MolNFT v1 · #182512 · protein
Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin and FAB6
7MTB · Rhodopsin kinase GRK1: “Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin and FAB6”. Electron microscopy, 2 ligands (SGV, RET), 9 pockets (best druggability 0.85). MolNFT v1 #182512 on GenesisL1: 3D structure…
- PDB
- 7MTB
- Type
- protein
- Length
- 1,109 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin kinase GRK1; FAB6 heavy chain; FAB6 light chain; Rhodopsin
- EC
- 2.7.11.14
- UniProt
- P28327, P02699
- Ligands
- SGV, RET
- Pockets
- 9 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | Rhodopsin kinase GRK1 (EC 2.7.11.14) | protein | 346 | 38% helix, 15% strand | P28327 |
| H | FAB6 heavy chain | protein | 225 | 3% helix, 40% strand | — |
| L | FAB6 light chain | protein | 214 | 4% helix, 50% strand | — |
| R | Rhodopsin | protein | 324 | 68% helix, 4% strand | P02699 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 930 | 0.85 | 0.86 | 80 | empty |
| 2 | 186 | 0.83 | 0.96 | 27 | RET |
| 3 | 379 | 0.76 | 0.86 | 43 | SGV |
| 4 | 124 | 0.42 | 0.76 | 23 | empty |
| 5 | 80 | 0.39 | 0.78 | 22 | empty |
Interfaces
4 interfaces between chains.
- H–L · 2395 Ų buried · 22 hydrogen bonds · protein-protein
- G–R · 1370 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 493 Ų buried · 4 hydrogen bonds · protein-protein
- G–L · 189 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 cofactor (disulfide, retinal Schiff base).
Compared structures
- 7MTB · Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin and Fab6 · the same entry in another collection · chain G against G, 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 0.94
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 7MTB · PDBe 7MTB · UniProt P28327 · UniProt P02699
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