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:Y10 4.6225407
2R:R:V11 4.15418
3R:R:V20 7.42333616
4R:R:S22 7.3975415
5R:R:P23 7.908515
6R:R:F24 5.145615
7R:R:Q28 7.8075415
8R:R:Y29 6.2775404
9R:R:Y30 6.89333614
10R:R:L31 5.346514
11R:R:M44 6.378547
12R:R:H65 5.696555
13R:R:L68 4.752557
14R:R:L72 5.3625408
15R:R:N73 6.265408
16R:R:I75 5.275407
17R:R:F91 5.00167647
18R:R:F103 7.372518
19R:R:F115 8.575426
20R:R:E122 7.48426
21R:R:W126 8.60833625
22R:R:R135 12.2725409
23R:R:V138 4.2025408
24R:R:W161 5.64409
25R:R:P170 4.36427
26R:R:P171 7.62425
27R:R:W175 7.92525
28R:R:R177 14.23415
29R:R:Y178 7.24286723
30R:R:P180 5.286513
31R:R:E181 7.162534
32R:R:M183 7.055402
33R:R:Q184 6.8825413
34R:R:I189 7.3424
35R:R:D190 11.078514
36R:R:Y191 7.44406
37R:R:Y192 6.85535
38R:R:T193 7.485615
39R:R:H195 11.64614
40R:R:F203 10.28626
41R:R:H211 9.26167626
42R:R:F261 7.3525409
43R:R:W265 8.398508
44R:R:Y268 5.88436
45R:R:F283 7.32434
46R:R:P285 3.6025403
47R:R:F287 8.0825434
48R:R:M288 6.2475434
49R:R:Y306 14.66479
50R:R:F313 8.38167678
51H:H:?1 20.1943710
52H:H:?3 35.8175410
   

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
1H:H:?1 R:R:S281 23.51644.02YesNo004
2R:R:F283 R:R:S281 24.22275.28YesNo044
3R:R:F283 R:R:Y192 26.11064.13YesYes345
4R:R:Y10 R:R:Y192 44.82078.94YesYes075
5H:H:?1 R:R:V20 15.9133.99YesYes106
6R:R:T193 R:R:Y10 42.71393.75YesYes057
7R:R:V20 R:R:Y30 10.47617.57YesYes164
8R:R:Q28 R:R:Y30 11.699511.27YesYes154
9R:R:P23 R:R:Q28 12.12929.47YesYes155
10R:R:P180 R:R:Q184 15.61067.9YesYes133
11R:R:F24 R:R:P180 31.22335.78YesYes153
12R:R:P180 R:R:P23 18.18693.9YesYes135
13R:R:F24 R:R:S22 11.83683.96YesYes155
14R:R:F103 R:R:F24 28.44615.36YesYes185
15R:R:C187 R:R:P180 22.55953.77NoYes193
16R:R:C187 R:R:F103 20.29966.98NoYes198
17R:R:E181 R:R:Y192 41.5746.73YesYes345
18R:R:E181 R:R:S186 57.65214.31YesNo045
19R:R:F293 R:R:S186 57.52086.61NoNo055
20R:R:F293 R:R:L40 21.15315.83NoNo055
21R:R:L40 R:R:M183 17.29375.65NoYes052
22R:R:F37 R:R:M183 14.93038.71NoYes052
23R:R:F37 R:R:Y29 14.13458.25NoYes054
24R:R:L31 R:R:P285 10.44224.93YesYes043
25R:R:F293 R:R:Y43 55.8025.16NoNo054
26R:R:L47 R:R:Y43 56.036814.07NoNo074
27R:R:F91 R:R:L47 48.01763.65YesNo477
28R:R:E113 R:R:F103 46.10784.66NoYes058
29R:R:E113 R:R:K296 41.9549.45NoNo057
30R:R:F91 R:R:M86 77.17794.98YesNo077
31R:R:A299 R:R:M86 75.98423.22NoNo097
32R:R:A299 R:R:D83 75.38154.63NoNo099
33R:R:D83 R:R:N55 74.774713.46NoNo099
34R:R:N55 R:R:P303 73.54926.52NoNo099
35R:R:P303 R:R:T58 71.68125.25NoNo099
36R:R:F313 R:R:T58 70.4165.19YesNo089
37R:R:F313 R:R:Y306 41.128424.76YesYes789
38R:R:N73 R:R:Y306 33.79358.14YesYes089
39R:R:N73 R:R:T70 25.30897.31YesNo087
40R:R:P71 R:R:T70 24.47535.25NoNo067
41R:R:E134 R:R:P71 17.727311NoNo086
42R:R:F313 R:R:N310 14.33153.62YesNo788
