MolNFT v1 · #63794 · protein
Crystal structure of putative pyridoxamine 5'-phosphate oxidase (NP_601736.1) from corynebacterium glutamicum atcc 13032 kitasato at 2.51 a resolution
3FKH: “Crystal structure of putative pyridoxamine 5'-phosphate oxidase (NP_601736.1) from corynebacterium glutamicum…”. X-ray diffraction, 1 ligand (CA), 11 pockets (best druggability 0.78). MolNFT v1 #63794 on GenesisL1: 3D structure…
- PDB
- 3FKH
- Type
- protein
- Length
- 773 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative pyridoxamine 5'-phosphate oxidase
- UniProt
- Q6M2U2
- Ligands
- CA
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 16% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative pyridoxamine 5'-phosphate oxidase | protein | 125 | 14% helix, 57% strand | Q6M2U2 |
| B | Putative pyridoxamine 5'-phosphate oxidase | protein | 133 | 17% helix, 51% strand | Q6M2U2 |
| C | Putative pyridoxamine 5'-phosphate oxidase | protein | 127 | 18% helix, 54% strand | Q6M2U2 |
| D | Putative pyridoxamine 5'-phosphate oxidase | protein | 134 | 16% helix, 51% strand | Q6M2U2 |
| E | Putative pyridoxamine 5'-phosphate oxidase | protein | 126 | 17% helix, 55% strand | Q6M2U2 |
| F | Putative pyridoxamine 5'-phosphate oxidase | protein | 128 | 16% helix, 54% strand | Q6M2U2 |
Ligands and binding sites
- CA · Calcium ion · metal · chains C, F
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · 5 copies · chains B, C, D, E, F
- GOL · Glycerol · additive · 3 copies · chains C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 847 | 0.78 | 0.81 | 79 | P33, GOL |
| 2 | 562 | 0.73 | 0.81 | 50 | P33 |
| 3 | 652 | 0.73 | 0.79 | 48 | P33 |
| 4 | 527 | 0.71 | 0.80 | 53 | P33 |
| 5 | 463 | 0.70 | 0.80 | 41 | P33 |
Interfaces
7 interfaces between chains.
- A–B · 1261 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1237 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1124 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 458 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 320 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 3FKH · Crystal structure of Putative pyridoxamine 5'-phosphate oxidase (NP_601736.1) from… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q6M2U2
- Elsewhere: RCSB PDB 3FKH · PDBe 3FKH · UniProt Q6M2U2
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