5HPW

Mode of binding of antithyroid drug, propylthiouracil to lactoperoxidase: Binding studies and structure determination

PDB DOI: https://doi.org/10.2210/pdb5HPW/pdb

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

Deposited: 2016-01-21 Released: 2016-04-20
Deposition Author(s): Singh, R.P., Singh, A., Sharma, P., Kaur, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.311
R-Value Work: 0.260
R-Value Observed: 0.262

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Mode of binding of antithyroid drug, propylthiouracil to lactoperoxidase: Binding studies and structure determination

Singh, R.P., Singh, A., Sharma, P., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 277.42 kDa
Atom Count: 20,141
Modelled Residue Count: 2,380
Deposited Residue Count: 2,380
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, B, C, D	595	Capra hircus	Mutation(s): 0
UniProt
Find proteins for A0A452E9Y6 (Capra hircus) Explore A0A452E9Y6 Go to UniProtKB: A0A452E9Y6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A452E9Y6
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
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	E, G, H	2		N-Glycosylation	Interactions Focus chain E Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	2		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G79924RM GlyCosmos: G79924RM GlyGen: G79924RM

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain MA [auth D] SDF format, chain P [auth A] SDF format, chain V [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain V [auth B]	EA [auth C], MA [auth D], P [auth A], V [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain EA [auth C] Focus chain MA [auth D] Focus chain P [auth A] Focus chain V [auth B] Interactions & Density Focus chain EA [auth C] Focus chain MA [auth D] Focus chain P [auth A] Focus chain V [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain Q [auth B] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C]	FA [auth D] GA [auth D] I [auth A] J [auth A] Q [auth B] FA [auth D], GA [auth D], I [auth A], J [auth A], Q [auth B], X [auth C], Y [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain FA [auth D] Focus chain GA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth B] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain FA [auth D] Focus chain GA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth B] Focus chain X [auth C] Focus chain Y [auth C]
3CJ Query on 3CJ Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain LA [auth D] SDF format, chain O [auth A] SDF format, chain W [auth B] MOL2 format, chain DA [auth C] MOL2 format, chain LA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain W [auth B]	DA [auth C], LA [auth D], O [auth A], W [auth B]	6-propyl-2-thioxo-2,3-dihydropyrimidin-4(1H)-one C₇ H₁₀ N₂ O S KNAHARQHSZJURB-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain LA [auth D] Focus chain O [auth A] Focus chain W [auth B] Interactions & Density Focus chain DA [auth C] Focus chain LA [auth D] Focus chain O [auth A] Focus chain W [auth B]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B]	AA [auth C] BA [auth C] CA [auth C] IA [auth D] JA [auth D] AA [auth C], BA [auth C], CA [auth C], IA [auth D], JA [auth D], KA [auth D], L [auth A], M [auth A], N [auth A], S [auth B], T [auth B], U [auth B]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain K [auth A] SDF format, chain R [auth B] SDF format, chain Z [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Z [auth C]	HA [auth D], K [auth A], R [auth B], Z [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain HA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain Z [auth C] Interactions & Density Focus chain HA [auth D] Focus chain K [auth A] Focus chain R [auth B] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.311
R-Value Work: 0.260
R-Value Observed: 0.262
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.221	α = 80.91
b = 82.588	β = 73.71
c = 95.083	γ = 89.96

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-04-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-04-20
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary