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Embp heparin complex

Analyse Embp heparin complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2BRS
Type: protein
Length: 230 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Eosinophil-granule major basic protein
UniProt: P13727
Ligands: IDU, SGN, SO4
Pockets: 3 · best druggability 0.30

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Eosinophil-granule major basic protein	protein	115	20% helix, 34% strand	P13727

Ligands and binding sites

IDU · 2-O-sulfo-beta-L-altropyranuronic acid · ligand · chains B
SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · chains B
SO4 · Sulfate ion · ion · 8 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	72	0.30	0.74	12	empty
2	58	0.25	0.73	16	empty
3	53	0.25	0.73	12	empty

Interfaces

1 interface between chains.

A–B · 166 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2BRS · EMBP Heparin complex · the same entry in another collection · chain A against A, TM-score 1.00
P13727 · AlphaFold monomer V2.0 prediction for bone marrow proteoglycan (P13727) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P13727
Elsewhere: RCSB PDB 2BRS · PDBe 2BRS · UniProt P13727

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