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
1S:S:V54 3.208517
2S:S:E57 4.5725418
3S:S:N58 5.452519
4S:S:V61 2.3425419
5S:S:I65 1.8375407
6S:S:F71 5.8875408
7S:S:M75 3.3075448
8S:S:F76 8.1325449
9S:S:V79 1.575407
10S:S:A83 1.7275419
11S:S:D86 5.992519
12S:S:A89 2.0125408
13S:S:G90 1.84407
14S:S:G92 1.71434
15S:S:L95 3.5675437
16S:S:F97 6.26254115
17S:S:L112 3.5175435
18S:S:I124 2.194518
19S:S:L127 3.2125418
20S:S:Y135 6.5945108
21S:S:W161 4.0945129
22S:S:P171 5.2675425
23S:S:W175 5.28424
24S:S:V186 2.0025404
25S:S:P189 3.56493
26S:S:L190 3.2075423
27S:S:H194 5.77833627
28S:S:F202 5.8875418
29S:S:F203 5.804514
30S:S:F206 3.3875406
31S:S:Q211 7.4925402
32S:S:Y213 5.18509
33S:S:Q215 6.264106
34S:S:L249 4.2975407
35S:S:F256 3.6275419
36S:S:W260 4.36718
37S:S:L261 2.025414
38S:S:Y266 5.89503
39S:S:N293 6.74419
40S:S:P294 6.4275419
41S:S:Y297 3.665419
42R:R:D44 6.43404
43R:R:V54 3.208557
44R:R:N58 6.014559
45R:R:V61 2.36459
46R:R:F71 7.025488
47R:R:F76 4.962589
48R:R:L78 3.458508
49R:R:D86 6.852559
50R:R:A89 2.0125408
51R:R:L95 3.574157
52R:R:L112 3.4375405
53R:R:Y135 4.945108
54R:R:Y144 9.4125408
55R:R:P189 3.4375463
56R:R:V196 3.7625413
57R:R:F202 5.252578
58R:R:F203 5.814574
59R:R:F206 4.275406
60R:R:M209 3.6075408
61R:R:Q211 7.135402
62R:R:Y213 3.946509
63R:R:Q215 7.18254106
64R:R:W260 4.965408
65R:R:L261 2.732574
66R:R:T264 5.025475
67R:R:Y266 3.5856163
68R:R:L284 2.6475404
69R:R:P294 5.166559
70R:R:I296 2.7075408
71R:R:Y297 3.6325409
72R:R:D303 6.19587
   

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
1S:S:T279 S:S:Y266 58.74464.99NoYes043
2S:S:T282 S:S:Y266 63.4594.99NoYes083
3S:S:P262 S:S:T282 64.12183.5NoNo098
4S:S:L261 S:S:P262 64.78191.64YesNo049
5S:S:F202 S:S:L261 21.84352.44YesYes184
6S:S:F202 S:S:W260 25.03683.01YesYes188
7S:S:F120 S:S:W260 28.27047.02NoYes048
8S:S:F120 S:S:L116 11.81212.44NoNo045
9S:S:G92 S:S:L116 11.13861.71YesNo045
10S:S:A89 S:S:D86 11.44791.54YesYes089
11S:S:A89 S:S:F120 19.80422.77YesNo084
12S:S:F71 S:S:F76 26.355717.15YesYes089
13S:S:F76 S:S:I65 16.88132.51YesYes097
14S:S:I65 S:S:V79 13.35461.54YesYes077
15S:S:F256 S:S:W260 34.63034.01YesYes198
16S:S:F256 S:S:L127 66.92422.44YesYes198
17S:S:L127 S:S:Y297 50.38433.52YesYes189
18S:S:I130 S:S:Y297 40.58994.84NoYes099
19S:S:I130 S:S:V79 37.72191.54NoYes097
20S:S:D303 S:S:F71 11.632.39NoYes078
21S:S:A73 S:S:P74 10.45981.87NoNo475
22S:S:F76 S:S:M75 12.12548.71YesYes498
23S:S:M75 S:S:V79 23.52111.52YesYes087
24S:S:C177 S:S:P189 11.34883.77NoYes953
25S:S:C177 S:S:T182 17.81993.38NoNo054
26S:S:S191 S:S:T182 19.4244.8NoNo064
