MolNFT v1 · #31016 · protein
Crystal structure of the carbinolamine intermediate in the reductive half-reaction of aromatic amine dehydrogenase (aadh) with tryptamine. F222 form
2AGZ: “Crystal structure of the carbinolamine intermediate in the reductive half-reaction of aromatic amine…”. X-ray diffraction, 2 ligands (TSC, ZN), 8 pockets (best druggability 0.82). MolNFT v1 #31016 on GenesisL1: 3D structure, binding…
- PDB
- 2AGZ
- Type
- protein
- Length
- 946 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
- TSC, ZN
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Aromatic amine dehydrogenase (EC 1.4.99.4) | protein | 109 | 8% helix, 39% strand | P84887 |
| H | Aromatic amine dehydrogenase (EC 1.4.99.4) | protein | 115 | 14% helix, 36% strand | P84887 |
| A, B | Aromatic amine dehydrogenase (EC 1.4.99.4) | protein | 361 | 6% helix, 48% strand | P84888 |
Ligands and binding sites
- TSC · (1S)-1-amino-2-(1H-indol-3-yl)ethanol · ligand · 2 copies · chains D, B, H, A
- ZN · Zinc ion · metal · 2 copies · chains D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.82 | 0.87 | 43 | empty |
| 2 | 561 | 0.80 | 0.86 | 43 | empty |
| 3 | 62 | 0.73 | 0.98 | 22 | empty |
| 4 | 50 | 0.68 | 0.97 | 17 | TSC |
| 5 | 151 | 0.50 | 0.79 | 24 | empty |
Interfaces
5 interfaces between chains.
- H–A · 1408 Ų buried · 28 hydrogen bonds · protein-protein
- D–B · 1382 Ų buried · 25 hydrogen bonds · protein-protein
- H–B · 946 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 930 Ų buried · 18 hydrogen bonds · protein-protein
- D–A · 913 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 covalent, 2 modified (disulfide, covalent ligand, cofactor).
Compared structures
- 2AGZ · Crystal structure of the carbinolamine intermediate in the reductive half-reaction of… · 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 0.99
- 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 2AGZ · PDBe 2AGZ · UniProt P84887 · UniProt P84888
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