Research workbench
Crystal structure of S. pneumoniae enoyl-acyl carrier protein reductase (fabk) in complex with an inhibitor
Analyse Crystal structure of S. pneumoniae 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
- 2Z6J
- Type
- protein
- Length
- 614 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trans-2-enoyl-acp reductase II
- EC
- 1.3.1.9
- UniProt
- Q9FBC5
- Ligands
- FMN, TUI, CA
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trans-2-enoyl-acp reductase II (EC 1.3.1.9) | protein | 307 | 45% helix, 16% strand | Q9FBC5 |
| B | Trans-2-enoyl-acp reductase II (EC 1.3.1.9) | protein | 307 | 46% helix, 16% strand | Q9FBC5 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- TUI · 2-(4-(2-((3-(5-(pyridin-2-ylthio)thiazol-2-yl)ureido)methyl)-1H-imidazol-4-yl)phenoxy)acetic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
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 | 613 | 0.79 | 0.84 | 66 | FMN, TUI |
| 2 | 527 | 0.77 | 0.84 | 63 | FMN, TUI |
| 3 | 272 | 0.57 | 0.77 | 35 | empty |
| 4 | 54 | 0.33 | 0.77 | 14 | empty |
| 5 | 61 | 0.31 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2220 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2Z6J · Crystal Structure of S. pneumoniae 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 Q9FBC5
- Elsewhere: RCSB PDB 2Z6J · PDBe 2Z6J · UniProt Q9FBC5
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