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Crystal structure of heparan sulfate lyase hepc mutant from pedobacter heparinus

Analyse Crystal structure of heparan sulfate lyase hepc mutant from pedobacter heparinus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4MMI
Type: protein
Length: 636 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heparinase III protein
EC: 4.2.2.8
UniProt: Q59289
Ligands: CA
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heparinase III protein (EC 4.2.2.8)	protein	636	37% helix, 22% strand	Q59289

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	128	0.72	0.92	19	empty
2	783	0.70	0.76	80	empty
3	82	0.37	0.76	16	empty
4	54	0.29	0.75	16	empty

Compared structures

4MMI · Crystal structure of heparan sulfate lyase HepC mutant from Pedobacter heparinus · the same entry in another collection · chain A against A, TM-score 1.00
Q59289 · AlphaFold monomer V2.0 prediction for heparin-sulfate lyase (Q59289) · a predicted model of the same protein · chain A against A, TM-score 0.79

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 Q59289
Elsewhere: RCSB PDB 4MMI · PDBe 4MMI · UniProt Q59289

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