Research workbench
Crystal structure of the phenylhydrazine adduct of aromatic amine dehydrogenase from alcaligenes faecalis
Analyse Crystal structure of the phenylhydrazine adduct of aromatic amine dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AGL
- Type
- protein
- Length
- 948 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
- PHZ
- Pockets
- 5 · 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 (EC 1.4.99.4) | protein | 109 | 11% helix, 37% strand | P84887 |
| H | Aromatic amine dehydrogenase (EC 1.4.99.4) | protein | 119 | 13% helix, 34% strand | P84887 |
| A | Aromatic amine dehydrogenase (EC 1.4.99.4) | protein | 360 | 6% helix, 49% strand | P84888 |
| B | Aromatic amine dehydrogenase (EC 1.4.99.4) | protein | 360 | 6% helix, 48% strand | P84888 |
Ligands and binding sites
- PHZ · 1-phenylhydrazine · ligand · 2 copies · chains D, B, H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.81 | 0.87 | 43 | empty |
| 2 | 560 | 0.80 | 0.86 | 41 | empty |
| 3 | 262 | 0.59 | 0.79 | 45 | empty |
| 4 | 82 | 0.37 | 0.77 | 21 | empty |
| 5 | 63 | 0.33 | 0.76 | 15 | empty |
Interfaces
5 interfaces between chains.
- H–A · 1410 Ų buried · 29 hydrogen bonds · protein-protein
- D–B · 1401 Ų buried · 28 hydrogen bonds · protein-protein
- D–A · 933 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 926 Ų buried · 18 hydrogen bonds · protein-protein
- H–B · 868 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 covalent, 2 modified (disulfide, covalent ligand, cofactor).
Compared structures
- 2AGL · Crystal structure of the phenylhydrazine adduct of aromatic amine dehydrogenase from… · 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 2AGL · PDBe 2AGL · UniProt P84887 · UniProt P84888
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