Research workbench
Crystal structure of 3-hydroxydecanoyl-acyl carrier protein dehydratase (faba) from pseudomonas aeruginosa in complex with 3-(pentylthio)-4H-1,2,4-triazole
Analyse Crystal structure of 3-hydroxydecanoyl-acyl carrier protein dehydratase (faba)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B0C
- Type
- protein
- Length
- 842 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
- EC
- 4.2.1.60
- UniProt
- O33877
- Ligands
- C9H
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.60) | protein | 168 | 19% helix, 38% strand | O33877 |
| B | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.60) | protein | 170 | 19% helix, 38% strand | O33877 |
| C | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.60) | protein | 166 | 19% helix, 38% strand | O33877 |
| D | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.60) | protein | 169 | 19% helix, 37% strand | O33877 |
| E | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.60) | protein | 169 | 19% helix, 37% strand | O33877 |
Ligands and binding sites
- C9H · 5-(pentylsulfanyl)-1H-1,2,4-triazole · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.79 | 0.98 | 27 | C9H |
| 2 | 125 | 0.79 | 0.97 | 29 | C9H |
| 3 | 106 | 0.77 | 0.97 | 25 | C9H |
| 4 | 165 | 0.73 | 0.91 | 31 | C9H |
| 5 | 134 | 0.65 | 0.88 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1661 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1502 Ų buried · 25 hydrogen bonds · protein-protein
- A–E · 823 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 809 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 52 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4B0C · Crystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehydratase (FabA) from… · the same entry in another collection · chain E against E, TM-score 1.00
- O33877 · AlphaFold monomer V2.0 prediction for 3-hydroxydecanoyl-[acyl- carrier-protein]… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O33877
- Elsewhere: RCSB PDB 4B0C · PDBe 4B0C · UniProt O33877
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