MolNFT v1 · #140655 · protein
Crystal structure of an aminotransferase from mycobacterium tuberculosis
5YHV: “Crystal structure of an aminotransferase from mycobacterium tuberculosis”. X-ray diffraction, 3 ligands (PLP, AKG, GLU), 20 pockets (best druggability 0.78). MolNFT v1 #140655 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5YHV
- Type
- protein
- Length
- 1,529 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase
- EC
- 2.6.1.-
- UniProt
- P96847
- Ligands
- PLP, AKG, GLU
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminotransferase (EC 2.6.1.-) | protein | 394 | 46% helix, 14% strand | P96847 |
| B | Aminotransferase (EC 2.6.1.-) | protein | 387 | 47% helix, 14% strand | P96847 |
| C | Aminotransferase (EC 2.6.1.-) | protein | 384 | 47% helix, 14% strand | P96847 |
| D | Aminotransferase (EC 2.6.1.-) | protein | 364 | 43% helix, 13% strand | P96847 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 4 copies · chains A, B, C, D
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains B, C
- GLU · Glutamic acid · ligand · chains A
- GOL · Glycerol · additive · 3 copies · chains A, B, C
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 | 149 | 0.78 | 0.94 | 29 | empty |
| 2 | 278 | 0.75 | 0.88 | 57 | empty |
| 3 | 380 | 0.73 | 0.84 | 65 | PLP |
| 4 | 453 | 0.73 | 0.82 | 64 | PLP |
| 5 | 68 | 0.72 | 0.97 | 28 | PLP |
Interfaces
6 interfaces between chains.
- A–B · 2976 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 2831 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 380 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 375 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 132 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 5YHV · Crystal structure of an aminotransferase from Mycobacterium tuberculosis · the same entry in another collection · chain A against A, TM-score 1.00
- P96847 · AlphaFold monomer V2.0 prediction for valine--pyruvate aminotransferase (P96847) · a predicted model of the same protein · chain C 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 P96847
- Elsewhere: RCSB PDB 5YHV · PDBe 5YHV · UniProt P96847
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