MolNFT v1 · #53194 · protein
Crystal structure of a mammalian sialyltransferase in complex with disaccharide and cmp
2WNB: “Crystal structure of a mammalian sialyltransferase in complex with disaccharide and cmp”. X-ray diffraction, 4 ligands (C5P, CG3, A2G), 4 pockets (best druggability 0.56). MolNFT v1 #53194 on GenesisL1: 3D structure, binding sites…
- PDB
- 2WNB
- Type
- protein
- Length
- 273 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- EC
- 2.4.99.4
- UniProt
- Q02745
- Ligands
- C5P, CG3, A2G, GAL
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (EC 2.4.99.4) | protein | 273 | 33% helix, 14% strand | Q02745 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · chains A
- CG3 · Hydroxy(2-hydroxyphenyl)oxoammonium · ligand · chains A
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.56 | 0.77 | 33 | C5P |
| 2 | 55 | 0.40 | 0.82 | 15 | empty |
| 3 | 62 | 0.37 | 0.79 | 13 | empty |
| 4 | 51 | 0.26 | 0.74 | 16 | empty |
Modifications
Observed in the structure: 3 disulfide, 3 modified (disulfide, engineered).
Compared structures
- 2WNB · Crystal Structure of a Mammalian Sialyltransferase in complex with disaccharide and CMP · the same entry in another collection · chain A against A, TM-score 1.00
- Q02745 · AlphaFold monomer V2.0 prediction for cmp-N-acetylneuraminate-beta… · a predicted model of the same protein · chain A 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 Q02745
- Elsewhere: RCSB PDB 2WNB · PDBe 2WNB · UniProt Q02745
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