27S:S:S191 S:S:W175 21.0088.65NoYes264
28S:S:H194 S:S:W175 28.93584.23YesYes274
29S:S:H194 S:S:L190 36.64542.57YesYes273
30S:S:L190 S:S:V187 25.45194.47YesNo035
31S:S:V186 S:S:V187 26.2031.6YesNo045
32S:S:T279 S:S:V186 55.29681.59NoYes044
33S:S:L190 S:S:L195 25.49474.15YesNo035
34S:S:L195 S:S:V186 26.9972.98NoYes054
35S:S:L190 S:S:P171 12.74541.64YesYes235
36S:S:Y213 S:S:Y297 13.46843.97YesYes099
37S:S:F206 S:S:F256 74.61644.29YesYes069
38S:S:F206 S:S:G207 99.97321.51YesNo064
39R:R:I208 S:S:G207 1001.76NoNo054
40R:R:I208 S:S:Q211 26.20974.12NoYes052
41S:S:Q211 S:S:Q215 12.87268.96YesYes026
42R:R:F202 R:R:I124 57.7232.51YesNo088
43R:R:I124 R:R:V205 52.02984.61NoNo088
44R:R:M209 R:R:V205 52.36461.52YesNo088
45R:R:L128 R:R:M209 95.3867.07NoYes078
46R:R:I208 R:R:L128 95.47712.85NoNo057
47R:R:L127 R:R:M209 40.65422.83NoYes088
48S:S:A257 S:S:F206 43.42052.77NoYes056
49S:S:A257 S:S:L261 43.02811.58NoYes054
50R:R:I103 R:R:S105 14.67613.1NoNo057
51R:R:A99 R:R:S105 17.81991.71NoNo047
52R:R:A99 R:R:L112 18.59921.58NoYes045
53R:R:L112 R:R:L95 14.68155.54YesYes057
54R:R:G92 R:R:L95 15.73251.71NoYes1547
55R:R:G92 R:R:L116 17.06211.71NoNo045
56R:R:F120 R:R:L116 19.20442.44NoNo045
57R:R:F120 R:R:W260 40.39317.02NoYes048
58R:R:F202 R:R:W260 41.20182YesYes088
59R:R:C102 R:R:F101 10.68616.98NoNo054
60R:R:C102 R:R:I103 11.48941.64NoNo055
61R:R:A89 R:R:D86 11.16681.54YesYes089
62R:R:A89 R:R:F120 22.18092.77YesNo084
63R:R:L261 R:R:P262 21.40161.64YesNo049
64R:R:F202 R:R:L261 22.08043.65YesYes784
65R:R:A298 R:R:V61 12.46281.7NoYes079
66R:R:A298 R:R:V79 12.7441.7NoNo077
67R:R:I130 R:R:V79 21.50341.54NoNo097
68R:R:I130 R:R:Y297 44.48622.42NoYes099
69R:R:L127 R:R:Y297 43.42853.52NoYes089
70R:R:F76 R:R:M75 18.29933.73YesNo098
71R:R:M75 R:R:V79 17.54551.52NoNo087
72R:R:I130 R:R:L78 24.33795.71NoYes098
73R:R:L157 R:R:L78 18.52962.77NoYes078
74R:R:A122 R:R:W161 15.56926.48NoNo079
75R:R:L157 R:R:W161 16.68052.28NoNo079
76R:R:A119 R:R:A89 14.84351.79NoYes068
77R:R:A119 R:R:L88 14.13653.15NoNo067
78R:R:L110 R:R:L173 11.41982.77NoNo054
79R:R:L173 R:R:V172 13.67191.49NoNo045
80R:R:G114 R:R:V172 14.79395.52NoNo055
81R:R:G114 R:R:L169 17.031.71NoNo053
82R:R:L169 R:R:M118 12.11474.24NoNo034
83R:R:A164 R:R:M118 13.8421.61NoNo084
84R:R:A122 R:R:A164 14.55961.79NoNo078
85R:R:L169 R:R:V115 13.33581.49NoNo034
86R:R:L88 R:R:V115 13.49251.49NoNo074
87R:R:L110 R:R:P189 10.28971.64NoYes053
88R:R:F263 R:R:T282 10.02735.19NoNo068
89R:R:P262 R:R:T282 18.20565.25NoNo098
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 9LYD
Class A
SubFamily Orphan
Type Orphan
