MolNFT v1 · #127642 · protein
Udp-glucose glycoprotein glucosyltransferase from chaetomium thermophilum (closed form)
5N2J · Udp-glucose-glycoprotein glucosyltransferase-like protein: “Udp-glucose glycoprotein glucosyltransferase from chaetomium thermophilum (closed form)”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.82).…
- PDB
- 5N2J
- Type
- protein
- Length
- 2,754 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glucose-glycoprotein glucosyltransferase-like protein
- UniProt
- G0SB58
- Ligands
- NAG, BMA, MAN, CA
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-glucose-glycoprotein glucosyltransferase-like protein | protein | 1373 | 37% helix, 18% strand | G0SB58 |
| B | Udp-glucose-glycoprotein glucosyltransferase-like protein | protein | 1381 | 37% helix, 17% strand | G0SB58 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- CA · Calcium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 893 | 0.82 | 0.84 | 95 | CA |
| 2 | 1149 | 0.80 | 0.82 | 102 | CA |
| 3 | 393 | 0.79 | 0.88 | 47 | empty |
| 4 | 467 | 0.78 | 0.86 | 52 | empty |
| 5 | 386 | 0.76 | 0.86 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 645 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 5N2J · UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum (closed form) · 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 G0SB58
- Elsewhere: RCSB PDB 5N2J · PDBe 5N2J · UniProt G0SB58
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