Research workbench
Structure of the phenylhydrazine adduct of the quinohemoprotein amine dehydrogenase from paracoccus denitrificans at 1.7 a resolution
Analyse Structure of the phenylhydrazine adduct of the quinohemoprotein amine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PBY
- Type
- protein
- Length
- 905 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Quinohemoprotein amine dehydrogenase 60 kda subunit; Quinohemoprotein amine dehydrogenase…
- EC
- 1.4.99.3
- UniProt
- Q8VUT0
- Ligands
- HEC
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Quinohemoprotein amine dehydrogenase 60 kda subunit (EC 1.4.99.3) | protein | 489 | 22% helix, 40% strand | Q8VUT0 |
| B | Quinohemoprotein amine dehydrogenase 40 kda subunit | protein | 337 | 2% helix, 52% strand | — |
| C | Quinohemoprotein amine dehydrogenase 9 kda subunit | protein | 79 | 19% helix, 3% strand | — |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A, B, C
- TBU · Tertiary-butyl alcohol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.82 | 0.86 | 67 | HEC |
| 2 | 288 | 0.76 | 0.88 | 41 | HEC |
| 3 | 521 | 0.72 | 0.81 | 73 | empty |
| 4 | 138 | 0.67 | 0.88 | 24 | empty |
| 5 | 306 | 0.66 | 0.81 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2452 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 1104 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1082 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor, 1 modified (heme c attachment, nonstandard).
Compared structures
- 1PBY · Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase from… · the same entry in another collection · chain A against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 1PBY · PDBe 1PBY · UniProt Q8VUT0
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