MolNFT v1 · #180430 · protein
Crystal structure of kaba from bacillus cereus UW85 with bound cofactor pmp
7KZ6 · Aminotransferase class I/II-fold pyridoxal phosphate…: “Crystal structure of kaba from bacillus cereus UW85 with bound cofactor pmp”. X-ray diffraction, 1 ligand (PMP), 20 pockets (best druggability 0.78). MolNFT v1 #180430 on…
- PDB
- 7KZ6
- Type
- protein
- Length
- 1,753 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase class I/II-fold pyridoxal phosphate- dependent enzyme
- EC
- 2.6.1.1
- UniProt
- C0JRF5
- Ligands
- PMP
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Aminotransferase class I/II-fold pyridoxal phosphate- dependent enzyme (EC 2.6.1.1) | protein | 438 | 43% helix, 15% strand | C0JRF5 |
| D | Aminotransferase class I/II-fold pyridoxal phosphate- dependent enzyme (EC 2.6.1.1) | protein | 439 | 43% helix, 16% strand | C0JRF5 |
Ligands and binding sites
- PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 28 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.78 | 0.81 | 92 | EDO |
| 2 | 568 | 0.76 | 0.83 | 59 | EDO |
| 3 | 470 | 0.75 | 0.84 | 77 | PMP |
| 4 | 426 | 0.75 | 0.85 | 74 | PMP, EDO |
| 5 | 498 | 0.74 | 0.83 | 62 | PMP, EDO |
Interfaces
5 interfaces between chains.
- C–D · 2584 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2583 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 572 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 569 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 96 Ų buried · 0 hydrogen bonds · protein-protein
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 C0JRF5
- Elsewhere: RCSB PDB 7KZ6 · PDBe 7KZ6 · UniProt C0JRF5
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