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
1L:L:?1 7.54530
2R:R:K26 7.3975424
3R:R:Y27 6.7075404
4R:R:Y30 5.9375425
5R:R:F38 5.6975406
6R:R:F52 4.284516
7R:R:R59 7.26407
8R:R:Y65 6.914537
9R:R:V70 3.93408
10R:R:D73 6.304519
11R:R:F76 6.5507
12R:R:L80 3.7875408
13R:R:F87 7.29405
14R:R:W92 8.42571758
15R:R:F94 8.88507
16R:R:K100 12.326567
17R:R:F106 7.668526
18R:R:T108 5405
19R:R:F116 9.63417
20R:R:D123 6.14438
21R:R:R124 6.58549
22R:R:F125 7.4775408
23R:R:R133 6.19404
24R:R:W151 5.174519
25R:R:L159 5.0725464
26R:R:E199 7.8405
27R:R:N210 8.7525417
28R:R:T226 2.96402
29R:R:M241 6.11447
30R:R:I242 5.215407
31R:R:I248 3.5975406
32R:R:F249 5.952519
33R:R:F253 7.665418
34R:R:I254 3.578506
35R:R:Y256 6.71571726
36R:R:L265 2.3875404
37R:R:R281 6.99524
38R:R:P285 6.6275423
39R:R:N294 8.4225419
40R:R:F297 3.785406
41R:R:D298 8.536519
42R:R:Y302 8.568519
   

