Research workbench
Structure of a quinohemoprotein amine dehydrogenase with a unique redox cofactor and highly unusual crosslinking
Analyse Structure of a quinohemoprotein amine dehydrogenase with a unique redox… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JJU
- Type
- protein
- Length
- 905 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Quinohemoprotein amine dehydrogenase
- UniProt
- Q8VUT0, Q8VUS7, Q8VUS8
- Ligands
- HEM, NA
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Quinohemoprotein amine dehydrogenase | protein | 489 | 22% helix, 40% strand | Q8VUT0 |
| B | Quinohemoprotein amine dehydrogenase | protein | 337 | 2% helix, 53% strand | Q8VUS7 |
| C | Quinohemoprotein amine dehydrogenase | protein | 79 | 19% helix, 0% strand | Q8VUS8 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B, C
- NA · Sodium ion · metal · chains B, C
- TBU · Tertiary-butyl alcohol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.86 | 0.87 | 96 | HEM |
| 2 | 258 | 0.78 | 0.90 | 44 | empty |
| 3 | 342 | 0.68 | 0.81 | 41 | empty |
| 4 | 201 | 0.62 | 0.83 | 26 | empty |
| 5 | 364 | 0.58 | 0.76 | 55 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2434 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 1087 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1052 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 1 modified (heme attachment, cofactor).
Compared structures
- 1JJU · Structure of a Quinohemoprotein Amine Dehydrogenase with a Unique Redox Cofactor and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8VUS8 · AlphaFold monomer V2.0 prediction for quinohemoprotein amine dehydrogenase subunit gamma… · a predicted model of the same protein · chain C against A, TM-score 0.93
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 Q8VUT0
- Every structure of UniProt Q8VUS7
- Every structure of UniProt Q8VUS8
- Elsewhere: RCSB PDB 1JJU · PDBe 1JJU · UniProt Q8VUT0 · UniProt Q8VUS7 · UniProt Q8VUS8
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