Color ConSurf Grade
      No Conservation data available
      1
      2
      3
      4
      5
      6
      7
      8
      9

Index: hub id, click on each number to highlight the corresponding hub in the 3D visualization.

Hub: the hub being considered.

Avg Int. Strength: the average interaction strength of all the links of the corresponding hub.

Num Of Links: the number of links of the corresponding hub.

Community: the id of the community the link belong to, otherwise 0.

ConSurf: this column reports the ConSurf conservation grades of each hub.

Index Hub Avg Int. Strength Num Of Links Community ConSurf
1R:R:P39 7.46438
2R:R:F40 4.784535
3R:R:W59 6.0475404
4R:R:N71 5.26519
5R:R:L75 1.5175407
6R:R:I91 5.526518
7R:R:N94 5.5419
8R:R:L95 2.8075419
9R:R:D99 5.54419
10R:R:N113 5.1825436
11R:R:Q114 5.27405
12R:R:F119 5.144538
13R:R:L121 4.134536
14R:R:H123 3.91432
15R:R:V133 2.325446
16R:R:T139 4.785407
17R:R:W142 5.716525
18R:R:S143 4.126518
19R:R:W152 6.576507
20R:R:P158 7.93407
21R:R:F164 5.12333617
22R:R:W177 7.6675409
23R:R:W179 7.836524
24R:R:W183 10.054525
25R:R:P186 4.6675423
26R:R:W191 5.9475425
27R:R:Y194 6.14571726
28R:R:W195 5.602533
29R:R:P196 6.88533
30R:R:H197 3.87833643
31R:R:T201 4.3925406
32R:R:C203 5.0425439
33R:R:F208 6.068545
34R:R:Y213 5.4525403
35R:R:Y219 7.22667626
36R:R:C227 4.59525
37R:R:Y239 5.356519
38R:R:W243 5.8925466
39R:R:E263 3.948568
40R:R:Y277 5.6975409
41R:R:W281 5.31408
42R:R:Y284 8.015447
43R:R:N294 4.165404
44R:R:F299 4.7125404
45R:R:P307 4.152546
46R:R:T315 4.85419
47R:R:Y322 6.96519
48R:R:F324 3.2425416
49R:R:F329 7.846558
50L:L:?1 6.25286740
   

Color ConSurf Grade
      No Conservation data available
      1
      2
      3
      4
      5
      6
      7
      8
      9

Index: link id, click on each number to highlight the corresponding link in the 3D visualization.

Node1 Node2: the two nodes of the corresponding link.

Recurrence: the relative Recurrence in the pool of shortest paths.

Int. Strength: the interaction strength between the two nodes.

Hub1?, Hub2?: "Yes" if the corresponding node has more than 3 links, otherwise "No".

Community: the id of the community the link belong to, otherwise 0.

ConSurf1, ConSurf2: these columns report the ConSurf conservation grades of the two nodes involved in a link.

