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Structure of the blood group glycosyltransferase aaglyb in complex with a pyridine inhibitor as a neutral pyrophosphate surrogate
Analyse Structure of the blood group glycosyltransferase aaglyb in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KC2
- Type
- protein
- Length
- 289 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase soluble form
- EC
- 2.4.1.40, 2.4.1.37
- UniProt
- P16442
- Ligands
- BHE, WS2, MN
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase soluble form (EC 2.4.1.40, 2.4.1.37) | protein | 289 | 33% helix, 19% strand | P16442 |
Ligands and binding sites
- BHE · octyl 2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-galactopyranoside · ligand · chains A
- WS2 · 6-(1-beta-D-Galactopyranosyloxymethyl)-N-(5'-deoxyluridine-5'-yl)picolinamide · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.65 | 0.79 | 35 | MN, BHE, WS2 |
| 2 | 52 | 0.31 | 0.76 | 16 | empty |
| 3 | 52 | 0.29 | 0.75 | 12 | empty |
Compared structures
- 4KC2 · Structure of the blood group glycosyltransferase AAglyB in complex with a pyridine… · the same entry in another collection · chain A against A, TM-score 1.00
- P16442 · AlphaFold monomer V2.0 prediction for histo-blood group abo system transferase (P16442) · 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 P16442
- Elsewhere: RCSB PDB 4KC2 · PDBe 4KC2 · UniProt P16442
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