9KU6 | pdb_00009ku6

Crystal structure of the complex of lactoperoxidase with nitric oxide at 1.72 A resolution

PDB DOI: https://doi.org/10.2210/pdb9KU6/pdb

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

Deposited: 2024-12-03 Released: 2024-12-18
Deposition Author(s): Maurya, A., Sharma, P., Sharma, S., Singh, T.P.
Funding Organization(s): Indian Council of Medical Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.235 (Depositor), 0.244 (DCC)
R-Value Work:
0.186 (Depositor), 0.196 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of the complex of lactoperoxidase with nitric oxide at 1.72 A resolution

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

To be published.

Macromolecule Content

Total Structure Weight: 73.89 kDa
Atom Count: 5,522
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 [auth C]	2		N-Glycosylation	Interactions Focus chain B [auth C] Interactions & Density Focus chain B [auth C]
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 OA [auth A] MOL2 format, chain OA [auth A] mmCIF format, chain OA [auth A]	OA [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain OA [auth A] Interactions & Density Focus chain OA [auth A]
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain NA [auth A] SDF format, chain Q [auth A] MOL2 format, chain C [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain C [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain Q [auth A]	C [auth A], NA [auth A], Q [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Focus chain NA [auth A] Focus chain Q [auth A] Interactions & Density Focus chain C [auth A] Focus chain NA [auth A] Focus chain Q [auth A]
PGE (Subject of Investigation/LOI) Query on PGE 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]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain HA [auth A] Interactions & Density Focus chain HA [auth A]
IOD (Subject of Investigation/LOI) Query on IOD Download:Ideal Coordinates CCD File SDF format, chain AB [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [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 QA [auth A] SDF format, chain RA [auth A] SDF format, chain SA [auth A] SDF format, chain TA [auth A] SDF format, chain UA [auth A] SDF format, chain VA [auth A] SDF format, chain WA [auth A] SDF format, chain XA [auth A] SDF format, chain YA [auth A] SDF format, chain ZA [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] MOL2 format, chain AB [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [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 QA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain ZA [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] mmCIF format, chain AB [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [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 QA [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain TA [auth A] mmCIF format, chain UA [auth A] mmCIF format, chain VA [auth A] mmCIF format, chain WA [auth A] mmCIF format, chain XA [auth A] mmCIF format, chain YA [auth A] mmCIF format, chain ZA [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A]	AB [auth A] D [auth A] E [auth A] F [auth A] G [auth A] AB [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], QA [auth A], RA [auth A], SA [auth A], TA [auth A], UA [auth A], VA [auth A], WA [auth A], XA [auth A], YA [auth A], ZA [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain AB [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [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 M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth A] Interactions & Density Focus chain AB [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [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 M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth A]
SCN (Subject of Investigation/LOI) Query on SCN Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain R [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] SDF format, chain Z [auth A] SDF format, chain IA [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain R [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] MOL2 format, chain Z [auth A] MOL2 format, chain IA [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain R [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] mmCIF format, chain Z [auth A] mmCIF format, chain IA [auth A]	AA [auth A] BA [auth A] CA [auth A] DA [auth A] EA [auth A] AA [auth A], BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], IA [auth A], R [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]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain IA [auth A] Focus chain R [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 BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain IA [auth A] Focus chain R [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]
NO2 (Subject of Investigation/LOI) Query on NO2 Download:Ideal Coordinates CCD File SDF format, chain JA [auth A] SDF format, chain MA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain MA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain MA [auth A]	JA [auth A], MA [auth A]	NITRITE ION N O₂ IOVCWXUNBOPUCH-UHFFFAOYSA-M		Interactions Focus chain JA [auth A] Focus chain MA [auth A] Interactions & Density Focus chain JA [auth A] Focus chain MA [auth A]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain PA [auth A] MOL2 format, chain PA [auth A] mmCIF format, chain PA [auth A]	PA [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain PA [auth A] Interactions & Density Focus chain PA [auth A]
NO (Subject of Investigation/LOI) Query on NO Download:Ideal Coordinates CCD File SDF format, chain KA [auth A] SDF format, chain LA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain LA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain LA [auth A]	KA [auth A], LA [auth A]	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYSA-N		Interactions Focus chain KA [auth A] Focus chain LA [auth A] Interactions & Density Focus chain KA [auth A] Focus chain LA [auth A]