Index Node1 Node2 Recurrence Int. Strength Hub1? Hub2? Community ConSurf1 ConSurf2
1R:R:N113 R:R:T201 20.12012.92YesYes066
2R:R:L199 R:R:T201 10.822.95NoYes056
3R:R:S202 R:R:T201 35.95623.2NoYes056
4R:R:H197 R:R:S202 37.04012.79YesNo035
5R:R:Q114 R:R:T201 11.63038.5YesYes056
6R:R:P205 R:R:Y194 13.18312.78NoYes056
7L:L:?1 R:R:P205 12.90957.64YesNo005
8L:L:?1 R:R:W281 74.76915.3YesYes008
9R:R:L141 R:R:W281 75.93736.83NoYes088
10R:R:L141 R:R:Y277 76.24178.21NoYes089
11R:R:I235 R:R:Y277 1002.42NoYes089
12R:R:I235 R:R:Y239 80.15752.42NoYes189
13R:R:R151 R:R:Y239 50.36928.23NoYes199
14R:R:R151 R:R:Y322 37.19026.17NoYes199
15R:R:L144 R:R:Y322 72.34859.38NoYes189
16R:R:L144 R:R:L95 35.9112.77NoYes189
17R:R:D99 R:R:L95 41.63872.71YesYes199
18R:R:D99 R:R:T315 10.17838.67YesYes199
19R:R:M273 R:R:Y239 38.79655.99NoYes089
20R:R:M273 R:R:Y322 38.06029.58NoYes089
21R:R:L144 R:R:N318 35.71564.12NoNo189
22R:R:D99 R:R:N318 34.90125.39YesNo199
23R:R:D99 R:R:N71 65.15235.39YesYes199
24R:R:L100 R:R:N71 18.24866.87NoYes079
25R:R:F324 R:R:P319 12.2022.89YesNo169
26R:R:N71 R:R:P319 14.20736.52YesNo199
27R:R:A96 R:R:N71 30.09483.13NoYes099
28R:R:A96 R:R:V74 28.10813.39NoNo099
29R:R:V323 R:R:V74 26.11739.62NoNo079
30R:R:L100 R:R:L75 14.21761.38NoYes077
31R:R:C332 R:R:L84 10.1686.35NoNo068
32R:R:F329 R:R:L84 12.189717.05YesNo088
33R:R:F329 R:R:V323 20.0795.24YesNo587
34R:R:I235 R:R:S148 20.00086.19NoNo189
35R:R:C238 R:R:S148 28.36935.16NoNo079
36R:R:C238 R:R:W152 27.69685.22NoYes077
37R:R:F164 R:R:M153 15.40013.73YesNo074
38R:R:P158 R:R:W152 10.178310.81YesYes077
39R:R:I147 R:R:R151 12.96096.26NoNo199
40R:R:I147 R:R:I91 13.32917.36NoYes198
41R:R:E150 R:R:I91 13.37436.83NoYes188
42R:R:E150 R:R:F164 11.897712.83NoYes187
43R:R:C227 R:R:L223 15.26853.17YesNo255
44R:R:L223 R:R:Y219 16.46559.38NoYes256
45R:R:S192 R:R:Y219 20.17985.09NoYes066
46R:R:S192 R:R:V216 16.76168.08NoNo064
47R:R:V216 R:R:Y213 15.78273.79NoYes043
48R:R:C227 R:R:W142 18.61052.61YesYes255
49R:R:P231 R:R:W142 24.188110.81NoYes095
50R:R:Q241 R:R:W152 20.21066.57NoYes047
51R:R:L244 R:R:Q241 19.17413.99NoNo014
52R:R:L244 R:R:W243 17.08863.42NoYes016
53R:R:E263 R:R:W243 12.8545.45YesYes686
54R:R:H197 R:R:Y284 36.74193.27YesYes437
55L:L:?1 R:R:Y284 50.685916.37YesYes407
56R:R:M220 R:R:Y219 17.45685.99NoYes056
57L:L:?1 R:R:M220 19.29952.82YesNo005
58R:R:P231 R:R:Y277 25.42622.78NoYes099
Download PSN data

2D representation of the global metapath, ligand(s) interactions and
histograms of path distribution according to several parameters
(click on the image to enlarge it 🔍):

A 2D representation of the global communication in the network.

ConSurf Conservation Grade (See documentation): 

 n/a   1    2    3    4    5    6    7    8    9  

Number of shortest communication paths as a function of the average residue correlation.

Number of shortest communication paths as a function of the average interaction strength of their links.

Number of shortest communication paths as a function of the % of hub nodes in each path.

Number of shortest communication paths as a function of the number of nodes in each path.

Number of shortest communication paths as a function of the % of correlated nodes in each path.


2D representation of the interactions of this orthosteric/allosteric ligand.