SubType GPR3
Species Homo Sapiens
Ligand -
Other Ligand(s) -
Protein Partners -
PDB Resolution 3.66
Date 2025-04-09
D.O.I. doi.org/10.1016/j.celrep.2025.115478
Net Summary
Imin 1.51
Number of Linked Nodes 473
Number of Links 539
Number of Hubs 72
Number of Links mediated by Hubs 248
Number of Communities 17
Number of Nodes involved in Communities 95
Number of Links involved in Communities 120
Path Summary
Number Of Nodes in MetaPath 90
Number Of Links MetaPath 89
Number of Shortest Paths 158420
Length Of Smallest Path 3
Average Path Length 17.9499
Length of Longest Path 42
Minimum Path Strength 1.35
Average Path Strength 3.66013
Maximum Path Strength 15.85
Minimum Path Correlation 0.7
Average Path Correlation 0.959236
Maximum Path Correlation 1
Minimum % Of Corr. Nodes 2.94118
Average % Of Corr. Nodes 50.3706
Maximum % Of Corr. Nodes 100
Minimum Path Hubs % 0
Average Path Hubs % 42.7861
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   • adenylate cyclase-activating G protein-coupled receptor signaling pathway   • cell communication   • adenylate cyclase-modulating G protein-coupled receptor signaling pathway   • G protein-coupled receptor signaling pathway   • cellular process   • signal transduction   • metabolic process   • regulation of metabolic process   • multicellular organismal process   • homeostatic process   • positive regulation of biological process   • adaptive thermogenesis   • positive regulation of metabolic process   • multicellular organismal-level homeostasis   • regulation of cold-induced thermogenesis   • cold-induced thermogenesis   • temperature homeostasis   • positive regulation of cold-induced thermogenesis   • positive regulation of multicellular organismal process   • regulation of multicellular organismal process   • positive regulation of cellular process   • regulation of cellular component organization   • sexual reproduction   • regulation of reproductive process   • reproductive process   • meiotic cell cycle process   • cellular component organization   • meiotic nuclear division   • cell cycle   • cellular component organization or biogenesis   • regulation of cell cycle   • cell cycle process   • regulation of meiotic cell cycle   • regulation of cell cycle process   • meiotic cell cycle   • organelle fission   • regulation of organelle organization   • regulation of meiotic nuclear division   • organelle organization   • nuclear division   • regulation of nuclear division   • cell periphery   • cellular anatomical structure   • plasma membrane   • membrane   • intracellular anatomical structure   • cytoplasm
