Research workbench
Soluble quinoprotein glucose dehydrogenase from acinetobacter calcoaceticus in complex with pqq and methylhydrazine
Analyse Soluble quinoprotein glucose dehydrogenase from acinetobacter calcoaceticus in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CRU
- Type
- protein
- Length
- 900 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (soluble quinoprotein glucose dehydrogenase)
- EC
- 1.1.99.17
- UniProt
- P13650
- Ligands
- PQQ, HDN, CA
- Pockets
- 13 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (soluble quinoprotein glucose dehydrogenase) (EC 1.1.99.17) | protein | 448 | 6% helix, 35% strand | P13650 |
| B | Protein (soluble quinoprotein glucose dehydrogenase) (EC 1.1.99.17) | protein | 452 | 7% helix, 36% strand | P13650 |
Ligands and binding sites
- PQQ · Pyrroloquinoline quinone · ligand · 2 copies · chains A, B
- HDN · Methylhydrazine · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.71 | 0.81 | 55 | CA, PQQ, HDN |
| 2 | 520 | 0.70 | 0.80 | 57 | HDN, CA, PQQ |
| 3 | 69 | 0.69 | 0.95 | 23 | empty |
| 4 | 451 | 0.68 | 0.79 | 37 | empty |
| 5 | 375 | 0.68 | 0.81 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 1195 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1CRU · Soluble quinoprotein glucose dehydrogenase from acinetobacter calcoaceticus in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P13650 · AlphaFold monomer V2.0 prediction for quinoprotein glucose dehydrogenase B (P13650) · a predicted model of the same protein · chain B 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 P13650
- Elsewhere: RCSB PDB 1CRU · PDBe 1CRU · UniProt P13650
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