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Crystal structure of C. difficile enoyl-acyl carrier protein reductase (fabk) in complex with an inhibitor
Analyse Crystal structure of C. difficile enoyl-acyl carrier protein reductase (fabk)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L00
- Type
- protein
- Length
- 1,251 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enoyl-acyl carrier protein reductase fabk
- EC
- 1.3.1.9, 1.13.12.16
- UniProt
- A0A031WIF2
- Ligands
- FMN, XCJ, NA
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enoyl-acyl carrier protein reductase fabk (EC 1.3.1.9, 1.13.12.16) | protein | 310 | 45% helix, 16% strand | A0A031WIF2 |
| B | Enoyl-acyl carrier protein reductase fabk (EC 1.3.1.9, 1.13.12.16) | protein | 311 | 43% helix, 16% strand | A0A031WIF2 |
| C, D | Enoyl-acyl carrier protein reductase fabk (EC 1.3.1.9, 1.13.12.16) | protein | 315 | 45% helix, 16% strand | A0A031WIF2 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- XCJ · N-[6-(methylsulfonyl)-1,3-benzothiazol-2-yl]-2-[2-(1H-pyrrol-1-yl)-1,3-thiazol-4-yl]acetamide · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.83 | 0.86 | 81 | empty |
| 2 | 405 | 0.81 | 0.90 | 65 | FMN, XCJ, NA |
| 3 | 612 | 0.80 | 0.85 | 71 | FMN, XCJ, NA, GOL |
| 4 | 1154 | 0.79 | 0.81 | 110 | FMN, XCJ, NA |
| 5 | 679 | 0.77 | 0.82 | 71 | FMN, XCJ, NA, GOL |
Interfaces
6 interfaces between chains.
- A–B · 1523 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1491 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 387 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 381 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 112 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7L00 · Crystal Structure of C. difficile Enoyl-Acyl Carrier Protein Reductase (FabK) in Complex… · 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 A0A031WIF2
- Elsewhere: RCSB PDB 7L00 · PDBe 7L00 · UniProt A0A031WIF2
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