2EHA

Crystal structure of goat lactoperoxidase complexed with formate anion at 3.3 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history. 


Literature

Crystal structure of goat lactoperoxidase complexed with formate anion at 3.3 A resolution

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

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lactoperoxidase
A, B
595Capra hircusMutation(s): 0 
EC: 1.11.1.7
UniProt
Find proteins for A0A452E9Y6 (Capra hircus)
Explore A0A452E9Y6 
Go to UniProtKB:  A0A452E9Y6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A452E9Y6
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D 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
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO
GlyCosmos:  G62182OO
GlyGen:  G62182OO
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D 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
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, J
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
N [auth A],
S [auth B]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
OSM
Query on OSM
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T [auth B]1-(OXIDOSULFANYL)METHANAMINE
C H5 N O S
KONFWJXIYYGXOO-UHFFFAOYSA-N
CO3
Query on CO3
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L [auth A],
R [auth B]		CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
SCN
Query on SCN
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M [auth A]THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
FMT
Query on FMT
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O [auth A],
P [auth A],
U [auth B],
V [auth B]		FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
K [auth A],
Q [auth B]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.991α = 85.45
b = 72.272β = 84.04
c = 83.652γ = 75.89
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
CNSrefinement
AUTOMARdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-24
    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: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-25
    Changes: Data collection, Database references, Refinement description, Structure summary