Gene OntologyCellular Component
SCOP2Domain Identifier• Aspartate/glutamate racemase
SCOP2Family Identifier• Aspartate/glutamate racemase
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
ChainS
ProteinReceptor
UniProtP46089
Sequence
>9LYD_Chain_S
APLPSPKAW DVVLCISGT LVSCENALV VAIIVGTPA FRAPMFLLV 
GSLAVADLL AGLGLVLHF AAVFCIGSA EMSLVLVGV LAMAFTASI 
GSLLAITVD RYLSLYNAL TYYSETTVT RTYVMLALV WGGALGLGL 
LPVLAWNCL DGLTTCGVV YPLSKNHLV VLAIAFFMV FGIMLQLYA 
QICRIVCRH AATRKGIAT LAVVLGAFA ACWLPFTVY CLLGDAHSP 
PLYTYLTLL PATYNSMIN PIIYAFRNQ DVQKVLWAV C


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  

ChainR
ProteinReceptor
UniProtP46089
Sequence
>9LYD_Chain_R
APLPSPKAW DVVLCISGT LVSCENALV VAIIVGTPA FRAPMFLLV 
GSLAVADLL AGLGLVLHF AAVFCIGSA EMSLVLVGV LAMAFTASI 
GSLLAITVD RYLSLYNAL TYYSETTVT RTYVMLALV WGGALGLGL 
LPVLAWNCL DGLTTCGVV YPLSKNHLV VLAIAFFMV FGIMLQLYA 
QICRIVCRH AATRKGIAT LAVVLGAFA ACWLPFTVY CLLGDAHSP 
PLYTYLTLL PATYNSMIN PIIYAFRNQ DVQKVLWAV C


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
8H8JAOrphanOrphanGPR35Homo sapiensLodoxamideCachim(NtGi1L-G13)/β1/γ23.22023-02-08doi.org/10.1038/s41421-022-00499-8
8H8J (No Gprot) AOrphanOrphanGPR35Homo sapiensLodoxamideCa3.22023-02-08doi.org/10.1038/s41421-022-00499-8
8U8FAOrphanOrphanGPR3Homo sapiensPalmitic Acid-Gs/β1/γ23.492024-03-06doi.org/10.1021/acs.biochem.3c00647
8U8F (No Gprot) AOrphanOrphanGPR3Homo sapiensPalmitic Acid-3.492024-03-06doi.org/10.1021/acs.biochem.3c00647
8WW2AOrphanOrphanGPR3Homo sapiens--chim(NtGi1-Gs)/β1/γ22.792024-02-14doi.org/10.1038/s41422-024-00932-5
8WW2 (No Gprot) AOrphanOrphanGPR3Homo sapiens--2.792024-02-14doi.org/10.1038/s41422-024-00932-5
9LYBAOrphanOrphanGPR3Homo sapiens--Gs/β1/γ23.162025-04-09doi.org/10.1016/j.celrep.2025.115478
9LYB (No Gprot) AOrphanOrphanGPR3Homo sapiens--3.162025-04-09doi.org/10.1016/j.celrep.2025.115478
9LYCAOrphanOrphanGPR3Homo sapiens--Gs/β1/γ23.062025-04-09doi.org/10.1016/j.celrep.2025.115478
9LYC (No Gprot) AOrphanOrphanGPR3Homo sapiens--3.062025-04-09doi.org/10.1016/j.celrep.2025.115478
9LYDAOrphanOrphanGPR3Homo sapiens---3.662025-04-09doi.org/10.1016/j.celrep.2025.115478
8X2KAOrphanOrphanGPR3Homo sapiensOleic monoethanolamide-chim(NtGi1-Gs)/β1/γ23.032024-04-03doi.org/10.1038/s41422-023-00919-8
8X2K (No Gprot) AOrphanOrphanGPR3Homo sapiensOleic monoethanolamide-3.032024-04-03doi.org/10.1038/s41422-023-00919-8
8XOFAOrphanOrphanGPR30Homo sapiensLys05-chim(NtGi1-Gs-CtGq)/β1/γ22.62024-04-10doi.org/10.1038/s41422-024-00963-y
