2QQT

Crystal structure of the complex of bovine lactoperoxidase with acetyl salicylic acid at 2.5 A resolution

PDB DOI: https://doi.org/10.2210/pdb2QQT/pdb

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

Deposited: 2007-07-27 Released: 2007-08-07
Deposition Author(s): Singh, A.K., Singh, N., Sharma, S., Kaur, P., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.211
R-Value Work: 0.194
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of the complex of bovine lactoperoxidase with acetyl salicylic acid at 2.5 A resolution

Singh, A.K., Singh, N., Sharma, S., Kaur, P., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 71.66 kDa
Atom Count: 5,295
Modelled Residue Count: 595
Deposited Residue Count: 595
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactoperoxidase	A	595	Bos taurus	Mutation(s): 0 Gene Names: LPO EC: 1.11.1.7
UniProt
Find proteins for P80025 (Bos taurus) Explore P80025 Go to UniProtKB: P80025
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80025
Protein Feature View Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Chain 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	Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Entity ID: 3
Molecule	Chains	Chain 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	Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A]	P [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Ligand Interaction
AIN Query on AIN Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	2-(ACETYLOXY)BENZOIC ACID C₉ H₈ O₄ BSYNRYMUTXBXSQ-UHFFFAOYSA-N		Ligand Interaction
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain K [auth A] SDF format, chain O [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth A]	I [auth A] J [auth A] K [auth A] L [auth A] M [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		Ligand Interaction
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Ligand Interaction
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Ligand Interaction

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.211
R-Value Work: 0.194
R-Value Observed: 0.194
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.66	α = 90
b = 80.52	β = 102.65
c = 77.97	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-08-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-08-07
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