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:F40 4.764534
2R:R:P43 6.6275456
3R:R:Y53 6.174504
4R:R:M60 5.235477
5R:R:N71 4.702509
6R:R:F81 9.035485
7R:R:L84 6.09587
8R:R:L88 6.7225408
9R:R:W90 4.5405
10R:R:I91 4.67507
11R:R:D99 6.5975429
12R:R:E102 5.3325417
13R:R:N113 5.2275406
14R:R:Q114 5.724575
15R:R:F119 5.77437
16R:R:L121 3.1975406
17R:R:C126 4.5075439
18R:R:W142 7.726515
19R:R:W152 5.741676108
20R:R:P158 5.50754107
21R:R:F164 5.0675406
22R:R:W183 10.43415
23R:R:W191 5.668545
24R:R:Y194 5.742504
25R:R:P196 6.142533
26R:R:F208 5.026515
27R:R:Y219 7.586547
28R:R:M224 3.5875405
29R:R:C227 4.255416
30R:R:Y239 8.4425409
31R:R:F277 4.87419
32R:R:W281 7.972518
33R:R:Y284 5.295417
34R:R:F287 6.086515
35R:R:F299 3.6025413
36R:R:P307 5.366516
37R:R:T315 6.0275428
38R:R:I321 2.735118
39R:R:Y322 7.46409
40R:R:V323 5.3507
41R:R:F324 3.2025406
42R:R:F329 8.0025408
43L:L:?1 6.175810
   

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:F40 R:R:P39 13.43382.89YesNo048
2R:R:F119 R:R:F40 33.68596.43YesYes374
3R:R:F119 R:R:N113 60.53489.67YesYes076
4R:R:L121 R:R:N113 18.56065.49YesYes066
5R:R:L121 R:R:V120 12.562.98YesNo063
6R:R:P39 R:R:W195 10.14852.7NoNo083
7R:R:F40 R:R:P196 12.32755.78YesYes343
8R:R:P196 R:R:W195 29.800512.16YesNo033
9R:R:C126 R:R:F119 13.02132.79YesYes397
10R:R:C126 R:R:P196 11.97493.77YesYes393
11R:R:C203 R:R:F119 13.02514.19NoYes397
12R:R:C203 R:R:P196 12.05375.65NoYes393
13R:R:A48 R:R:Y53 10.62862.67NoYes034
14R:R:Q114 R:R:Y53 14.63773.38YesYes054
15R:R:Q114 R:R:T201 59.74358.5YesNo055
16R:R:N113 R:R:T201 62.93882.92YesNo065
17R:R:M60 R:R:Q114 67.7586.8YesYes775
18R:R:M60 R:R:W59 69.28443.49YesNo074
19R:R:F309 R:R:W59 70.07958.02NoNo054
20R:R:D99 R:R:N318 44.31076.73YesNo299
21R:R:A314 R:R:N318 46.31714.69NoNo099
22R:R:A314 R:R:Y317 47.23222.67NoNo096
23R:R:C280 R:R:Y317 49.03992.69NoNo096
24R:R:C280 R:R:W281 49.932511.75NoYes098
25L:L:?1 R:R:W281 1004.54YesYes108
26L:L:?1 R:R:Y284 87.3657.02YesYes107
27R:R:P307 R:R:Y284 74.8359.74YesYes167
28R:R:P283 R:R:P307 72.20973.9NoYes096
29R:R:F310 R:R:P283 71.36215.78NoNo079
30R:R:F309 R:R:F310 70.52957.5NoNo057
31R:R:D99 R:R:N71 35.2615.39YesYes099
32R:R:P319 R:R:V323 26.44763.53NoYes097
33R:R:N71 R:R:P319 28.57796.52YesNo099
34R:R:F329 R:R:L84 14.412710.96YesYes087
35R:R:F329 R:R:V323 17.80686.55YesYes087
36R:R:E150 R:R:L88 29.68427.95NoYes088
37R:R:E150 R:R:I91 30.74184.1NoYes087
38R:R:I147 R:R:I91 43.71445.89NoYes097
39R:R:I147 R:R:R151 43.21186.26NoNo099
40R:R:R151 R:R:Y239 44.08195.14NoYes099
41R:R:S148 R:R:Y239 57.920815.26NoYes089
