6A4Y

Crystal structure of bovine lactoperoxidase with partial occupancies of iodide and SCN- ions at the substrate binding site on the distal heme side at 1.92 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

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


Literature

Crystal structure of bovine lactoperoxidase with partial occupancies of iodide and SCN- ions at the substrate binding site on the distal heme side at 1.92 A resolution

Singh, P.K.Sirohi, H.V.Kaur, P.Sharma, S.Singh, T.P.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lactoperoxidase595Bos taurusMutation(s): 0 
EC: 1.11.1.7
UniProt
Find proteins for P80025 (Bos taurus)
Explore P80025 
Go to UniProtKB:  P80025
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80025
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
B
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

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C [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NAG
Query on NAG

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D [auth A],
E [auth A],
F [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
IOD
Query on IOD

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G [auth A]
H [auth A]
I [auth A]
J [auth A]
T [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
T [auth A],
U [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
OSM
Query on OSM

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V [auth A]1-(OXIDOSULFANYL)METHANAMINE
C H5 N O S
KONFWJXIYYGXOO-UHFFFAOYSA-N
SCN
Query on SCN

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L [auth A]
M [auth A]
N [auth A]
O [auth A]
P [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]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CA
Query on CA

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K [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.74α = 90
b = 79.8β = 91.43
c = 65.18γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary