Research workbench
Crystal structure of kaba from bacillus cereus UW85 in complex with the plp external aldimine adduct with kanosamine-6-phosphate
Analyse Crystal structure of kaba from bacillus cereus UW85 in complex with the plp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KZ5
- 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
- O1G, NA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% 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 | 42% helix, 16% strand | C0JRF5 |
Ligands and binding sites
- O1G · 3-deoxy-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy) methyl]pyridin-4-yl}methylidene)amino]-6-O-phosphono-alpha-D-gluco pyranose · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 51 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 | 1098 | 0.79 | 0.81 | 88 | EDO |
| 2 | 645 | 0.78 | 0.83 | 69 | EDO |
| 3 | 615 | 0.77 | 0.83 | 85 | O1G, EDO |
| 4 | 559 | 0.75 | 0.82 | 78 | EDO, O1G |
| 5 | 480 | 0.73 | 0.83 | 57 | O1G |
Interfaces
5 interfaces between chains.
- C–D · 2562 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2555 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 649 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 635 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 123 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7KZ5 · Crystal structure of KabA from Bacillus cereus UW85 in complex with the plp external… · 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 7KZ5 · PDBe 7KZ5 · UniProt C0JRF5
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