MolNFT v1 · #114376 · protein
E. COLI fabh with small molecule inhibitor 1
5BNM · 3-oxoacyl-[acyl-carrier-protein] synthase 3: “E. COLI fabh with small molecule inhibitor 1”. X-ray diffraction, 2 ligands (4VK, SO4), 6 pockets (best druggability 0.77). MolNFT v1 #114376 on GenesisL1: 3D structure, binding sites…
- PDB
- 5BNM
- Type
- protein
- Length
- 634 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] synthase 3
- EC
- 2.3.1.180
- UniProt
- P0A6R0
- Ligands
- 4VK, SO4
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-oxoacyl-[acyl-carrier-protein] synthase 3 (EC 2.3.1.180) | protein | 317 | 40% helix, 27% strand | P0A6R0 |
Ligands and binding sites
- 4VK · N-{[3'-(hydroxymethyl)biphenyl-4-yl]methyl}benzenesulfonamide · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.77 | 0.90 | 53 | empty |
| 2 | 186 | 0.61 | 0.82 | 33 | 4VK |
| 3 | 132 | 0.59 | 0.84 | 27 | PG4 |
| 4 | 109 | 0.39 | 0.75 | 19 | empty |
| 5 | 98 | 0.35 | 0.74 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 2262 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
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 P0A6R0
- Elsewhere: RCSB PDB 5BNM · PDBe 5BNM · UniProt P0A6R0
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