MolNFT v1 · #82616 · protein
Crystal structure of 1,6-apd (2-animophenol-1,6-dioxygenase) complexed with intermediate products
3VSJ · 2-amino-5-chlorophenol 1,6-dioxygenase alpha subunit: “Crystal structure of 1,6-apd (2-animophenol-1,6-dioxygenase) complexed with intermediate products”. X-ray diffraction, 5 ligands (2XP, 2X7, FE2), 6 pockets (best druggability…
- PDB
- 3VSJ
- Type
- protein
- Length
- 1,142 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
- 2XP, 2X7, FE2, CL, OH
- Pockets
- 6 · 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 | 303 | 40% helix, 26% strand | Q38M41 |
| D | 2-amino-5-chlorophenol 1,6-dioxygenase beta subunit (EC 1.13.11.8) | protein | 299 | 39% helix, 24% strand | Q38M41 |
Ligands and binding sites
- 2XP · (2Z,4Z)-2-imino-6-oxohex-4-enoic acid · ligand · chains B
- 2X7 · (3E)-3-iminooxepin-2(3H)-one · ligand · chains D
- FE2 · Fe (II) ion · metal · 2 copies · chains B, D
- CL · Chloride ion · ion · chains A
- OH · Hydroxide ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.85 | 0.98 | 24 | empty |
| 2 | 1104 | 0.84 | 0.85 | 87 | 2X7, OH |
| 3 | 1154 | 0.82 | 0.83 | 86 | CL, 2XP |
| 4 | 217 | 0.58 | 0.80 | 36 | empty |
| 5 | 73 | 0.36 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1635 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1561 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1085 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3VSJ · Crystal structure of 1,6-APD (2-ANIMOPHENOL-1,6-DIOXYGENASE) complexed with intermediate… · 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 3VSJ · PDBe 3VSJ · UniProt Q38M40 · UniProt Q38M41
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