Research workbench
Crystal structure of double-domain arginine kinase from anthopleura japonicas in complex with ADP
Analyse Crystal structure of double-domain arginine kinase from anthopleura japonicas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RF8
- Type
- protein
- Length
- 1,379 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
- ADP, NO3
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginine kinase (EC 2.7.3.3) | protein | 686 | 41% helix, 17% strand | O15992 |
| B | Arginine kinase (EC 2.7.3.3) | protein | 693 | 40% helix, 17% strand | O15992 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · 20 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.77 | 0.84 | 61 | NO3, EPE |
| 2 | 1052 | 0.74 | 0.77 | 103 | ADP |
| 3 | 598 | 0.70 | 0.78 | 60 | NO3 |
| 4 | 376 | 0.54 | 0.74 | 52 | ADP |
| 5 | 81 | 0.51 | 0.84 | 23 | NO3 |
Interfaces
1 interface between chains.
- A–B · 966 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4RF8 · 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 0.96
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 4RF8 · PDBe 4RF8 · UniProt O15992
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