Research workbench
Crystal structure of carbohydrate oxidase from microdochium nivale
Analyse Crystal structure of carbohydrate oxidase from microdochium nivale in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RJ8
- Type
- protein
- Length
- 473 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbohydrate oxidase
- EC
- 1.1.3.4
- Ligands
- FAD, NAG, ZN, K
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbohydrate oxidase (EC 1.1.3.4) | protein | 473 | 36% helix, 22% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- K · Potassium ion · metal · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 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 | 546 | 0.84 | 0.89 | 64 | FAD |
| 2 | 51 | 0.72 | 0.99 | 13 | empty |
| 3 | 64 | 0.36 | 0.78 | 18 | empty |
Modifications
Observed in the structure: 2 cofactor, 1 glycan (flavinylation, N-glycosylation).
Compared structures
- 3RJ8 · Crystal structure of carbohydrate oxidase from Microdochium nivale · 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 3RJ8 · PDBe 3RJ8
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