MolNFT v1 · #180437 · protein
Crystal structure of kaba from bacillus cereus UW85 in complex with the reduced internal aldimine and with bound glutarate
7KZD · Aminotransferase class I/II-fold pyridoxal phosphate…: “Crystal structure of kaba from bacillus cereus UW85 in complex with the reduced internal aldimine and with…”. X-ray diffraction, 2 ligands (PLR, GUA), 20 pockets (best…
- 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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