MolNFT v1 · #137418 · protein
Crystal structure of an 8-amino-7-oxononanoate synthase from burkholderia multivorans with a potential glycine-plp-LYS242 cyclized intermediate or byproduct
5VNX: “Crystal structure of an 8-amino-7-oxononanoate synthase from burkholderia multivorans with a potential…”. X-ray diffraction, 3 ligands (BEN, 9EV, SO4), 6 pockets (best druggability 0.82). MolNFT v1 #137418 on GenesisL1: 3D…
- PDB
- 5VNX
- Type
- protein
- Length
- 1,174 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 8-amino-7-oxononanoate synthase
- EC
- 2.3.1.47
- UniProt
- A9AE46
- Ligands
- BEN, 9EV, SO4
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 8-amino-7-oxononanoate synthase (EC 2.3.1.47) | protein | 392 | 44% helix, 19% strand | A9AE46 |
| B, C | 8-amino-7-oxononanoate synthase (EC 2.3.1.47) | protein | 391 | 44% helix, 19% strand | A9AE46 |
Ligands and binding sites
- BEN · Benzamidine · ligand · 5 copies · chains A, B, C
- 9EV · 6-[(2R)-2-{3-hydroxy-2-methyl-5-[(phosphonooxy) methyl]pyridin-4-yl}-5-oxo-1,3-oxazolidin-3-yl]-L-norleucine · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 777 | 0.82 | 0.85 | 108 | 9EV, SO4, BEN |
| 2 | 614 | 0.81 | 0.86 | 104 | 9EV, BEN |
| 3 | 495 | 0.62 | 0.75 | 60 | EDO |
| 4 | 358 | 0.59 | 0.76 | 55 | 9EV, BEN |
| 5 | 78 | 0.38 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4116 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 542 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 448 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 5VNX · Crystal structure of an 8-amino-7-oxononanoate synthase from Burkholderia multivorans… · the same entry in another collection · chain A against A, TM-score 1.00
- A9AE46 · AlphaFold monomer V2.0 prediction for 8-amino-7-oxononanoate synthase (A9AE46) · a predicted model of the same protein · chain B 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 A9AE46
- Elsewhere: RCSB PDB 5VNX · PDBe 5VNX · UniProt A9AE46
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