MolNFT v1 · #20471 · protein
Crystal structure of pyridoxal kinase complexed with AMP- pcp and pyridoxamine
1RFT: “Crystal structure of pyridoxal kinase complexed with AMP- pcp and pyridoxamine”. X-ray diffraction, 4 ligands (ACP, PXM, ZN), 2 pockets (best druggability 0.75). MolNFT v1 #20471 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1RFT
- Type
- protein
- Length
- 309 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal kinase
- EC
- 2.7.1.35
- UniProt
- P82197
- Ligands
- ACP, PXM, ZN, K
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal kinase (EC 2.7.1.35) | protein | 309 | 39% helix, 22% strand | P82197 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · chains A
- PXM · 4-(aminomethyl)-5-(hydroxymethyl)-2-methylpyridin-3-ol · ligand · chains A
- ZN · Zinc ion · metal · chains A
- K · Potassium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.75 | 0.80 | 62 | ZN, K, ACP, PXM |
| 2 | 118 | 0.42 | 0.77 | 22 | empty |
Compared structures
- 1RFT · Crystal structure of pyridoxal kinase complexed with AMP-PCP and pyridoxamine · the same entry in another collection · chain A against A, TM-score 1.00
- P82197 · AlphaFold monomer V2.0 prediction for pyridoxal kinase (P82197) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P82197
- Elsewhere: RCSB PDB 1RFT · PDBe 1RFT · UniProt P82197
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