MolNFT v1 · #3919 · protein
Cytochrome domain of cellobiose dehydrogenase, pH 7.5
1D7B: “Cytochrome domain of cellobiose dehydrogenase, pH 7.5”. X-ray diffraction, 5 ligands (HEM, 1PG, NAG), 3 pockets (best druggability 0.66). MolNFT v1 #3919 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1D7B
- Type
- protein
- Length
- 372 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellobiose dehydrogenase
- EC
- 1.1.3.25
- Ligands
- HEM, 1PG, NAG, BMA, CD
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cellobiose dehydrogenase (EC 1.1.3.25) | protein | 186 | 4% helix, 45% strand | — |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- 1PG · 2-(2-{2-[2-(2-methoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethanol · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- CD · Cadmium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.66 | 0.86 | 23 | CD |
| 2 | 144 | 0.62 | 0.85 | 26 | HEM |
| 3 | 138 | 0.62 | 0.85 | 24 | HEM |
Interfaces
1 interface between chains.
- A–B · 306 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 1D7B · Cytochrome domain of cellobiose dehydrogenase, pH 7.5 · 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
- Elsewhere: RCSB PDB 1D7B · PDBe 1D7B
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