MolNFT v1 · #31105 · protein
Crystal structure of a human pyridoxal kinase
2AJP: “Crystal structure of a human pyridoxal kinase”. X-ray diffraction, 3 ligands (ANP, MG, UNX), 7 pockets (best druggability 0.77). MolNFT v1 #31105 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2AJP
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal kinase
- EC
- 2.7.1.35
- UniProt
- O00764
- Ligands
- ANP, MG, UNX
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal kinase (EC 2.7.1.35) | protein | 303 | 40% helix, 21% strand | O00764 |
| B | Pyridoxal kinase (EC 2.7.1.35) | protein | 301 | 41% helix, 23% strand | O00764 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 40 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.77 | 0.82 | 63 | MG, UNX, ANP |
| 2 | 82 | 0.76 | 0.99 | 17 | UNX |
| 3 | 780 | 0.75 | 0.79 | 65 | MG, UNX, ANP |
| 4 | 97 | 0.61 | 0.88 | 17 | empty |
| 5 | 52 | 0.38 | 0.81 | 18 | UNX |
Interfaces
1 interface between chains.
- A–B · 2090 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
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 O00764
- Elsewhere: RCSB PDB 2AJP · PDBe 2AJP · UniProt O00764
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