MolNFT v1 · #183922 · protein

Structural basis of the activation of the cc chemokine receptor 5 by a chemokine agonist

7O7F · Guanine nucleotide-binding protein G(I) subunit alpha-1: “Structural basis of the activation of the cc chemokine receptor 5 by a chemokine agonist”. Electron microscopy, 14 pockets (best druggability 0.82). MolNFT v1 #183922 on…

PDB: 7O7F
Type: protein
Length: 1,420 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine nucleotide-binding…
UniProt: P63096, P62871, P51681, P02698, P13501
Pockets: 14 · best druggability 0.82

Structure

electron microscopy · 7 distinct chains · 31% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Guanine nucleotide-binding protein G(I) subunit alpha-1	protein	219	44% helix, 18% strand	P63096
B	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	protein	338	8% helix, 47% strand	P62871
C	C-C chemokine receptor type 5	protein	300	79% helix, 2% strand	P51681
G	Guanine nucleotide-binding protein G(T) subunit gamma-T1	protein	58	60% helix, 0% strand	P02698
I	C-C motif chemokine 5	protein	67	19% helix, 19% strand	P13501
H	Fab antibody fragment heavy chain	protein	221	5% helix, 51% strand	—
F	Fab antibody fragment light chain	protein	217	6% helix, 48% strand	—

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	724	0.82	0.86	60	empty
2	1023	0.72	0.76	85	empty
3	229	0.63	0.82	32	empty
4	327	0.59	0.77	49	empty
5	450	0.57	0.74	52	empty

Interfaces

8 interfaces between chains.

B–G · 2439 Å² buried · 16 hydrogen bonds · protein-protein
C–I · 1803 Å² buried · 13 hydrogen bonds · protein-protein
H–F · 1779 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1264 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 1217 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 1 modified (disulfide, cyclization).

Compared structures

7O7F · Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist · the same entry in another collection · chain F against F, TM-score 1.00
P62871 · 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
P51681 · AlphaFold monomer V2.0 prediction for C-C chemokine receptor type 5 (P51681) · a predicted model of the same protein · chain C against A, TM-score 0.93
P02698 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(T) subunit… · a predicted model of the same protein · chain G against A, TM-score 0.89
P63096 · 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 0.81
P13501 · AlphaFold monomer V2.0 prediction for C-C motif chemokine 5 (P13501) · a predicted model of the same protein · chain I against A, TM-score 0.79

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 P63096
Every structure of UniProt P62871
Every structure of UniProt P51681
Every structure of UniProt P02698
Every structure of UniProt P13501
Elsewhere: RCSB PDB 7O7F · PDBe 7O7F · UniProt P63096 · UniProt P62871 · UniProt P51681 · UniProt P02698 · UniProt P13501

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