MolNFT v1 · #38073 · protein
Crystal structure of (3R)-hydroxyacyl-acyl carrier protein DEHYDRATASE(FABZ) MUTANT(Y100A) from helicobacter pylori
2GLV · (3R)-hydroxymyristoyl-acyl carrier protein dehydratase: “Crystal structure of (3R)-hydroxyacyl-acyl carrier protein DEHYDRATASE(FABZ) MUTANT(Y100A) from helicobacter…”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability…
- PDB
- 2GLV
- Type
- protein
- Length
- 1,813 residues
- Chains
- 12
- 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
- CL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 23% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F, I, J, K | (3R)-hydroxymyristoyl-acyl carrier protein dehydratase (EC 4.2.1.-) | protein | 152 | 24% helix, 38% strand | Q5G940 |
| B | (3R)-hydroxymyristoyl-acyl carrier protein dehydratase (EC 4.2.1.-) | protein | 150 | 23% helix, 39% strand | Q5G940 |
| D, E, L | (3R)-hydroxymyristoyl-acyl carrier protein dehydratase (EC 4.2.1.-) | protein | 151 | 24% helix, 38% strand | Q5G940 |
| G | (3R)-hydroxymyristoyl-acyl carrier protein dehydratase (EC 4.2.1.-) | protein | 150 | 23% helix, 42% strand | Q5G940 |
| H | (3R)-hydroxymyristoyl-acyl carrier protein dehydratase (EC 4.2.1.-) | protein | 148 | 23% helix, 38% strand | Q5G940 |
Ligands and binding sites
- CL · Chloride ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.76 | 0.78 | 85 | empty |
| 2 | 1199 | 0.75 | 0.78 | 110 | empty |
| 3 | 78 | 0.74 | 0.97 | 21 | empty |
| 4 | 77 | 0.74 | 0.97 | 17 | empty |
| 5 | 77 | 0.74 | 0.97 | 19 | empty |
Interfaces
14 interfaces between chains.
- C–D · 1499 Ų buried · 15 hydrogen bonds · protein-protein
- K–L · 1432 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1420 Ų buried · 16 hydrogen bonds · protein-protein
- I–J · 1378 Ų buried · 17 hydrogen bonds · protein-protein
- G–L · 1314 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2GLV · Crystal structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase(FabZ)… · 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 2GLV · PDBe 2GLV · UniProt Q5G940
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