MolNFT v1 · #151852 · protein
Structure of human D-glucuronyl C5 epimerase
6HZZ · D-glucuronyl C5-epimerase: “Structure of human D-glucuronyl C5 epimerase”. X-ray diffraction, 7 ligands (NAG, MAN, BMA), 10 pockets (best druggability 0.77). MolNFT v1 #151852 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6HZZ
- Type
- protein
- Length
- 1,027 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
- NAG, MAN, BMA, FUC, CA, SO4, CL
- Pockets
- 10 · best druggability 0.77
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 | 511 | 32% helix, 30% strand | O94923 |
| B | D-glucuronyl C5-epimerase (EC 5.1.3.17) | protein | 516 | 31% helix, 29% strand | O94923 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.77 | 0.88 | 49 | ACT |
| 2 | 305 | 0.60 | 0.78 | 48 | empty |
| 3 | 240 | 0.59 | 0.80 | 38 | empty |
| 4 | 286 | 0.55 | 0.76 | 34 | SO4 |
| 5 | 221 | 0.53 | 0.77 | 31 | SO4, CL |
Interfaces
1 interface between chains.
- A–B · 3321 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan (N-glycosylation).
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 O94923
- Elsewhere: RCSB PDB 6HZZ · PDBe 6HZZ · UniProt O94923
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