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:V20 8.41833616
2R:R:F24 7.64333615
3R:R:Y29 8.1075474
4R:R:Y30 9.608514
5R:R:L31 6.058514
6R:R:F37 7.1575475
7R:R:Y43 8.065434
8R:R:I48 2.985406
9R:R:H65 7.302595
10R:R:N78 6.042569
11R:R:D83 8.2325459
12R:R:V87 3.52406
13R:R:F91 6.88537
14R:R:F103 5.72833618
15R:R:F115 5.915426
16R:R:I123 4.74567
17R:R:W126 9.256505
18R:R:Y136 7.4865117
19R:R:F148 5.705407
20R:R:W175 11.3925425
21R:R:R177 12.15445
22R:R:Y178 7.442523
23R:R:C185 3.545405
24R:R:D190 9.84544
25R:R:Y191 6.1675446
26R:R:Y192 8.3225445
27R:R:H195 14.91444
28R:R:T198 5.97441
29R:R:N200 7.605444
30R:R:F203 8.56571726
31R:R:Y206 8.285424
32R:R:H211 7.23571726
33R:R:F212 4.1325408
34R:R:Y223 8.885409
35R:R:E247 5.855407
36R:R:Y268 5.782506
37R:R:F276 4.5975404
38R:R:F283 10.075404
39R:R:P285 5.035413
40R:R:P303 7.81459
41R:R:I307 7.4475457
42R:R:F313 8.796558
43H:H:?1 15.495610
   

