MolNFT v1 · #105557 · protein
Crystal structure of RV1600 encoded aminotransferase in complex with plp-mes from mycobacterium tuberculosis
4R8D · Histidinol-phosphate aminotransferase: “Crystal structure of RV1600 encoded aminotransferase in complex with plp-mes from mycobacterium tuberculosis”. X-ray diffraction, 2 ligands (PLP, SO4), 7 pockets (best druggability 0.72).…
- PDB
- 4R8D
- Type
- protein
- Length
- 734 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidinol-phosphate aminotransferase
- EC
- 2.6.1.9
- UniProt
- I6XYD8
- Ligands
- PLP, SO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidinol-phosphate aminotransferase (EC 2.6.1.9) | protein | 369 | 44% helix, 15% strand | I6XYD8 |
| B | Histidinol-phosphate aminotransferase (EC 2.6.1.9) | protein | 365 | 44% helix, 15% strand | I6XYD8 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · 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 | 401 | 0.72 | 0.83 | 58 | PLP, MES, SO4 |
| 2 | 414 | 0.70 | 0.81 | 51 | PLP, MES, SO4 |
| 3 | 139 | 0.62 | 0.85 | 22 | empty |
| 4 | 118 | 0.58 | 0.85 | 25 | empty |
| 5 | 96 | 0.35 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3701 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 4R8D · Crystal structure of Rv1600 encoded aminotransferase in complex with PLP-MES from… · 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 I6XYD8
- Elsewhere: RCSB PDB 4R8D · PDBe 4R8D · UniProt I6XYD8
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