43R:R:M253 R:R:N310 13.61134.21NoNo088
44R:R:L72 R:R:V250 13.91178.94YesNo088
45R:R:E181 R:R:Y268 69.809210.1YesYes346
46R:R:Y191 R:R:Y268 1005.96YesYes066
47R:R:I189 R:R:Y191 59.86639.67YesYes046
48R:R:I189 R:R:Y178 25.50784.84YesYes243
49R:R:F115 R:R:Y178 22.6595.16YesYes263
50R:R:F115 R:R:L119 17.47078.53YesNo065
51R:R:L119 R:R:L165 16.40444.15NoNo053
52R:R:L165 R:R:W161 15.33413.42NoYes039
53R:R:M288 R:R:Y192 29.24585.99YesYes345
54R:R:M288 R:R:Y268 31.20344.79YesYes346
55R:R:F203 R:R:I189 37.573410.05YesYes264
56R:R:F203 R:R:W175 68.790718.04YesYes265
57R:R:W175 R:R:Y206 66.31797.72YesNo254
58R:R:H211 R:R:Y206 61.147513.07YesNo264
59R:R:E122 R:R:H211 35.07679.85YesYes266
60R:R:E122 R:R:L125 33.78163.98YesNo067
61R:R:F261 R:R:L125 32.45879.74YesNo097
62R:R:F261 R:R:W265 16.360612.03YesYes098
63R:R:M207 R:R:Y191 39.79354.79NoYes056
64R:R:F203 R:R:M207 36.03364.98YesNo065
65R:R:H211 R:R:W126 21.10135.29YesYes265
66R:R:V129 R:R:W126 11.09876.13NoYes075
67R:R:F261 R:R:L128 12.79374.87YesNo098
68R:R:L128 R:R:V258 10.97947.45NoNo088
69R:R:E134 R:R:V138 17.48074.28NoYes088
70R:R:V138 R:R:V139 16.33081.6YesNo088
71R:R:L226 R:R:V139 15.40185.96NoNo088
72R:R:C140 R:R:L226 10.69693.17NoNo078
73R:R:I179 R:R:P180 45.52895.08NoYes113
74R:R:R177 R:R:T193 21.02176.47YesYes155
75R:R:D190 R:R:T193 21.696113.01YesYes145
76R:R:P194 R:R:T193 14.59213.5NoYes015
77R:R:I179 R:R:R177 22.768411.27NoYes115
78R:R:D190 R:R:I179 23.38718.4YesNo141
79R:R:F91 R:R:K296 37.61123.72YesNo477
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.


PDB Summary
PDB 8FD0
Class A
SubFamily Sensory
Type Opsins
SubType Rhodopsin
Species Bos Taurus
Ligand -
Other Ligand(s) -
Protein Partners -
PDB Resolution 3.71
Date 2023-08-30
D.O.I. 10.1038/s41467-023-40911-9
Net Summary
Imin 3.5
Number of Linked Nodes 299
Number of Links 355
Number of Hubs 52
Number of Links mediated by Hubs 192
Number of Communities 7
Number of Nodes involved in Communities 71
Number of Links involved in Communities 107
Path Summary
Number Of Nodes in MetaPath 80
Number Of Links MetaPath 79
Number of Shortest Paths 104932
Length Of Smallest Path 3
Average Path Length 17.3981
Length of Longest Path 45
Minimum Path Strength 1.47
Average Path Strength 7.36529
Maximum Path Strength 54.0033
Minimum Path Correlation 0.7
Average Path Correlation 0.965931
Maximum Path Correlation 1
Minimum % Of Corr. Nodes 3.22581
Average % Of Corr. Nodes 64.8323
Maximum % Of Corr. Nodes 100
Minimum Path Hubs % 0
Average Path Hubs % 49.3583
Maximum Path Hubs % 100
AnnotationTypeLinks
Gene OntologyMolecular Function
Gene OntologyBiological Process
Gene OntologyCellular Component
SCOP2Domain Identifier
SCOP2Family Identifier
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 .
