Research workbench
Structure of a bacterial polysialyltransferase in complex with fondaparinux
Analyse Structure of a bacterial polysialyltransferase in complex with fondaparinux in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WD7
- Type
- protein
- Length
- 764 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Siad
- UniProt
- G4RIN4
- Ligands
- ZDO, SUS, IDS, BDP, SGN, SO4
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, M | Siad | protein | 382 | 44% helix, 15% strand | G4RIN4 |
Ligands and binding sites
- ZDO · methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside · ligand · chains A
- SUS · 2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · ligand · chains A
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · chains A
- BDP · beta-D-glucopyranuronic acid · sugar · chains A
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 648 | 0.66 | 0.76 | 48 | empty |
| 2 | 331 | 0.66 | 0.81 | 44 | empty |
| 3 | 327 | 0.53 | 0.74 | 34 | empty |
| 4 | 204 | 0.50 | 0.76 | 29 | empty |
| 5 | 175 | 0.46 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–M · 1334 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5WD7 · Structure of a bacterial polysialyltransferase in complex with fondaparinux · the same entry in another collection · 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 G4RIN4
- Elsewhere: RCSB PDB 5WD7 · PDBe 5WD7 · UniProt G4RIN4
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