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
1L:L:?1 R:R:L115 29.07793.66YesNo005
2R:R:L115 R:R:V150 30.69655.96NoNo057
3R:R:F116 R:R:V150 21.799813.11YesNo077
4R:R:F116 R:R:L69 30.32038.53YesNo179
5R:R:D298 R:R:L69 23.95999.5YesNo199
6R:R:D298 R:R:D73 55.84756.65YesYes199
7R:R:D73 R:R:N109 77.85256.73YesNo098
8R:R:F76 R:R:N109 93.890313.29YesNo078
9R:R:F106 R:R:F76 1006.43YesYes067
10R:R:F106 R:R:Y256 65.90115.16YesYes266
11R:R:Y256 R:R:Y284 27.088810.92YesNo265
12R:R:R281 R:R:Y284 23.81745.14YesNo245
13R:R:G112 R:R:V150 12.80631.84NoNo077
14R:R:G112 R:R:V154 12.73791.84NoNo077
15R:R:T108 R:R:V154 12.80634.76YesNo057
16R:R:L105 R:R:T108 20.87664.42NoYes055
17R:R:L105 R:R:T79 30.84464.42NoNo056
18R:R:F76 R:R:T79 31.93323.89YesNo076
19R:R:L288 R:R:Y30 14.98355.86NoYes255
20R:R:F106 R:R:R83 49.85186.41YesNo066
21R:R:F87 R:R:R83 51.3454.28YesNo056
22R:R:F87 R:R:Y27 62.019814.44YesYes054
23R:R:Y27 R:R:Y86 56.26353.97YesNo045
24R:R:F76 R:R:L80 26.08573.65YesYes078
25R:R:W92 R:R:Y86 42.46554.82YesNo085
26R:R:F94 R:R:W92 23.942821.05YesYes078
27R:R:F94 R:R:P93 15.39387.22YesNo073
28R:R:N91 R:R:P93 13.22816.52NoNo043
29R:R:N91 R:R:Q89 11.0519.24NoNo043
30R:R:L80 R:R:V37 11.10792.98YesNo087
31R:R:F38 R:R:L80 11.10793.65YesYes068
32R:R:F52 R:R:Y302 15.83276.19YesYes169
33R:R:R59 R:R:T63 11.54116.47YesNo078
34R:R:M66 R:R:Y302 45.748311.97NoYes189
35R:R:M241 R:R:R124 28.03494.96YesYes479
36R:R:M241 R:R:T305 45.2246.02YesNo076
37R:R:M66 R:R:T305 47.21874.52NoNo086
38L:L:?1 R:R:Y65 13.718210.34YesYes307
39R:R:A143 R:R:Y65 11.67795.34NoYes077
40R:R:F116 R:R:W151 11.52976.01YesYes179
41R:R:D298 R:R:N294 13.62712.12YesYes199
42R:R:L155 R:R:W151 13.01155.69NoYes039
43R:R:N294 R:R:S113 16.3577.45YesNo099
44R:R:N257 R:R:Y256 32.46895.81NoYes076
45R:R:E199 R:R:N257 28.148913.15YesNo057
46R:R:D298 R:R:L117 19.04714.07YesNo098
47R:R:F249 R:R:L117 18.3864.87YesNo098
48R:R:F249 R:R:L207 23.83456.09YesNo097
49R:R:I254 R:R:L207 23.2194.28YesNo067
50R:R:F203 R:R:I254 23.56093.77NoYes086
51R:R:F203 R:R:N257 23.720524.17NoNo087
52R:R:L260 R:R:Y256 25.43039.38NoYes066
53R:R:E199 R:R:L260 19.2753.98YesNo056
54R:R:F253 R:R:N294 44.89916.04YesYes189
55R:R:F249 R:R:N210 15.41669.67YesYes197
56R:R:A127 R:R:R138 21.48645.53NoNo087
57R:R:A127 R:R:R124 22.66615.53NoYes089
58R:R:R138 R:R:S134 24.79777.91NoNo076
59R:R:L126 R:R:S134 12.58419.01NoNo056
60R:R:F125 R:R:L126 11.04534.87YesNo085
61R:R:R133 R:R:S134 11.02826.59YesNo046
62R:R:I242 R:R:M241 22.01642.92YesYes077
63R:R:I242 R:R:V217 15.95244.61YesNo078
64R:R:I128 R:R:V217 14.40783.07NoNo088
65R:R:I128 R:R:I238 12.85197.36NoNo088
66R:R:S177 R:R:Y86 13.22811.27NoNo035
67R:R:E199 R:R:V261 41.64482.85YesNo055
68R:R:L265 R:R:V261 38.23661.49YesNo045
69R:R:L265 R:R:N269 17.54824.12YesNo044
70R:R:N269 R:R:T268 14.06025.85NoNo042
71R:R:R267 R:R:T268 10.56082.59NoNo042
72R:R:L265 R:R:S264 14.06021.5YesNo045
73R:R:I238 R:R:L221 11.28465.71NoNo088
74R:R:C252 R:R:F253 42.73914.19NoYes078
75R:R:C252 R:R:F297 40.71014.19NoYes076
76R:R:F297 R:R:I248 30.39443.77YesYes066
77R:R:I248 R:R:V244 24.06823.07YesNo065
78R:R:F304 R:R:V244 21.93666.55NoNo075
79R:R:F304 R:R:R240 11.10793.21NoNo075
80R:R:R281 R:R:Y263 26.6675.14YesNo044
81R:R:V280 R:R:Y263 24.68375.05NoNo054
82R:R:N259 R:R:V280 12.54422.96NoNo055
83R:R:I283 R:R:N259 10.48111.33NoNo055
84R:R:V266 R:R:V280 10.4813.21NoNo035
85R:R:L101 R:R:L105 10.32142.77NoNo055
86R:R:F52 R:R:T63 12.70943.89YesNo068
87R:R:F87 R:R:Y30 17.22335.16YesYes055
88R:R:D298 R:R:Y302 56.40610.34YesYes199
89R:R:D73 R:R:N294 17.92438.08YesYes199
90R:R:N109 R:R:S113 16.40265.96NoNo089
91R:R:F249 R:R:F253 13.62135.36YesYes198
92R:R:L288 R:R:Y256 10.64634.69NoYes256
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
L:L:?1 R:R:Y65 10.34 3 Yes Yes 0 7 0 1
L:L:?1 R:R:L115 3.66 3 Yes No 0 5 0 1
L:L:?1 R:R:C119 8.4 3 Yes No 0 6 0 1
L:L:?1 R:R:V122 10.51 3 Yes No 0 6 0 1
L:L:?1 R:R:D123 4.79 3 Yes Yes 0 8 0 1
R:R:D123 R:R:E61 6.5 3 Yes No 8 6 1 2
R:R:D123 R:R:T62 8.67 3 Yes No 8 7 1 2
R:R:C119 R:R:Y65 6.72 3 No Yes 6 7 1 1
R:R:D123 R:R:Y65 4.6 3 Yes Yes 8 7 1 1
R:R:A143 R:R:Y65 5.34 0 No Yes 7 7 2 1
R:R:V146 R:R:Y65 7.57 0 No Yes 5 7 2 1
R:R:L115 R:R:V150 5.96 0 No No 5 7 1 2
R:R:L209 R:R:V122 2.98 0 No No 7 6 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

