MolNFT v1 · #61553 · protein
Crystal structure of (3R)-hydroxyacyl-acyl carrier protein dehydratase (fabz) from helicobacter pylori in complex with compound 3N
3DP1 · (3R)-hydroxymyristoyl-acyl carrier protein dehydratase: “Crystal structure of (3R)-hydroxyacyl-acyl carrier protein dehydratase (fabz) from helicobacter pylori in…”. X-ray diffraction, 3 ligands (BEN, 2RB, CL), 10 pockets (best…
- PDB
- 3DP1
- Type
- protein
- Length
- 899 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (3R)-hydroxymyristoyl-acyl carrier protein dehydratase
- EC
- 4.2.1.-
- UniProt
- Q5G940
- Ligands
- BEN, 2RB, CL
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | (3R)-hydroxymyristoyl-acyl carrier protein dehydratase (EC 4.2.1.-) | protein | 151 | 24% helix, 42% strand | Q5G940 |
| B, D, F | (3R)-hydroxymyristoyl-acyl carrier protein dehydratase (EC 4.2.1.-) | protein | 149 | 24% helix, 42% strand | Q5G940 |
| C | (3R)-hydroxymyristoyl-acyl carrier protein dehydratase (EC 4.2.1.-) | protein | 150 | 24% helix, 42% strand | Q5G940 |
Ligands and binding sites
- BEN · Benzamidine · ligand · 5 copies · chains B, D, E, F
- 2RB · N'-[(1E)-(3,5-dibromo-2,4-dihydroxyphenyl)methylidene]-4-methoxybenzohydrazide · ligand · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.76 | 0.78 | 78 | empty |
| 2 | 340 | 0.75 | 0.85 | 41 | 2RB, CL |
| 3 | 64 | 0.72 | 0.97 | 19 | empty |
| 4 | 305 | 0.71 | 0.84 | 40 | CL, BEN, 2RB |
| 5 | 68 | 0.70 | 0.95 | 19 | empty |
Interfaces
6 interfaces between chains.
- E–F · 1517 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1298 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 1284 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1241 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1222 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3DP1 · Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (FabZ) from… · 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
- Elsewhere: RCSB PDB 3DP1 · PDBe 3DP1 · UniProt Q5G940
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