Research workbench
Cellobiose dehydrogenase from neurospora crassa, nccdh
Analyse Cellobiose dehydrogenase from neurospora crassa, nccdh in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QI7
- Type
- protein
- Length
- 1,597 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellobiose dehydrogenase
- UniProt
- Q7RXM0
- Ligands
- HEM, FAD, NAG, MAN, PT, MG
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellobiose dehydrogenase | protein | 805 | 20% helix, 28% strand | Q7RXM0 |
| B | Cellobiose dehydrogenase | protein | 792 | 21% helix, 28% strand | Q7RXM0 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- PT · Platinum (II) ion · metal · 20 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 880 | 0.85 | 0.87 | 82 | FAD, PT, MG |
| 2 | 908 | 0.84 | 0.86 | 84 | FAD, PT |
| 3 | 665 | 0.79 | 0.84 | 63 | PT, HEM |
| 4 | 1197 | 0.75 | 0.78 | 108 | PT |
| 5 | 142 | 0.62 | 0.85 | 26 | HEM |
Interfaces
1 interface between chains.
- A–B · 988 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 glycan, 11 disulfide (N-glycosylation, disulfide, O-glycosylation).
Compared structures
- 4QI7 · Cellobiose dehydrogenase from Neurospora crassa, NcCDH · 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 Q7RXM0
- Elsewhere: RCSB PDB 4QI7 · PDBe 4QI7 · UniProt Q7RXM0
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