ShowSimilarityNetwork TypeNameLigandDescription
40.00Single8G2YLPC8G2Y-ADGRF1-LPC-chim(Gs-CtGq)/β1/γ2
30.77Single9IYBA1D5Q9IYB-DP2-Prostaglandin-A1D5Q-Gi1/β1/γ2
30.00Single8K9LVV98K9L-μ-Damgo-VV9-Gi3/β1/γ1
30.00Single9K1CDHA9K1C-FFA1-DHA-Gi1/β1/γ2
28.57Single7WU4K6G7WU4-ADGRF1-K6G-Gi1/β1/γ2
28.57Single8XXVA1D5Q8XXV-DP2-Indomethacin-A1D5Q-Gi1/β1/γ2
27.78Single5KW2PubChem 1330539535KW2-FFA1-PubChem 133053953
25.00Single7WU3K6G7WU3-ADGRF1-K6G-Gs/β1/γ2
23.53Single5TZYMK8666; PubChem 1270535975TZY-FFA1-MK8666; PubChem 127053597
23.08Single6C1RAvacopan; Na6C1R-C5a1-PMX53-Avacopan; Na
21.43Single7WU5K6G7WU5-ADGRF1-K6G-Gi1/β1/γ2
20.00Single6OBAGTPL110746OBA-β2-S-Alprenolol-GTPL11074
20.00Single8XXUA1D5Q8XXU-DP2-A1D5Q-Gi1/β1/γ2
18.18Single7CKZMevidalen7CKZ-D1-Dopamine-Mevidalen-Gs/β1/γ2
16.67Single6C1QNDT95137276C1Q-C5a1-PMX53-NDT9513727
15.38Single5O9HNDT95137275O9H-C5a1-NDT9513727
15.38Single8IYXYL-3658IYX-GPR34-YL-365
14.29Single9K1DCholesterol9K1D-FFA2-Butanoic acid-Cholesterol-Gi1/β1/γ2
11.11Single9GE2Cholesterol9GE2-GPR55-ML184-Cholesterol-chim(CtGi1-G13)/β1/γ2
11.11Single9K1DCholesterol9K1D-FFA2-Butanoic acid-Cholesterol-Gi1/β1/γ2
8.33Single8X2KOleic monoethanolamide8X2K-GPR3-Oleic monoethanolamide-chim(NtGi1-Gs)/β1/γ2
7.69Single8U8FPalmitic Acid8U8F-GPR3-Palmitic Acid-Gs/β1/γ2
7.14Single6N48PubChem 1384542566N48-β2-BI167107-PubChem 138454256
5.88Single8JLPRalmitaront8JLP-TA1-Ralmitaront-Gs/β1/γ2
5.88Single8ZR5Firuglipel8ZR5-GPR119-Firuglipel-Gs/β1/γ2
5.56Single7SHEPI; PE7SHE-GPR158-PI; PE
5.56Single7T6BS1P7T6B-S1P2-S1P-chim(NtGi1L-G13)/β1/γ2
5.56Single7XZ5Lysophosphatidylcholine7XZ5-GPR119-Lysophosphatidylcholine-Gs/β1/γ2
5.56Single8VHFMBX-29828VHF-GPR119-MBX-2982-Gs/β1/γ2
5.26Single7SHFPI; PE7SHF-GPR158-PI; PE-B5; RGS7
5.26Single8ZX4Lysophosphatidylinositol 8ZX4-GPR55-Lysophosphatidylinositol-chim(NtGi1-G13)/β1/γ2
5.00Single8SAI1-Oleoyl-2-Hydroxy-Sn-Glycero-3-Phospho-L-Serine8SAI-GPR34-1-Oleoyl-2-Hydroxy-Sn-Glycero-3-Phospho-L-Serine-Gi1/β1/γ2
4.76Single6RZ8ONO-20803656RZ8-CysLT2-ONO-2080365
4.55Single7SHEPI; PE7SHE-GPR158-PI; PE
4.55Single7SHFPI; PE7SHF-GPR158-PI; PE-B5; RGS7
4.00Consensusp2y10_onOrthosteric Ligand8KGG-P2Y10-LPS-chim(NtGi2-G13)/β1/γ2
3.70Consensusp2y10_on_gpOrthosteric Ligand8KGG-P2Y10-LPS-chim(NtGi2-G13)/β1/γ2
3.57Single8KGGLPS8KGG-P2Y10-LPS-chim(NtGi2-G13)/β1/γ2

