7WYJ | pdb_00007wyj

Structure of the complex of lactoperoxidase with nitric oxide catalytic product nitrite at 1.89 A resolution

PDB DOI: https://doi.org/10.2210/pdb7WYJ/pdb
Entry: 7WYJ supersedes: 7VIN

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

Deposited: 2022-02-16 Released: 2023-01-11
Deposition Author(s): Viswanathan, V., Pandey, N., Singh, A.K., Sinha, M., Singh, R.P., Sharma, P., Kaur, P., Sharma, S., Singh, T.P.
Funding Organization(s): Department of Science & Technology (DST, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.258 (Depositor), 0.270 (DCC)
R-Value Work:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural evidence of the conversion of nitric oxide (NO) to nitrite ion (NO2-) by lactoperoxidase (LPO): Structure of the complex of LPO with NO2- at 1.89 angstrom resolution

Viswanathan, V., Ahmad, M.I., Singh, P.K., Ahmad, N., Sharma, P., Sharma, S., Singh, T.P.

(2023) J Inorg Biochem 247: 112311

DOI: https://doi.org/10.1016/j.jinorgbio.2023.112311

Macromolecule Content

Total Structure Weight: 72.78 kDa
Atom Count: 5,454
Modeled Residue Count: 595
Deposited Residue Count: 595
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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	D 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 8 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 R [auth A] MOL2 format, chain R [auth A] mmCIF format, chain R [auth A]	R [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain KA [auth A] SDF format, chain JA [auth A] SDF format, chain IA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain IA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain IA [auth A]	IA [auth A], JA [auth A], KA [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Interactions & Density Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A]
IOD (Subject of Investigation/LOI) Query on IOD Download:Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain GA [auth A] SDF format, chain I [auth A] SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain FA [auth A] SDF format, chain F [auth A] SDF format, chain EA [auth A] SDF format, chain DA [auth A] SDF format, chain CA [auth A] SDF format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain I [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain I [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain AA [auth A]	AA [auth A] BA [auth A] CA [auth A] D [auth A] DA [auth A] AA [auth A], BA [auth A], CA [auth A], D [auth A], DA [auth A], E [auth A], EA [auth A], F [auth A], FA [auth A], G [auth A], GA [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain E [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain FA [auth A] Focus chain G [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [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] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain E [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain FA [auth A] Focus chain G [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [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] Focus chain Z [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain HA [auth A] MOL2 format, chain HA [auth A] mmCIF format, chain HA [auth A]	HA [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain HA [auth A] Interactions & Density Focus chain HA [auth A]
EDO (Subject of Investigation/LOI) Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A]	N [auth A], O [auth A], Q [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth A]
SCN (Subject of Investigation/LOI) Query on SCN Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain M [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain M [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain M [auth A]	M [auth A], S [auth A], T [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain M [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain M [auth A] Focus chain S [auth A] Focus chain T [auth A]
NO2 (Subject of Investigation/LOI) Query on NO2 Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	NITRITE ION N O₂ IOVCWXUNBOPUCH-UHFFFAOYSA-M		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]