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The crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (fabg) from yersinia pestis at 2.85A resolution
Analyse The crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (fabg)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CDY
- Type
- protein
- Length
- 832 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier protein] reductase
- EC
- 1.1.1.100
- UniProt
- Q7CJ23
- Ligands
- PO4
- Pockets
- 12 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) | protein | 213 | 50% helix, 17% strand | Q7CJ23 |
| B | 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) | protein | 205 | 51% helix, 18% strand | Q7CJ23 |
| C | 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) | protein | 209 | 49% helix, 18% strand | Q7CJ23 |
| D | 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) | protein | 205 | 52% helix, 18% strand | Q7CJ23 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.62 | 0.80 | 41 | PO4 |
| 2 | 76 | 0.59 | 0.89 | 26 | empty |
| 3 | 227 | 0.59 | 0.80 | 39 | empty |
| 4 | 192 | 0.56 | 0.79 | 35 | empty |
| 5 | 124 | 0.49 | 0.80 | 15 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1464 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 1437 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1113 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1067 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5CDY · The crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG) from Yersinia… · 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 Q7CJ23
- Elsewhere: RCSB PDB 5CDY · PDBe 5CDY · UniProt Q7CJ23
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