PDB Summary
PDB 5XSZ
Class A
SubFamily Lipid
Type Lysophospholipid
SubType LPA6
Species Danio Rerio
Ligand Glyceryl-mono-oleate
Other Ligand(s) -
Protein Partners -
PDB Resolution 3.2
Date 2017-08-16
D.O.I. 10.1038/nature23448
Net Summary
Imin 3.64
Number of Linked Nodes 259
Number of Links 287
Number of Hubs 42
Number of Links mediated by Hubs 160
Number of Communities 7
Number of Nodes involved in Communities 41
Number of Links involved in Communities 52
Path Summary
Number Of Nodes in MetaPath 93
Number Of Links MetaPath 92
Number of Shortest Paths 44988
Length Of Smallest Path 3
Average Path Length 13.0188
Length of Longest Path 30
Minimum Path Strength 1.385
Average Path Strength 6.44883
Maximum Path Strength 22.725
Minimum Path Correlation 0.7
Average Path Correlation 0.938807
Maximum Path Correlation 0.99
Minimum % Of Corr. Nodes 4.7619
Average % Of Corr. Nodes 59.2472
Maximum % Of Corr. Nodes 100
Minimum Path Hubs % 0
Average Path Hubs % 46.2202
Maximum Path Hubs % 100
AnnotationTypeLinks
Gene OntologyMolecular Function
Gene OntologyBiological Process• cellular response to stimulus   • regulation of biological process   • regulation of cellular process   • response to stimulus   • signaling   • biological regulation   • G protein-coupled receptor signaling pathway   • cellular process   • signal transduction   • cell communication   • adenylate cyclase-modulating G protein-coupled receptor signaling pathway   • developmental process   • multicellular organismal process   • blood vessel morphogenesis   • tube development   • angiogenesis   • vasculature development   • circulatory system development   • anatomical structure morphogenesis   • multicellular organism development   • tube morphogenesis   • anatomical structure formation involved in morphogenesis   • anatomical structure development   • blood vessel development   • system development   • biological process involved in interspecies interaction between organisms   • response to other organism   • defense response   • response to external stimulus   • response to biotic stimulus   • defense response to bacterium   • defense response to other organism   • response to stress   • response to bacterium   • response to external biotic stimulus   • carbohydrate derivative catabolic process   • catabolic process   • peptidoglycan catabolic process   • glycosaminoglycan metabolic process   • carbohydrate derivative metabolic process   • aminoglycan catabolic process   • macromolecule catabolic process   • glycosaminoglycan catabolic process   • aminoglycan metabolic process   • peptidoglycan metabolic process   • metabolic process   • macromolecule metabolic process   • symbiont-mediated cytolysis of host cell   • viral life cycle   • disruption of cell in another organism   • cytolysis   • biological process involved in interaction with host   • biological process involved in symbiotic interaction   • viral release from host cell by cytolysis   • exit from host cell   • viral process   • cytolysis in another organism   • viral release from host cell   • disruption of anatomical structure in another organism   • symbiont-mediated killing of host cell   • killing of cells of another organism   • cell killing   • cell wall organization or biogenesis   • cell wall macromolecule catabolic process   • cell wall macromolecule metabolic process   • cell periphery   • cellular anatomical structure   • plasma membrane   • membrane   • host cellular component   • host intracellular part   • host cell cytoplasm   • host cell part   • host intracellular region
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 .
CodeOLC
PDB ResiduesL:L:?1
Environment DetailsOpen EMBL-EBI Page
CodeOLC
Name(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
Synonyms1-Oleoyl-R-glycerol
Identifier
FormulaC21 H40 O4
Molecular Weight356.54
SMILES
PubChem11451146
Formal Charge0
Total Atoms65
Total Chiral Atoms1
Total Bonds64
Total Aromatic Bonds0

PDBsumOpen PDBsum Page
ChainR
ProteinReceptor
UniProtQ08BG4
Sequence
>5XSZ_Chain_R
DNFKYPLYS MVFSIVFMV GLITNVAAM YIFMCSLKL RNETTTYMM 
NLVVSDLLF VLTLPLRVF YFVQQNWPF GSLLCKLSV SLFYTNMYG 
SILFLTCIS VDRFLAIVY PFRSRGLRT KRNAKIVCA AVWVLVLSG 
SLPTGFMLN STNKLENNS ISCFEWKSH LSKVVIFIE TVGFLIPLM 
LNVVCSAMV LQTLRRPNT VLNKKKILR MIIVHLFIF CFCFIPYNV 
NLVFYSLVR TNTLKGCAA ESVVRTIYP IALCIAVSN CCFDPIVYY 
FTSETIQNS ASSEDLYFQ


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
9ITBALipidLysophospholipidLPA6Homo sapiensLPA-chim(NtGi1-Gs-CtGq)/β1/γ22.892025-01-15doi.org/10.1073/pnas.2415426122
9ITB (No Gprot) ALipidLysophospholipidLPA6Homo sapiensLPA-2.892025-01-15doi.org/10.1073/pnas.2415426122
9ITEALipidLysophospholipidLPA6Homo sapiensLPA-chim(NtGi2-G13)/β1/γ23.062025-01-15doi.org/10.1073/pnas.2415426122
9ITE (No Gprot) ALipidLysophospholipidLPA6Homo sapiensLPA-3.062025-01-15doi.org/10.1073/pnas.2415426122




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 5XSZ.zip



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