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Crystallographic structure of a bacterial heparanase

Analyse Crystallographic structure of a bacterial heparanase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5BWI
Type: protein
Length: 880 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycoside hydrolase family 79
UniProt: A0A095J205
Ligands: NA
Pockets: 8 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycoside hydrolase family 79	protein	442	31% helix, 31% strand	A0A095J205
B	Glycoside hydrolase family 79	protein	438	31% helix, 32% strand	A0A095J205

Ligands and binding sites

NA · Sodium ion · metal · chains A
GOL · Glycerol · additive · 2 copies · chains A, B
ACT · Acetate ion · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1016	0.75	0.78	84	GOL
2	166	0.57	0.81	27	empty
3	172	0.56	0.81	24	empty
4	203	0.52	0.77	31	empty
5	200	0.50	0.76	31	ACT

Interfaces

1 interface between chains.

A–B · 1281 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

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Every structure of UniProt A0A095J205
Elsewhere: RCSB PDB 5BWI · PDBe 5BWI · UniProt A0A095J205

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