Research workbench
Adenosylmethionine-8-amino-7-oxononanoate aminotransferase from mycobacterium tuberculosis complexed with a fragment from dsf screening
Analyse Adenosylmethionine-8-amino-7-oxononanoate aminotransferase from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WYD
- Type
- protein
- Length
- 860 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
- P9WQ81
- Ligands
- PLP, 3VR
- Pockets
- 7 · best druggability 0.76
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 | 430 | 41% helix, 20% strand | P9WQ81 |
| B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 430 | 42% helix, 20% strand | P9WQ81 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- 3VR · N-methyl-1-[4-(1H-pyrazol-1-ylmethyl)phenyl]methanamine · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.76 | 0.85 | 65 | PLP, 3VR, EPE |
| 2 | 444 | 0.75 | 0.84 | 64 | PLP, 3VR, EPE |
| 3 | 210 | 0.62 | 0.82 | 26 | empty |
| 4 | 74 | 0.35 | 0.76 | 20 | empty |
| 5 | 70 | 0.35 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 4935 Ų buried · 65 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- P9WQ81 · AlphaFold monomer V2.0 prediction for adenosylmethionine-8-amino-7-oxononanoate… · a predicted model of the same protein · chain B 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 P9WQ81
- Elsewhere: RCSB PDB 4WYD · PDBe 4WYD · UniProt P9WQ81
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