MolNFT v1 · #93220 · protein
Crystal structure of arginine kinase in complex with D-arginine, mgadp, and nitrate.
4GVZ: “Crystal structure of arginine kinase in complex with D-arginine, mgadp, and nitrate.”. X-ray diffraction, 4 ligands (ADP, DAR, MG), 1 pocket (best druggability 0.77). MolNFT v1 #93220 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4GVZ
- Type
- protein
- Length
- 356 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arginine kinase
- EC
- 2.7.3.3
- UniProt
- P51541
- Ligands
- ADP, DAR, MG, NO3
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arginine kinase (EC 2.7.3.3) | protein | 356 | 40% helix, 17% strand | P51541 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- DAR · D-arginine · ligand · chains A
- MG · Magnesium ion · metal · chains A
- NO3 · Nitrate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.77 | 0.84 | 62 | ADP, MG, NO3, DAR |
Compared structures
- 4GVZ · Crystal structure of arginine kinase in complex with D-arginine, MgADP, and nitrate. · the same entry in another collection · chain A against A, TM-score 1.00
- P51541 · AlphaFold monomer V2.0 prediction for arginine kinase (P51541) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P51541
- Elsewhere: RCSB PDB 4GVZ · PDBe 4GVZ · UniProt P51541
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