Research workbench
Crystal structure of 3-hydroxydecanoyl-acyl carrier protein dehydratase (faba) from pseudomonas aeruginosa in complex with DDD00084774
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
- 7BHJ
- Type
- protein
- Length
- 839 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
- TQH
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.59, 5.3.3.14) | protein | 170 | 18% helix, 36% strand | O33877 |
| B | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.59, 5.3.3.14) | protein | 163 | 20% helix, 37% strand | O33877 |
| 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 | 169 | 18% helix, 36% strand | O33877 |
Ligands and binding sites
- TQH · ~{N}-[(5-methylfuran-2-yl)methyl]-5-thiophen-2-yl-4~{H}-1,2,4-triazol-3-amine · ligand · 4 copies · chains B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.78 | 0.98 | 29 | TQH |
| 2 | 103 | 0.78 | 0.98 | 27 | TQH |
| 3 | 138 | 0.74 | 0.92 | 32 | TQH |
| 4 | 380 | 0.68 | 0.81 | 64 | TQH |
| 5 | 149 | 0.61 | 0.85 | 27 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1579 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1553 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 814 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 810 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 25 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7BHJ · 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 D 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 7BHJ · PDBe 7BHJ · UniProt O33877
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