9IT8

Crystal structure of the ternary complex of lactoperoxidase with nitric oxide and nitrite ion at 1.95 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.188 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the ternary complex of lactoperoxidase with nitric oxide and nitrite ion at 1.95 A resolution

Maurya, A.Ahmad, N.Sharma, 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 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

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Z [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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C [auth A],
D [auth A],
E [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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EA [auth A]
FA [auth A]
GA [auth A]
HA [auth A]
NA [auth A]
EA [auth A],
FA [auth A],
GA [auth A],
HA [auth A],
NA [auth A],
OA [auth A],
PA [auth A],
QA [auth A],
R [auth A],
RA [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
OSM (Subject of Investigation/LOI)
Query on OSM

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

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AA [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3 (Subject of Investigation/LOI)
Query on NO3

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H [auth A]
I [auth A]
IA [auth A]
M [auth A]
N [auth A]
H [auth A],
I [auth A],
IA [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
SCN (Subject of Investigation/LOI)
Query on SCN

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CA [auth A]
J [auth A]
K [auth A]
L [auth A]
LA [auth A]
CA [auth A],
J [auth A],
K [auth A],
L [auth A],
LA [auth A],
MA [auth A]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
NO2 (Subject of Investigation/LOI)
Query on NO2

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G [auth A],
KA [auth A]
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
CA (Subject of Investigation/LOI)
Query on CA

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BA [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NO (Subject of Investigation/LOI)
Query on NO

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F [auth A],
JA [auth A]
NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.048α = 90
b = 80.503β = 102.849
c = 75.951γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Indian Council of Medical ResearchIndiaIR-661

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Structure summary