Research workbench

Crystal structure of bovine lactoperoxidase

Analyse Crystal structure of bovine lactoperoxidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GC1
Type: protein
Length: 595 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lactoperoxidase
EC: 1.11.1.7
UniProt: P80025
Ligands: HEM, NAG, MAN, CA, IOD, SCN
Pockets: 7 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lactoperoxidase (EC 1.11.1.7)	protein	595	35% helix, 9% strand	P80025

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
MAN · alpha-D-mannopyranose · sugar · 2 copies
CA · Calcium ion · metal · chains A
IOD · Iodide ion · ion · 7 copies · chains A
SCN · Thiocyanate ion · ion · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	988	0.80	0.82	82	HEM, IOD
2	261	0.58	0.78	41	empty
3	110	0.42	0.77	24	empty
4	100	0.41	0.77	24	empty
5	110	0.40	0.76	20	empty

Modifications

Observed in the structure: 7 disulfide, 4 glycan, 2 cofactor, 1 modified (disulfide, N-glycosylation, heme attachment, phosphorylation).

Compared structures

3GC1 · Crystal structure of bovine lactoperoxidase · the same entry in another collection · chain A against A, TM-score 1.00
P80025 · AlphaFold monomer V2.0 prediction for lactoperoxidase (P80025) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P80025
Elsewhere: RCSB PDB 3GC1 · PDBe 3GC1 · UniProt P80025

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