3R55

Crystal structure of the complex of goat lactoperoxidase with Pyrazinamide at 2.1 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3R55/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Capra hircus
• Mutation(s): No 


• Deposited: 2011-03-18 Released: 2011-08-03 
• Deposition Author(s): Singh, R.P., Pandey, N., Singh, A.K., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.264 
• R-Value Work: 0.219 
• R-Value Observed: 0.222 

Starting Model: experimental

Literature

Crystal structure of the complex of goat lactoperoxidase with Pyrazinamide at 2.1 A resolution

Singh, R.P., Pandey, N., Singh, A.K., Sinha, M., Kaur, P., 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: 72.17 kDa 
• Atom Count: 5,298 
• 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	Capra hircus	Mutation(s): 0  EC: 1.11.1.7
UniProt
Find proteins for A0A452E9Y6 (Capra hircus) Explore A0A452E9Y6  Go to UniProtKB:  A0A452E9Y6
Glycosylation
Glycosylation Sites: 4

Oligosaccharides

Help

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, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 11 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
NAG	D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
IOD	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]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
PZA	V [auth A], W [auth A]	PYRAZINE-2-CARBOXAMIDE C5 H5 N3 O IPEHBUMCGVEMRF-UHFFFAOYSA-N
MRD	EA [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
PEG	FA [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	CA [auth A], DA [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	AA [auth A], BA [auth A], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
SCN	U [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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.264 
• R-Value Work: 0.219 
• R-Value Observed: 0.222 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.991	α = 90
b = 79.62	β = 102.24
c = 77.52	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-03 
Deposition Author(s): Singh, R.P., Pandey, N., Singh, A.K., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2011-08-03
  Type: Initial release
  
• Version 1.1: 2014-10-29
  Changes: Structure summary
• Version 1.2: 2016-04-06
  Changes: Non-polymer description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary