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- PDB-7lag: CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH... -

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Database: PDB / ID: 7lag
TitleCRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH Compound-14 AKA 7-({1-[(3-phenoxyphenyl)methyl]-1H-pyrazol-4-yl}methyl)-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine
Components
  • Isoform H14 of Myeloperoxidase
  • Myeloperoxidase light chain
KeywordsOXIDOREDUCTASE / Myeloperoxidase / MPO / HEME-DEPENDENT PEROXIDASE
Function / homology
Function and homology information


myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / phagocytic vesicle lumen / response to gold nanoparticle / response to yeast / respiratory burst involved in defense response / low-density lipoprotein particle remodeling / azurophil granule / response to food ...myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / phagocytic vesicle lumen / response to gold nanoparticle / response to yeast / respiratory burst involved in defense response / low-density lipoprotein particle remodeling / azurophil granule / response to food / defense response to fungus / response to mechanical stimulus / removal of superoxide radicals / secretory granule / hydrogen peroxide catabolic process / peroxidase activity / defense response / azurophil granule lumen / heparin binding / response to oxidative stress / response to lipopolysaccharide / lysosome / defense response to bacterium / intracellular membrane-bounded organelle / heme binding / Neutrophil degranulation / chromatin binding / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-XSD / Myeloperoxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsKhan, J.A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2021
Title: Small molecule and macrocyclic pyrazole derived inhibitors of myeloperoxidase (MPO).
Authors: Hu, C.H. / Neissel Valente, M.W. / Halpern, O.S. / Jusuf, S. / Khan, J.A. / Locke, G.A. / Duke, G.J. / Liu, X. / Duclos, F.J. / Wexler, R.R. / Kick, E.K. / Smallheer, J.M.
History
DepositionJan 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 2.0Jul 28, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / pdbx_branch_scheme / 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_assembly_prop / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / reflns_shell / struct_asym / struct_conn / struct_conn_type
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value ..._pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.ls_d_res_high / _refine_hist.d_res_high / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_number_atoms_ligand / _reflns_shell.number_unique_obs
Description: Polymer backbone linkage / Provider: author / Type: Coordinate replacement
Revision 2.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myeloperoxidase light chain
B: Isoform H14 of Myeloperoxidase
D: Myeloperoxidase light chain
E: Isoform H14 of Myeloperoxidase
F: Myeloperoxidase light chain
G: Isoform H14 of Myeloperoxidase
H: Myeloperoxidase light chain
I: Isoform H14 of Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,31135
Polymers260,7708
Non-polymers10,54127
Water00
1
A: Myeloperoxidase light chain
B: Isoform H14 of Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,02010
Polymers65,1932
Non-polymers2,8278
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14700 Å2
ΔGint-86 kcal/mol
Surface area21860 Å2
MethodPISA
2
D: Myeloperoxidase light chain
E: Isoform H14 of Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5828
Polymers65,1932
Non-polymers3,3896
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13940 Å2
ΔGint-69 kcal/mol
Surface area21740 Å2
MethodPISA
3
F: Myeloperoxidase light chain
G: Isoform H14 of Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,07711
Polymers65,1932
Non-polymers3,8849
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14760 Å2
ΔGint-86 kcal/mol
Surface area22030 Å2
MethodPISA
4
H: Myeloperoxidase light chain
I: Isoform H14 of Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8039
Polymers65,1932
Non-polymers3,6107
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14250 Å2
ΔGint-66 kcal/mol
Surface area21850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.459, 149.886, 228.642
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 8 molecules ADFHBEGI

#1: Protein
Myeloperoxidase light chain / MPO


Mass: 11974.420 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Blood Neutrophill / Source: (natural) Homo sapiens (human) / References: UniProt: P05164, myeloperoxidase
#2: Protein
Isoform H14 of Myeloperoxidase / MPO


Mass: 53218.188 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05164, myeloperoxidase

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Sugars , 3 types, 11 molecules

#3: 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.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#7: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / 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 , 4 types, 16 molecules

#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#9: Chemical
ChemComp-XSD / 7-({1-[(3-phenoxyphenyl)methyl]-1H-pyrazol-4-yl}methyl)-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine


Mass: 397.433 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H19N7O / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.1M Hepes pH 7.5, 150mM NaCl, 20-25%(V/V)PEG3350.Crystals were cryoprotected by supplementing the mother liquor with 15% (v/v) ethylene glycol and harvested by flash-cooling in liquid nitrogen
PH range: 7.5?

