Research workbench
Crystal structure of (3R)-hydroxyacyl-acyl carrier protein DEHYDRATASE(FABZ) in complex with holo-acp from helicobacter pylori
Analyse Crystal structure of (3R)-hydroxyacyl-acyl carrier protein DEHYDRATASE(FABZ) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZJB
- Type
- protein
- Length
- 382 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz; Acyl carrier protein
- EC
- 4.2.1.59
- UniProt
- Q5G940, Q5EDC8
- Ligands
- PNS
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz (EC 4.2.1.59) | protein | 150 | 22% helix, 41% strand | Q5G940 |
| B | 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz (EC 4.2.1.59) | protein | 151 | 24% helix, 42% strand | Q5G940 |
| G | Acyl carrier protein | protein | 81 | 62% helix, 2% strand | Q5EDC8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.76 | 0.90 | 45 | PNS |
| 2 | 262 | 0.73 | 0.87 | 41 | empty |
| 3 | 215 | 0.65 | 0.83 | 34 | CIT |
| 4 | 211 | 0.47 | 0.74 | 37 | empty |
| 5 | 99 | 0.40 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1361 Ų buried · 16 hydrogen bonds · protein-protein
- B–G · 343 Ų buried · 3 hydrogen bonds · protein-protein
- A–G · 159 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (phosphopantetheinylation).
Compared structures
- 4ZJB · Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ) 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 Q5G940
- Every structure of UniProt Q5EDC8
- Elsewhere: RCSB PDB 4ZJB · PDBe 4ZJB · UniProt Q5G940 · UniProt Q5EDC8
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