MolNFT v1 · #105780 · protein
Crystal structure of double-domain arginine kinase from anthopleura japonicas in complex with L-arginine and atpgs
4RF9: “Crystal structure of double-domain arginine kinase from anthopleura japonicas in complex with L-arginine and…”. X-ray diffraction, 2 ligands (ARG, AGS), 11 pockets (best druggability 0.79). MolNFT v1 #105780 on GenesisL1: 3D…
- PDB
- 4RF9
- Type
- protein
- Length
- 1,376 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine kinase
- EC
- 2.7.3.3
- UniProt
- O15992
- Ligands
- ARG, AGS
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginine kinase (EC 2.7.3.3) | protein | 690 | 39% helix, 18% strand | O15992 |
| B | Arginine kinase (EC 2.7.3.3) | protein | 686 | 38% helix, 17% strand | O15992 |
Ligands and binding sites
- ARG · Arginine · ligand · 2 copies · chains A, B
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · chains B
- ACT · Acetate ion · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.79 | 0.88 | 53 | empty |
| 2 | 1089 | 0.74 | 0.77 | 97 | empty |
| 3 | 934 | 0.73 | 0.77 | 92 | ACT |
| 4 | 131 | 0.43 | 0.76 | 19 | empty |
| 5 | 135 | 0.40 | 0.75 | 24 | ARG |
Interfaces
1 interface between chains.
- A–B · 908 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4RF9 · Crystal structure of double-domain arginine kinase from Anthopleura japonicas in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- O15992 · AlphaFold monomer V2.0 prediction for arginine kinase (O15992) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 O15992
- Elsewhere: RCSB PDB 4RF9 · PDBe 4RF9 · UniProt O15992
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