Research workbench
Crystal structure of indol-3-acetaldehyde derived ttq-amide adduct of aromatic amine dehydrogenase
Analyse Crystal structure of indol-3-acetaldehyde derived ttq-amide adduct of aromatic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OJY
- Type
- protein
- Length
- 950 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
- TSR
- Pockets
- 9 · best druggability 0.80
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 | 11% helix, 37% strand | Q0VKG6 |
| H | Aromatic amine dehydrogenase, small subunit (EC 1.4.99.4) | protein | 119 | 13% helix, 31% strand | Q0VKG6 |
| A | Aromatic amine dehydrogenase, large subunit (EC 1.4.99.4) | protein | 360 | 6% helix, 48% strand | Q0VKG7 |
| B | Aromatic amine dehydrogenase, large subunit (EC 1.4.99.4) | protein | 361 | 6% helix, 48% strand | Q0VKG7 |
Ligands and binding sites
- TSR · 2-(1H-indol-3-yl)acetamide · ligand · 2 copies · chains D, B, H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 552 | 0.80 | 0.87 | 44 | empty |
| 2 | 523 | 0.79 | 0.86 | 39 | empty |
| 3 | 58 | 0.70 | 0.97 | 19 | empty |
| 4 | 51 | 0.68 | 0.97 | 17 | TSR |
| 5 | 180 | 0.63 | 0.84 | 35 | TSR |
Interfaces
5 interfaces between chains.
- H–A · 1420 Ų buried · 28 hydrogen bonds · protein-protein
- D–B · 1400 Ų buried · 28 hydrogen bonds · protein-protein
- H–B · 1006 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 927 Ų buried · 19 hydrogen bonds · protein-protein
- D–A · 924 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 covalent, 2 modified (disulfide, covalent ligand, cofactor).
Compared structures
- 2OJY · Crystal structure of indol-3-acetaldehyde derived TTQ-amide adduct of aromatic amine… · 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 2OJY · PDBe 2OJY · UniProt Q0VKG6 · UniProt Q0VKG7
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