MolNFT v1 · #123510 · protein

Heparinase III-BT4657 gene product

5JMF · Heparinase III protein: “Heparinase III-BT4657 gene product”. X-ray diffraction, 1 ligand (MG), 5 pockets (best druggability 0.53). MolNFT v1 #123510 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5JMF
Type: protein
Length: 638 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heparinase III protein
UniProt: Q89YS4
Ligands: MG
Pockets: 5 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heparinase III protein	protein	638	37% helix, 23% strand	Q89YS4

Ligands and binding sites

MG · Magnesium ion · metal · chains A
GOL · Glycerol · additive · chains A
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

5 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	65	0.53	0.87	20	empty
2	285	0.52	0.74	34	empty
3	82	0.41	0.79	17	empty
4	119	0.40	0.75	21	empty
5	91	0.34	0.74	27	empty

Modifications

Observed in the structure: 25 modified (methylation).

Compared structures

5JMF · Heparinase III-BT4657 gene product · the same entry in another collection · 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 Q89YS4
Elsewhere: RCSB PDB 5JMF · PDBe 5JMF · UniProt Q89YS4

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