MolNFT v1 · #57228 · protein
Crystal structure of aldoxime dehydratase (oxdre) in complex with propionaldoxime
3A16: “Crystal structure of aldoxime dehydratase (oxdre) in complex with propionaldoxime”. X-ray diffraction, 3 ligands (HEM, PXO, MG), 20 pockets (best druggability 0.83). MolNFT v1 #57228 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3A16
- Type
- protein
- Length
- 1,412 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aldoxime dehydratase
- EC
- 4.99.1.5
- UniProt
- Q76K71
- Ligands
- HEM, PXO, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Aldoxime dehydratase (EC 4.99.1.5) | protein | 353 | 33% helix, 31% strand | Q76K71 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- PXO · (1Z)-propanal oxime · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1056 | 0.83 | 0.84 | 90 | MG |
| 2 | 704 | 0.82 | 0.86 | 69 | HEM, PXO |
| 3 | 673 | 0.82 | 0.86 | 64 | HEM, PXO |
| 4 | 654 | 0.82 | 0.86 | 64 | HEM, PXO |
| 5 | 705 | 0.82 | 0.85 | 66 | HEM, PXO |
Interfaces
4 interfaces between chains.
- C–D · 1180 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1151 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 897 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 163 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3A16 · Crystal Structure of Aldoxime Dehydratase (OxdRE) in Complex with Propionaldoxime · the same entry in another collection · chain A 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 Q76K71
- Elsewhere: RCSB PDB 3A16 · PDBe 3A16 · UniProt Q76K71
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