MolNFT v1 · #152435 · protein
Crystal structure of (3R)-hydroxyacyl-acyl carrier protein DEHYDRATASE(FABZ) Y100A mutant in complex with holo-acp from helicobacter pylori
6IHC · 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz: “Crystal structure of (3R)-hydroxyacyl-acyl carrier protein DEHYDRATASE(FABZ) Y100A mutant in complex with…”. X-ray diffraction, 1 ligand (PN7), 12 pockets (best druggability…
- PDB
- 6IHC
- Type
- protein
- Length
- 970 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz; Holo-form acyl carrier protein…
- EC
- 4.2.1.59
- UniProt
- A0A1Q4MZN5, B6JLE2
- Ligands
- PN7
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz (EC 4.2.1.59) | protein | 151 | 24% helix, 42% strand | A0A1Q4MZN5 |
| C, D | 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz (EC 4.2.1.59) | protein | 150 | 23% helix, 41% strand | A0A1Q4MZN5 |
| E | 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz (EC 4.2.1.59) | protein | 150 | 24% helix, 42% strand | A0A1Q4MZN5 |
| F | 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz (EC 4.2.1.59) | protein | 153 | 24% helix, 42% strand | A0A1Q4MZN5 |
| G | Holo-form acyl carrier protein (holo-acp) | protein | 65 | 48% helix, 3% strand | B6JLE2 |
Ligands and binding sites
- PN7 · N~3~-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy) butanoyl]-N-(2-sulfanylethyl)-beta-alaninamide · ligand · chains A, B, G
- CIT · Citric acid · additive · 3 copies · chains A, B, C, F, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.77 | 0.97 | 20 | CIT |
| 2 | 87 | 0.77 | 0.98 | 18 | CIT |
| 3 | 100 | 0.76 | 0.96 | 19 | CIT |
| 4 | 1009 | 0.76 | 0.78 | 78 | empty |
| 5 | 272 | 0.74 | 0.87 | 47 | empty |
Interfaces
8 interfaces between chains.
- A–F · 1359 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1300 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1276 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 1263 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 1251 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6IHC · Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) Y100A mutant… · the same entry in another collection · chain G against G, TM-score 1.00
- B6JLE2 · AlphaFold monomer V2.0 prediction for acyl carrier protein (B6JLE2) · a predicted model of the same protein · chain G against A, TM-score 0.94
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 A0A1Q4MZN5
- Every structure of UniProt B6JLE2
- Elsewhere: RCSB PDB 6IHC · PDBe 6IHC · UniProt A0A1Q4MZN5 · UniProt B6JLE2
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