Research workbench
Beta-ketoacyl-acp synthase I (kas) from E. COLI, apo structure
Analyse Beta-ketoacyl-acp synthase I (kas) from E. COLI, apo structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VB9
- Type
- protein
- Length
- 1,618 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] synthase 1
- EC
- 2.3.1.41
- UniProt
- P0A953
- Ligands
- CL
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | 3-oxoacyl-[acyl-carrier-protein] synthase 1 (EC 2.3.1.41) | protein | 404 | 38% helix, 22% strand | P0A953 |
| C | 3-oxoacyl-[acyl-carrier-protein] synthase 1 (EC 2.3.1.41) | protein | 406 | 38% helix, 22% strand | P0A953 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.74 | 0.87 | 48 | empty |
| 2 | 148 | 0.64 | 0.86 | 34 | empty |
| 3 | 127 | 0.63 | 0.87 | 34 | empty |
| 4 | 165 | 0.61 | 0.84 | 35 | empty |
| 5 | 160 | 0.45 | 0.76 | 33 | empty |
Interfaces
5 interfaces between chains.
- A–B · 3019 Ų buried · 51 hydrogen bonds · protein-protein
- C–D · 2981 Ų buried · 51 hydrogen bonds · protein-protein
- A–C · 255 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 124 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 120 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2VB9 · beta-ketoacyl-ACP synthase I (KAS) from E. coli, apo structure · the same entry in another collection · chain D against D, TM-score 1.00
- P0A953 · AlphaFold monomer V2.0 prediction for 3-oxoacyl-[acyl-carrier- protein] synthase 1… · 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 P0A953
- Elsewhere: RCSB PDB 2VB9 · PDBe 2VB9 · UniProt P0A953
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