MolNFT v1 · #25590 · protein
Roles of active site tryptophans in substrate binding and catalysis by alpha-1,3 galactosyltransferase
1VZX · N-acetyllactosaminide alpha-1,3-galactosyltransferase: “Roles of active site tryptophans in substrate binding and catalysis by alpha-1,3 galactosyltransferase”. X-ray diffraction, 4 ligands (UDP, NAG, GAL), 5 pockets (best…
- PDB
- 1VZX
- 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
- 2.4.1.151
- UniProt
- P14769
- Ligands
- UDP, NAG, GAL, MN
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | N-acetyllactosaminide alpha-1,3-galactosyltransferase (EC 2.4.1.151) | protein | 287 | 37% helix, 21% strand | P14769 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-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
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.72 | 0.84 | 41 | GAL, MN, UDP |
| 2 | 332 | 0.71 | 0.84 | 42 | GAL, MN, UDP |
| 3 | 223 | 0.63 | 0.82 | 38 | empty |
| 4 | 95 | 0.39 | 0.76 | 20 | empty |
| 5 | 64 | 0.28 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 828 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1VZX · Roles of active site tryptophans in substrate binding and catalysis by ALPHA-1,3… · 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 1VZX · PDBe 1VZX · UniProt P14769
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