MolNFT v1 · #100067 · protein

Crystal structure of heparan sulfate lyase hepc from pedobacter heparinus

4MMH · Heparinase III protein: “Crystal structure of heparan sulfate lyase hepc from pedobacter heparinus”. X-ray diffraction, 1 ligand (CA), 2 pockets (best druggability 0.75). MolNFT v1 #100067 on GenesisL1: 3D structure, binding sites…

PDB: 4MMH
Type: protein
Length: 637 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: 2 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heparinase III protein (EC 4.2.2.8)	protein	637	35% helix, 23% 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

2 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	124	0.75	0.94	19	empty
2	802	0.71	0.77	81	empty

Compared structures

4MMH · Crystal structure of heparan sulfate lyase HepC 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 0.75

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 4MMH · PDBe 4MMH · UniProt Q59289

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