CodeNAG
PDB ResiduesH:H:?1 H:H:?2 H:H:?5
Environment DetailsOpen EMBL-EBI Page
CodeNAG
NameN-Acetylglucosamine
SynonymsN-Acetyl-D-glucosamine
IdentifierN-[(2R,3R,4R,5S,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]ethanamide
FormulaC8 H15 N O6
Molecular Weight221.208
SMILESCC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1O)CO)O)O
PubChem24139
Formal Charge0
Total Atoms30
Total Chiral Atoms5
Total Bonds30
Total Aromatic Bonds0

CodeBMA
PDB ResiduesH:H:?3
Environment DetailsOpen EMBL-EBI Page
CodeBMA
Namebeta-D-mannopyranose
Synonymsbeta-D-mannose; D-mannose; mannose
Identifier(2R,3S,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol
FormulaC6 H12 O6
Molecular Weight180.156
SMILESC([C@@H]1[C@H]([C@@H]([C@@H]([C@@H](O1)O)O)O)O)O
PubChem439680
Formal Charge0
Total Atoms24
Total Chiral Atoms5
Total Bonds24
Total Aromatic Bonds0

CodeMAN
PDB ResiduesH:H:?4 H:H:?6
Environment DetailsOpen EMBL-EBI Page
CodeMAN
Namealpha-D-mannopyranose
Synonymsalpha-D-mannose; D-mannose; mannose
Identifier(2S,3S,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol
FormulaC6 H12 O6
Molecular Weight180.156
SMILESC([C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O)O)O)O)O
PubChem185698
Formal Charge0
Total Atoms24
Total Chiral Atoms5
Total Bonds24
Total Aromatic Bonds0

PDBsumOpen PDBsum Page
ChainR
ProteinReceptor
UniProtP02699
Sequence
>8FD0_Chain_R
MNGTEGPNF YVPFSNKTG VVRSPFEAP QYYLAEPWQ FSMLAAYMF 
LLIMLGFPI NFLTLYVTV QHKKLRTPL NYILLNLAV ADLFMVFGG 
FTTTLYTSL HGYFVFGPT GCNLEGFFA TLGGEIALW SLVVLAIER 
YVVVCKPMS NFRNHAIMG VAFTWVMAL ACAAPPLVG WSRYIPEGM 
QCSCGIDYY TPHEETNNE SFVIYMFVV HFIIPLIVI FFCYGQLVF 
TVATTQKAE KEVTRMVII MVIAFLICW LPYAGVAFY IFTHQGSDF 
GPIFMTIPA FFAKTSAVY NPVIYIMMN KQFRNCMVT TLCC


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
1F88ASensoryOpsinsRhodopsinBos taurus11-cis-Retinal--2.82000-08-0410.1126/science.289.5480.739
1GZMASensoryOpsinsRhodopsinBos taurus11-cis-Retinal--2.652003-11-2010.1016/j.jmb.2004.08.090
1HZXASensoryOpsinsRhodopsinBos taurus11-cis-Retinal--2.82001-07-0410.1021/bi0155091
1L9HASensoryOpsinsRhodopsinBos taurus11-cis-Retinal--2.62002-05-1510.1073/pnas.082666399
1U19ASensoryOpsinsRhodopsinBos taurus11-cis-Retinal--2.22004-10-1210.1016/j.jmb.2004.07.044
2G87ASensoryOpsinsRhodopsinBos taurusAll-trans-retinal--2.62006-09-0210.1002/anie.200600595
2HPYASensoryOpsinsRhodopsinBos taurusAll-trans-retinal--2.82006-08-2210.1073/pnas.0601765103
2I35ASensoryOpsinsRhodopsinBos taurus11-cis-Retinal--3.82006-10-1710.1073/pnas.0608022103
2I36ASensoryOpsinsRhodopsinBos taurus---4.12006-10-1710.1073/pnas.0608022103
2I37ASensoryOpsinsRhodopsinBos taurus---4.152006-10-1710.1073/pnas.0608022103
2J4YASensoryOpsinsRhodopsinBos taurus11-cis-Retinal--3.42007-09-2510.1016/j.jmb.2007.03.007
2PEDASensoryOpsinsRhodopsinBos taurus9-cis-Retinal--2.952007-10-3010.1529/biophysj.107.108225
2X72ASensoryOpsinsRhodopsinBos taurusAll-trans-retinal-Gt(CT)32011-03-1610.1038/nature09795
