9IT8 | pdb_00009it8

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 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.198 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9IT8

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structure of the Complex of Lactoperoxidase With Nitric Oxide at 1.95 angstrom Resolution.

Maurya, A.Ahmad, N.Sharma, P.Sharma, S.Singh, T.P.

(2025) Proteins 93: 1079-1089

  • DOI: https://doi.org/10.1002/prot.26797
  • Primary Citation Related Structures: 
    9IT8

  • PubMed Abstract: 

    Lactoperoxidase (LPO) is a heme-containing mammalian enzyme that is found in the extracellular fluids of animals including plasma, saliva, airway epithelial and nasal lining fluids, milk, tears, and gastric juices. LPO uses hydrogen peroxide (H 2 O 2 ) to convert substrates into oxidized products. Previous structural studies have shown that H 2 O 2 , CO, and CN are bound to LPO at the distal heme cavity by coordinating with heme iron. The structure of the complex of LPO with NO shows that NO also binds to LPO at the distal heme cavity and forms a coordinate linkage with heme iron. The structure shows that the nitrogen atom of NO is linked to heme iron at a distance of 1.97 while the oxygen atom is attached to the N ε2 atom of His109 at a distance of 2.23 Å. On the other hand, N atom of NO is located with an interatomic distance of 3.25 Å allowing a hydrogen-bonding interaction with the N ε2 atom of Gln105. A comparison of the bindings of NO, CO, CN, and H 2 O 2 in coordination with heme iron indicates stereochemical compatibility of the distal heme cavity for the binding of diatomic molecules. However, notable differences are observed in their orientations in the distal heme cavity indicating functional differences. The bindings of NO, CO, and CN by coordinating with heme iron result in the inhibition of LPO while the binding of H 2 O 2 to heme iron produces an intermediate of LPO known as Compound I.


  • Organizational Affiliation
    • Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.

Macromolecule Content 

  • Total Structure Weight: 72.81 kDa 
  • Atom Count: 5,322 
  • Modeled Residue Count: 595 
  • Deposited Residue Count: 595 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD 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



Download:Ideal Coordinates CCD File
Z [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NAG
(Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
DA [auth A]1-(OXIDOSULFANYL)METHANAMINE
C H5 N O S
KONFWJXIYYGXOO-UHFFFAOYSA-N
EDO
(Subject of Investigation/LOI)

Query on EDO



Download:Ideal Coordinates CCD File
AA [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3
(Subject of Investigation/LOI)

Query on NO3



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
G [auth A],
KA [auth A]
NITRITE ION
N O2
IOVCWXUNBOPUCH-UHFFFAOYSA-M
CA
(Subject of Investigation/LOI)

Query on CA



Download:Ideal Coordinates CCD File
BA [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NO
(Subject of Investigation/LOI)

Query on NO



Download:Ideal Coordinates CCD File
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 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.198 (DCC) 
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

View Full Validation Report



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
  • Version 1.2: 2025-03-19
    Changes: Database references
  • Version 1.3: 2025-05-14
    Changes: Database references