MolNFT v1 · #12327 · protein
Crystal structure of the flavin domain of cellobiose dehydrogenase
1KDG: “Crystal structure of the flavin domain of cellobiose dehydrogenase”. X-ray diffraction, 6 ligands (6FA, EMT, NAG), 4 pockets (best druggability 0.88). MolNFT v1 #12327 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KDG
- Type
- protein
- Length
- 1,087 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cellobiose dehydrogenase
- EC
- 1.1.99.18
- UniProt
- Q01738
- Ligands
- 6FA, EMT, NAG, MAN, HG, UNX
- Pockets
- 4 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cellobiose dehydrogenase (EC 1.1.99.18) | protein | 541 | 33% helix, 21% strand | Q01738 |
| B | Cellobiose dehydrogenase (EC 1.1.99.18) | protein | 546 | 32% helix, 21% strand | Q01738 |
Ligands and binding sites
- 6FA · 6-hydroxy-flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- EMT · 2-(ethylmercuri-thio)-benzoic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- HG · Mercury (II) ion · metal · 9 copies · chains A, B
- UNX · Unknown atom or ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.88 | 0.91 | 100 | 6FA |
| 2 | 599 | 0.86 | 0.91 | 68 | 6FA |
| 3 | 293 | 0.76 | 0.89 | 40 | empty |
| 4 | 59 | 0.42 | 0.82 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 940 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 glycan, 2 disulfide (N-glycosylation, O-glycosylation, disulfide).
Compared structures
- 1KDG · Crystal structure of the flavin domain of cellobiose dehydrogenase · the same entry in another collection · chain A against A, TM-score 1.00
- Q01738 · AlphaFold monomer V2.0 prediction for cellobiose dehydrogenase (Q01738) · a predicted model of the same protein · 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 Q01738
- Elsewhere: RCSB PDB 1KDG · PDBe 1KDG · UniProt Q01738
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