2Z73ASensoryOpsinsRhodopsinTodarodes pacificus11-cis-Retinal--2.52008-05-1310.1038/nature06925
2ZIYASensoryOpsinsRhodopsinTodarodes pacificus11-cis-Retinal--3.72008-05-0610.1074/jbc.C800040200
3AYMASensoryOpsinsRhodopsinTodarodes pacificusAll-trans-retinal--2.82011-08-1710.1016/j.jmb.2011.08.044
3AYNASensoryOpsinsRhodopsinTodarodes pacificus9-cis-Retinal--2.72011-08-1710.1016/j.jmb.2011.08.044
3C9LASensoryOpsinsRhodopsinBos taurus11-cis-Retinal--2.652008-08-0510.1107/S0907444908017162
3C9MASensoryOpsinsRhodopsinBos taurus11-cis-Retinal--3.42008-08-0510.1107/S0907444908017162
3CAPASensoryOpsinsRhodopsinBos taurus---2.92008-06-2410.1038/nature07063
3DQBASensoryOpsinsRhodopsinBos taurus--Gt(CT)3.22008-09-2310.1038/nature07330
3OAXASensoryOpsinsRhodopsinBos taurus11-cis-Retinal--2.62011-01-1910.1016/j.bpj.2010.08.003
3PQRASensoryOpsinsRhodopsinBos taurusAll-trans-retinal-Gt(CT)2.852011-03-0910.1038/nature09789
3PXOASensoryOpsinsRhodopsinBos taurusAll-trans-retinal--32011-03-0910.1038/nature09789
4A4MASensoryOpsinsRhodopsinBos taurusAll-trans-retinal-Gt(CT)3.32012-01-2510.1073/pnas.1114089108
4BEYASensoryOpsinsRhodopsinBos taurus--Gt(CT)2.92013-05-0810.1038/embor.2013.44
4BEZASensoryOpsinsRhodopsinBos taurus---3.32013-04-2410.1038/embor.2013.44
4J4QASensoryOpsinsRhodopsinBos taurusOctyl Beta-D-Glucopyranoside-Gt(CT)2.652013-10-3010.1002/anie.201302374
4PXFASensoryOpsinsRhodopsinBos taurusOctyl Beta-D-Glucopyranoside-Arrestin1_Finger_loop2.752014-09-1710.1038/ncomms5801
4WW3ASensoryOpsinsRhodopsinTodarodes pacificusAll-trans-retinal--2.82015-06-1710.1371/journal.pone.0126970
4X1HASensoryOpsinsRhodopsinBos taurusNonyl Beta-D-Glucopyranoside-Gt(CT)2.292015-11-0410.1016/j.str.2015.09.015
4ZWJASensoryOpsinsRhodopsinHomo sapiens--Arrestin13.32015-07-2910.1038/nature14656
5DGYASensoryOpsinsRhodopsinHomo sapiens--Arrestin17.72016-03-2310.1038/sdata.2016.21
5DYSASensoryOpsinsRhodopsinBos taurusAll-trans-retinal--2.32016-08-1010.15252/embr.201642671
5EN0ASensoryOpsinsRhodopsinBos taurusAll-trans-retinal-Gt(CT)2.812016-08-1010.15252/embr.201642671
5TE3ASensoryOpsinsRhodopsinBos taurusOctyl Beta-D-Glucopyranoside--2.72017-03-1510.1073/pnas.1617446114
5TE5ASensoryOpsinsRhodopsinBos taurus20-Methanoretinal--4.012017-03-1510.1073/pnas.1617446114
5W0PASensoryOpsinsRhodopsinHomo sapiens--Arrestin13.012017-08-0910.1016/j.cell.2017.07.002
5WKTASensoryOpsinsRhodopsinBos taurusOctyl Beta-D-Glucopyranoside-Gt(CT)3.22017-12-1310.1038/nprot.2017.135
6CMOASensoryOpsinsRhodopsinHomo sapiens--Gi1/&β;1/&γ;24.52018-06-2010.1038/s41586-018-0215-y
6FK6ASensoryOpsinsRhodopsinBos taurus-PubChem 132473033-2.362018-04-0410.1073/pnas.1718084115
6FK7ASensoryOpsinsRhodopsinBos taurus-PubChem 132473034-2.622018-04-0410.1073/pnas.1718084115
6FK8ASensoryOpsinsRhodopsinBos taurus-PubChem 132473035-2.872018-04-0410.1073/pnas.1718084115
6FK9ASensoryOpsinsRhodopsinBos taurus-PubChem 132473036-2.632018-04-0410.1073/pnas.1718084115