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:D190 R:R:N200 47.22076.73YesYes444
2R:R:N200 R:R:S176 56.87587.45YesNo045
3R:R:F203 R:R:S176 58.01787.93YesNo065
4R:R:F203 R:R:P171 96.95465.78YesNo265
5R:R:P171 R:R:Y178 97.614915.3NoYes253
6R:R:G114 R:R:Y178 92.74694.35NoYes053
7R:R:E113 R:R:G114 91.8714.91NoNo055
8R:R:E113 R:R:F103 89.20297NoYes058
9R:R:F103 R:R:F24 57.92684.29YesYes185
10R:R:F24 R:R:P180 46.29097.22YesNo153
11R:R:P180 R:R:Q184 43.83846.32NoNo133
12R:R:P12 R:R:Q184 43.43756.32NoNo183
13R:R:L31 R:R:P12 38.26644.93YesNo148
14R:R:L31 R:R:V11 14.67464.47YesNo148
15R:R:V11 R:R:V20 13.41134.81NoYes186
16R:R:L31 R:R:Y30 21.34484.69YesYes144
17R:R:V20 R:R:Y30 13.542612.62YesYes164
18H:H:?1 R:R:V20 18.88227.97YesYes106
19R:R:F103 R:R:F105 34.59447.5YesNo087
20R:R:F105 R:R:V104 30.75397.87NoNo074
21R:R:V104 R:R:Y102 28.294710.09NoNo044
22R:R:P27 R:R:Y102 27.01465.56NoNo084
23R:R:P27 R:R:Y29 25.72778.34NoYes084
24R:R:F37 R:R:Y29 13.80887.22YesYes754
25R:R:F203 R:R:Y206 53.97525.16YesYes264
26R:R:H211 R:R:Y206 54.71639.8YesYes264
27R:R:E122 R:R:H211 1006.15NoYes266
28R:R:E122 R:R:L125 99.68333.98NoNo067
29R:R:L125 R:R:W265 96.06529.11NoNo078
30R:R:C264 R:R:W265 90.30457.84NoNo088
31R:R:C264 R:R:Y301 78.44975.38NoNo385
32R:R:T297 R:R:Y301 94.08774.99NoNo365
33R:R:L47 R:R:T297 83.54335.9NoNo376
34R:R:F203 R:R:M207 53.40594.98YesNo065
35R:R:H211 R:R:M207 53.29473.94YesNo065
36R:R:F91 R:R:L47 83.597212.18YesNo377
37R:R:F91 R:R:V87 17.23153.93YesYes076
38R:R:F91 R:R:M86 61.85153.73YesNo077
39R:R:A299 R:R:M86 56.62314.83NoNo097
40R:R:A299 R:R:D83 55.29924.63NoYes099
41R:R:D83 R:R:P303 49.70698.05YesYes599
42R:R:I307 R:R:P303 44.4653.39YesYes579
43R:R:F313 R:R:I307 38.798710.05YesYes587
44R:R:F313 R:R:L68 28.8647.31YesNo087
45R:R:C316 R:R:L68 18.51176.35NoNo057
46R:R:C316 R:R:H65 17.005817.69NoYes055
47R:R:F115 R:R:Y178 43.48474.13YesYes263
48R:R:F115 R:R:L119 38.47534.87YesNo065
49R:R:I123 R:R:L119 36.59554.28YesNo075
50R:R:I123 R:R:N78 33.7694.25YesYes679
51R:R:N78 R:R:S127 33.04145.96YesNo698
52R:R:I75 R:R:S127 33.3586.19NoNo078
53R:R:I75 R:R:V130 17.95927.68NoNo077
54R:R:E134 R:R:V130 14.92725.7NoNo087
55R:R:E134 R:R:F148 12.87239.33NoYes087
56R:R:I75 R:R:L131 30.27894.28NoNo079
57R:R:H211 R:R:W126 12.98686.35YesYes065
58R:R:C264 R:R:S298 11.20815.16NoNo389
59R:R:N302 R:R:S298 26.85965.96NoNo099
60R:R:L128 R:R:N302 25.78165.49NoNo089
61R:R:L128 R:R:Y306 24.764214.07NoNo089
62R:R:L131 R:R:R135 30.049918.22NoNo099
63R:R:R135 R:R:Y223 29.94889.26NoYes099
64R:R:V254 R:R:Y223 22.20738.83NoYes089
65R:R:V227 R:R:V254 20.33764.81NoNo058
66R:R:K231 R:R:V227 15.30454.55NoNo1255
67R:R:E247 R:R:K231 14.516216.2YesNo075
68R:R:D190 R:R:Y192 35.34910.34YesYes445
69R:R:Y191 R:R:Y192 12.46810.92YesYes465
70R:R:Y191 R:R:Y268 10.11324.96YesYes066
71R:R:M288 R:R:Y192 22.18375.99NoYes445
72R:R:F287 R:R:M288 21.32136.22NoNo044
73R:R:F283 R:R:F287 18.565610.72YesNo044
74R:R:F283 R:R:Y274 12.97334.13YesNo044
75R:R:H278 R:R:Y274 11.558426.13NoNo034
76R:R:H278 R:R:T277 10.13685.48NoNo035
77R:R:F212 R:R:W265 12.47472YesNo088
78R:R:M257 R:R:Y306 23.692911.97NoNo089
79R:R:M257 R:R:Y223 23.504210.78NoYes089
80R:R:S298 R:R:Y301 16.73976.36NoNo395
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 4BEZ
Class A
SubFamily Sensory
Type Opsins
SubType Rhodopsin
Species Bos taurus
Ligand -
Other Ligand(s) -
Protein Partners -
PDB Resolution 3.3
Date 2013-04-24
D.O.I. 10.1038/embor.2013.44
Net Summary
Imin 3.93
Number of Linked Nodes 316
Number of Links 352
Number of Hubs 43
Number of Links mediated by Hubs 169
Number of Communities 12
Number of Nodes involved in Communities 81
Number of Links involved in Communities 106
Path Summary
Number Of Nodes in MetaPath 81
Number Of Links MetaPath 80
Number of Shortest Paths 66560
Length Of Smallest Path 3
Average Path Length 18.2758
Length of Longest Path 40
Minimum Path Strength 1.795
Average Path Strength 6.96494
Maximum Path Strength 38.77
Minimum Path Correlation 0.7
Average Path Correlation 0.950915
Maximum Path Correlation 0.99
Minimum % Of Corr. Nodes 3.125
Average % Of Corr. Nodes 56.356
Maximum % Of Corr. Nodes 100
Minimum Path Hubs % 0
Average Path Hubs % 36.703
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
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:?4
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

CodeMAN
PDB ResiduesH:H:?5
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
>4BEZ_Chain_R
MCGTEGPNF YVPFSNKTG VVRSPFEAP QYYLAEPWQ FSMLAAYMF 
LLIMLGFPI NFLTLYVTV QHKKLRTPL NYILLNLAV ADLFMVFGD 
FTTTLYTSL HGYFVFGPT GCNLEGFFA TLGGEIALW SLVVLAIER 
YVVVCKPMS NFRFGENHA IMGVAFTWV MALACAAPP LVGWSRYIP 
EGMQCSCGI DYYTPHEET NNESFVIYM FVVHFIIPL IVIFFCYGQ 
LVFTVKEAA AQQQESATT QKAEKEVTR MVIIMVIAF LICWLPYAG 
VAFYIFTHQ GSCFGPIFM 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 4BEZ.zip



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