Research workbench
Mycobaterium tuberculosis transaminase bioa complexed with substrate kapa
Analyse Mycobaterium tuberculosis transaminase bioa complexed with substrate kapa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CXQ
- Type
- protein
- Length
- 853 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
- EC
- 2.6.1.62
- UniProt
- P0A4X6
- Ligands
- PLP, KAP
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 427 | 41% helix, 20% strand | P0A4X6 |
| B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 426 | 41% helix, 20% strand | P0A4X6 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- KAP · 7-keto-8-aminopelargonic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.72 | 0.86 | 46 | PLP, KAP |
| 2 | 379 | 0.72 | 0.83 | 65 | PLP, KAP |
| 3 | 284 | 0.66 | 0.82 | 29 | EDO |
| 4 | 225 | 0.52 | 0.76 | 36 | empty |
| 5 | 83 | 0.38 | 0.77 | 23 | EDO |
Interfaces
1 interface between chains.
- A–B · 4857 Ų buried · 61 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4CXQ · Mycobaterium tuberculosis transaminase BioA complexed with substrate KAPA · the same entry in another collection · chain B against B, 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 P0A4X6
- Elsewhere: RCSB PDB 4CXQ · PDBe 4CXQ · UniProt P0A4X6
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