MolNFT v1 · #70791 · protein
Crystal structure of mycobacterium tuberculosis 7,8-diaminopelargonic acid synthase in complex with substrate analog sinefungin
3LV2 · Adenosylmethionine-8-amino-7-oxononanoate aminotransferase: “Crystal structure of mycobacterium tuberculosis 7,8-diaminopelargonic acid synthase in complex with substrate…”. X-ray diffraction, 2 ligands (PLP, SFG), 7 pockets (best…
- PDB
- 3LV2
- Type
- protein
- Length
- 836 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, SFG
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 421 | 42% helix, 20% strand | P0A4X6 |
| B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 415 | 42% helix, 20% strand | P0A4X6 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- SFG · Sinefungin · ligand · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.81 | 0.89 | 64 | PLP, SFG |
| 2 | 635 | 0.77 | 0.82 | 79 | PLP |
| 3 | 80 | 0.50 | 0.83 | 18 | empty |
| 4 | 65 | 0.44 | 0.82 | 18 | empty |
| 5 | 75 | 0.39 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 4619 Ų buried · 49 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 3LV2 · Crystal structure of Mycobacterium tuberculosis 7,8-diaminopelargonic acid synthase in… · 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 3LV2 · PDBe 3LV2 · UniProt P0A4X6
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