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- PDB-6wev: Crystal structures of human E-NPP 1: bound to N-{[1-(6,7-dimethox... -

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Basic information

Entry
Database: PDB / ID: 6wev
TitleCrystal structures of human E-NPP 1: bound to N-{[1-(6,7-dimethoxy-5,8-dihydroquinazolin-4-yl)piperidin-4-yl]methyl}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 / GTP diphosphatase activity / Vitamin B2 (riboflavin) metabolism / UTP diphosphatase activity / 3'-phosphoadenosine 5'-phosphosulfate binding / dinucleotide phosphatase activity / nucleoside triphosphate catabolic process / phosphodiesterase I ...cyclic-GMP-AMP hydrolase activity / negative regulation of hh target transcription factor activity / inorganic diphosphate transport / GTP diphosphatase activity / Vitamin B2 (riboflavin) metabolism / UTP diphosphatase activity / 3'-phosphoadenosine 5'-phosphosulfate binding / dinucleotide phosphatase activity / nucleoside triphosphate catabolic process / phosphodiesterase I / nucleotide diphosphatase / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / nucleic acid metabolic process / Vitamin B5 (pantothenate) metabolism / nucleoside triphosphate diphosphatase activity / negative regulation of glycogen biosynthetic process / ATP diphosphatase activity / negative regulation of bone mineralization / phosphate ion homeostasis / negative regulation of D-glucose import / melanocyte differentiation / intracellular phosphate ion homeostasis / regulation of bone mineralization / phosphate-containing compound metabolic process / phosphodiesterase I activity / scavenger receptor activity / exonuclease activity / response to ATP / negative regulation of fat cell differentiation / bone mineralization / polysaccharide binding / 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 / basolateral plasma membrane / gene expression / 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-TZS / Ectonucleotide pyrophosphatase/phosphodiesterase family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
Revision 1.3Nov 13, 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
AbA: Ectonucleotide pyrophosphatase/phosphodiesterase family member 1
BbB: Ectonucleotide pyrophosphatase/phosphodiesterase family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,52317
Polymers210,1172
Non-polymers4,40615
Water36020
1
AbA: Ectonucleotide pyrophosphatase/phosphodiesterase family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6239
Polymers105,0581
Non-polymers2,5658
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BbB: Ectonucleotide pyrophosphatase/phosphodiesterase family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,9008
Polymers105,0581
Non-polymers1,8417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.278, 158.993, 209.230
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 AbABbB

#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 , 4 types, 7 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-alpha-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: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_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)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: 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.: 2
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
#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
#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.: 2
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

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Non-polymers , 5 types, 28 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-TZS / N-{[1-(6,7-dimethoxy-5,8-dihydroquinazolin-4-yl)piperidin-4-yl]methyl}sulfuric diamide


Mass: 383.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N5O4S / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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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: 3.26 Å3/Da / Density % sol: 62.23 %
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: 0.953736 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953736 Å / Relative weight: 1
ReflectionResolution: 2.9→47.322 Å / Num. obs: 61713 / % possible obs: 99.9 % / Redundancy: 26 % / CC1/2: 0.993 / Rpim(I) all: 0.085 / Net I/σ(I): 9.9
Reflection shellResolution: 2.9→2.98 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4478 / CC1/2: 0.569 / Rpim(I) all: 0.74

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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: 2.9→47.28 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.877 / SU B: 16.889 / SU ML: 0.297 / Cross valid method: FREE R-VALUE / ESU R: 0.897 / ESU R Free: 0.353
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2534 3122 5.066 %
Rwork0.2112 58507 -
all0.213 --
obs-61629 99.893 %
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: 62.639 Å2
Baniso -1Baniso -2Baniso -3
1-1.945 Å20 Å2-0 Å2
2--4.251 Å2-0 Å2
3----6.196 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12734 0 278 20 13032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01313438
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711792
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.66918315
X-RAY DIFFRACTIONr_angle_other_deg1.2331.5927497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg20.7165.4731679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62622.589649
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.288152051
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg3.466153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1021564
X-RAY DIFFRACTIONr_chiral_restr0.0840.21757
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216749
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022804
X-RAY DIFFRACTIONr_nbd_refined0.2070.22459
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.210925
X-RAY DIFFRACTIONr_nbtor_refined0.1690.26382
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.25966
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2197
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0150.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1570.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.22
X-RAY DIFFRACTIONr_nbd_other0.180.223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0710.22
X-RAY DIFFRACTIONr_mcbond_it4.4366.7736455
X-RAY DIFFRACTIONr_mcbond_other4.4366.7726454
X-RAY DIFFRACTIONr_mcangle_it7.0410.158060
X-RAY DIFFRACTIONr_mcangle_other7.03910.1518061
X-RAY DIFFRACTIONr_scbond_it4.3817.016983
X-RAY DIFFRACTIONr_scbond_other4.3467.0086973
X-RAY DIFFRACTIONr_scangle_it7.01310.41610255
X-RAY DIFFRACTIONr_scangle_other7.00810.41410244
X-RAY DIFFRACTIONr_lrange_it11.852124.96254922
X-RAY DIFFRACTIONr_lrange_other11.849124.96854918
X-RAY DIFFRACTIONr_ncsr_local_group_10.0950.0524808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.9750.3412010.3514276X-RAY DIFFRACTION99.7771
2.975-3.0570.3562280.3234169X-RAY DIFFRACTION99.841
3.057-3.1450.3532360.3094023X-RAY DIFFRACTION100
3.145-3.2420.2972060.2793932X-RAY DIFFRACTION99.8793
3.242-3.3480.282280.2553771X-RAY DIFFRACTION99.925
3.348-3.4660.291830.2453737X-RAY DIFFRACTION99.8981
3.466-3.5970.2341800.2193600X-RAY DIFFRACTION99.9736
3.597-3.7430.231980.2093427X-RAY DIFFRACTION99.6975
3.743-3.910.2171860.1893294X-RAY DIFFRACTION100
3.91-4.10.2211650.1843190X-RAY DIFFRACTION100
4.1-4.3220.2041590.1643017X-RAY DIFFRACTION100
4.322-4.5840.2141590.1482853X-RAY DIFFRACTION100
4.584-4.90.1931520.1362669X-RAY DIFFRACTION100
4.9-5.2910.2091310.162538X-RAY DIFFRACTION100
5.291-5.7950.2391110.1782342X-RAY DIFFRACTION100
5.795-6.4780.2191050.1922130X-RAY DIFFRACTION100
6.478-7.4770.274980.1951912X-RAY DIFFRACTION100
7.477-9.1490.263830.1841620X-RAY DIFFRACTION100
9.149-12.9050.219710.1981264X-RAY DIFFRACTION100
12.905-47.280.475420.372743X-RAY DIFFRACTION96.9136

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