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Crystal structure of D-glucuronyl C5-epimerase in complex with heparin hexasaccharide
Analyse Crystal structure of D-glucuronyl C5-epimerase in complex with heparin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PXQ
- Type
- protein
- Length
- 1,031 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-glucuronyl C5 epimerase B
- EC
- 5.1.3.17
- UniProt
- Q6TS32
- Ligands
- UAP, SGN, IDS
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-glucuronyl C5 epimerase B (EC 5.1.3.17) | protein | 516 | 32% helix, 27% strand | Q6TS32 |
| B | D-glucuronyl C5 epimerase B (EC 5.1.3.17) | protein | 515 | 32% helix, 28% strand | Q6TS32 |
Ligands and binding sites
- UAP · 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid · ligand · 2 copies · chains A, B
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 6 copies · chains A, B
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.79 | 0.91 | 44 | empty |
| 2 | 278 | 0.61 | 0.80 | 43 | empty |
| 3 | 317 | 0.58 | 0.77 | 40 | SGN, IDS, UAP |
| 4 | 257 | 0.58 | 0.79 | 42 | empty |
| 5 | 304 | 0.57 | 0.76 | 34 | SGN, IDS, UAP |
Interfaces
1 interface between chains.
- A–B · 3204 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 4PXQ · Crystal structure of D-glucuronyl C5-epimerase in complex with heparin hexasaccharide · 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 Q6TS32
- Elsewhere: RCSB PDB 4PXQ · PDBe 4PXQ · UniProt Q6TS32
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