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- PDB-6wet: Crystal structures of human E-NPP 1: apo -

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Basic information

Entry
Database: PDB / ID: 6wet
TitleCrystal structures of human E-NPP 1: apo
ComponentsEctonucleotide pyrophosphatase/phosphodiesterase family member 1
KeywordsHYDROLASE / human E-NPP 1 / drug discovery / inhibitors
Function / homology
Function and homology information


GTP diphosphatase activity / cyclic-GMP-AMP hydrolase activity / negative regulation of hh target transcription factor activity / inorganic diphosphate transport / Vitamin B2 (riboflavin) metabolism / UTP diphosphatase activity / phosphodiesterase I / 3'-phosphoadenosine 5'-phosphosulfate binding / dinucleotide phosphatase activity / Vitamin B5 (pantothenate) metabolism ...GTP diphosphatase activity / cyclic-GMP-AMP hydrolase activity / negative regulation of hh target transcription factor activity / inorganic diphosphate transport / Vitamin B2 (riboflavin) metabolism / 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 / intracellular phosphate ion homeostasis / negative regulation of protein autophosphorylation / nucleoside triphosphate diphosphatase activity / nucleic acid metabolic process / sequestering of triglyceride / ATP diphosphatase activity / negative regulation of glycogen biosynthetic process / negative regulation of bone mineralization / phosphate ion homeostasis / melanocyte differentiation / phosphodiesterase I activity / scavenger receptor activity / negative regulation of glucose import / regulation of bone mineralization / phosphate-containing compound metabolic process / exonuclease activity / negative regulation of fat cell differentiation / polysaccharide binding / response to ATP / bone mineralization / phosphatase activity / 3',5'-cyclic-AMP phosphodiesterase activity / response to inorganic substance / 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
Ectonucleotide pyrophosphatase/phosphodiesterase family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 2, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)214,00818
Polymers210,2772
Non-polymers3,73116
Water1,29772
1
AaA: Ectonucleotide pyrophosphatase/phosphodiesterase family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,28911
Polymers105,1381
Non-polymers2,15010
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)106,7197
Polymers105,1381
Non-polymers1,5816
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.111, 158.885, 209.832
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 AaABaB

#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: 105138.383 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, 9 molecules

#2: 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: obtained synthetically
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
#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: obtained synthetically
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.: 1
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
#6: 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.: 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 , 3 types, 79 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.3 Å3/Da / Density % sol: 62.69 %
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: 0.953731 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953731 Å / Relative weight: 1
ReflectionResolution: 2.6→44.423 Å / Num. obs: 86202 / % possible obs: 100 % / Redundancy: 26.1 % / CC1/2: 0.998 / Rpim(I) all: 0.053 / Net I/σ(I): 12.9
Reflection shellResolution: 2.6→2.65 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4500 / CC1/2: 0.539 / Rpim(I) all: 0.916 / % possible all: 100

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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 4B56

4b56


Resolution: 2.6→44.4 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.928 / SU B: 12.886 / SU ML: 0.251 / Cross valid method: FREE R-VALUE / ESU R: 0.368 / ESU R Free: 0.258
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2442 4461 5.177 %
Rwork0.2104 81708 -
all0.212 --
obs-86169 99.962 %
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: 68.659 Å2
Baniso -1Baniso -2Baniso -3
1-2.237 Å2-0 Å2-0 Å2
2--2.855 Å2-0 Å2
3----5.092 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12653 0 237 72 12962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01313300
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711634
X-RAY DIFFRACTIONr_angle_refined_deg1.371.67418102
X-RAY DIFFRACTIONr_angle_other_deg1.1921.59327121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg19.3315.4891676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90922.601642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.057152012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3281561
X-RAY DIFFRACTIONr_chiral_restr0.0580.21735
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216638
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022774
X-RAY DIFFRACTIONr_nbd_refined0.2040.22377
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.210555
X-RAY DIFFRACTIONr_nbtor_refined0.1650.26286
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.25715
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2224
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1250.22
X-RAY DIFFRACTIONr_metal_ion_refined0.2180.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2690.210
X-RAY DIFFRACTIONr_nbd_other0.2680.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2430.22
X-RAY DIFFRACTIONr_mcbond_it4.2547.4786438
X-RAY DIFFRACTIONr_mcbond_other4.2547.4776437
X-RAY DIFFRACTIONr_mcangle_it6.61511.2088037
X-RAY DIFFRACTIONr_mcangle_other6.61411.2088038
X-RAY DIFFRACTIONr_scbond_it4.5257.7146862
X-RAY DIFFRACTIONr_scbond_other4.5247.7146863
X-RAY DIFFRACTIONr_scangle_it7.13611.45410065
X-RAY DIFFRACTIONr_scangle_other7.13611.45410066
X-RAY DIFFRACTIONr_lrange_it11.668137.90353546
X-RAY DIFFRACTIONr_lrange_other11.668137.90953538
X-RAY DIFFRACTIONr_ncsr_local_group_10.1050.0524191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6680.3713240.3635930X-RAY DIFFRACTION99.968
2.668-2.7410.3692940.3425841X-RAY DIFFRACTION100
2.741-2.820.323430.3095633X-RAY DIFFRACTION100
2.82-2.9070.3173180.2845523X-RAY DIFFRACTION100
2.907-3.0020.2772700.2775342X-RAY DIFFRACTION99.9822
3.002-3.1070.2862840.2495171X-RAY DIFFRACTION100
3.107-3.2250.2752610.2355010X-RAY DIFFRACTION100
3.225-3.3560.2522490.2244820X-RAY DIFFRACTION100
3.356-3.5050.2492480.224624X-RAY DIFFRACTION100
3.505-3.6760.272350.2084435X-RAY DIFFRACTION100
3.676-3.8750.2412350.1944224X-RAY DIFFRACTION100
3.875-4.110.2222330.1784002X-RAY DIFFRACTION100
4.11-4.3930.2061890.1583786X-RAY DIFFRACTION100
4.393-4.7450.1931870.1433497X-RAY DIFFRACTION100
4.745-5.1970.1641970.1473253X-RAY DIFFRACTION100
5.197-5.8090.2211820.192922X-RAY DIFFRACTION100
5.809-6.7050.2371490.2092633X-RAY DIFFRACTION100
6.705-8.2060.225980.1952276X-RAY DIFFRACTION99.9579
8.206-11.5810.1861040.1771769X-RAY DIFFRACTION100
11.581-44.40.377610.3141018X-RAY DIFFRACTION97.3827

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