3GCJ

Mode of ligand binding and assignment of subsites in mammalian peroxidases: crystal structure of lactoperoxidase complexes with acetyl salycylic acid, salicylhydroxamic acid and benzylhydroxamic acid

• PDB DOI: https://doi.org/10.2210/pdb3GCJ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2009-02-22 Released: 2009-03-31 
• Deposition Author(s): Singh, A.K., Singh, N., Sinha, M., Kaur, P., Srinivasan, A., Sharma, S., Singh, T.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.212 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 

Starting Model: experimental

Literature

Mode of ligand binding and assignment of subsites in mammalian peroxidases: crystal structure of lactoperoxidase complexes with acetyl salycylic acid, salicylhydroxamic acid and benzylhydroxamic acid

Singh, A.K., Singh, N., Sinha, M., Kaur, P., Srinivasan, A., Sharma, S., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 71.76 kDa 
• Atom Count: 5,326 
• Modelled Residue Count: 595 
• Deposited Residue Count: 595 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactoperoxidase	A	595	Bos taurus	Mutation(s): 0  EC: 1.11.1.7
UniProt
Find proteins for P80025 (Bos taurus) Explore P80025  Go to UniProtKB:  P80025
Glycosylation
Glycosylation Sites: 4

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	F [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SHA	Q [auth A]	SALICYLHYDROXAMIC ACID C7 H7 N O3 HBROZNQEVUILML-UHFFFAOYSA-N
IOD	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
SCN	P [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CA	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Binding Affinity Annotations
ID	Source	Binding Affinity
SHA	BindingDB:  3GCJ	IC50: 400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 0.212 
• R-Value Work: 0.204 
• R-Value Observed: 0.204 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.618	α = 90
b = 80.553	β = 102.55
c = 77.803	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-31 
Deposition Author(s): Singh, A.K., Singh, N., Sinha, M., Kaur, P., Srinivasan, A., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2009-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary