Research workbench
A native ternary complex of alpha-1,3-galactosyltransferase (alpha- 3GALT) supports a conserved reaction mechanism for retaining glycosyltransferases - unliganded alpha-3GALT
Analyse A native ternary complex of alpha-1,3-galactosyltransferase (alpha- 3GALT)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NR9
- Type
- protein
- Length
- 558 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
- Pockets
- 5 · best druggability 0.76
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 | 278 | 37% helix, 21% strand | P14769 |
| B | N-acetyllactosaminide alpha-1,3-galactosyltransferase (EC 2.4.1.87) | protein | 280 | 36% helix, 20% strand | P14769 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 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 | 989 | 0.76 | 0.78 | 75 | GOL |
| 2 | 327 | 0.58 | 0.76 | 34 | GOL |
| 3 | 323 | 0.55 | 0.75 | 48 | empty |
| 4 | 56 | 0.42 | 0.82 | 16 | empty |
| 5 | 103 | 0.38 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 475 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5NR9 · A Native Ternary Complex of Alpha-1,3-Galactosyltransferase (alpha-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 A 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 P14769
- Elsewhere: RCSB PDB 5NR9 · PDBe 5NR9 · UniProt P14769
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