MolNFT v1 · #174083 · protein
Crystal structure of 3-hydroxydecanoyl-acyl carrier protein dehydratase (faba) from pseudomonas aeruginosa in complex with DDD01870824
7BKA · 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase: “Crystal structure of 3-hydroxydecanoyl-acyl carrier protein dehydratase (faba) from pseudomonas aeruginosa in…”. X-ray diffraction, 1 ligand (4JC), 18 pockets (best druggability…
- PDB
- 7BKA
- Type
- protein
- Length
- 844 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
- EC
- 4.2.1.59, 5.3.3.14
- UniProt
- O33877
- Ligands
- 4JC
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.59, 5.3.3.14) | protein | 169 | 18% helix, 36% strand | O33877 |
| B | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.59, 5.3.3.14) | protein | 170 | 19% helix, 36% strand | O33877 |
| C, D | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.59, 5.3.3.14) | protein | 167 | 19% helix, 37% strand | O33877 |
| E | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.59, 5.3.3.14) | protein | 171 | 18% helix, 36% strand | O33877 |
Ligands and binding sites
- 4JC · 4-ethylbenzenesulfonamide · ligand · 5 copies · chains A, B, C, D, E
- DMS · Dimethyl sulfoxide · additive · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.78 | 0.98 | 28 | 4JC, DMS |
| 2 | 84 | 0.77 | 0.99 | 28 | 4JC, DMS |
| 3 | 89 | 0.77 | 0.98 | 29 | 4JC, DMS |
| 4 | 89 | 0.76 | 0.98 | 28 | 4JC, DMS |
| 5 | 142 | 0.63 | 0.86 | 26 | empty |
Interfaces
7 interfaces between chains.
- B–C · 1730 Ų buried · 34 hydrogen bonds · protein-protein
- D–E · 1707 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 801 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 800 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 64 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7BKA · 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 C 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 7BKA · PDBe 7BKA · UniProt O33877
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