MolNFT v1 · #128476 · protein
A native ternary complex of alpha-1,3-galactosyltransferase (a-3GALT) supports a conserved reaction mechanism for retaining glycosyltransferases - alpha-3GALT in complex with CO2+, udp-gal and lactose - A3GALT-CO2+-udp-gal-lat-2
5NRD · N-acetyllactosaminide alpha-1,3-galactosyltransferase: “A native ternary complex of alpha-1,3-galactosyltransferase (a-3GALT) supports a conserved reaction mechanism…”. X-ray diffraction, 4 ligands (GDU, BGC, GAL), 7 pockets (best…
- PDB
- 5NRD
- Type
- protein
- Length
- 561 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
- GDU, BGC, GAL, CO
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetyllactosaminide alpha-1,3-galactosyltransferase (EC 2.4.1.87) | protein | 284 | 36% helix, 20% strand | P14769 |
| B | N-acetyllactosaminide alpha-1,3-galactosyltransferase (EC 2.4.1.87) | protein | 277 | 37% helix, 21% strand | P14769 |
Ligands and binding sites
- GDU · Galactose-uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.75 | 0.81 | 49 | CO, GDU |
| 2 | 307 | 0.74 | 0.86 | 34 | GAL, CO, GDU |
| 3 | 253 | 0.52 | 0.75 | 32 | empty |
| 4 | 74 | 0.37 | 0.77 | 18 | empty |
| 5 | 74 | 0.32 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 494 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5NRD · A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (a-3GalT) Supports a… · 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 5NRD · PDBe 5NRD · UniProt P14769
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