Research workbench
Crystal structure of the sialyltransferase cst-II in complex with trisaccharide acceptor and cmp
Analyse Crystal structure of the sialyltransferase cst-II in complex with trisaccharide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X61
- Type
- protein
- Length
- 488 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-2,3-/2,8-sialyltransferase
- EC
- 2.4.99.-
- UniProt
- Q9LAK3
- Ligands
- CH, NGA, GAL, SIA
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-2,3-/2,8-sialyltransferase (EC 2.4.99.-) | protein | 245 | 41% helix, 16% strand | Q9LAK3 |
| B | Alpha-2,3-/2,8-sialyltransferase (EC 2.4.99.-) | protein | 243 | 42% helix, 16% strand | Q9LAK3 |
Ligands and binding sites
- CH · N3-protonated cytidine-5'-monophosphate · ligand · 2 copies · chains A, B
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.72 | 0.81 | 57 | empty |
| 2 | 312 | 0.65 | 0.81 | 42 | SIA, CH |
| 3 | 303 | 0.63 | 0.80 | 40 | SIA, CH |
Interfaces
1 interface between chains.
- A–B · 479 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2X61 · Crystal structure of the sialyltransferase CST-II in complex with trisaccharide acceptor… · the same entry in another collection · chain B against B, 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 Q9LAK3
- Elsewhere: RCSB PDB 2X61 · PDBe 2X61 · UniProt Q9LAK3
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