8ING | pdb_00008ing

Structure of the ternary complex of lactoperoxidase with substrate nitric oxide (NO) and product nitrite ion (NO2) at 1.98 A resolution

PDB DOI: https://doi.org/10.2210/pdb8ING/pdb
Entry: 8ING supersedes: 7WCS

Classification: OXIDOREDUCTASE
Organism(s): Capra hircus
Mutation(s): No

Deposited: 2023-03-09 Released: 2023-04-05
Deposition Author(s): Ahmad, M.I., Viswanathan, V., Kumar, M., Singh, R.P., Singh, A.K., Sinha, M., Kaur, P., Sharma, P., Sharma, S., Singh, T.P.
Funding Organization(s): Science and Engineering Research Board (SERB)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free:
0.234 (Depositor), 0.236 (DCC)
R-Value Work:
0.183 (Depositor), 0.189 (DCC)

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

Structure of the ternary complex of lactoperoxidase with substrate nitric oxide (NO) and product nitrite ion (NO2) at 1.98 A resolution

Ahmad, M.I., Viswanathan, V., Kumar, M., Singh, R.P., Singh, A.K., Sinha, M., Kaur, P., Sharma, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 72.13 kDa
Atom Count: 5,333
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	Capra hircus	Mutation(s): 0 EC: 1.11.1.7
UniProt
Find proteins for A0A452E9Y6 (Capra hircus) Explore A0A452E9Y6 Go to UniProtKB: A0A452E9Y6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A452E9Y6
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 11 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 BA [auth A] MOL2 format, chain BA [auth A] mmCIF format, chain BA [auth A]	BA [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain BA [auth A] Interactions & Density Focus chain BA [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain C [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 Query on IOD Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain IA [auth A] SDF format, chain KA [auth A] SDF format, chain LA [auth A] SDF format, chain S [auth A] SDF format, chain U [auth A] SDF format, chain W [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain X [auth A] SDF format, chain V [auth A] SDF format, chain T [auth A] SDF format, chain JA [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain S [auth A] MOL2 format, chain U [auth A] MOL2 format, chain W [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain X [auth A] MOL2 format, chain V [auth A] MOL2 format, chain T [auth A] MOL2 format, chain JA [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain S [auth A] mmCIF format, chain U [auth A] mmCIF format, chain W [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain X [auth A] mmCIF format, chain V [auth A] mmCIF format, chain T [auth A] mmCIF format, chain JA [auth A]	AA [auth A] IA [auth A] JA [auth A] KA [auth A] LA [auth A] AA [auth A], IA [auth A], JA [auth A], KA [auth A], LA [auth A], S [auth A], T [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 IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [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] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [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] Focus chain Z [auth A]
OSM Query on OSM 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]	1-(OXIDOSULFANYL)METHANAMINE C H₅ N O S KONFWJXIYYGXOO-UHFFFAOYSA-N		Interactions Focus chain HA [auth A] Interactions & Density Focus chain HA [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain L [auth A] SDF format, chain EA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain L [auth A] MOL2 format, chain EA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain L [auth A] mmCIF format, chain EA [auth A]	CA [auth A], EA [auth A], L [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain EA [auth A] Focus chain L [auth A] Interactions & Density Focus chain CA [auth A] Focus chain EA [auth A] Focus chain L [auth A]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [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] SDF format, chain R [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [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] MOL2 format, chain R [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [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] mmCIF format, chain R [auth A]	H [auth A] I [auth A] N [auth A] O [auth A] P [auth A] H [auth A], I [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]
SCN Query on SCN Download:Ideal Coordinates CCD File SDF format, chain GA [auth A] SDF format, chain J [auth A] SDF format, chain M [auth A] SDF format, chain K [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A]	GA [auth A], J [auth A], K [auth A], M [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain GA [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Interactions & Density Focus chain GA [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A]
NO2 (Subject of Investigation/LOI) Query on NO2 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]	NITRITE ION N O₂ IOVCWXUNBOPUCH-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CA Query on CA 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]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain DA [auth A] Interactions & Density Focus chain DA [auth A]
NO (Subject of Investigation/LOI) Query on NO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain FA [auth A] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth A] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth A]	F [auth A], FA [auth A]	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain FA [auth A] Interactions & Density Focus chain F [auth A] Focus chain FA [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain MA [auth A] SDF format, chain NA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain NA [auth A]	MA [auth A], NA [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain MA [auth A] Focus chain NA [auth A] Interactions & Density Focus chain MA [auth A] Focus chain NA [auth A]