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:F9 8.965417
2R:R:V11 4.23418
3R:R:N15 12.06417
4R:R:V20 9.436516
5R:R:S22 5.415415
6R:R:P23 8.09515
7R:R:F24 6.94857715
8R:R:Y29 7.3375404
9R:R:Y30 7.05833614
10R:R:L31 5.8425414
11R:R:Y43 7.0775434
12R:R:N55 6.424539
13R:R:H65 7.824555
14R:R:Y74 5.765405
15R:R:N78 6.634569
16R:R:D83 7.5525439
17R:R:F103 5.42518
18R:R:E113 4.558515
19R:R:F115 6.9075406
20R:R:I123 4.21667
21R:R:W126 8.63525
22R:R:Y136 6.0225117
23R:R:F146 7.4275495
24R:R:F148 6.09167697
25R:R:T160 5.4775467
26R:R:W161 5.605469
27R:R:L172 4.7975405
28R:R:W175 11.0875425
29R:R:R177 13.065445
30R:R:Y178 6.67403
31R:R:P180 6.09513
32R:R:Q184 6.735413
33R:R:C187 6.3475419
34R:R:D190 8.802544
35R:R:Y191 4.468546
36R:R:Y192 6.0675445
37R:R:H195 16.8375444
38R:R:N200 5.68544
39R:R:F203 9.21333626
40R:R:Y206 6.076524
41R:R:H211 9.024526
42R:R:F212 5.00754128
43R:R:Y223 7.1185109
44R:R:E247 5.265137
45R:R:M257 8.244108
46R:R:Y268 6.2875406
47R:R:F283 6.355604
48R:R:M288 3.9125444
49R:R:Y301 5.3325435
50R:R:N302 4.84439
51R:R:P303 5.7125439
52R:R:I305 3.8125408
53R:R:F313 6.342558
54H:H:?1 16.558510
55H:H:?4 18.062570
   

