2IKC

Crystal structure of sheep lactoperoxidase at 3.25 A resolution reveals the binding sites for formate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history. 


Literature

Crystal structure of sheep lactoperoxidase at 3.25 A resolution reveals the binding sites for formate

Sheikh, I.A., Singh, N., Singh, A.K., Sharma, S., Singh, T.P.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
milk lactoperoxidase
A, B
595Ovis ariesMutation(s): 0 
EC: 1.11.1.7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, F, G
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
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
E, H
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G62182OO
GlyCosmos:  G62182OO
GlyGen:  G62182OO
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
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L [auth A],
S [auth B]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NAG
Query on NAG
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I [auth A],
P [auth B]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CO3
Query on CO3
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K [auth A],
R [auth B]		CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
FMT
Query on FMT
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M [auth A]
N [auth A]
O [auth A]
T [auth B]
U [auth B]
M [auth A],
N [auth A],
O [auth A],
T [auth B],
U [auth B],
V [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
J [auth A],
Q [auth B]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.08α = 85.2
b = 72.59β = 84.07
c = 84.47γ = 75.41
Software Package:
Software NamePurpose
CNSrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-10-25
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-30
    Changes: Structure summary