Research workbench
Crystal structure of kaba from bacillus cereus UW85 in complex with the reduced internal aldimine and with bound glutarate
Analyse Crystal structure of kaba from bacillus cereus UW85 in complex with the reduced… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KZD
- Type
- protein
- Length
- 3,504 residues
- Chains
- 8
- 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
- PLR, GUA
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, H | Aminotransferase class I/II-fold pyridoxal phosphate- dependent enzyme (EC 2.6.1.1) | protein | 438 | 42% helix, 14% strand | C0JRF5 |
| B, G | Aminotransferase class I/II-fold pyridoxal phosphate- dependent enzyme (EC 2.6.1.1) | protein | 439 | 44% helix, 15% strand | C0JRF5 |
| E, F | Aminotransferase class I/II-fold pyridoxal phosphate- dependent enzyme (EC 2.6.1.1) | protein | 437 | 43% helix, 15% strand | C0JRF5 |
Ligands and binding sites
- PLR · (5-hydroxy-4,6-dimethylpyridin-3-yl)methyl dihydrogen phosphate · ligand · 8 copies · chains A, C, B, D, E, H, F, G
- GUA · Glutaric acid · ligand · 4 copies · chains A, C, B, D, E, H, F, G
- EDO · 1,2-ethanediol · additive · 46 copies · chains A, C, B, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.78 | 0.87 | 79 | GUA, PLR, EDO |
| 2 | 489 | 0.77 | 0.85 | 80 | EDO, GUA, PLR |
| 3 | 486 | 0.76 | 0.84 | 83 | EDO, GUA, PLR |
| 4 | 513 | 0.75 | 0.83 | 65 | PLR, EDO |
| 5 | 441 | 0.74 | 0.84 | 68 | GUA, PLR |
Interfaces
11 interfaces between chains.
- E–H · 2694 Ų buried · 25 hydrogen bonds · protein-protein
- B–D · 2629 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 2606 Ų buried · 21 hydrogen bonds · protein-protein
- F–G · 2596 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 353 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 7KZD · Crystal structure of KabA from Bacillus cereus UW85 in complex with the reduced internal… · 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 7KZD · PDBe 7KZD · UniProt C0JRF5
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