Research workbench
Holo form of pyranose dehydrogenase pqq domain from coprinopsis cinerea
Analyse Holo form of pyranose dehydrogenase pqq domain from coprinopsis cinerea in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JWF
- Type
- protein
- Length
- 818 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular pqq-dependent sugar dehydrogenase
- UniProt
- A0A0A8IDB7
- Ligands
- PQQ, NAG, CA
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Extracellular pqq-dependent sugar dehydrogenase | protein | 409 | 7% helix, 39% strand | A0A0A8IDB7 |
Ligands and binding sites
- PQQ · Pyrroloquinoline quinone · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 806 | 0.82 | 0.85 | 83 | EDO, ACT |
| 2 | 62 | 0.67 | 0.95 | 21 | empty |
| 3 | 351 | 0.65 | 0.80 | 47 | empty |
| 4 | 263 | 0.62 | 0.80 | 29 | CA, PQQ, EDO |
| 5 | 231 | 0.60 | 0.80 | 26 | CA, PQQ, EDO |
Interfaces
1 interface between chains.
- A–B · 701 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6JWF · Holo form of Pyranose Dehydrogenase PQQ domain 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 6JWF · PDBe 6JWF · UniProt A0A0A8IDB7
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