7Y3U | pdb_00007y3u

Crystal structure of the complex of Lactoperoxidase with Nitric oxide at 2.50A resolution

PDB DOI: https://doi.org/10.2210/pdb7Y3U/pdb
Entry: 7Y3U supersedes: 6LRN

Classification: OXIDOREDUCTASE
Organism(s): Bos grunniens
Mutation(s): No

Deposited: 2022-06-13 Released: 2022-06-29
Deposition Author(s): Singh, P.K., Viswanathan, V., Ahmad, N., Rani, C., Sharma, P., Sharma, S., Singh, T.P.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.277 (Depositor), 0.275 (DCC)
R-Value Work:
0.219 (Depositor), 0.219 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7Y3U

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the complex of Lactoperoxidase with Nitric oxide at 2.50A resolution

Singh, P.K., Viswanathan, V., Ahmad, N.

To be published.

Macromolecule Content

Total Structure Weight: 139.52 kDa
Atom Count: 9,986
Modeled Residue Count: 1,190
Deposited Residue Count: 1,190
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactoperoxidase	A, B	595	Bos grunniens	Mutation(s): 0 EC: 1.11.1.7
UniProt
Find proteins for A0A8B9XNB5 (Bos mutus grunniens) Explore A0A8B9XNB5 Go to UniProtKB: A0A8B9XNB5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8B9XNB5
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	3		N-Glycosylation	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MH0 Query on MH0 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B]	E [auth A], M [auth B]	Mesoheme C₃₄ H₃₆ Fe N₄ O₄ CKMCSMAXNUVLQI-RGGAHWMASA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain M [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	H [auth A] I [auth A] J [auth A] O [auth B] P [auth B] H [auth A], I [auth A], J [auth A], O [auth B], P [auth B], Q [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain N [auth B]	F [auth A], N [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain N [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
NO (Subject of Investigation/LOI) Query on NO Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain K [auth A] mmCIF format, chain R [auth B] mmCIF format, chain K [auth A]	K [auth A], R [auth B]	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain R [auth B] Interactions & Density Focus chain K [auth A] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.277 (Depositor), 0.275 (DCC)
R-Value Work: 0.219 (Depositor), 0.219 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.731	α = 90
b = 93.173	β = 91.2
c = 82.319	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-06-29

Deposition Author(s):

Viswanathan, V.

This entry supersedes: 6LRN

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-06-29
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.