MolNFT v1 · #105610 · protein
Crystal structure of platelet factor 4 complexed with fondaparinux
4R9W: “Crystal structure of platelet factor 4 complexed with fondaparinux”. X-ray diffraction, 5 ligands (ZDO, SUS, IDS). MolNFT v1 #105610 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4R9W
- Type
- protein
- Length
- 126 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet factor 4
- UniProt
- P02776
- Ligands
- ZDO, SUS, IDS, BDP, SGN
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet factor 4 | protein | 62 | 23% helix, 29% strand | P02776 |
| B | Platelet factor 4 | protein | 64 | 22% helix, 28% strand | P02776 |
Ligands and binding sites
- ZDO · methyl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside · ligand · chains B
- SUS · 2-deoxy-3,6-di-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · ligand · chains A, B
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · chains A, B
- BDP · beta-D-glucopyranuronic acid · sugar · chains A
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 818 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 P02776
- Elsewhere: RCSB PDB 4R9W · PDBe 4R9W · UniProt P02776
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