Research workbench
Crystal structure of the benzylamine complex of aromatic amine dehydrogenase in N-semiquinone form
Analyse Crystal structure of the benzylamine complex of aromatic amine dehydrogenase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HXC
- Type
- protein
- Length
- 939 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aromatic amine dehydrogenase
- EC
- 1.4.99.4
- UniProt
- P84887, P84888
- Ligands
- ABN
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, H | Aromatic amine dehydrogenase (EC 1.4.99.4) | protein | 110 | 11% helix, 33% strand | P84887 |
| A | Aromatic amine dehydrogenase (EC 1.4.99.4) | protein | 359 | 6% helix, 49% strand | P84888 |
| B | Aromatic amine dehydrogenase (EC 1.4.99.4) | protein | 360 | 6% helix, 49% strand | P84888 |
Ligands and binding sites
- ABN · Benzylamine · ligand · 3 copies · chains D, B, H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.81 | 0.87 | 42 | empty |
| 2 | 523 | 0.79 | 0.86 | 41 | empty |
| 3 | 163 | 0.50 | 0.78 | 25 | empty |
| 4 | 134 | 0.46 | 0.78 | 22 | empty |
| 5 | 74 | 0.35 | 0.76 | 16 | empty |
Interfaces
5 interfaces between chains.
- H–A · 1397 Ų buried · 29 hydrogen bonds · protein-protein
- D–B · 1386 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 932 Ų buried · 19 hydrogen bonds · protein-protein
- D–A · 858 Ų buried · 15 hydrogen bonds · protein-protein
- H–B · 857 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 modified, 1 covalent (disulfide, nonstandard, covalent ligand).
Compared structures
- 2HXC · Crystal structure of the benzylamine complex of aromatic amine dehydrogenase in N-semiqui… · the same entry in another collection · chain B against B, TM-score 1.00
- P84887 · AlphaFold monomer V2.0 prediction for aralkylamine dehydrogenase light chain (P84887) · a predicted model of the same protein · chain D against A, TM-score 1.00
- P84888 · AlphaFold monomer V2.0 prediction for aralkylamine dehydrogenase heavy chain (P84888) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P84887
- Every structure of UniProt P84888
- Elsewhere: RCSB PDB 2HXC · PDBe 2HXC · UniProt P84887 · UniProt P84888
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