Research workbench
Crystal structure of kaba from bacillus cereus UW85 with bound cofactor pmp
Analyse Crystal structure of kaba from bacillus cereus UW85 with bound cofactor pmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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