Research workbench
Catalytic domain of udp-glucose glycoprotein glucosyltransferase from chaetomium thermophilum in complex with udp-2-deoxy-2-fluoro-D- glucose
Analyse Catalytic domain of udp-glucose glycoprotein glucosyltransferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZLU
- Type
- protein
- Length
- 834 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-glucose-glycoprotein glucosyltransferase-like protein
- UniProt
- G0SB58
- Ligands
- U2F, NAG, CA
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Udp-glucose-glycoprotein glucosyltransferase-like protein | protein | 278 | 44% helix, 15% strand | G0SB58 |
Ligands and binding sites
- U2F · Uridine-5'-diphosphate-2-deoxy-2-fluoro-alpha-D-glucose · ligand · 3 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, B, C
- PDO · 1,3-propandiol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.76 | 0.82 | 67 | empty |
| 2 | 352 | 0.65 | 0.80 | 29 | U2F, CA |
| 3 | 303 | 0.64 | 0.80 | 30 | U2F, CA |
| 4 | 351 | 0.64 | 0.79 | 29 | U2F, CA |
| 5 | 81 | 0.34 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- B–C · 573 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7ZLU · Catalytic domain of UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium… · 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 7ZLU · PDBe 7ZLU · UniProt G0SB58
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