MolNFT v1 · #123508 · protein

Heparinase III-BT4657 gene product, methylated lysines

5JMD · Heparinase III protein: “Heparinase III-BT4657 gene product, methylated lysines”. X-ray diffraction, 1 ligand (MG), 7 pockets (best druggability 0.60). MolNFT v1 #123508 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5JMD
Type: protein
Length: 646 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heparinase III protein
UniProt: Q89YS4
Ligands: MG
Pockets: 7 · best druggability 0.60

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heparinase III protein	protein	646	37% helix, 23% strand	Q89YS4

Ligands and binding sites

MG · Magnesium ion · metal · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	94	0.60	0.88	24	empty
2	70	0.41	0.80	13	empty
3	134	0.39	0.74	22	empty
4	78	0.35	0.75	17	empty
5	68	0.34	0.76	21	empty

Modifications

Observed in the structure: 1 modified (methylation).

Compared structures

5JMD · Heparinase III-BT4657 gene product, Methylated Lysines · 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 5JMD · PDBe 5JMD · UniProt Q89YS4

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