MolNFT v1 · #82615 · protein
Crystal structure of native 1,6-apd (2-animophenol-1,6-dioxygenase) complex with 4-nitrocatechol
3VSI · 2-amino-5-chlorophenol 1,6-dioxygenase alpha subunit: “Crystal structure of native 1,6-apd (2-animophenol-1,6-dioxygenase) complex with 4-nitrocatechol”. X-ray diffraction, 2 ligands (4NC, FE), 8 pockets (best druggability 0.85).…
- PDB
- 3VSI
- Type
- protein
- Length
- 1,143 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-amino-5-chlorophenol 1,6-dioxygenase alpha subunit; 2-amino-5-chlorophenol…
- EC
- 1.13.11.8
- UniProt
- Q38M40, Q38M41
- Ligands
- 4NC, FE
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 2-amino-5-chlorophenol 1,6-dioxygenase alpha subunit (EC 1.13.11.8) | protein | 270 | 41% helix, 26% strand | Q38M40 |
| B | 2-amino-5-chlorophenol 1,6-dioxygenase beta subunit (EC 1.13.11.8) | protein | 304 | 38% helix, 26% strand | Q38M41 |
| D | 2-amino-5-chlorophenol 1,6-dioxygenase beta subunit (EC 1.13.11.8) | protein | 299 | 40% helix, 24% strand | Q38M41 |
Ligands and binding sites
- 4NC · 4-nitrocatechol · ligand · 2 copies · chains B, D
- FE · Fe (III) ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.85 | 0.98 | 24 | empty |
| 2 | 1176 | 0.82 | 0.83 | 81 | FE, 4NC |
| 3 | 1133 | 0.82 | 0.83 | 83 | FE, 4NC |
| 4 | 72 | 0.63 | 0.91 | 19 | empty |
| 5 | 79 | 0.39 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1603 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1585 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1162 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3VSI · Crystal structure of native 1,6-APD (2-Animophenol-1,6-dioxygenase) complex with… · 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 Q38M40
- Every structure of UniProt Q38M41
- Elsewhere: RCSB PDB 3VSI · PDBe 3VSI · UniProt Q38M40 · UniProt Q38M41
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