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Crystal structure of aldoxime dehydratase (oxdre) in complex with butyraldoxime (co-crystal)
Analyse Crystal structure of aldoxime dehydratase (oxdre) in complex with butyraldoxime… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A17
- Type
- protein
- Length
- 2,843 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldoxime dehydratase
- EC
- 4.99.1.5
- UniProt
- Q76K71
- Ligands
- HEM, BXO
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aldoxime dehydratase (EC 4.99.1.5) | protein | 350 | 35% helix, 30% strand | Q76K71 |
| B, F, H | Aldoxime dehydratase (EC 4.99.1.5) | protein | 359 | 34% helix, 30% strand | Q76K71 |
| C | Aldoxime dehydratase (EC 4.99.1.5) | protein | 352 | 35% helix, 30% strand | Q76K71 |
| D | Aldoxime dehydratase (EC 4.99.1.5) | protein | 360 | 34% helix, 30% strand | Q76K71 |
| E | Aldoxime dehydratase (EC 4.99.1.5) | protein | 351 | 35% helix, 30% strand | Q76K71 |
| G | Aldoxime dehydratase (EC 4.99.1.5) | protein | 353 | 35% helix, 29% strand | Q76K71 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- BXO · (1Z)-butanal oxime · ligand · 8 copies · chains A, B, C, D, E, F, G, H
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 | 418 | 0.87 | 0.94 | 46 | HEM, BXO |
| 2 | 417 | 0.87 | 0.94 | 50 | HEM, BXO |
| 3 | 398 | 0.87 | 0.95 | 50 | HEM, BXO |
| 4 | 400 | 0.87 | 0.95 | 49 | HEM, BXO |
| 5 | 406 | 0.87 | 0.94 | 49 | HEM, BXO |
Interfaces
8 interfaces between chains.
- E–F · 1099 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1094 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1091 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 1083 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 697 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3A17 · Crystal Structure of Aldoxime Dehydratase (OxdRE) in Complex with Butyraldoxime… · the same entry in another collection · chain C against C, 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 Q76K71
- Elsewhere: RCSB PDB 3A17 · PDBe 3A17 · UniProt Q76K71
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