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- PDB-5wdj: CRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH... -

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Database: PDB / ID: 5wdj
TitleCRYSTAL STRUCTURE OF MYELOPEROXIDASE SUBFORM C (MPO) COMPLEX WITH COMPOUND-6 AKA 7-(BENZYLOXY)-1H-[1,2, 3]TRIAZOLO[4,5-D]PYRIMIDIN-5-AMINE
Components(Myeloperoxidase) x 2
KeywordsMETAL BINDING PROTEIN / MYELOPEROXIDASE
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 / response to food / azurophil granule ...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 / response to food / azurophil granule / removal of superoxide radicals / defense response to fungus / response to mechanical stimulus / peroxidase activity / hydrogen peroxide catabolic process / secretory granule / defense response / azurophil granule lumen / heparin binding / response to oxidative stress / response to lipopolysaccharide / lysosome / defense response to bacterium / intracellular membrane-bounded organelle / chromatin binding / heme binding / Neutrophil degranulation / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / nucleus
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. / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-AEY / alpha-L-fucopyranose / PROTOPORPHYRIN IX CONTAINING FE / alpha-D-mannopyranose / Myeloperoxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsKhan, J.A.
CitationJournal: Medchemcomm / Year: 2017
Title: Triazolopyrimidines identified as reversible myeloperoxidase inhibitors.
Authors: Duclos, F. / Abell, L.M. / Harden, D.G. / Pike, K. / Nowak, K. / Locke, G.A. / Duke, G.J. / Liu, X. / Fernando, G. / Shaw, S.A. / Vokits, B.P. / Wurtz, N.R. / Viet, A. / Valente, M.N. / ...Authors: Duclos, F. / Abell, L.M. / Harden, D.G. / Pike, K. / Nowak, K. / Locke, G.A. / Duke, G.J. / Liu, X. / Fernando, G. / Shaw, S.A. / Vokits, B.P. / Wurtz, N.R. / Viet, A. / Valente, M.N. / Stachura, S. / Sleph, P. / Khan, J.A. / Gao, J. / Dongre, A.R. / Zhao, L. / Wexler, R.R. / Gordon, D.A. / Kick, E.K.
History
DepositionJul 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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.type_symbol / _chem_comp.name / _chem_comp.type / _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_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myeloperoxidase
B: Myeloperoxidase
D: Myeloperoxidase
E: Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,60626
Polymers130,5594
Non-polymers5,04622
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34100 Å2
ΔGint-171 kcal/mol
Surface area39720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.925, 103.925, 242.276
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 102
2114D1 - 102
1124B114 - 560
2124E114 - 560

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein Myeloperoxidase / / MPO


Mass: 11974.420 Da / Num. of mol.: 2 / Fragment: UNP residues 167-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPO / Production host: Homo sapiens (human) / References: UniProt: P05164, myeloperoxidase
#2: Protein Myeloperoxidase / / MPO


Mass: 53305.266 Da / Num. of mol.: 2 / Fragment: UNP residues 183-649
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPO / Production host: Homo sapiens (human) / References: UniProt: P05164, myeloperoxidase

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Sugars , 5 types, 12 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 545.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-3/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#9: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
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
#10: Sugar ChemComp-FUC / alpha-L-fucopyranose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#11: Sugar ChemComp-MAN / alpha-D-mannopyranose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 532 molecules

#5: Chemical ChemComp-AEY / 7-(benzyloxy)-1H-[1,2,3]triazolo[4,5-d]pyrimidin-5-amine


Mass: 242.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H10N6O
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 522 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 296 K / Method: vapor diffusion
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
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→95.51 Å / Num. obs: 52722 / % possible obs: 99.8 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 15.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 3.1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTERrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2.4→95.51 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.903 / SU B: 17.365 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.463 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 2676 5.1 %RANDOM
Rwork0.194 ---
obs0.1967 49966 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.25 Å2 / Biso mean: 24.457 Å2 / Biso min: 9.15 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å20 Å2
2---1.64 Å20 Å2
3---3.28 Å2
Refinement stepCycle: final / Resolution: 2.4→95.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9048 0 326 522 9896
Biso mean--28.02 28.92 -
Num. residues----1138
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A813MEDIUM POSITIONAL0.110.5
1A813MEDIUM THERMAL0.282
2B3545MEDIUM POSITIONAL0.180.5
2B3545MEDIUM THERMAL0.312
LS refinement shellResolution: 2.398→2.461 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 188 -
Rwork0.23 3455 -
all-3643 -
obs--95.04 %

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