MolNFT v1 · #104687 · protein
Dehydrogenase domain of myriococcum thermophilum cellobiose dehydrogenase with bound cellobionolactam, mtdh
4QI5: “Dehydrogenase domain of myriococcum thermophilum cellobiose dehydrogenase with bound cellobionolactam, mtdh”. X-ray diffraction, 4 ligands (FAD, ABL, NAG), 3 pockets (best druggability 0.85). MolNFT v1 #104687 on GenesisL1: 3D…
- PDB
- 4QI5
- Type
- protein
- Length
- 585 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellobiose dehydrogenase
- UniProt
- A9XK88
- Ligands
- FAD, ABL, NAG, CD
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellobiose dehydrogenase | protein | 585 | 27% helix, 23% strand | A9XK88 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- ABL · (2R,3R,4R,5R)-4,5-dihydroxy-2-(hydroxymethyl)-6-oxopiperidin-3-yl beta-D-glucopyranoside · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- CD · Cadmium ion · metal · 2 copies · 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 | 754 | 0.85 | 0.88 | 78 | FAD, ABL |
| 2 | 153 | 0.61 | 0.84 | 24 | empty |
| 3 | 59 | 0.34 | 0.77 | 19 | empty |
Modifications
Observed in the structure: 3 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4QI5 · Dehydrogenase domain of Myriococcum thermophilum cellobiose dehydrogenase with bound… · 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 4QI5 · PDBe 4QI5 · UniProt A9XK88
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