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:T4 5.1175436
2R:R:F9 7.2525467
3R:R:V11 3.9675438
4R:R:V20 6.6625436
5R:R:F24 5.295445
6R:R:Q28 7.7225435
7R:R:Y30 6.364534
8R:R:L47 5.2875407
9R:R:N55 5.22489
10R:R:P71 3.3175416
11R:R:N73 4.0075418
12R:R:F91 5.28407
13R:R:Y102 3.5625404
14R:R:F103 6.48571748
15R:R:E113 3.938545
16R:R:L119 3.4525405
17R:R:E122 4.26254116
18R:R:I123 3.5965117
19R:R:F148 6.985417
20R:R:V157 3.45497
21R:R:P171 6.4375425
22R:R:S176 6.275425
23R:R:P180 5.718503
24R:R:C187 4.22449
25R:R:Y191 4.745406
26R:R:P194 4.0225401
27R:R:H195 11.682524
28R:R:T198 7.245421
29R:R:N200 7.222524
30R:R:F203 6.83526
31R:R:H211 8.68426
32R:R:I219 2.2575408
33R:R:E232 6.205454
34R:R:Q244 3.595134
35R:R:E247 6.3085137
36R:R:K248 4.1775454
37R:R:R252 6.436557
38R:R:M257 5.414108
39R:R:F283 3.3875404
40R:R:F293 5.388575
41R:R:Y301 4.5175405
42R:R:Y306 11.064519
43R:R:M317 5.3025406
44R:R:T320 4.4405
   

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:I275 14.04085.02YesNo044
2R:R:E181 R:R:Y192 13.67064.49NoNo045
3R:R:E181 R:R:I179 15.62642.73NoNo041
4R:R:I179 R:R:P180 16.74923.39NoYes013
5R:R:F9 R:R:P180 31.41782.89YesYes073
6R:R:P23 R:R:Q28 25.75966.32NoYes055
7R:R:F9 R:R:P23 28.427718.78YesNo075
8R:R:P12 R:R:V11 11.90393.53NoYes088
9R:R:P12 R:R:Q184 30.97114.74NoNo083
10R:R:P180 R:R:Q184 31.832314.21YesNo033
11R:R:C187 R:R:P180 73.6693.77YesYes093
12R:R:A26 R:R:Q28 20.40731.52NoYes025
13R:R:A26 R:R:P27 19.19191.87NoNo028
14R:R:C187 R:R:E113 72.36113.04YesYes495
15R:R:E113 R:R:T94 1007.06YesNo057
16R:R:M44 R:R:T94 99.87523.01NoNo077
17R:R:F91 R:R:M44 98.35817.46YesNo077
18R:R:F91 R:R:L47 94.75233.65YesYes077
19R:R:L47 R:R:T297 91.52885.9YesNo076
20R:R:T297 R:R:Y301 91.09822.5NoYes065
21R:R:F261 R:R:Y301 89.87896.19NoYes095
22R:R:F261 R:R:N302 80.92489.67NoNo1099
23R:R:L79 R:R:N302 84.2775.49NoNo099
24R:R:L76 R:R:L79 83.75795.54NoNo089
25R:R:L76 R:R:Y306 83.21067.03NoYes089
26R:R:F313 R:R:Y306 12.813431.98NoYes189
27R:R:F313 R:R:M317 11.879813.68NoYes086
28R:R:L68 R:R:N73 10.17756.87NoYes178
29R:R:N73 R:R:Y306 40.77033.49YesYes189
30R:R:L72 R:R:Y306 32.48823.52NoYes189
31R:R:L72 R:R:T70 31.67932.95NoNo187
32R:R:P71 R:R:T70 63.32253.5YesNo167
33R:R:N73 R:R:T70 33.45812.92YesNo187
34R:R:E134 R:R:P71 50.01413.14NoYes186
35R:R:E113 R:R:G114 76.61883.27YesNo055
36R:R:G114 R:R:Y178 75.3315.79NoNo053
37R:R:P171 R:R:Y178 73.3395.56YesNo053
38R:R:F203 R:R:P171 56.9487.22YesYes265
39R:R:F203 R:R:M207 56.51748.71YesNo265
40R:R:H211 R:R:M207 54.58976.57YesNo265
41R:R:H211 R:R:W126 52.1515.29YesNo065
42R:R:E122 R:R:W126 39.85674.36YesNo065
43R:R:E122 R:R:I123 32.56074.1YesYes1167
44R:R:I123 R:R:S127 17.12343.1YesNo078
45R:R:S127 R:R:T160 15.95246.4NoNo087
46R:R:T160 R:R:V157 14.77323.17NoYes077
47R:R:I123 R:R:L119 14.77324.28YesYes075
48R:R:P215 R:R:W126 14.773216.21NoNo095
49R:R:P215 R:R:V129 12.39081.77NoNo097
50R:R:E134 R:R:R135 48.72233.49NoNo089
51R:R:E247 R:R:R135 44.99988.14YesNo079
52R:R:E247 R:R:T251 25.42968.47YesNo076
53R:R:P171 R:R:S176 13.85577.13YesYes255
54R:R:N200 R:R:S176 14.86982.98YesYes245
55R:R:I275 R:R:Y191 11.61822.42NoYes046
56R:R:R252 R:R:T251 21.73937.76YesNo076
57R:R:F283 R:R:P12 27.3214.33YesNo048
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 6OFJ
Class A
SubFamily Sensory
Type Opsins
SubType Rhodopsin
Species Bos taurus
Ligand -
Other Ligand(s) -
Protein Partners -
PDB Resolution 4.5
Date 2019-08-21
D.O.I. 10.1074/jbc.RA119.010089
Net Summary
Imin 2.5
Number of Linked Nodes 296
Number of Links 332
Number of Hubs 44
Number of Links mediated by Hubs 164
Number of Communities 14
Number of Nodes involved in Communities 72
Number of Links involved in Communities 91
Path Summary
Number Of Nodes in MetaPath 58
Number Of Links MetaPath 57
Number of Shortest Paths 48498
Length Of Smallest Path 3
Average Path Length 17.7336
Length of Longest Path 41
Minimum Path Strength 1.26
Average Path Strength 5.46979
Maximum Path Strength 22.83
Minimum Path Correlation 0.7
Average Path Correlation 0.925283
Maximum Path Correlation 0.99
Minimum % Of Corr. Nodes 3.33333
Average % Of Corr. Nodes 39.3964
Maximum % Of Corr. Nodes 100
Minimum Path Hubs % 0
Average Path Hubs % 41.1097
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 .
PDBsumOpen PDBsum Page
ChainR
ProteinReceptor
UniProtP02699
Sequence
>6OFJ_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 K


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 6OFJ.zip



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