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Structure of human D-glucuronyl C5 epimerase

Analyse Structure of human D-glucuronyl C5 epimerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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 Å² buried · 46 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 glycan (N-glycosylation).

Compared structures

6HZZ · Structure of human D-glucuronyl C5 epimerase · 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 B against A, TM-score 0.99

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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