MolNFT v1 · #104685 · protein
Cytochrome domain of myriococcum thermophilum cellobiose dehydrogenase, mtcyt
4QI3: “Cytochrome domain of myriococcum thermophilum cellobiose dehydrogenase, mtcyt”. X-ray diffraction, 4 ligands (HEM, MAN, NAG), 6 pockets (best druggability 0.68). MolNFT v1 #104685 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4QI3
- Type
- protein
- Length
- 416 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellobiose dehydrogenase
- UniProt
- A9XK88
- Ligands
- HEM, MAN, NAG, MG
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cellobiose dehydrogenase | protein | 208 | 7% helix, 46% strand | A9XK88 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.68 | 0.86 | 30 | HEM, MG |
| 2 | 194 | 0.67 | 0.86 | 30 | HEM |
| 3 | 392 | 0.60 | 0.76 | 38 | empty |
| 4 | 171 | 0.45 | 0.75 | 29 | empty |
| 5 | 117 | 0.44 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 466 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan, 4 disulfide, 2 modified (O-glycosylation, disulfide, N-glycosylation, cyclization).
Compared structures
- 4QI3 · Cytochrome domain of Myriococcum thermophilum cellobiose dehydrogenase, MtCYT · 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 A9XK88
- Elsewhere: RCSB PDB 4QI3 · PDBe 4QI3 · UniProt A9XK88
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