Links and nodes colored according to ConSurf Conservation Grade (See documentation): 

 n/a   1    2    3    4    5    6    7    8    9  

Node1 Node2 LinkStrength Comm IsNode1Hub? IsNode2Hub? Node1Cons Node2Cons Node1Shell Node2Shell
R:R:K312 R:R:V133 3.04 4 No Yes 8 6 1 1
L:L:?1 R:R:V133 2.97 4 Yes Yes 0 6 0 1
R:R:L141 R:R:W281 6.83 0 No Yes 8 8 2 1
R:R:P205 R:R:Y194 2.78 0 No Yes 5 6 1 2
R:R:G204 R:R:H197 3.18 0 No Yes 4 3 2 2
R:R:F208 R:R:H197 7.92 4 Yes Yes 5 3 2 2
R:R:H197 R:R:Y284 3.27 4 Yes Yes 3 7 2 1
R:R:G204 R:R:P205 4.06 0 No No 4 5 2 1
L:L:?1 R:R:P205 7.64 4 Yes No 0 5 0 1
R:R:M220 R:R:V207 7.61 0 No No 5 4 1 2
R:R:F208 R:R:Y284 8.25 4 Yes Yes 5 7 2 1
R:R:F208 R:R:P307 4.33 4 Yes Yes 5 6 2 2
R:R:M220 R:R:Y219 5.99 0 No Yes 5 6 1 2
L:L:?1 R:R:M220 2.82 4 Yes No 0 5 0 1
R:R:C280 R:R:W281 5.22 0 No Yes 8 8 2 1
R:R:A311 R:R:W281 3.89 0 No Yes 7 8 2 1
L:L:?1 R:R:W281 5.3 4 Yes Yes 0 8 0 1
R:R:P307 R:R:Y284 4.17 4 Yes Yes 6 7 2 1
L:L:?1 R:R:Y284 16.37 4 Yes Yes 0 7 0 1
L:L:?1 R:R:K312 6.56 4 Yes No 0 8 0 1
L:L:?1 R:R:C228 2.11 4 Yes No 0 8 0 1
R:R:A106 R:R:V133 1.7 0 No Yes 6 6 2 1
R:R:T132 R:R:V133 1.59 0 No Yes 4 6 2 1

Location and physicochemical properties of the interaction partners of this ligand

