MolNFT v1 · #49010 · protein
Crystal structure of a thermostable mutant of bacillus subtilis adenylate kinase (Q199R/G213E)
2QAJ: “Crystal structure of a thermostable mutant of bacillus subtilis adenylate kinase (Q199R/G213E)”. X-ray diffraction, 3 ligands (AP5, ZN, MG), 5 pockets (best druggability 0.82). MolNFT v1 #49010 on GenesisL1: 3D structure, binding…
- PDB
- 2QAJ
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenylate kinase
- EC
- 2.7.4.3
- UniProt
- P16304
- Ligands
- AP5, ZN, MG
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenylate kinase (EC 2.7.4.3) | protein | 216 | 50% helix, 16% strand | P16304 |
Ligands and binding sites
- AP5 · Bis(adenosine)-5'-pentaphosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.82 | 0.84 | 107 | MG, AP5 |
| 2 | 483 | 0.81 | 0.88 | 57 | MG, AP5 |
| 3 | 61 | 0.53 | 0.87 | 19 | empty |
| 4 | 61 | 0.52 | 0.87 | 19 | empty |
| 5 | 112 | 0.47 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 563 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2QAJ · Crystal structure of a thermostable mutant of Bacillus subtilis Adenylate Kinase… · the same entry in another collection · chain A against A, TM-score 1.00
- P16304 · AlphaFold monomer V2.0 prediction for adenylate kinase (P16304) · 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 P16304
- Elsewhere: RCSB PDB 2QAJ · PDBe 2QAJ · UniProt P16304
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