MolNFT v1 · #151854 · protein
Structure of human D-glucuronyl C5 epimerase in complex with substrate
6I01 · D-glucuronyl C5-epimerase: “Structure of human D-glucuronyl C5 epimerase in complex with substrate”. X-ray diffraction, 6 ligands (GNS, NAG, BDP), 11 pockets (best druggability 0.79). MolNFT v1 #151854 on GenesisL1: 3D structure…
- PDB
- 6I01
- Type
- protein
- Length
- 1,028 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-glucuronyl C5-epimerase
- EC
- 5.1.3.17
- UniProt
- O94923
- Ligands
- GNS, NAG, BDP, MAN, BMA, CA
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-glucuronyl C5-epimerase (EC 5.1.3.17) | protein | 512 | 31% helix, 30% strand | O94923 |
| B | D-glucuronyl C5-epimerase (EC 5.1.3.17) | protein | 516 | 30% helix, 30% strand | O94923 |
Ligands and binding sites
- GNS · 2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose · ligand · 6 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
- BDP · beta-D-glucopyranuronic acid · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 14 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.79 | 0.89 | 47 | GOL |
| 2 | 320 | 0.62 | 0.79 | 48 | GOL |
| 3 | 293 | 0.62 | 0.80 | 47 | GOL |
| 4 | 327 | 0.60 | 0.78 | 46 | GNS, BDP |
| 5 | 275 | 0.60 | 0.79 | 34 | GNS, BDP |
Interfaces
1 interface between chains.
- A–B · 3371 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan (N-glycosylation).
Compared structures
- 6I01 · Structure of human D-glucuronyl C5 epimerase in complex with substrate · the same entry in another collection · chain A against A, TM-score 1.00
- O94923 · AlphaFold monomer V2.0 prediction for D-glucuronyl C5-epimerase (O94923) · 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 O94923
- Elsewhere: RCSB PDB 6I01 · PDBe 6I01 · UniProt O94923
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