Research workbench
E.COLI beta-ketoacyl (acyl carrier protein) synthase I in complex with octanoic acid, 120K
Analyse E.COLI beta-ketoacyl (acyl carrier protein) synthase I in complex with octanoic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BUI
- Type
- protein
- Length
- 1,622 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] synthase I
- EC
- 2.3.1.41
- UniProt
- P14926
- Ligands
- OCA, NH4
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 3-oxoacyl-[acyl-carrier-protein] synthase I (EC 2.3.1.41) | protein | 406 | 38% helix, 22% strand | P14926 |
| D | 3-oxoacyl-[acyl-carrier-protein] synthase I (EC 2.3.1.41) | protein | 404 | 38% helix, 22% strand | P14926 |
Ligands and binding sites
- OCA · Octanoic acid (caprylic acid) · ligand · 4 copies · chains A, B, C, D
- NH4 · Ammonium ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.72 | 0.88 | 40 | OCA |
| 2 | 51 | 0.69 | 0.97 | 16 | OCA |
| 3 | 209 | 0.64 | 0.83 | 36 | empty |
| 4 | 174 | 0.64 | 0.85 | 36 | empty |
| 5 | 171 | 0.63 | 0.84 | 37 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2987 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2978 Ų buried · 50 hydrogen bonds · protein-protein
- A–D · 103 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 2BUI · E. COLI beta-ketoacyl (acyl carrier protein) synthase I in complex with octanoic acid… · the same entry in another collection · chain D against D, 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 P14926
- Elsewhere: RCSB PDB 2BUI · PDBe 2BUI · UniProt P14926
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