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Crystal structure of substrate-free form of aldoxime dehydratase (oxdre)
Analyse Crystal structure of substrate-free form of aldoxime dehydratase (oxdre) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A15
- Type
- protein
- Length
- 1,430 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
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Aldoxime dehydratase (EC 4.99.1.5) | protein | 353 | 35% helix, 31% strand | Q76K71 |
| B, D | Aldoxime dehydratase (EC 4.99.1.5) | protein | 362 | 34% helix, 29% strand | Q76K71 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.87 | 0.95 | 47 | HEM |
| 2 | 408 | 0.87 | 0.94 | 49 | HEM |
| 3 | 1094 | 0.81 | 0.82 | 95 | HEM |
| 4 | 1128 | 0.81 | 0.82 | 101 | HEM |
| 5 | 71 | 0.71 | 0.97 | 27 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1109 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1085 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 398 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 103 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3A15 · Crystal Structure of Substrate-Free Form of Aldoxime Dehydratase (OxdRE) · 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 3A15 · PDBe 3A15 · UniProt Q76K71
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