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- PDB-5ff1: Two way mode of binding of antithyroid drug methimazole to mammal... -

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Basic information

Entry
Database: PDB / ID: 5ff1
TitleTwo 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
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / Inhibitor / peroxidase
Function / homology
Function and homology information


thiocyanate catabolic process / thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / lactoperoxidase activity / peroxidase / antifungal humoral response / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / basolateral plasma membrane ...thiocyanate catabolic process / thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / lactoperoxidase activity / peroxidase / antifungal humoral response / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / basolateral plasma membrane / response to oxidative stress / calcium ion binding / heme binding / extracellular space / cytoplasm
Similarity search - Function
Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 1-METHYL-1,3-DIHYDRO-2H-IMIDAZOLE-2-THIONE / NITRATE ION / Lactoperoxidase / Lactoperoxidase
Similarity search - Component
Biological speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsSingh, R.P. / Singh, A. / Sirohi, H. / Singh, A.K. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: Febs Open Bio / Year: 2016
Title: Dual binding mode of antithyroid drug methimazole to mammalian heme peroxidases - structural determination of the lactoperoxidase-methimazole complex at 1.97 angstrom resolution.
Authors: Singh, R.P. / Singh, A. / Sirohi, H.V. / Singh, A.K. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionDec 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactoperoxidase
B: Lactoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,09735
Polymers135,0602
Non-polymers5,03733
Water13,962775
1
A: Lactoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,97818
Polymers67,5301
Non-polymers2,44817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lactoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,11917
Polymers67,5301
Non-polymers2,58916
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.310, 93.020, 81.530
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 1 - 595 / Label seq-ID: 1 - 595

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lactoperoxidase /


Mass: 67529.781 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 118-712 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) / References: UniProt: A3F9D6, UniProt: A0A452E9Y6*PLUS

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Sugars , 2 types, 8 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 800 molecules

#3: Chemical
ChemComp-MMZ / 1-METHYL-1,3-DIHYDRO-2H-IMIDAZOLE-2-THIONE / METHIMAZOLE / Thiamazole


Mass: 114.169 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6N2S / Comment: medication*YM
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: NO3
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 775 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Sodium nitrate, PEG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 12, 2015
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.97→40.43 Å / Num. obs: 78463 / % possible obs: 93.8 % / Redundancy: 4 % / Net I/σ(I): 7.2
Reflection shellResolution: 1.966→2.017 Å / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OEK

4oek


Resolution: 1.97→40.43 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22586 2415 3 %RANDOM
Rwork0.17675 ---
obs0.17819 78463 94.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.345 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20.38 Å2
2--1.12 Å2-0 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 1.97→40.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9507 0 326 775 10608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01910109
X-RAY DIFFRACTIONr_bond_other_d00.029433
X-RAY DIFFRACTIONr_angle_refined_deg1.851.98713751
X-RAY DIFFRACTIONr_angle_other_deg3.5543.00321602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.40351188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.8823.75480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.377151610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3291576
X-RAY DIFFRACTIONr_chiral_restr0.1250.21453
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111441
X-RAY DIFFRACTIONr_gen_planes_other0.020.022421
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0483.0924758
X-RAY DIFFRACTIONr_mcbond_other3.0463.094757
X-RAY DIFFRACTIONr_mcangle_it4.6244.6235944
X-RAY DIFFRACTIONr_mcangle_other4.6244.6255945
X-RAY DIFFRACTIONr_scbond_it3.2563.3385351
X-RAY DIFFRACTIONr_scbond_other3.2563.3385352
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0494.9247808
X-RAY DIFFRACTIONr_long_range_B_refined8.39925.1712550
X-RAY DIFFRACTIONr_long_range_B_other8.39925.1712551
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3815 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.966→2.017 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 145 -
Rwork0.27 5009 -
obs--81.95 %

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