2E9E

Crystal structure of the complex of goat lactoperoxidase with Nitrate at 3.25 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2E9E/pdb

• Classification: METAL BINDING PROTEIN, OXIDOREDUCTASE
• Organism(s): Capra hircus
• Mutation(s): No 


• Deposited: 2007-01-25 Released: 2007-02-06 
• Deposition Author(s): Singh, A.K., Prem kumar, R., Singh, N., Sharma, S., Singh, S.B., Bhushan, A., Kaur, P., Singh, T.P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 0.203 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Literature

Crystal structure of the complex of goat lactoperoxidase with Nitrate at 3.25 A resolution

Singh, A.K., Prem kumar, R., Singh, N., Sharma, S., Singh, S.B., Bhushan, A., Kaur, P., Singh, T.P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 141.27 kDa 
• Atom Count: 10,299 
• Modelled Residue Count: 1,190 
• Deposited Residue Count: 1,190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactoperoxidase	A, B	595	Capra hircus	Mutation(s): 0  EC: 1.11.1.7
UniProt
Find proteins for A0A452E9Y6 (Capra hircus) Explore A0A452E9Y6  Go to UniProtKB:  A0A452E9Y6

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	C, D, G	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO GlyCosmos:  G62182OO GlyGen:  G62182OO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, H, I	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

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

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	Q [auth A], V [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
OSM	W [auth B]	1-(OXIDOSULFANYL)METHANAMINE C H5 N O S KONFWJXIYYGXOO-UHFFFAOYSA-N
NO3	K [auth A], L [auth A], R [auth B], S [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CO3	M [auth A], T [auth B]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L
SCN	P [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CA	N [auth A], U [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CYN	O [auth A]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 0.203 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.522	α = 85.3
b = 72.537	β = 84.06
c = 83.983	γ = 75.68

Software Package:

Software Name	Purpose
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-06 
Deposition Author(s): Singh, A.K., Prem kumar, R., Singh, N., Sharma, S., Singh, S.B., Bhushan, A., Kaur, P., Singh, T.P.

Revision History  

• Version 1.0: 2007-02-06
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 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: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary