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- PDB-5lqq: Structure of Autotaxin (ENPP2) with LM350 -

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Basic information

Entry
Database: PDB / ID: 5lqq
TitleStructure of Autotaxin (ENPP2) with LM350
ComponentsEctonucleotide pyrophosphatase/phosphodiesterase family member 2
KeywordsHYDROLASE / Autotaxin / ENPP2 / Inhibitor / LM350 / Ectonucleotide pyrophosphatase/phosphodiesterase
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 / phosphatidylcholine 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 / phosphatidylcholine 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 / nucleic acid binding / immune response / positive regulation of cell population proliferation / calcium ion binding / extracellular space / zinc ion binding / membrane
Similarity search - Function
Factor Xa Inhibitor - #20 / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Factor Xa Inhibitor / Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily ...Factor Xa Inhibitor - #20 / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Factor Xa Inhibitor / 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 / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-72P / IODIDE ION / Autotaxin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsKeune, W.J. / Heidebrecht, T. / Castelmur, E. / Joosten, R.P. / Perrakis, A.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Structure-Activity Relationships of Small Molecule Autotaxin Inhibitors with a Discrete Binding Mode.
Authors: Miller, L.M. / Keune, W.J. / Castagna, D. / Young, L.C. / Duffy, E.L. / Potjewyd, F. / Salgado-Polo, F. / Engel Garcia, P. / Semaan, D. / Pritchard, J.M. / Perrakis, A. / Macdonald, S.J. / ...Authors: Miller, L.M. / Keune, W.J. / Castagna, D. / Young, L.C. / Duffy, E.L. / Potjewyd, F. / Salgado-Polo, F. / Engel Garcia, P. / Semaan, D. / Pritchard, J.M. / Perrakis, A. / Macdonald, S.J. / Jamieson, C. / Watson, A.J.
History
DepositionAug 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_validate_chiral / struct_asym / struct_conn / struct_conn_type / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _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_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,29217
Polymers95,0381
Non-polymers3,25416
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-30 kcal/mol
Surface area32370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.655, 89.067, 77.509
Angle α, β, γ (deg.)90.000, 102.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 95037.656 Da / Num. of mol.: 1 / Fragment: UNP residues 36-862 / Mutation: N410A, L581F, R591T, N806A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Enpp2, Atx, Npps2 / Plasmid: pcDNA5 / Cell line (production host): HEK293 / Organ (production host): kidney / Production host: Homo sapiens (human) / Variant (production host): FlP-in
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-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-h1_f2-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+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, 94 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#6: Chemical ChemComp-72P / 3-(6-chloranyl-2-methyl-1-phenyl-indol-3-yl)sulfanylbenzoic acid


Mass: 393.886 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H16ClNO2S
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 22% PEG 3350, NH4I (0.2M), NaSCN (0.1M)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97925 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.4→46 Å / Num. obs: 32432 / % possible obs: 99.6 % / Redundancy: 3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.05 / Rrim(I) all: 0.09 / Net I/σ(I): 12.9 / Num. measured all: 98094
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.4-2.4930.6550.784199.4
8.98-463.10.0230.999198.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.6 Å46 Å
Translation7.6 Å46 Å

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Processing

Software
NameVersionClassification
Aimless0.5.26data scaling
PHASER2.6.1phasing
REFMACrefmac_5.8.0155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XR9

2xr9


Resolution: 2.4→46 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / Matrix type: sparse / SU B: 30.617 / SU ML: 0.311 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.609 / ESU R Free: 0.293
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2621 1569 4.8 %RANDOM
Rwork0.2173 ---
obs0.2194 30843 99.54 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 159.56 Å2 / Biso mean: 61.503 Å2 / Biso min: 24.48 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å20 Å20.69 Å2
2--2.5 Å20 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 2.4→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6252 0 135 79 6466
Biso mean--69.01 43.52 -
Num. residues----775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196575
X-RAY DIFFRACTIONr_bond_other_d0.0010.025975
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.9698939
X-RAY DIFFRACTIONr_angle_other_deg0.9512.99713832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3535772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23823.226310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.051151068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.711547
X-RAY DIFFRACTIONr_chiral_restr0.0920.2954
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217285
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021548
X-RAY DIFFRACTIONr_mcbond_it0.4712.7393097
X-RAY DIFFRACTIONr_mcbond_other0.4712.7383096
X-RAY DIFFRACTIONr_mcangle_it0.8744.1073866
X-RAY DIFFRACTIONr_sphericity_free65.95551
X-RAY DIFFRACTIONr_sphericity_bonded511
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
2.4-2.4620.42980.342251236599.3230.301
2.462-2.530.3161220.3272211234199.6580.283
2.53-2.6030.3041200.3062151228599.3870.255
2.603-2.6830.3391040.2942078219199.5890.247
2.683-2.7710.334980.2792038214199.7660.232
2.771-2.8680.29870.2691992208699.6640.219
2.868-2.9760.393960.2641885198599.7980.217
2.976-3.0970.2541050.2551803191499.6870.214
3.097-3.2350.346740.2381772185499.5680.205
3.235-3.3920.318840.2171691177999.7750.189
3.392-3.5760.212880.2081571166899.460.182
3.576-3.7920.268820.2031501159099.560.186
3.792-4.0530.212690.1891427150699.3360.17
4.053-4.3770.212660.1581332140399.6440.145
4.377-4.7930.233640.1531213128599.3770.141
4.793-5.3560.26670.1791082115199.8260.167
5.356-6.1790.238500.213989104899.1410.198
6.179-7.5550.239410.21482787299.5410.203
7.555-10.6320.178320.15665669499.1350.157
10.632-75.5590.152220.18337340497.7720.194
Refinement TLS params.Method: refined / Origin x: -13.3486 Å / Origin y: -13.7286 Å / Origin z: -16.122 Å
111213212223313233
T0.159 Å20.012 Å2-0.0303 Å2-0.5658 Å20.0109 Å2--0.0147 Å2
L1.0174 °20.3062 °20.2572 °2-0.8401 °20.3866 °2--2.2 °2
S-0.015 Å °0.0754 Å °0.0138 Å °-0.1074 Å °0.094 Å °0.0475 Å °-0.177 Å °0.0028 Å °-0.079 Å °

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