MolNFT v1 · #38067 · protein
Crystal structure of (3R)-hydroxyacyl-acyl carrier protein DEHYDRATASE(FABZ) from helicobacter pylori complexed with compound 1
2GLP · (3R)-hydroxymyristoyl-acyl carrier protein dehydratase: “Crystal structure of (3R)-hydroxyacyl-acyl carrier protein DEHYDRATASE(FABZ) from helicobacter pylori…”. X-ray diffraction, 3 ligands (BEN, BDE, CL), 16 pockets (best…
- PDB
- 2GLP
- Type
- protein
- Length
- 905 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, BDE, CL
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E | (3R)-hydroxymyristoyl-acyl carrier protein dehydratase (EC 4.2.1.-) | protein | 152 | 24% helix, 42% strand | Q5G940 |
| B, C | (3R)-hydroxymyristoyl-acyl carrier protein dehydratase (EC 4.2.1.-) | protein | 151 | 25% helix, 42% strand | Q5G940 |
| F | (3R)-hydroxymyristoyl-acyl carrier protein dehydratase (EC 4.2.1.-) | protein | 147 | 24% helix, 41% strand | Q5G940 |
Ligands and binding sites
- BEN · Benzamidine · ligand · 10 copies · chains A, B, C, E, F
- BDE · N'-[(1E)-(3,5-dibromo-2,4-dihydroxyphenyl)methylene]nicotinohydrazide · 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
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.77 | 0.87 | 44 | BDE, CL |
| 2 | 997 | 0.76 | 0.78 | 86 | empty |
| 3 | 88 | 0.74 | 0.96 | 19 | empty |
| 4 | 81 | 0.74 | 0.96 | 22 | CL |
| 5 | 373 | 0.73 | 0.84 | 45 | CL, BDE, BEN |
Interfaces
6 interfaces between chains.
- E–F · 1461 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1449 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1225 Ų buried · 26 hydrogen bonds · protein-protein
- C–E · 1222 Ų buried · 25 hydrogen bonds · protein-protein
- B–F · 1197 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 2GLP · 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 2GLP · PDBe 2GLP · UniProt Q5G940
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.