Research workbench
Crystal structure of plp bound 7,8-diaminopelargonic acid synthase in mycobacterium tuberculosis
Analyse Crystal structure of plp bound 7,8-diaminopelargonic acid synthase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BV0
- Type
- protein
- Length
- 824 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
- Pockets
- 5 · best druggability 0.77
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 | 410 | 42% helix, 21% strand | P0A4X6 |
| B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 414 | 40% helix, 20% strand | P0A4X6 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 665 | 0.77 | 0.82 | 76 | PLP |
| 2 | 680 | 0.74 | 0.80 | 63 | PLP |
| 3 | 237 | 0.64 | 0.82 | 28 | empty |
| 4 | 81 | 0.38 | 0.77 | 19 | empty |
| 5 | 72 | 0.33 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 4325 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 3BV0 · Crystal Structure of PLP Bound 7,8-Diaminopelargonic Acid Synthase in Mycobacterium… · 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 P0A4X6
- Elsewhere: RCSB PDB 3BV0 · PDBe 3BV0 · UniProt P0A4X6
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