6FKAASensoryOpsinsRhodopsinBos taurus-PubChem 132473037-2.72018-04-0410.1073/pnas.1718084115
6FKBASensoryOpsinsRhodopsinBos taurus-PubChem 132473038-3.032018-04-0410.1073/pnas.1718084115
6FKCASensoryOpsinsRhodopsinBos taurus-PubChem 132473039-2.462018-04-0410.1073/pnas.1718084115
6FKDASensoryOpsinsRhodopsinBos taurus-PubChem 137349183-2.492018-04-0410.1073/pnas.1718084115
6FUFASensoryOpsinsRhodopsinBos taurusAll-trans-retinal-Go/&β;1/&γ;23.122018-10-0310.1126/sciadv.aat7052
6I9KASensoryOpsinsRhodopsinHasarius adansoni9-cis-Retinal--2.152019-07-0310.1073/pnas.1902192116
6NWEASensoryOpsinsRhodopsinBos taurusOctyl Beta-D-Glucopyranoside-Gt(CT)2.712020-02-12To be published
6OFJASensoryOpsinsRhodopsinBos taurus---4.52019-08-2110.1074/jbc.RA119.010089
6OY9ASensoryOpsinsRhodopsinBos taurusAll-trans-retinal-Gt/&β;1/&γ;13.92019-07-2410.1016/j.molcel.2019.06.007
6OYAASensoryOpsinsRhodopsinBos taurusAll-trans-retinal-Gt/&β;1/&γ;13.32019-07-2410.1016/j.molcel.2019.06.007
6PELASensoryOpsinsRhodopsinBos taurus-CitronellolGt(CT)3.192020-06-24To be published
6PGSASensoryOpsinsRhodopsinBos taurus-GeraniolGt(CT)2.92020-07-01To be published
6PH7ASensoryOpsinsRhodopsinBos taurus-NerolGt(CT)2.92020-07-01To be published
6QNOASensoryOpsinsRhodopsinBos taurusAll-trans-retinal-Gi1/&β;1/&γ;14.382019-07-1010.7554/eLife.46041
7MT8ASensoryOpsinsRhodopsinBos taurusAll-trans-retinal-GRK15.82021-07-0710.1038/s41586-021-03721-x
7MT9ASensoryOpsinsRhodopsinBos taurusAll-trans-retinal-GRK172021-07-0710.1038/s41586-021-03721-x
7MTAASensoryOpsinsRhodopsinBos taurusAll-trans-retinal-GRK14.12021-07-0710.1038/s41586-021-03721-x
7MTBASensoryOpsinsRhodopsinBos taurusAll-trans-retinal-GRK142021-07-0710.1038/s41586-021-03721-x
7ZBCASensoryOpsinsRhodopsinBos taurus11-cis-Retinal--1.82023-03-2910.1038/s41586-023-05863-6
7ZBEASensoryOpsinsRhodopsinBos taurus11-cis-Retinal--1.82023-03-2910.1038/s41586-023-05863-6
8A6CASensoryOpsinsRhodopsinBos taurusAll-trans-retinal--1.82023-03-2910.1038/s41586-023-05863-6
8A6DASensoryOpsinsRhodopsinBos taurusAll-trans-retinal--1.82023-03-2910.1038/s41586-023-05863-6
8A6EASensoryOpsinsRhodopsinBos taurusAll-trans-retinal--1.82023-03-2910.1038/s41586-023-05863-6
8FCZASensoryOpsinsRhodopsinBos taurus11-cis-Retinal--3.72023-08-3010.1038/s41467-023-40911-9
8FD0ASensoryOpsinsRhodopsinBos taurus---3.712023-08-3010.1038/s41467-023-40911-9
8FD1ASensoryOpsinsRhodopsinBos taurus---4.252023-08-3010.1038/s41467-023-40911-9
3CAP (Dimer)ASensoryOpsinsRhodopsinBos taurus---2.92008-06-2410.1038/nature07063
6OFJ (Dimer)ASensoryOpsinsRhodopsinBos taurus---4.52019-08-2110.1074/jbc.RA119.010089
8FCZ (Dimer)ASensoryOpsinsRhodopsinBos taurus11-cis-Retinal--3.72023-08-3010.1038/s41467-023-40911-9
8FD0 (Dimer)ASensoryOpsinsRhodopsinBos taurus---3.712023-08-3010.1038/s41467-023-40911-9
8FD1 (Dimer)ASensoryOpsinsRhodopsinBos taurus---4.252023-08-3010.1038/s41467-023-40911-9




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