42R:R:I235 R:R:S148 81.06814.64NoNo088
43R:R:F277 R:R:I235 82.21572.51YesNo098
44R:R:F277 R:R:W281 80.70816.01YesYes198
45R:R:F164 R:R:L88 18.38439.74YesYes068
46R:R:P87 R:R:W90 13.83145.4NoYes065
47R:R:A166 R:R:W90 13.78643.89NoYes025
48R:R:P205 R:R:Y194 19.17574.17NoYes044
49R:R:G204 R:R:P205 18.69944.06NoNo044
50R:R:G204 R:R:H197 18.20063.18NoNo045
51R:R:H197 R:R:S202 16.81294.18NoNo055
52R:R:E129 R:R:S202 16.39662.87NoNo055
53R:R:E129 R:R:I109 16.130416.4NoNo055
54R:R:I109 R:R:N113 15.82662.83NoYes056
55R:R:L223 R:R:Y219 21.88724.69NoYes057
56R:R:P187 R:R:Y219 19.760712.52NoYes467
57R:R:P187 R:R:Y194 22.85111.13NoYes064
58R:R:M273 R:R:Y239 10.46359.58NoYes089
59R:R:C238 R:R:S148 35.84985.16NoNo078
60R:R:C238 R:R:W152 34.83727.84NoYes078
61R:R:V242 R:R:W152 22.22852.45NoYes088
62R:R:V155 R:R:V242 21.11843.21NoNo088
63R:R:A166 R:R:D165 10.28731.54NoNo027
64R:R:R193 R:R:W195 35.519823.99NoNo043
65R:R:D206 R:R:R193 22.254711.91NoNo044
66R:R:D206 R:R:S209 13.37382.94NoNo045
67R:R:F287 R:R:P307 13.39637.22YesYes156
68R:R:F287 R:R:F299 17.00053.22YesYes153
69R:R:E263 R:R:I246 17.79931.37NoNo078
70R:R:I246 R:R:V155 19.99321.54NoNo088
71R:R:A250 R:R:E263 10.92484.53NoNo047
72L:L:?1 R:R:L223 24.51625.52YesNo005
73R:R:F208 R:R:Y284 12.07623.09YesYes157
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:C136 R:R:E102 6.08 0 No Yes 7 7 2 1
R:R:E102 R:R:G137 3.27 1 Yes No 7 7 1 2
R:R:E102 R:R:K312 4.05 1 Yes No 7 7 1 1
L:L:?1 R:R:E102 7.93 1 Yes Yes 0 7 0 1
R:R:A106 R:R:K312 3.21 0 No No 6 7 2 1
R:R:F277 R:R:L141 6.09 1 Yes No 9 7 2 2
R:R:L141 R:R:W281 13.67 1 No Yes 7 8 2 1
R:R:F208 R:R:Y284 3.09 1 Yes Yes 5 7 2 1
R:R:F208 R:R:P307 4.33 1 Yes Yes 5 6 2 2
R:R:L223 R:R:Y219 4.69 0 No Yes 5 7 1 2
R:R:C227 R:R:L223 3.17 1 Yes No 6 5 2 1
L:L:?1 R:R:L223 5.52 1 Yes No 0 5 0 1
R:R:I229 R:R:M224 2.92 0 No Yes 4 5 2 1
R:R:C289 R:R:M224 3.24 0 No Yes 6 5 2 1
L:L:?1 R:R:M224 6.58 1 Yes Yes 0 5 0 1
L:L:?1 R:R:C228 6.33 1 Yes No 0 7 0 1
R:R:F277 R:R:W281 6.01 1 Yes Yes 9 8 2 1
R:R:C280 R:R:W281 11.75 0 No Yes 9 8 2 1
R:R:A311 R:R:W281 3.89 0 No Yes 7 8 2 1
L:L:?1 R:R:W281 4.54 1 Yes Yes 0 8 0 1
R:R:P307 R:R:Y284 9.74 1 Yes Yes 6 7 2 1
L:L:?1 R:R:Y284 7.02 1 Yes Yes 0 7 0 1
L:L:?1 R:R:K312 9.38 1 Yes No 0 7 0 1
L:L:?1 R:R:A288 2.1 1 Yes No 0 5 0 1
R:R:A285 R:R:M224 1.61 0 No Yes 6 5 2 1
R:R:A308 R:R:Y284 1.33 0 No Yes 5 7 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 9YDA_nogp
Class
SubFamily
Type
SubType
Species
Ligand
Other Ligand(s)
Protein Partners
PDB Resolution
Date
D.O.I.
Net Summary
Imin 2.67
Number of Linked Nodes 280
Number of Links 310
Number of Hubs 43
Number of Links mediated by Hubs 164
Number of Communities 11
Number of Nodes involved in Communities 57
Number of Links involved in Communities 69
Path Summary
Number Of Nodes in MetaPath 74
Number Of Links MetaPath 73
Number of Shortest Paths 53917
Length Of Smallest Path 3
Average Path Length 16.4218
Length of Longest Path 36
Minimum Path Strength 1.46
Average Path Strength 6.12082
Maximum Path Strength 18.17
Minimum Path Correlation 0.7
Average Path Correlation 0.927873
Maximum Path Correlation 0.99
Minimum % Of Corr. Nodes 3.125
Average % Of Corr. Nodes 44.5286
Maximum % Of Corr. Nodes 100
Minimum Path Hubs % 0
Average Path Hubs % 43.6273
Maximum Path Hubs % 100
AnnotationTypeLinks
Gene OntologyMolecular Function
Gene OntologyBiological Process• fibroblast proliferation   • cell population proliferation   • cellular process   • cellular response to nitrogen compound   • cellular response to stimulus   • response to dopamine   • regulation of cellular process   • response to stimulus   • signaling   • cellular response to dopamine   • response to monoamine   • cell communication   • response to catecholamine   • adenylate cyclase-activating dopamine receptor signaling pathway   • cellular response to catecholamine stimulus   • signal transduction   • regulation of biological process   • G protein-coupled dopamine receptor signaling pathway   • biological regulation   • response to oxygen-containing compound   • response to nitrogen compound   • adenylate cyclase-activating G protein-coupled receptor signaling pathway   • cellular response to oxygen-containing compound   • cellular response to chemical stimulus   • cellular response to monoamine stimulus   • response to chemical   • adenylate cyclase-modulating G protein-coupled receptor signaling pathway   • G protein-coupled receptor signaling pathway   • response to ketone   • response to prostaglandin   • response to lipid   • response to endogenous stimulus   • response to alcohol   • cellular response to prostaglandin stimulus   • cellular response to endogenous stimulus   • cellular response to prostaglandin E stimulus   • cellular response to alcohol   • response to hormone   • cellular response to lipid   • response to prostaglandin E   • cellular response to ketone   • cellular response to hormone stimulus   • cellular anatomical structure   • membrane   • protein-containing complex   • extrinsic component of plasma membrane   • catalytic complex   • plasma membrane protein complex   • cytoplasmic side of membrane   • plasma membrane   • membrane protein complex   • heterotrimeric G-protein complex   • side of membrane   • cell periphery   • cytoplasmic side of plasma membrane   • GTPase complex
Gene OntologyCellular Component• cellular anatomical structure   • membrane   • protein-containing complex   • extrinsic component of plasma membrane   • catalytic complex   • plasma membrane protein complex   • cytoplasmic side of membrane   • plasma membrane   • membrane protein complex   • heterotrimeric G-protein complex   • side of membrane   • cell periphery   • cytoplasmic side of plasma membrane   • GTPase complex   • extrinsic component of membrane   • extrinsic component of cytoplasmic side of plasma membrane   • extracellular exosome   • membrane-bounded organelle   • extracellular vesicle   • extracellular organelle   • extracellular region   • organelle   • extracellular space   • vesicle   • extracellular membrane-bounded organelle   • synapse   • cell junction   • protein binding   • binding   • enzyme binding   • GTPase binding   • protein-containing complex binding   • pyrophosphatase activity   • GTPase activity   • ribonucleoside triphosphate phosphatase activity   • hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides   • hydrolase activity   • hydrolase activity, acting on acid anhydrides   • catalytic activity   • 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 