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jan 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.81→50 Å / Num. obs: 59486 / % possible obs: 100 % / Redundancy: 6.2 % / Biso Wilson estimate: 57.76 Å2 / Rmerge(I) obs: 0.152 / Net I/σ(I): 12
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 5855 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WY7

6wy7


Resolution: 2.85→47.2 Å / Cor.coef. Fo:Fc: 0.9195 / Cor.coef. Fo:Fc free: 0.8924 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.357
RfactorNum. reflection% reflectionSelection details
Rfree0.2354 2988 5.03 %RANDOM
Rwork0.1925 ---
obs0.1947 59424 98.77 %-
Displacement parametersBiso max: 114.27 Å2 / Biso mean: 43.9 Å2 / Biso min: 9.94 Å2
Baniso -1Baniso -2Baniso -3
1--2.6232 Å20 Å20 Å2
2--3.9875 Å20 Å2
3----1.3644 Å2
Refine analyzeLuzzati coordinate error obs: 0.346 Å
Refinement stepCycle: final / Resolution: 2.85→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17748 0 710 0 18458
Biso mean--47.42 --
Num. residues----2269
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6453SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes448HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2886HARMONIC5
X-RAY DIFFRACTIONt_it18948HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2497SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact22121SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d18948HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg25865HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion17.78
LS refinement shellResolution: 2.81→2.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3011 197 5.31 %
Rwork0.2205 3511 -
all0.2247 3708 -
obs--98.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.91270.45820.42171.39810.05340.6079-0.0649-0.0456-0.0458-0.050.01550.003-0.0396-0.04110.0494-0.1069-0.02450.0664-0.0775-0.05860.0515138.5321.3843251.224
20.77040.46110.26431.27630.17670.62160.001-0.0165-0.21020.0059-0.0031-0.0140.025-0.08140.0021-0.15-0.05450.0665-0.097-0.03860.0222132.82312.5056254.079
31.31220.34370.53840.92640.56250.6726-0.0168-0.0607-0.0702-0.01930.02650.0308-0.0432-0.0173-0.0097-0.0838-0.01280.0369-0.0821-0.01180.0191162.47439.4562267.862
40.95220.19150.15880.71680.12340.9149-0.10420.0657-0.00620.04470.0863-0.0706-0.14030.05690.0178-0.0964-0.0590.002-0.0938-0.0395-0.0183170.85445.4856264.334
50.82830.23720.81620.6465-0.23280.7067-0.0134-0.08230.0518-0.1701-0.01530.0288-0.0459-0.06250.02860.0038-0.0194-0.0647-0.12270.04640.0015175.587-19.5786246.914
60.55820.36870.08060.8324-0.01710.65120.0246-0.0527-0.0447-0.1274-0.01150.14540.0696-0.1223-0.0131-0.039-0.0478-0.104-0.10990.0318-0.0026168.777-27.61250.388
70.65410.0356-0.04920.84850.22920.6573-0.0258-0.03810.0149-0.0603-0.0406-0.02-0.1147-0.03750.0663-0.0648-0.0323-0.0529-0.05770.03450.0215194.6553.185264.15
80.7160.35720.13360.49190.12180.7892-0.07020.01450.01740.0080.033-0.0846-0.17980.15840.0372-0.0411-0.0736-0.0545-0.1040.0350.0031204.0038.2305261.542
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 103
2X-RAY DIFFRACTION2{ B|* }B114 - 577
3X-RAY DIFFRACTION3{ D|* }D1 - 103
4X-RAY DIFFRACTION4{ E|* }E113 - 577
5X-RAY DIFFRACTION5{ F|* }F1 - 103
6X-RAY DIFFRACTION6{ G|* }G114 - 577
7X-RAY DIFFRACTION7{ H|* }H1 - 103
8X-RAY DIFFRACTION8{ I|* }I114 - 577

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