8XOF (No Gprot) AOrphanOrphanGPR30Homo sapiensLys05-2.62024-04-10doi.org/10.1038/s41422-024-00963-y
8XOGAOrphanOrphanGPR30Homo sapiens--chim(NtGi1-Gs-CtGq)/β1/γ22.92024-04-10doi.org/10.1038/s41422-024-00963-y
8XOG (No Gprot) AOrphanOrphanGPR30Homo sapiens--2.92024-04-10doi.org/10.1038/s41422-024-00963-y
8XOHAOrphanOrphanGPR30Homo sapiens--chim(NtGi1-Gs-CtGq)/β1/γ23.22024-04-10doi.org/10.1038/s41422-024-00963-y
8XOH (No Gprot) AOrphanOrphanGPR30Homo sapiens--3.22024-04-10doi.org/10.1038/s41422-024-00963-y
8XOIAOrphanOrphanGPR30Homo sapiens--chim(NtGi1-Gs-CtGq)/β1/γ23.22024-04-10doi.org/10.1038/s41422-024-00963-y
8XOI (No Gprot) AOrphanOrphanGPR30Homo sapiens--3.22024-04-10doi.org/10.1038/s41422-024-00963-y
8XOJAOrphanOrphanGPR30Homo sapiens--chim(NtGi1-Gs-CtGq)/β1/γ23.12024-04-10doi.org/10.1038/s41422-024-00963-y
8XOJ (No Gprot) AOrphanOrphanGPR30Homo sapiens--3.12024-04-10doi.org/10.1038/s41422-024-00963-y
8XBEAOrphanOrphanGPR34Homo sapiensS3E-LysoPS-Gi1/β1/γ13.42024-05-15doi.org/10.1038/s41467-024-45046-z
8XBE (No Gprot) AOrphanOrphanGPR34Homo sapiensS3E-LysoPS-3.42024-05-15doi.org/10.1038/s41467-024-45046-z
8XBGAOrphanOrphanGPR34Homo sapiensS3E-LysoPS--3.432024-05-15doi.org/10.1038/s41467-024-45046-z
8SAIAOrphanOrphanGPR34Homo sapiens1-Oleoyl-2-Hydroxy-Sn-Glycero-3-Phospho-L-Serine-Gi1/β1/γ23.272023-10-04doi.org/10.1073/pnas.2308435120
8SAI (No Gprot) AOrphanOrphanGPR34Homo sapiens1-Oleoyl-2-Hydroxy-Sn-Glycero-3-Phospho-L-Serine-3.272023-10-04doi.org/10.1073/pnas.2308435120
8IYXAOrphanOrphanGPR34Homo sapiensYL-365--3.342024-03-20doi.org/10.1073/pnas.2308435120
8WRBAOrphanOrphanGPR34Homo sapiensLysophosphatidylserine-Gi1/β1/γ22.912023-11-08doi.org/10.1371/journal.pbio.3002387
8WRB (No Gprot) AOrphanOrphanGPR34Homo sapiensLysophosphatidylserine-2.912023-11-08doi.org/10.1371/journal.pbio.3002387
8XBHAOrphanOrphanGPR34Homo sapiensS3E-LysoPS-Gi1/β1/γ22.832023-12-27doi.org/10.1038/s41467-024-45046-z
8XBH (No Gprot) AOrphanOrphanGPR34Homo sapiensS3E-LysoPS-2.832023-12-27doi.org/10.1038/s41467-024-45046-z
8XBIAOrphanOrphanGPR34Homo sapiensS3E-LysoPS--3.062023-12-27doi.org/10.1038/s41467-024-45046-z
8K4NAOrphanOrphanGPR34Homo sapiensVF0-Gi1/β1/γ22.832023-10-25To be published
8K4N (No Gprot) AOrphanOrphanGPR34Homo sapiensVF0-2.832023-10-25To be published
8IZ4AOrphanOrphanGPR34Homo sapiensLysophosphatidylserine-Gi1/β1/γ22.942024-04-10To be published
8IZ4 (No Gprot) AOrphanOrphanGPR34Homo sapiensLysophosphatidylserine-2.942024-04-10To be published




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 9LYD.zip



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