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:F283 R:R:M288 19.7964.98YesYes044
2R:R:M288 R:R:Y192 21.77643.59YesYes445
3R:R:D190 R:R:Y192 29.76836.9YesYes445
4R:R:D190 R:R:N200 34.76568.08YesYes444
5R:R:N200 R:R:S176 39.97664.47YesNo045
6R:R:F203 R:R:S176 40.68259.25YesNo065
7R:R:F203 R:R:P171 56.75944.33YesNo065
8R:R:P171 R:R:Y178 60.876111.13NoYes053
9R:R:G114 R:R:Y178 60.87245.79NoYes053
10R:R:E113 R:R:G114 60.27984.91YesNo055
11R:R:C187 R:R:E113 29.37644.56YesYes195
12R:R:C187 R:R:P180 29.60673.77YesYes193
13R:R:P180 R:R:P23 18.64247.79YesYes135
14R:R:P23 R:R:V11 16.01373.53YesYes158
15R:R:E113 R:R:F103 27.88274.66YesYes158
16R:R:F103 R:R:F24 10.66155.36YesYes185
17R:R:P180 R:R:Q184 12.12547.9YesYes133
18R:R:F103 R:R:F105 21.66124.29YesNo087
19R:R:F105 R:R:V104 18.9087.87NoNo074
20R:R:V104 R:R:Y102 17.11911.36NoNo044
21R:R:P27 R:R:Y102 16.19946.95NoNo084
22R:R:P27 R:R:Y29 15.27629.74NoYes084
23R:R:F37 R:R:Y29 12.4844.13NoYes054
24R:R:L172 R:R:Y178 97.64623.52YesYes053
25R:R:F115 R:R:L172 98.45447.31YesYes065
26R:R:F115 R:R:L119 99.72696.09YesNo065
27R:R:I123 R:R:L119 99.97035.71YesNo075
28R:R:I123 R:R:N78 50.17184.25YesYes679
29R:R:N78 R:R:S127 50.33725.96YesNo698
30R:R:I75 R:R:S127 1006.19NoNo078
31R:R:I75 R:R:L131 86.81014.28NoNo079
32R:R:L131 R:R:R135 86.299217.01NoNo099
33R:R:M257 R:R:R135 70.413.72YesNo1089
34R:R:M257 R:R:Y306 72.942115.57YesNo089
35R:R:L128 R:R:Y306 64.177316.41NoNo089
36R:R:L128 R:R:N302 63.5295.49NoYes089
37R:R:N302 R:R:Y301 28.96954.65YesYes395
38R:R:T297 R:R:Y301 24.04843.75NoYes365
39R:R:T297 R:R:Y43 16.954.99NoYes364
40R:R:I123 R:R:T160 49.83934.56YesYes677
41R:R:S127 R:R:T160 50.06046.4NoYes687
42R:R:N302 R:R:P303 34.72293.26YesYes399
43R:R:N55 R:R:P303 10.98858.15YesYes399
44R:R:I54 R:R:P303 18.22623.39NoYes089
45R:R:I54 R:R:M308 17.36614.37NoNo086
46R:R:F313 R:R:M308 15.64963.73YesNo086
47R:R:I305 R:R:Y306 10.46284.84YesNo089
48R:R:I75 R:R:V130 25.14636.14NoNo077
49R:R:E134 R:R:V130 22.58825.7NoNo087
50R:R:E134 R:R:F148 21.728113.99NoYes087
51R:R:F203 R:R:Y206 16.05834.13YesYes264
52R:R:H211 R:R:Y206 10.297410.89YesYes264
53R:R:R135 R:R:Y223 15.36728.23NoYes1099
54R:R:F146 R:R:F148 10.16744.29YesYes957
55R:R:F283 R:R:Y274 11.44553.09YesNo044
56R:R:H278 R:R:Y274 10.587227.22NoNo034
57R:R:V254 R:R:Y223 15.5797.57NoYes089
58R:R:V227 R:R:V254 13.81784.81NoNo058
59R:R:T251 R:R:V227 12.91873.17NoNo065
60R:R:E247 R:R:T251 11.09444.23YesNo1376
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 3CAP
Class A
SubFamily Sensory
Type Opsins
SubType Rhodopsin
Species Bos taurus
Ligand -
Other Ligand(s) -
Protein Partners -
PDB Resolution 2.9
Date 2008-06-24
D.O.I. 10.1038/nature07063
Net Summary
Imin 3.52
Number of Linked Nodes 316
Number of Links 365
Number of Hubs 55
Number of Links mediated by Hubs 201
Number of Communities 13
Number of Nodes involved in Communities 92
Number of Links involved in Communities 127
Path Summary
Number Of Nodes in MetaPath 61
Number Of Links MetaPath 60
Number of Shortest Paths 82427
Length Of Smallest Path 3
Average Path Length 19.6995
Length of Longest Path 43
Minimum Path Strength 1.24
Average Path Strength 6.65174
Maximum Path Strength 36.54
Minimum Path Correlation 0.7
Average Path Correlation 0.949327
Maximum Path Correlation 1
Minimum % Of Corr. Nodes 3.33333
Average % Of Corr. Nodes 51.6584
Maximum % Of Corr. Nodes 100
Minimum Path Hubs % 0
Average Path Hubs % 47.1
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:?4 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

CodePLM
PDB ResiduesH:H:?11
Environment DetailsOpen EMBL-EBI Page
CodePLM
NamePalmitic Acid
SynonymsHexadecylic acid
Identifierhexadecanoic acid
FormulaC16 H32 O2
Molecular Weight256.424
SMILESCCCCCCCCCCCCCCCC(=O)O
PubChem135369651
Formal Charge0
Total Atoms50
Total Chiral Atoms0
Total Bonds49
Total Aromatic Bonds0

PDBsumOpen PDBsum Page
ChainR
ProteinReceptor
UniProtP02699
Sequence
>3CAP_Chain_R
MNGTEGPNF YVPFSNKTG VVRSPFEAP QYYLAEPWQ FSMLAAYMF 
LLIMLGFPI NFLTLYVTV QHKKLRTPL NYILLNLAV ADLFMVFGG 
FTTTLYTSL HGYFVFGPT GCNLEGFFA TLGGEIALW SLVVLAIER 
YVVVCKPMS NFRFGENHA IMGVAFTWV MALACAAPP LVGWSRYIP 
EGMQCSCGI DYYTPHEET NNESFVIYM FVVHFIIPL IVIFFCYGQ 
LVFTVKEAA AQQQESATT QKAEKEVTR MVIIMVIAF LICWLPYAG 
VAFYIFTHQ GSDFGPIFM TIPAFFAKT SAVYNPVIY IMMNKQFRN 
CMVTTLCCG KN


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




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 3CAP.zip



You can click to copy the link of this page to easily come back here later

or use this QR code to link and share this page.



You can also  read or  download a guide explaining the meaning of all files and numerical data.