Research workbench
Human beta 1,3-glucuronyltransferase I (glcat-I) in complex with udp and gal-GAL(6-SO4)-XYL(2-PO4)-O-ser
Analyse Human beta 1,3-glucuronyltransferase I (glcat-I) in complex with udp and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CU0
- Type
- protein
- Length
- 497 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactosylgalactosylxylosylprotein 3-beta- glucuronosyltransferase 3
- EC
- 2.4.1.135
- UniProt
- O94766
- Ligands
- UDP, GAL, MN, SO4
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactosylgalactosylxylosylprotein 3-beta- glucuronosyltransferase 3 (EC 2.4.1.135) | protein | 250 | 28% helix, 25% strand | O94766 |
| B | Galactosylgalactosylxylosylprotein 3-beta- glucuronosyltransferase 3 (EC 2.4.1.135) | protein | 247 | 31% helix, 24% strand | O94766 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · 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 | 552 | 0.70 | 0.79 | 51 | GAL, MN, UDP |
| 2 | 448 | 0.65 | 0.78 | 47 | GAL, UDP, SO4, MN |
| 3 | 131 | 0.53 | 0.81 | 22 | empty |
| 4 | 157 | 0.50 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2121 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 3CU0 · human beta 1,3-glucuronyltransferase I (GlcAT-I) in complex with UDP and… · the same entry in another collection · chain A against A, TM-score 1.00
- O94766 · AlphaFold monomer V2.0 prediction for galactosylgalactosylxylosylprotein… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O94766
- Elsewhere: RCSB PDB 3CU0 · PDBe 3CU0 · UniProt O94766
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