Research workbench
Crystal structure of 3-hydroxydecanoyl-acyl carrier protein dehydratase (faba) mutant (H70N) from pseudomonas aeruginosa in complex with 3-hydroxydecanoyl-N-acetyl cysteamine
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
- 4B0I
- Type
- protein
- Length
- 845 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
- KBP
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.60) | protein | 168 | 18% helix, 36% strand | O33877 |
| B, C, D | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.60) | protein | 170 | 18% helix, 37% strand | O33877 |
| E | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.60) | protein | 167 | 19% helix, 36% strand | O33877 |
Ligands and binding sites
- KBP · S-[2-(acetylamino)ethyl] (3R)-3-hydroxydecanethioate · 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
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.81 | 0.98 | 33 | KBP |
| 2 | 123 | 0.81 | 0.98 | 29 | KBP |
| 3 | 126 | 0.80 | 0.98 | 29 | KBP |
| 4 | 497 | 0.72 | 0.81 | 68 | KBP |
| 5 | 186 | 0.66 | 0.85 | 29 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1685 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1582 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 692 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 671 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 67 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4B0I · Crystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehydratase (FabA) mutant… · 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 E 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 O33877
- Elsewhere: RCSB PDB 4B0I · PDBe 4B0I · UniProt O33877
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