9IT8

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

PDB DOI: https://doi.org/10.2210/pdb9IT8/pdb

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

Deposited: 2024-07-19 Released: 2024-09-11
Deposition Author(s): Maurya, A., Ahmad, N., Sharma, P., Sharma, S., Singh, T.P.
Funding Organization(s): Indian Council of Medical Research

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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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactoperoxidase	A	595	Bos taurus	Mutation(s): 0 EC: 1.11.1.7
UniProt
Find proteins for P80025 (Bos taurus) Explore P80025 Go to UniProtKB: P80025
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80025
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain Z [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain Z [auth A]	Z [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain Z [auth A] Interactions & Density Focus chain Z [auth A]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
IOD (Subject of Investigation/LOI) Query on IOD Download Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain NA [auth A] SDF format, chain OA [auth A] SDF format, chain PA [auth A] SDF format, chain QA [auth A] SDF format, chain R [auth A] SDF format, chain RA [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A]	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		Interactions Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain R [auth A] Focus chain RA [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain NA [auth A] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain R [auth A] Focus chain RA [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A]
OSM (Subject of Investigation/LOI) Query on OSM Download Ideal Coordinates CCD File SDF format, chain DA [auth A] MOL2 format, chain DA [auth A] mmCIF format, chain DA [auth A]	DA [auth A]	1-(OXIDOSULFANYL)METHANAMINE C H₅ N O S KONFWJXIYYGXOO-UHFFFAOYSA-N		Interactions Focus chain DA [auth A] Interactions & Density Focus chain DA [auth A]
EDO (Subject of Investigation/LOI) Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain AA [auth A]	AA [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Interactions & Density Focus chain AA [auth A]
NO3 (Subject of Investigation/LOI) Query on NO3 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain IA [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A]	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		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]
SCN (Subject of Investigation/LOI) Query on SCN Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth A] SDF format, chain MA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain MA [auth A]	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		Interactions Focus chain CA [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Interactions & Density Focus chain CA [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth A] Focus chain MA [auth A]
NO2 (Subject of Investigation/LOI) Query on NO2 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain KA [auth A] MOL2 format, chain G [auth A] MOL2 format, chain KA [auth A] mmCIF format, chain G [auth A] mmCIF format, chain KA [auth A]	G [auth A], KA [auth A]	NITRITE ION N O₂ IOVCWXUNBOPUCH-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain KA [auth A] Interactions & Density Focus chain G [auth A] Focus chain KA [auth A]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain BA [auth A] MOL2 format, chain BA [auth A] mmCIF format, chain BA [auth A]	BA [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Interactions & Density Focus chain BA [auth A]
NO (Subject of Investigation/LOI) Query on NO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain JA [auth A] MOL2 format, chain F [auth A] MOL2 format, chain JA [auth A] mmCIF format, chain F [auth A] mmCIF format, chain JA [auth A]	F [auth A], JA [auth A]	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain JA [auth A] Interactions & Density Focus chain F [auth A] Focus chain JA [auth A]