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- PDB-7g4a: Crystal Structure of rat Autotaxin in complex with (3-chloro-5-me... -

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Basic information

Entry
Database: PDB / ID: 7g4a
TitleCrystal Structure of rat Autotaxin in complex with (3-chloro-5-methylsulfonylphenyl)methyl 2-(1H-benzotriazole-5-carbonyl)-2,7-diazaspiro[3.5]nonane-7-carboxylate, i.e. SMILES c1c(cc(cc1S(=O)(=O)C)COC(=O)N1CCC2(CC1)CN(C2)C(=O)c1ccc2c(c1)N=NN2)Cl with IC50=0.332347 microM
ComponentsIsoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
KeywordsHYDROLASE / LYSOPHOSPHATIDIC ACID / LPA / LYSOPHOSPHATIDYLCHOLINE / LPC / SOMATOMEDIN / METASTASIS / NEUROPATHIC PAIN / VASCULAR DEVELOPMENT / NEURAL DEVELOPMENT
Function / homology
Function and homology information


response to polycyclic arene / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipase D / phospholipid catabolic process / phosphatidylcholine catabolic process / phospholipase D activity / positive regulation of lamellipodium morphogenesis / phosphodiesterase I activity / lysophospholipase activity ...response to polycyclic arene / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipase D / phospholipid catabolic process / phosphatidylcholine catabolic process / phospholipase D activity / positive regulation of lamellipodium morphogenesis / phosphodiesterase I activity / lysophospholipase activity / scavenger receptor activity / cellular response to cadmium ion / alkylglycerophosphoethanolamine phosphodiesterase activity / polysaccharide binding / positive regulation of oligodendrocyte differentiation / positive regulation of epithelial cell migration / negative regulation of cell-matrix adhesion / positive regulation of focal adhesion assembly / estrous cycle / phospholipid metabolic process / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / cell chemotaxis / cellular response to estradiol stimulus / positive regulation of peptidyl-tyrosine phosphorylation / nucleic acid binding / immune response / positive regulation of cell population proliferation / calcium ion binding / extracellular space / zinc ion binding / 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
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / : / Autotaxin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsStihle, M. / Benz, J. / Hunziker, D. / Mattei, P. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: To be published
Title: Crystal Structure of a rat Autotaxin complex
Authors: Hunziker, D. / Joachim, S.C. / Ullmer, C. / Rudolph, M.G.
History
DepositionJun 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,0338
Polymers97,3431
Non-polymers2,6897
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.806, 93.169, 119.884
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 / Sugars , 2 types, 2 molecules A

#1: Protein Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 / E-NPP 2 / Autotaxin / Extracellular lysophospholipase D / LysoPLD


Mass: 97343.305 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-862 / Mutation: N53A, N410A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Enpp2, Atx, Npps2 / Plasmid: pcDNA3.1(-)_neo_rAtx(1-862_N53A:N410A) / Production host: Homo sapiens (human) / Strain (production host): HEK 293-F
References: UniProt: Q64610, alkylglycerophosphoethanolamine phosphodiesterase
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-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: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-i1_g2-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 110 molecules

#3: Chemical ChemComp-YOQ / [3-chloro-5-(methanesulfonyl)phenyl]methyl 2-(1H-benzotriazole-5-carbonyl)-2,7-diazaspiro[3.5]nonane-7-carboxylate


Mass: 517.985 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H24ClN5O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 15.3 mg/mL protein in 20mM BICINE/NaOH pH8.5, 150mM NaCl, 0.02% NaN3 mixed 50-70% with 50-30% reservoir consisting of 11-17% PEG3350, 0.1M Na-acetate pH4.5, 0.2M Ca-acetate, total volume 200nL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.67→46.58 Å / Num. obs: 26978 / % possible obs: 97.5 % / Redundancy: 6.169 % / Biso Wilson estimate: 41.95 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.215 / Rrim(I) all: 0.236 / Χ2: 0.782 / Net I/σ(I): 8.43 / Num. measured all: 166439 / Scaling rejects: 3223
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.67-2.746.1212.0411.0612315201620120.5192.23299.8
2.74-2.815.9951.4031.411708195419530.6061.53799.9
2.81-2.96.1771.1761.7411650188718860.6811.28499.9
2.9-2.996.3020.8932.2311672185218520.7790.974100
2.99-3.086.6750.7082.912121181618160.8530.769100
3.08-3.196.7380.5653.6611697173617360.9170.612100
3.19-3.316.5570.4444.7711095169416920.9440.48399.9
3.31-3.456.0760.4195.299794162716120.950.4699.1
3.45-3.65.7450.4454.948802156415320.9330.49198
3.6-3.784.480.2088.14771149410650.990.24171.3
3.78-3.984.8180.2498.615888142512220.9770.28285.8
3.98-4.226.5970.13813.149071137713750.9910.1599.9
4.22-4.516.7250.10516.058494126312630.9950.113100
4.51-4.876.5920.09717.497845119011900.9950.105100
4.87-5.346.1170.09716.696765110711060.9950.10799.9
5.34-5.976.1380.09915.886175100810060.9940.10899.8
5.97-6.896.6770.07819.4660569079070.9960.085100
6.89-8.446.3620.05923.2649437787770.9980.06499.9
8.44-11.945.6620.03830.1934316066060.9990.042100
11.94-46.5845.80.03233.8621463803700.9990.03697.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_1019refinement
PDB_EXTRACT3.28data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2.67→46.584 Å / FOM work R set: 0.7227 / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2941 1289 5.3 %RANDOM
Rwork0.2115 23047 --
obs0.2158 24336 88.11 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.683 Å2 / ksol: 0.284 e/Å3
Displacement parametersBiso max: 208.61 Å2 / Biso mean: 50.39 Å2 / Biso min: 22.57 Å2
Baniso -1Baniso -2Baniso -3
1--10.6925 Å20 Å2-0 Å2
2--15.9952 Å2-0 Å2
3----5.3027 Å2
Refinement stepCycle: final / Resolution: 2.67→46.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6508 0 173 104 6785
Biso mean--82.07 33.41 -
Num. residues----806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136902
X-RAY DIFFRACTIONf_angle_d1.2579365
X-RAY DIFFRACTIONf_chiral_restr0.0841001
X-RAY DIFFRACTIONf_plane_restr0.0061185
X-RAY DIFFRACTIONf_dihedral_angle_d20.0272612
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.67-2.77690.4141460.36552646279293
2.7769-2.90330.42931580.329128513009100
2.9033-3.05630.39291620.27928593021100
3.0563-3.24780.36021560.24328693025100
3.2478-3.49850.37761340.25752491262586
3.4985-3.85040.4455490.30871183123240
3.8504-4.40720.25521240.16672139226374
4.4072-5.55110.20621860.136929323118100
5.5511-46.59160.20711740.151230773251100
Refinement TLS params.Method: refined / Origin x: -5.0721 Å / Origin y: 3.5447 Å / Origin z: -40.7645 Å
111213212223313233
T0.3192 Å2-0.0181 Å2-0.0138 Å2-0.2687 Å20.0344 Å2--0.2919 Å2
L1.1591 °2-0.1331 °2-0.2042 °2-0.4333 °2-0.0551 °2--1.1213 °2
S0.0235 Å °0.083 Å °0.1177 Å °0.03 Å °-0.006 Å °-0.0237 Å °-0.0057 Å °0.1232 Å °-0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA51 - 909
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allI1 - 3
6X-RAY DIFFRACTION1allS1 - 103
7X-RAY DIFFRACTION1allS104

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