MolNFT v1 · #179819 · protein

Cryo-EM structure of the human arginine vasopressin avp-vasopressin receptor V2R-gs signaling complex

7KH0 · Vasopressin V2 receptor: “Cryo-EM structure of the human arginine vasopressin avp-vasopressin receptor V2R-gs signaling complex”. Electron microscopy, 1 ligand (NH2), 18 pockets (best druggability 0.81). MolNFT v1 #179819 on…

PDB: 7KH0
Type: protein
Length: 1,273 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Vasopressin V2 receptor; Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit…
UniProt: P30518, P62873, P08754, P01185, P59768
Ligands: NH2
Pockets: 18 · best druggability 0.81

Structure

electron microscopy · 7 distinct chains · 30% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
R	Vasopressin V2 receptor	protein	276	76% helix, 0% strand	P30518
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	339	8% helix, 48% strand	P62873
A	Guanine nucleotide-binding protein G(I) subunit alpha-3, isoform gnas-2 of guanine nucleotide-binding protein G(S) subunit alpha isoforms short fusion	protein	227	44% helix, 19% strand	P08754
L	Arg-vasopressin	protein	9	0% helix, 0% strand	P01185
G	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	protein	60	52% helix, 0% strand	P59768
S	Single Fab chain (SCFV16)	protein	236	5% helix, 47% strand	—
N	Nanobody 35	protein	126	7% helix, 44% strand	—

Ligands and binding sites

NH2 · Amino group · ion · chains R, L

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	767	0.81	0.85	59	empty
2	834	0.72	0.77	62	empty
3	1064	0.72	0.75	75	empty
4	201	0.68	0.86	29	empty
5	298	0.67	0.83	48	empty

Interfaces

9 interfaces between chains.

B–G · 2270 Å² buried · 16 hydrogen bonds · protein-protein
B–A · 1399 Å² buried · 15 hydrogen bonds · protein-protein
R–A · 1191 Å² buried · 2 hydrogen bonds · protein-protein
R–L · 984 Å² buried · 14 hydrogen bonds · protein-protein
A–N · 911 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

7KH0 · Cryo-EM structure of the human arginine vasopressin AVP-vasopressin receptor V2R-Gs… · the same entry in another collection · chain N against N, TM-score 1.00
P62873 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain B against A, TM-score 0.99
P30518 · AlphaFold monomer V2.0 prediction for vasopressin V2 receptor (P30518) · a predicted model of the same protein · chain R against A, TM-score 0.90
P59768 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain G against A, TM-score 0.89
P08754 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.74
P01185 · AlphaFold monomer V2.0 prediction for vasopressin-neurophysin 2-copeptin (P01185) · a predicted model of the same protein · chain L against A, TM-score 0.38

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P30518
Every structure of UniProt P62873
Every structure of UniProt P08754
Every structure of UniProt P01185
Every structure of UniProt P59768
Elsewhere: RCSB PDB 7KH0 · PDBe 7KH0 · UniProt P30518 · UniProt P62873 · UniProt P08754 · UniProt P01185 · UniProt P59768

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