MolNFT v1 · #31004 · protein
Crystal structure of the phenylhydrazine adduct of aromatic amine dehydrogenase from alcaligenes faecalis
2AGL: “Crystal structure of the phenylhydrazine adduct of aromatic amine dehydrogenase from alcaligenes faecalis”. X-ray diffraction, 1 ligand (PHZ), 5 pockets (best druggability 0.81). MolNFT v1 #31004 on GenesisL1: 3D structure, binding…
- 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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