Research workbench
Apo form of the soluble pqq-dependent glucose dehydrogenase from acinetobacter calcoaceticus
Analyse Apo form of the soluble pqq-dependent glucose dehydrogenase from acinetobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MIN
- Type
- protein
- Length
- 905 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Quinoprotein glucose dehydrogenase B
- EC
- 1.1.5.2
- UniProt
- P13650
- Ligands
- CA, CL
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Quinoprotein glucose dehydrogenase B (EC 1.1.5.2) | protein | 452 | 6% helix, 36% strand | P13650 |
| B | Quinoprotein glucose dehydrogenase B (EC 1.1.5.2) | protein | 453 | 6% helix, 36% strand | P13650 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 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 | 0.73 | 0.82 | 57 | empty |
| 2 | 486 | 0.73 | 0.82 | 56 | CA |
| 3 | 63 | 0.69 | 0.96 | 20 | empty |
| 4 | 427 | 0.67 | 0.79 | 36 | empty |
| 5 | 447 | 0.67 | 0.79 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 1227 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5MIN · Apo form of the soluble PQQ-dependent Glucose Dehydrogenase from Acinetobacter… · 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 5MIN · PDBe 5MIN · UniProt P13650
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