Interactions of this ligand

Similarities between the interactions of this ligand and those of other networks

PDB Summary
PDB 8IU2_nogp
Class
SubFamily
Type
SubType
Species
Ligand
Other Ligand(s)
Protein Partners
PDB Resolution
Date
D.O.I.
Net Summary
Imin 2.42
Number of Linked Nodes 272
Number of Links 320
Number of Hubs 50
Number of Links mediated by Hubs 189
Number of Communities 8
Number of Nodes involved in Communities 75
Number of Links involved in Communities 103
Path Summary
Number Of Nodes in MetaPath 59
Number Of Links MetaPath 58
Number of Shortest Paths 77166
Length Of Smallest Path 3
Average Path Length 15.5867
Length of Longest Path 31
Minimum Path Strength 1.495
Average Path Strength 5.56074
Maximum Path Strength 14.605
Minimum Path Correlation 0.7
Average Path Correlation 0.928124
Maximum Path Correlation 0.99
Minimum % Of Corr. Nodes 4.34783
Average % Of Corr. Nodes 45.2869
Maximum % Of Corr. Nodes 100
Minimum Path Hubs % 0
Average Path Hubs % 49.374
Maximum Path Hubs % 100
AnnotationTypeLinks
Gene OntologyMolecular Function
Gene OntologyBiological Process• regulation of cytokinesis   • regulation of biological process   • regulation of cellular process   • positive regulation of cell division   • regulation of cell cycle process   • biological regulation   • positive regulation of biological process   • cytokinesis   • positive regulation of cell cycle   • regulation of cell division   • positive regulation of cytokinesis   • positive regulation of cell cycle process   • cellular process   • cell division   • cell cycle   • regulation of cell cycle   • positive regulation of cellular process   • cell cycle process   • cellular response to stimulus   • response to light stimulus   • response to stimulus   • cellular response to light stimulus   • response to radiation   • response to abiotic stimulus   • cellular response to radiation   • cellular response to abiotic stimulus   • cellular response to environmental stimulus   • multicellular organismal process   • sensory perception of light stimulus   • system process   • sensory perception   • nervous system process   • visual perception   • phototransduction   • detection of light stimulus   • detection of external stimulus   • signaling   • response to external stimulus   • detection of abiotic stimulus   • cell communication   • detection of stimulus   • signal transduction   • G protein-coupled receptor signaling pathway   • membrane-bounded organelle   • non-motile cilium   • membrane   • 9+0 non-motile cilium   • cilium   • neuron projection   • photoreceptor disc membrane   • photoreceptor outer segment   • plasma membrane bounded cell projection   • cell projection   • cellular anatomical structure   • photoreceptor cell cilium   • organelle   • organelle membrane
Gene OntologyCellular Component• membrane-bounded organelle   • non-motile cilium   • membrane   • 9+0 non-motile cilium   • cilium   • neuron projection   • photoreceptor disc membrane   • photoreceptor outer segment   • plasma membrane bounded cell projection   • cell projection   • cellular anatomical structure   • photoreceptor cell cilium   • organelle   • organelle membrane   • cell periphery   • plasma membrane   • D2 dopamine receptor binding   • protein binding   • binding   • signaling receptor binding   • G protein-coupled receptor binding   • dopamine receptor binding   • phosphorus-oxygen lyase activity   • enzyme regulator activity   • cyclase regulator activity   • molecular function regulator activity   • cyclase activity   • adenylate cyclase regulator activity   • lyase activity   • catalytic activity   • adenylate cyclase activity   • guanyl nucleotide binding   • GTP binding   • nucleotide binding   • guanyl ribonucleotide binding   • purine ribonucleotide binding   • purine ribonucleoside triphosphate binding   • nucleoside phosphate binding   • ion binding   • purine nucleotide binding   • anion binding   • heterocyclic compound binding   • carbohydrate derivative binding   • ribonucleotide binding   • small molecule binding   • cation binding   • magnesium ion binding   • metal ion binding   • GDP binding   • G protein-coupled serotonin receptor binding   • protein-containing complex binding   • G-protein beta/gamma-subunit complex binding   • pyrophosphatase activity   • GTPase activity   • G protein activity   • ribonucleoside triphosphate phosphatase activity   • hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides   • hydrolase activity   • hydrolase activity, acting on acid anhydrides   • cellular response to stimulus   • regulation of biological process   • regulation of cellular process   • response to stimulus   • signaling   • biological regulation   • adenylate cyclase-inhibiting serotonin receptor signaling pathway   • G protein-coupled serotonin receptor signaling pathway   • cell communication   • adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway   • adenylate cyclase-modulating G protein-coupled receptor signaling pathway   • G protein-coupled receptor signaling pathway   • cellular process   • signal transduction   • response to hormone   • response to chemical   • response to endogenous stimulus   • response to peptide hormone   • response to oxygen-containing compound   • response to nitrogen compound   • cell division   • leukocyte migration   • immune system process   • mononuclear cell migration   • lymphocyte migration   • cell migration   • T cell migration   • cell motility   • regulation of steroid biosynthetic process   • regulation of cholesterol biosynthetic process   • regulation of cholesterol metabolic process   • steroid metabolic process   • regulation of lipid metabolic process   • sterol metabolic process   • positive regulation of biological process   • cholesterol metabolic process   • lipid biosynthetic process   • alcohol metabolic process   • regulation of primary metabolic process   • positive regulation of metabolic process   • regulation of small molecule metabolic process   • positive regulation of biosynthetic process   • positive regulation of lipid metabolic process   • small molecule metabolic process   • steroid biosynthetic process   • positive regulation of cellular process   • regulation of biosynthetic process   • secondary alcohol biosynthetic process   • regulation of alcohol biosynthetic process   • small molecule biosynthetic process   • regulation of steroid metabolic process   • cholesterol biosynthetic process   • positive regulation of cholesterol biosynthetic process   • primary metabolic process   • secondary alcohol metabolic process   • positive regulation of steroid biosynthetic process   • biosynthetic process   • sterol biosynthetic process   • positive regulation of lipid biosynthetic process   • regulation of sterol biosynthetic process   • alcohol biosynthetic process   • positive regulation of cholesterol metabolic process   • positive regulation of steroid metabolic process   • metabolic process   • regulation of lipid biosynthetic process   • positive regulation of small molecule metabolic process   • regulation of metabolic process   • positive regulation of alcohol biosynthetic process   • positive regulation of sterol biosynthetic process   • lipid metabolic process   • regulation of cytoskeleton organization   • regulation of cellular component organization   • microtubule cytoskeleton organization   • regulation of mitotic spindle organization   • mitotic cell cycle   • cellular component organization   • cell cycle   • cellular component organization or biogenesis   • regulation of cell cycle   • microtubule cytoskeleton organization involved in mitosis   • spindle organization   • cell cycle process   • regulation of cell cycle process   • regulation of microtubule-based process   • regulation of spindle organization   • regulation of organelle organization   • mitotic spindle organization   • organelle organization   • mitotic cell cycle process   • microtubule-based process   • cytoskeleton organization   • regulation of microtubule cytoskeleton organization   • protein localization   • positive regulation of protein localization to cell periphery   • regulation of localization   • protein localization to cell periphery   • cellular localization   • regulation of protein localization   • positive regulation of protein localization to cell cortex   • regulation of protein localization to cell periphery   • localization   • regulation of cellular localization   • regulation of protein localization to cell cortex   • cellular macromolecule localization   • macromolecule localization   • positive regulation of protein localization   • protein localization to cell cortex   • response to ketone   • response to prostaglandin   • response to lipid   • response to alcohol   • response to prostaglandin E   • cellular response to forskolin   • cellular response to oxygen-containing compound   • cellular response to chemical stimulus   • cellular response to alcohol   • response to forskolin   • cellular response to lipid   • cellular response to ketone   • midbody   • intracellular anatomical structure   • nucleus   • membrane-enclosed lumen   • intracellular membraneless organelle   • intracellular membrane-bounded organelle   • nucleolus   • intracellular organelle lumen   • intracellular organelle   • organelle lumen   • membraneless organelle   • nuclear lumen   • cell cortex   • cytoplasm   • protein-containing complex   • extrinsic component of plasma membrane   • catalytic complex   • plasma membrane protein complex   • cytoplasmic side of membrane   • membrane protein complex   • heterotrimeric G-protein complex   • side of membrane   • cytoplasmic side of plasma membrane   • GTPase complex   • extrinsic component of membrane   • extrinsic component of cytoplasmic side of plasma membrane   • extracellular exosome   • extracellular vesicle   • extracellular organelle   • extracellular region   • extracellular space   • vesicle   • extracellular membrane-bounded organelle   • centrosome   • microtubule organizing center   • cytoskeleton   • microtubule cytoskeleton   • centriolar satellite   • cytosol   • nucleoplasm   • vacuolar membrane   • lytic vacuole   • vacuole   • lytic vacuole membrane   • bounding membrane of organelle   • lysosomal membrane   • lysosome   • Golgi apparatus   • endomembrane system   • ciliary basal body   • enzyme binding   • GTPase binding   • signaling receptor complex adaptor activity   • protein-macromolecule adaptor activity   • molecular adaptor activity   • signaling adaptor activity   • multicellular organismal process   • system process   • sensory perception of chemical stimulus   • sensory perception   • nervous system process   • sensory perception of taste   • developmental process   • sensory organ development   • eye development   • animal organ development   • retina development in camera-type eye   • visual system development   • multicellular organism development   • camera-type eye development   • anatomical structure development   • sensory system development   • system development   • cell population proliferation   • cellular response to prostaglandin stimulus   • cellular response to endogenous stimulus   • cellular response to prostaglandin E stimulus   • cellular response to hormone stimulus   • small GTPase-mediated signal transduction   • Ras protein signal transduction   • intracellular signal transduction   • intracellular signaling cassette   • phospholipase C-activating G protein-coupled receptor signaling pathway   • cellular response to nitrogen compound   • response to dopamine   • cellular response to dopamine   • response to monoamine   • response to catecholamine   • adenylate cyclase-activating dopamine receptor signaling pathway   • cellular response to catecholamine stimulus   • G protein-coupled dopamine receptor signaling pathway   • adenylate cyclase-activating G protein-coupled receptor signaling pathway   • cellular response to monoamine stimulus   • synaptic signaling   • cellular response to acetylcholine   • cell-cell signaling   • acetylcholine receptor signaling pathway   • postsynaptic signal transduction   • G protein-coupled acetylcholine receptor signaling pathway   • response to acetylcholine   • synapse   • cell junction   • G-protein beta-subunit binding
SCOP2Domain Identifier• Ras-like P-loop GTPases   • Transducin (heterotrimeric G protein), gamma chain
SCOP2Family Identifier• Ras-like P-loop GTPases   • Transducin (heterotrimeric G protein), gamma chain
Membrane Protein Annotations-• Orientations of Proteins in Membranes database (OPM)   • Protein Data Bank of Transmembrane Proteins (PDBTM)   • MemProtMD


