Research workbench
Crystal structure of pqq doamin of pyranose dehydrogenase from coprinopsis cinerea: apo-from
Analyse Crystal structure of pqq doamin of pyranose dehydrogenase from coprinopsis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JT5
- Type
- protein
- Length
- 409 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular pqq-dependent sugar dehydrogenase
- UniProt
- A0A0A8IDB7
- Ligands
- NAG, CA, SO4
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular pqq-dependent sugar dehydrogenase | protein | 409 | 7% helix, 39% strand | A0A0A8IDB7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- FMT · Formic acid · additive · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 320 | 0.66 | 0.81 | 46 | GOL |
| 2 | 218 | 0.61 | 0.81 | 25 | CA, SO4, FMT, GOL |
| 3 | 52 | 0.33 | 0.78 | 15 | empty |
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6JT5 · Crystal structure of PQQ doamin of Pyranose Dehydrogenase from Coprinopsis cinerea… · 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 A0A0A8IDB7
- Elsewhere: RCSB PDB 6JT5 · PDBe 6JT5 · UniProt A0A0A8IDB7
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