Research workbench
Crystal structure of carbohydrate oxidase from microdochium nivale in complex with substrate analogue
Analyse Crystal structure of carbohydrate oxidase from microdochium nivale in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RJA
- 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
- ABL, FAD, NAG, ZN, CL, SO4
- Pockets
- 3 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbohydrate oxidase (EC 1.1.3.4) | protein | 473 | 35% helix, 22% strand | — |
Ligands and binding sites
- ABL · (2R,3R,4R,5R)-4,5-dihydroxy-2-(hydroxymethyl)-6-oxopiperidin-3-yl beta-D-glucopyranoside · ligand · 2 copies · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- CL · Chloride ion · ion · 4 copies · chains A
- SO4 · Sulfate ion · ion · 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 | 516 | 0.84 | 0.90 | 65 | FAD, ABL |
| 2 | 57 | 0.73 | 0.99 | 18 | empty |
| 3 | 54 | 0.32 | 0.77 | 19 | empty |
Modifications
Observed in the structure: 2 cofactor, 1 disulfide, 1 glycan (flavinylation, disulfide, N-glycosylation).
Compared structures
- 3RJA · Crystal structure of carbohydrate oxidase from Microdochium nivale in complex with… · 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 3RJA · PDBe 3RJA
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