Research workbench
Crystal structure of an electron transfer complex between aromatic amine dephydrogenase and azurin from alcaligenes faecalis (form 1)
Analyse Crystal structure of an electron transfer complex between aromatic amine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H47
- Type
- protein
- Length
- 2,072 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aromatic amine dehydrogenase; Azurin
- EC
- 1.4.99.4
- UniProt
- P84888, P84887, P00281
- Ligands
- CU
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 9 distinct chains · 9% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aromatic amine dehydrogenase (EC 1.4.99.4) | protein | 360 | 6% helix, 47% strand | P84888 |
| B | Aromatic amine dehydrogenase (EC 1.4.99.4) | protein | 124 | 18% helix, 31% strand | P84887 |
| C | Azurin | protein | 128 | 17% helix, 35% strand | P00281 |
| D | Aromatic amine dehydrogenase (EC 1.4.99.4) | protein | 361 | 6% helix, 48% strand | P84888 |
| E | Aromatic amine dehydrogenase (EC 1.4.99.4) | protein | 125 | 15% helix, 34% strand | P84887 |
| F | Aromatic amine dehydrogenase (EC 1.4.99.4) | protein | 362 | 6% helix, 48% strand | P84888 |
| G | Aromatic amine dehydrogenase (EC 1.4.99.4) | protein | 126 | 17% helix, 33% strand | P84887 |
| H | Aromatic amine dehydrogenase (EC 1.4.99.4) | protein | 362 | 6% helix, 49% strand | P84888 |
| I | Aromatic amine dehydrogenase (EC 1.4.99.4) | protein | 124 | 15% helix, 30% strand | P84887 |
Ligands and binding sites
- CU · Copper (II) ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.80 | 0.85 | 43 | empty |
| 2 | 623 | 0.79 | 0.84 | 40 | empty |
| 3 | 578 | 0.79 | 0.85 | 40 | empty |
| 4 | 565 | 0.78 | 0.84 | 39 | empty |
| 5 | 67 | 0.71 | 0.97 | 19 | empty |
Interfaces
15 interfaces between chains.
- H–I · 1402 Ų buried · 26 hydrogen bonds · protein-protein
- F–G · 1400 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1396 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 1369 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 1042 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 disulfide, 4 modified (disulfide, cofactor).
Compared structures
- 2H47 · Crystal Structure of an Electron Transfer Complex Between Aromatic Amine Dephydrogenase… · the same entry in another collection · chain I against I, TM-score 1.00
- P84887 · AlphaFold monomer V2.0 prediction for aralkylamine dehydrogenase light chain (P84887) · a predicted model of the same protein · chain B 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 D 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 P84888
- Every structure of UniProt P84887
- Every structure of UniProt P00281
- Elsewhere: RCSB PDB 2H47 · PDBe 2H47 · UniProt P84888 · UniProt P84887 · UniProt P00281
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