Details about the values in these tables can be found in the corresponding documentation page .
CodeRET
PDB ResiduesL:L:?1
Environment DetailsOpen EMBL-EBI Page
CodeRET
NameRETINAL
Synonyms
Identifier
FormulaC20 H28 O
Molecular Weight284.436
SMILES
PubChem638015
Formal Charge0
Total Atoms49
Total Chiral Atoms0
Total Bonds49
Total Aromatic Bonds0

PDBsumOpen PDBsum Page
ChainR
ProteinReceptor
UniProtP04000
Sequence
>8IU2_nogp_Chain_R
GPFEGPNYH IAPRWVYHL TSVWMIFVV TASVFTNGL VLAATMKFK 
KLRHPLNWI LVNLAVADL AETVIASTI SIVNQVSGY FVLGHPMCV 
LQGYTVSLC GITGLWSLA IISWERWMV VCKPFGNVR FDAKLAIVG 
IAFSWIWAA VWTAPPIFG WSRYWPHGL KTSCGPDVF SGSSYPGVQ 
SYMIVLMVT CCIIPLAII MLCYLQVWL AIRAVAKQQ KESESTQKA 
EKEVTRMVV VMIFAYCVC WGPYTFFAC FAAANPGYA FHPLMAALP 
AYFAKSATI YNPVIYVFM NRQFRNCIL Q


Click on each residue to open a popup with some information about it.

ConSurf Conservation Grade (See documentation): 

 n/a   1    2    3    4    5    6    7    8    9  




This receptor, from the same or other species and bound to the same or other ligands, is also present in the following networks:
Show PDB Class SubFamily Type SubType Species Orthosteric Ligand Other Ligand(s) Protein Partners Resolution Date DOI
8IU2ASensoryOpsinsOpsin1LWHomo sapiensRetinal-Gi1/β1/γ23.352024-03-27To be published
8IU2 (No Gprot) ASensoryOpsinsOpsin1LWHomo sapiensRetinal-3.352024-03-27To be published




You can download a compressed (zip) file with structure(s), 3D outputs (as PyMol and VMD scripts) and numerical data files (as csv and plain text files).

Download 8IU2_nogp.zip



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