6M7E

Structure of bovine lactoperoxidase with multiple iodide ions in the distaline heme cavity.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.184 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Structure of bovine lactoperoxidase with multiple iodide ions in the distaline heme cavity.

Maurya, A.Viswanathan, V.Pandey, N.Singh, A.K.Sinha, M.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 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

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D [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NAG (Subject of Investigation/LOI)
Query on NAG

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E [auth A],
F [auth A],
G [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
IOD (Subject of Investigation/LOI)
Query on IOD

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AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
H [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
X [auth A],
Y [auth A],
Z [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL (Subject of Investigation/LOI)
Query on GOL

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R [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
OSM (Subject of Investigation/LOI)
Query on OSM

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U [auth A]1-(OXIDOSULFANYL)METHANAMINE
C H5 N O S
KONFWJXIYYGXOO-UHFFFAOYSA-N
SCN (Subject of Investigation/LOI)
Query on SCN

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Q [auth A],
S [auth A],
T [auth A],
V [auth A]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
CA (Subject of Investigation/LOI)
Query on CA

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C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)
Query on CL

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W [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.81α = 90
b = 80.673β = 103.07
c = 74.442γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata 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: 2020-04-15
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2022-05-04
    Changes: Database references, Structure summary
  • Version 2.2: 2023-11-29
    Changes: Data collection, Derived calculations, Refinement description