5FF1

Two way mode of binding of antithyroid drug methimazole to mammalian heme peroxidases: Structure of the complex of lactoperoxidase with methimazole at 1.97 Angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb5FF1/pdb

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

Deposited: 2015-12-17 Released: 2016-01-13
Deposition Author(s): Singh, R.P., Singh, A., Sirohi, H., Singh, A.K., Kaur, P., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.226
R-Value Work: 0.177
R-Value Observed: 0.178

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Dual binding mode of antithyroid drug methimazole to mammalian heme peroxidases - structural determination of the lactoperoxidase-methimazole complex at 1.97 angstrom resolution.

Singh, R.P., Singh, A., Sirohi, H.V., Singh, A.K., Kaur, P., Sharma, S., Singh, T.P.

(2016) FEBS Open Bio 6: 640-650

PubMed: 27398304 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/2211-5463.12051
Primary Citation of Related Structures:
5FF1

PubMed Abstract:
Lactoperoxidase (LPO, EC 1.11.1.7) is a member of the mammalian heme peroxidase family which also includes thyroid peroxidase (TPO). These two enzymes have a sequence homology of 76%. The structure of LPO is known but not that of TPO. In order to determine the mode of binding of antithyroid drugs to thyroid peroxidase, we have determined the crystal structure of LPO complexed with an antithyroid drug, methimazole (MMZ) at 1.97 Å resolution. LPO was isolated from caprine colostrum, purified to homogeneity and crystallized with 20% poly(ethylene glycol)-3350. Crystals of LPO were soaked in a reservoir solution containing MMZ. The structure determination showed the presence of two crystallographically independent molecules in the asymmetric unit. Both molecules contained one molecule of MMZ, but with different orientations. MMZ was held tightly between the heme moiety on one side and the hydrophobic parts of the side chains of Arg255, Glu258, and Leu262 on the opposite side. The back of the cleft contained the side chains of Gln105 and His109 which also interacted with MMZ. In both orientations, MMZ had identical buried areas and formed a similar number of interactions. It appears that the molecules of MMZ can enter the substrate-binding channel of LPO in two opposite orientations. But once they reach the distal heme pocket, their orientations are frozen due to equally tight packing of MMZ in both orientations. This is a novel example of an inhibitor binding to an enzyme with two orientations at the same site with nearly equal occupancies.

Organizational Affiliation

Department of Biophysics All India Institute of Medical Sciences New Delhi India.

Macromolecule Content

Total Structure Weight: 140.1 kDa
Atom Count: 10,608
Modelled Residue Count: 1,190
Deposited Residue Count: 1,190
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	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A452E9Y6
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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	C	2		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain J [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain J [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain J [auth A]	J [auth A], Y [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain J [auth A] Focus chain Y [auth B] Interactions & Density Focus chain J [auth A] Focus chain Y [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File 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 V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] 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 V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] 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 V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	F [auth A] G [auth A] H [auth A] I [auth A] V [auth B] F [auth A], G [auth A], H [auth A], I [auth A], V [auth B], W [auth B], X [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B]
MMZ Query on MMZ Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain EA [auth B] SDF format, chain U [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain U [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain U [auth B]	D [auth A], E [auth A], EA [auth B], U [auth B]	1-METHYL-1,3-DIHYDRO-2H-IMIDAZOLE-2-THIONE C₄ H₆ N₂ S PMRYVIKBURPHAH-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain EA [auth B] Focus chain U [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain EA [auth B] Focus chain U [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A]	FA [auth B] GA [auth B] HA [auth B] IA [auth B] Q [auth A] FA [auth B], GA [auth B], HA [auth B], IA [auth B], Q [auth A], R [auth A], S [auth A], T [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain L [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] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain L [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] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain L [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]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] L [auth A] AA [auth B], BA [auth B], CA [auth B], DA [auth B], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] 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] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] 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]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain Z [auth B] MOL2 format, chain K [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain K [auth A] mmCIF format, chain Z [auth B]	K [auth A], Z [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain Z [auth B] Interactions & Density Focus chain K [auth A] Focus chain Z [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
MMZ	BindingDB: 5FF1	IC50: 8400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.226
R-Value Work: 0.177
R-Value Observed: 0.178
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.31	α = 90
b = 93.02	β = 89.97
c = 81.53	γ = 90

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: 2016-01-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-01-13
Type: Initial release
Version 1.1: 2016-07-27
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-16
Changes: Structure summary