Research workbench
Crystal structure of kaba from bacillus cereus UW85 in complex with the internal aldimine
Analyse Crystal structure of kaba from bacillus cereus UW85 in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KZ3
- Type
- protein
- Length
- 1,756 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
- NA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Aminotransferase class I/II-fold pyridoxal phosphate- dependent enzyme (EC 2.6.1.1) | protein | 439 | 43% helix, 15% strand | C0JRF5 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains C, D
- EDO · 1,2-ethanediol · additive · 69 copies · chains A, C, B, 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 | 505 | 0.77 | 0.85 | 62 | EDO |
| 2 | 348 | 0.76 | 0.87 | 41 | EDO, NA |
| 3 | 446 | 0.70 | 0.81 | 44 | EDO |
| 4 | 404 | 0.70 | 0.81 | 46 | EDO |
| 5 | 379 | 0.69 | 0.81 | 34 | EDO |
Interfaces
5 interfaces between chains.
- B–D · 2545 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 2523 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 675 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 560 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 186 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 7KZ3 · Crystal structure of KabA from Bacillus cereus UW85 in complex with the internal aldimine · 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 C0JRF5
- Elsewhere: RCSB PDB 7KZ3 · PDBe 7KZ3 · UniProt C0JRF5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.