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The binding of udp-galactose by an active site mutant of alpha-1,3 galactosyltransferase (ALPHA3GT)
Analyse The binding of udp-galactose by an active site mutant of alpha-1,3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VS3
- Type
- protein
- Length
- 574 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetyllactosaminide alpha-1,3-galactosyltransferase
- EC
- 2.4.1.87
- UniProt
- P14769
- Ligands
- UDP, NDG, GAL, MN
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-acetyllactosaminide alpha-1,3-galactosyltransferase (EC 2.4.1.87) | protein | 287 | 36% helix, 20% strand | P14769 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.76 | 0.87 | 43 | GAL, UDP, MN |
| 2 | 315 | 0.75 | 0.87 | 40 | GAL, UDP, MN |
| 3 | 222 | 0.63 | 0.83 | 38 | empty |
| 4 | 89 | 0.57 | 0.86 | 21 | empty |
| 5 | 113 | 0.40 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 841 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2VS3 · THE BINDING OF UDP-GALACTOSE BY AN ACTIVE SITE MUTANT OF alpha-1,3 GALACTOSYLTRANSFERASE… · the same entry in another collection · chain A against A, TM-score 1.00
- P14769 · AlphaFold monomer V2.0 prediction for N-acetyllactosaminide… · a predicted model of the same protein · chain B 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 P14769
- Elsewhere: RCSB PDB 2VS3 · PDBe 2VS3 · UniProt P14769
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