3PY4

Crystal structure of bovine lactoperoxidase in complex with paracetamol at 2.4A resolution

PDB DOI: https://doi.org/10.2210/pdb3PY4/pdb

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

Deposited: 2010-12-11 Released: 2011-01-05
Deposition Author(s): Pandey, N., Sing, R.P., Singh, A.K., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.258
R-Value Work: 0.225
R-Value Observed: 0.225

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 72.41 kDa
Atom Count: 5,150
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 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
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
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	C	3		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
TYL Query on TYL Download Ideal Coordinates CCD File SDF format, chain W [auth A] MOL2 format, chain W [auth A]	W [auth A]	N-(4-HYDROXYPHENYL)ACETAMIDE (TYLENOL) C₈ H₉ N O₂ RZVAJINKPMORJF-UHFFFAOYSA-N		Interactions Focus chain W [auth A] Interactions & Density Focus chain W [auth A]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain I [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth A]	H [auth A] I [auth A] J [auth A] K [auth A] L [auth A] H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain X [auth A] MOL2 format, chain X [auth A]	X [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain X [auth A] Interactions & Density Focus chain X [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth A] MOL2 format, chain BA [auth A]	BA [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Interactions & Density Focus chain BA [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain Z [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain Z [auth A]	AA [auth A], Z [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain Z [auth A]
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain Y [auth A] MOL2 format, chain Y [auth A]	Y [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain Y [auth A] Interactions & Density Focus chain Y [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

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: 2.42 Å
R-Value Free: 0.258
R-Value Work: 0.225
R-Value Observed: 0.225
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.81	α = 90
b = 80.673	β = 103.07
c = 74.442	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-01-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-01-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: 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