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- PDB-6wew: Crystal structures of human E-NPP 1: bound to N-{4-[(7-methoxyqui... -

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Basic information

Entry
Database: PDB / ID: 6wew
TitleCrystal structures of human E-NPP 1: bound to N-{4-[(7-methoxyquinolin-4-yl)oxy]phenyl}sulfuric diamide
ComponentsEctonucleotide pyrophosphatase/phosphodiesterase family member 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / human E-NPP 1 / drug discovery / inhibitors / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


cyclic-GMP-AMP hydrolase activity / negative regulation of hh target transcription factor activity / inorganic diphosphate transport / Vitamin B2 (riboflavin) metabolism / GTP diphosphatase activity / UTP diphosphatase activity / phosphodiesterase I / 3'-phosphoadenosine 5'-phosphosulfate binding / dinucleotide phosphatase activity / Vitamin B5 (pantothenate) metabolism ...cyclic-GMP-AMP hydrolase activity / negative regulation of hh target transcription factor activity / inorganic diphosphate transport / Vitamin B2 (riboflavin) metabolism / GTP diphosphatase activity / UTP diphosphatase activity / phosphodiesterase I / 3'-phosphoadenosine 5'-phosphosulfate binding / dinucleotide phosphatase activity / Vitamin B5 (pantothenate) metabolism / nucleoside triphosphate catabolic process / nucleotide diphosphatase / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / nucleic acid metabolic process / negative regulation of protein autophosphorylation / nucleoside triphosphate diphosphatase activity / sequestering of triglyceride / intracellular phosphate ion homeostasis / ATP diphosphatase activity / negative regulation of glycogen biosynthetic process / negative regulation of bone mineralization / phosphate ion homeostasis / phosphodiesterase I activity / melanocyte differentiation / scavenger receptor activity / negative regulation of D-glucose import / regulation of bone mineralization / phosphate-containing compound metabolic process / exonuclease activity / polysaccharide binding / response to ATP / bone mineralization / negative regulation of fat cell differentiation / phosphatase activity / 3',5'-cyclic-AMP phosphodiesterase activity / ATP metabolic process / negative regulation of insulin receptor signaling pathway / generation of precursor metabolites and energy / insulin receptor binding / negative regulation of cell growth / cellular response to insulin stimulus / gene expression / basolateral plasma membrane / nucleic acid binding / immune response / lysosomal membrane / calcium ion binding / cell surface / protein homodimerization activity / extracellular space / zinc ion binding / ATP binding / membrane / plasma membrane
Similarity search - Function
Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Extracellular Endonuclease, subunit A ...Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / His-Me finger superfamily / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Chem-TZV / Ectonucleotide pyrophosphatase/phosphodiesterase family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsPeat, T.S. / Dennis, M. / Newman, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Other government Australia
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Crystal structures of human ENPP1 in apo and bound forms.
Authors: Dennis, M.L. / Newman, J. / Dolezal, O. / Hattarki, M. / Surjadi, R.N. / Nuttall, S.D. / Pham, T. / Nebl, T. / Camerino, M. / Khoo, P.S. / Monahan, B.J. / Peat, T.S.
History
DepositionApr 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AbA: Ectonucleotide pyrophosphatase/phosphodiesterase family member 1
BaB: Ectonucleotide pyrophosphatase/phosphodiesterase family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,03521
Polymers210,1172
Non-polymers4,91919
Water3,333185
1
AbA: Ectonucleotide pyrophosphatase/phosphodiesterase family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,01813
Polymers105,0581
Non-polymers2,95912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BaB: Ectonucleotide pyrophosphatase/phosphodiesterase family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,0188
Polymers105,0581
Non-polymers1,9597
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.131, 161.578, 209.978
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AbABaB

#1: Protein Ectonucleotide pyrophosphatase/phosphodiesterase family member 1 / E-NPP 1 / Membrane component chromosome 6 surface marker 1 / Phosphodiesterase I/nucleotide ...E-NPP 1 / Membrane component chromosome 6 surface marker 1 / Phosphodiesterase I/nucleotide pyrophosphatase 1 / Plasma-cell membrane glycoprotein PC-1


Mass: 105058.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ENPP1, M6S1, NPPS, PC1, PDNP1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: P22413, phosphodiesterase I, nucleotide diphosphatase

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Sugars , 5 types, 9 molecules

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


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: 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: isolated from a genetically manipulated source
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
#5: 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
#8: 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.: 4 / 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 , 5 types, 195 molecules

#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: Zn
#9: Chemical ChemComp-TZV / N-{4-[(7-methoxyquinolin-4-yl)oxy]phenyl}sulfuric diamide


Mass: 345.373 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H15N3O4S / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.36 Å3/Da / Density % sol: 63.35 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 7.5 mg/mL protein against 19-22% PEG4000, 240-270 mM trilithium/triammonium/tripotassium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.73→47.967 Å / Num. obs: 76020 / % possible obs: 100 % / Redundancy: 11.8 % / CC1/2: 0.99 / Rpim(I) all: 0.105 / Net I/σ(I): 8.4
Reflection shellResolution: 2.73→2.79 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4480 / CC1/2: 0.548 / Rpim(I) all: 0.765

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6WET

6wet


Resolution: 2.73→47.92 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.905 / SU B: 12.878 / SU ML: 0.244 / Cross valid method: FREE R-VALUE / ESU R: 0.485 / ESU R Free: 0.287
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2409 3771 4.966 %
Rwork0.2102 72171 -
all0.212 --
obs-75942 99.955 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 51.507 Å2
Baniso -1Baniso -2Baniso -3
1-0.982 Å20 Å20 Å2
2--2.553 Å2-0 Å2
3----3.535 Å2
Refinement stepCycle: LAST / Resolution: 2.73→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12688 0 308 185 13181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01313477
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711757
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.67418374
X-RAY DIFFRACTIONr_angle_other_deg1.1871.59427407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg21.1765.4821692
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96122.504651
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.441152030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7771564
X-RAY DIFFRACTIONr_chiral_restr0.0580.21762
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216874
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022845
X-RAY DIFFRACTIONr_nbd_refined0.20.22390
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.210628
X-RAY DIFFRACTIONr_nbtor_refined0.1650.26371
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.25806
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2315
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0040.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1130.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2180.25
X-RAY DIFFRACTIONr_nbd_other0.230.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2450.26
X-RAY DIFFRACTIONr_mcbond_it3.295.6016476
X-RAY DIFFRACTIONr_mcbond_other3.2895.6016475
X-RAY DIFFRACTIONr_mcangle_it5.3858.3898095
X-RAY DIFFRACTIONr_mcangle_other5.3858.398096
X-RAY DIFFRACTIONr_scbond_it3.4345.8197001
X-RAY DIFFRACTIONr_scbond_other3.4355.826998
X-RAY DIFFRACTIONr_scangle_it5.6368.64610279
X-RAY DIFFRACTIONr_scangle_other5.6378.64710274
X-RAY DIFFRACTIONr_lrange_it10.497102.29954879
X-RAY DIFFRACTIONr_lrange_other10.499102.34854816
X-RAY DIFFRACTIONr_ncsr_local_group_10.0890.0524627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.8010.3332710.3285285X-RAY DIFFRACTION99.982
2.801-2.8780.3032920.3075141X-RAY DIFFRACTION99.9816
2.878-2.9610.3272420.294997X-RAY DIFFRACTION100
2.961-3.0520.3192310.2664878X-RAY DIFFRACTION100
3.052-3.1520.2812690.2514674X-RAY DIFFRACTION100
3.152-3.2630.2912380.2434581X-RAY DIFFRACTION100
3.263-3.3860.2992220.2364398X-RAY DIFFRACTION100
3.386-3.5240.2432330.2244258X-RAY DIFFRACTION100
3.524-3.680.2411950.2144100X-RAY DIFFRACTION100
3.68-3.860.2322050.1993897X-RAY DIFFRACTION99.9026
3.86-4.0690.2291770.1863742X-RAY DIFFRACTION99.898
4.069-4.3150.1821930.163513X-RAY DIFFRACTION99.973
4.315-4.6130.1731830.1453345X-RAY DIFFRACTION100
4.613-4.9820.1861540.1433100X-RAY DIFFRACTION100
4.982-5.4560.1821620.1562859X-RAY DIFFRACTION100
5.456-6.0990.2181410.1792613X-RAY DIFFRACTION100
6.099-7.040.2441350.212321X-RAY DIFFRACTION100
7.04-8.6150.215900.2041992X-RAY DIFFRACTION100
8.615-12.1570.211810.171572X-RAY DIFFRACTION100
12.157-47.920.34570.359905X-RAY DIFFRACTION97.665

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