Research workbench
Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin and FAB1
Analyse Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin and FAB1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MTA
- Type
- protein
- Length
- 1,108 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhodopsin kinase GRK1; FAB1 heavy chain; FAB1 light chain; Rhodopsin
- EC
- 2.7.11.14
- UniProt
- P28327, P02699
- Ligands
- SGV, RET
- Pockets
- 13 · best druggability 0.86
Structure
electron microscopy · 4 distinct chains · 35% helix, 26% 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 |
| H | FAB1 heavy chain | protein | 223 | 7% helix, 52% strand | — |
| L | FAB1 light chain | protein | 215 | 5% helix, 49% strand | — |
| R | Rhodopsin | protein | 324 | 70% helix, 4% strand | P02699 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.86 | 0.92 | 47 | empty |
| 2 | 194 | 0.83 | 0.96 | 32 | RET |
| 3 | 695 | 0.75 | 0.81 | 55 | SGV |
| 4 | 56 | 0.52 | 0.88 | 18 | empty |
| 5 | 122 | 0.47 | 0.79 | 17 | empty |
Interfaces
4 interfaces between chains.
- H–L · 2224 Ų buried · 22 hydrogen bonds · protein-protein
- G–R · 1766 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 600 Ų buried · 2 hydrogen bonds · protein-protein
- G–L · 86 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 cofactor (disulfide, retinal Schiff base).
Compared structures
- 7MTA · Rhodopsin kinase (GRK1)-S5E/S488E/T489E in complex with rhodopsin and Fab1 · 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 0.89
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 7MTA · PDBe 7MTA · UniProt P28327 · UniProt P02699
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