process   • cellular response to stimulus   • regulation of biological process   • regulation of cellular process   • response to stimulus   • signaling   • biological regulation   • signal transduction   • cell communication   • response to ketone   • response to prostaglandin   • response to lipid   • response to endogenous stimulus   • response to alcohol   • cellular response to prostaglandin stimulus   • response to oxygen-containing compound   • cellular response to oxygen-containing compound   • cellular response to endogenous stimulus   • cellular response to prostaglandin E stimulus   • cellular response to chemical stimulus   • cellular response to alcohol   • response to hormone   • response to chemical   • cellular response to lipid   • response to prostaglandin E   • cellular response to ketone   • 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   • 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   • response to nitrogen compound   • adenylate cyclase-activating G protein-coupled receptor signaling pathway   • cellular response to monoamine stimulus   • adenylate cyclase-modulating G protein-coupled receptor signaling pathway   • 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   • non-motile cilium   • 9+0 non-motile cilium   • cilium   • neuron projection   • photoreceptor disc membrane   • photoreceptor outer segment   • plasma membrane bounded cell projection   • cell projection   • photoreceptor cell cilium   • organelle membrane   • intracellular anatomical structure   • cytoplasm   • cytosol   • vacuolar membrane   • lytic vacuole   • vacuole   • intracellular membrane-bounded organelle   • intracellular organelle   • lytic vacuole membrane   • bounding membrane of organelle   • lysosomal membrane   • lysosome   • G protein-coupled photoreceptor activity   • molecular transducer activity   • photoreceptor activity   • G protein-coupled receptor activity   • transmembrane signaling receptor activity   • signaling receptor activity   • identical protein binding   • regulation of cytokinesis   • positive regulation of cell division   • regulation of cell cycle process   • 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   • cell division   • cell cycle   • regulation of cell cycle   • positive regulation of cellular process   • cell cycle process   • detection of light stimulus   • response to light stimulus   • detection of external stimulus   • response to external stimulus   • detection of abiotic stimulus   • absorption of visible light   • detection of stimulus   • light absorption   • response to abiotic stimulus   • response to radiation   • cellular response to light stimulus   • cellular response to radiation   • cellular response to abiotic stimulus   • cellular response to environmental stimulus   • sensory perception of light stimulus   • visual perception   • phototransduction
SCOP2Domain Identifier• Transducin (heterotrimeric G protein), gamma chain
SCOP2Family Identifier• 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
UniProtP04001
Sequence
>9YDA_nogp_Chain_R
RGPFEGPNY HIAPRWVYH LTSVWMIFV VIASVFTNG LVLAATMKF 
KKLRHPLNW ILVNLAVAD LAETVIAST ISVVNQVYG YFVLGHPMC 
VLEGYTVSL CGITGLWSL AIISWERWM VVCKPFGNV RFDAKLAIV 
GIAFSWIWA AVWTAPPIF GWSRYWPHG LKTSCGPDV FSGSSYPGV 
QSYMIVLMV TCCITPLSI IVLCYLQVW LAIRAVAKQ QKESESTQK 
AEKEVTRMV VVMVLAFCF CWGPYAFFA CFAAANPGY PFHPLMAAL 
PAFFAKSAT IYNPVIYVF MNRQFRNCI LQL


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
8Y01ASensoryOpsinsOpsin1MWHomo sapiensAll-trans-Retinal-Gi1/β1/γ22.482025-02-12To be published
8Y01 (No Gprot) ASensoryOpsinsOpsin1MWHomo sapiensAll-trans-Retinal-2.482025-02-12To be published
9YDAASensoryOpsinsOpsin1MWHomo sapiensAll-trans-Retinal-chim(NtGi1L-Gs-CtGt)/β1/γ22.92025-12-2410.1073/pnas.2516318122
9YDA (No Gprot) ASensoryOpsinsOpsin1MWHomo sapiensAll-trans-Retinal-2.92025-12-2410.1073/pnas.2516318122




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 9YDA_nogp.zip



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