Research workbench
Crystal structure of aromatic amine dehydrogenase ttq-formamide adduct oxidized with ferricyanide.
Analyse Crystal structure of aromatic amine dehydrogenase ttq-formamide adduct oxidized… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OK6
- Type
- protein
- Length
- 949 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aromatic amine dehydrogenase, small subunit; Aromatic amine dehydrogenase, large subunit
- EC
- 1.4.99.4
- UniProt
- Q0VKG6, Q0VKG7
- Ligands
- BEZ
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Aromatic amine dehydrogenase, small subunit (EC 1.4.99.4) | protein | 110 | 8% helix, 37% strand | Q0VKG6 |
| H | Aromatic amine dehydrogenase, small subunit (EC 1.4.99.4) | protein | 120 | 13% helix, 34% strand | Q0VKG6 |
| A | Aromatic amine dehydrogenase, large subunit (EC 1.4.99.4) | protein | 359 | 6% helix, 49% strand | Q0VKG7 |
| B | Aromatic amine dehydrogenase, large subunit (EC 1.4.99.4) | protein | 360 | 6% helix, 47% strand | Q0VKG7 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 2 copies · chains D, B, H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.81 | 0.87 | 44 | empty |
| 2 | 551 | 0.79 | 0.85 | 42 | empty |
| 3 | 59 | 0.69 | 0.96 | 22 | empty |
| 4 | 169 | 0.50 | 0.77 | 33 | empty |
| 5 | 108 | 0.44 | 0.78 | 19 | empty |
Interfaces
5 interfaces between chains.
- H–A · 1418 Ų buried · 29 hydrogen bonds · protein-protein
- D–B · 1392 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 924 Ų buried · 20 hydrogen bonds · protein-protein
- H–B · 869 Ų buried · 13 hydrogen bonds · protein-protein
- D–A · 864 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 2OK6 · Crystal structure of aromatic amine dehydrogenase TTQ-formamide adduct oxidized with… · the same entry in another collection · chain D against D, 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 Q0VKG6
- Every structure of UniProt Q0VKG7
- Elsewhere: RCSB PDB 2OK6 · PDBe 2OK6 · UniProt Q0VKG6 · UniProt Q0VKG7
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