MolNFT v1 · #25192 · protein
Crystal structure of pyridoxamine kinase
1VI9: “Crystal structure of pyridoxamine kinase”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.78). MolNFT v1 #25192 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1VI9
- Type
- protein
- Length
- 1,152 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxamine kinase
- EC
- 2.7.1.35
- UniProt
- P77150
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pyridoxamine kinase (EC 2.7.1.35) | protein | 288 | 42% helix, 18% strand | P77150 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- BME · Beta-mercaptoethanol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.78 | 0.87 | 45 | SO4, BME |
| 2 | 402 | 0.77 | 0.86 | 51 | SO4, BME |
| 3 | 643 | 0.77 | 0.82 | 56 | SO4 |
| 4 | 640 | 0.76 | 0.81 | 49 | SO4 |
| 5 | 622 | 0.63 | 0.74 | 52 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1898 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1862 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 133 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 36 modified, 2 covalent (engineered, oxidation, additive adduct).
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 P77150
- Elsewhere: RCSB PDB 1VI9 · PDBe 1VI9 · UniProt P77150
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