Research workbench
Structure of mycobacterium tuberculosis ilve, a branched-chain amino acid transaminase, in complex with D-cycloserine derivative
Analyse Structure of mycobacterium tuberculosis ilve, a branched-chain amino acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U3F
- Type
- protein
- Length
- 654 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Branched-chain-amino-acid aminotransferase
- EC
- 2.6.1.42
- UniProt
- P9WQ75
- Ligands
- 7TS
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Branched-chain-amino-acid aminotransferase (EC 2.6.1.42) | protein | 326 | 27% helix, 34% strand | P9WQ75 |
| B | Branched-chain-amino-acid aminotransferase (EC 2.6.1.42) | protein | 328 | 27% helix, 34% strand | P9WQ75 |
Ligands and binding sites
- 7TS · (5-hydroxy-6-methyl-4-{[(3-oxo-2,3-dihydro-1,2-oxazol-4-yl)amino]methyl}pyridin-3-yl)methyl dihydrogen phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.72 | 0.99 | 21 | empty |
| 2 | 388 | 0.70 | 0.82 | 51 | 7TS |
| 3 | 329 | 0.65 | 0.81 | 38 | 7TS |
| 4 | 54 | 0.36 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2219 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5U3F · Structure of Mycobacterium tuberculosis IlvE, a branched-chain amino acid transaminase… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WQ75 · AlphaFold monomer V2.0 prediction for branched-chain-amino-acid aminotransferase (P9WQ75) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P9WQ75
- Elsewhere: RCSB PDB 5U3F · PDBe 5U3F · UniProt P9WQ75
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