MolNFT v1 · #182509 · protein

Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin

7MT8 · Rhodopsin kinase GRK1: “Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin”. Electron microscopy, 2 ligands (SGV, RET), 6 pockets (best druggability 0.86). MolNFT v1 #182509 on GenesisL1: 3D structure, binding sites…

PDB: 7MT8
Type: protein
Length: 670 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rhodopsin kinase GRK1; Rhodopsin
EC: 2.7.11.14
UniProt: P28327, P02699
Ligands: SGV, RET
Pockets: 6 · best druggability 0.86

Structure

electron microscopy · 2 distinct chains · 52% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	Rhodopsin kinase GRK1 (EC 2.7.11.14)	protein	346	38% helix, 14% strand	P28327
R	Rhodopsin	protein	324	68% helix, 3% strand	P02699

Ligands and binding sites

SGV · Sangivamycin · ligand · chains G
RET · Retinal · ligand · chains R

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	400	0.86	0.94	53	empty
2	227	0.85	0.97	26	RET
3	528	0.77	0.84	54	SGV
4	135	0.46	0.77	20	empty
5	63	0.35	0.78	15	empty

Interfaces

1 interface between chains.

G–R · 1861 Å² buried · 28 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 cofactor, 1 disulfide (retinal Schiff base, disulfide).

Compared structures

7MT8 · Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin · the same entry in another collection · chain R against R, TM-score 1.00
P28327 · AlphaFold monomer V2.0 prediction for rhodopsin kinase GRK1 (P28327) · a predicted model of the same protein · chain G against A, TM-score 0.92

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 P28327
Every structure of UniProt P02699
Elsewhere: RCSB PDB 7MT8 · PDBe 7MT8 · UniProt P28327 · UniProt P02699

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