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- PDB-2xrg: Crystal structure of Autotaxin (ENPP2) in complex with the HA155 ... -

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Basic information

Entry
Database: PDB / ID: 2xrg
TitleCrystal structure of Autotaxin (ENPP2) in complex with the HA155 boronic acid inhibitor
ComponentsECTONUCLEOTIDE 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 / lysophospholipase activity / phosphodiesterase I 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 / lysophospholipase activity / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity / polysaccharide binding / negative regulation of cell-matrix adhesion / positive regulation of oligodendrocyte differentiation / positive regulation of epithelial cell migration / positive regulation of focal adhesion assembly / estrous cycle / phospholipid metabolic process / positive regulation of substrate adhesion-dependent cell spreading / cellular response to cadmium ion / 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
Similarity search - Function
Factor Xa Inhibitor - #20 / Extracellular Endonuclease; Chain A / 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. ...Factor Xa Inhibitor - #20 / Extracellular Endonuclease; Chain A / 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 / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / His-Me finger superfamily / Factor Xa Inhibitor / Alkaline-phosphatase-like, core domain superfamily / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Chem-SWH / Autotaxin
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHausmann, J. / Albers, H.M.H.G. / Perrakis, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structural Basis of Substrate Discrimination and Integrin Binding by Autotaxin.
Authors: Hausmann, J. / Kamtekar, S. / Christodoulou, E. / Day, J.E. / Wu, T. / Fulkerson, Z. / Albers, H.M.H.G. / Van Meeteren, L.A. / Houben, A.J. / Van Zeijl, L. / Jansen, S. / Andries, M. / Hall, ...Authors: Hausmann, J. / Kamtekar, S. / Christodoulou, E. / Day, J.E. / Wu, T. / Fulkerson, Z. / Albers, H.M.H.G. / Van Meeteren, L.A. / Houben, A.J. / Van Zeijl, L. / Jansen, S. / Andries, M. / Hall, T. / Pegg, L.E. / Benson, T.E. / Kasiem, M. / Harlos, K. / Kooi, C.W. / Smyth, S.S. / Ovaa, H. / Bollen, M. / Morris, A.J. / Moolenaar, W.H. / Perrakis, A.
History
DepositionSep 14, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
A: ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,74111
Polymers98,8691
Non-polymers1,87210
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.995, 90.204, 152.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 2 / AUTOTAXIN ENPP2 / EXTRACELLULAR LYSOPHOSPHOLIPASE D / LYSOPLD / AUTOTAXIN / E-NPP 2


Mass: 98869.211 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-862 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / Variant (production host): FLIPIN
References: UniProt: Q64610, alkylglycerophosphoethanolamine phosphodiesterase
#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.: 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

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Non-polymers , 5 types, 20 molecules

#3: Chemical ChemComp-SWH / {4-[(4-{(Z)-[3-(4-FLUOROBENZYL)-2,4-DIOXO-1,3-THIAZOLIDIN-5-YLIDENE]METHYL}PHENOXY)METHYL]PHENYL}(TRIHYDROXY)BORATE(1-) / HA155 INHIBITOR


Mass: 480.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H20BFNO6S
#4: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 410 TO ALA
Nonpolymer detailsHA155 INHIBITOR (SWH): CO-CRYSTALLIZATION IODIDE ION (IOD): FROM CRYSTALLIZATION BUFFER CALCIUM ION ...HA155 INHIBITOR (SWH): CO-CRYSTALLIZATION IODIDE ION (IOD): FROM CRYSTALLIZATION BUFFER CALCIUM ION (CA): IN ANALOGY WITH NATIVE ZINC ION (ZN): IN ANALOGY WITH NATIVE ALPHA-D-MANNOSE (MAN): GLYCOSYLATION N-ACETYL-D-GLUCOSAMINE (NAG): GLYCOSYLATION

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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: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.283
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 15159 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 97.64 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.3
Reflection shellResolution: 3.2→3.36 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.5 / % possible all: 98.5

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.8.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XR9

2xr9


Resolution: 3.2→49.39 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.8216 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2547 760 5.1 %RANDOM
Rwork0.201 ---
obs0.2036 15034 98.5 %-
Displacement parametersBiso mean: 57.39 Å2
Baniso -1Baniso -2Baniso -3
1-15.6734 Å20 Å20 Å2
2---13.1624 Å20 Å2
3----2.511 Å2
Refine analyzeLuzzati coordinate error obs: 0.578 Å
Refinement stepCycle: LAST / Resolution: 3.2→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6116 0 80 11 6207
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086382HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.938675HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2142SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes145HARMONIC2
X-RAY DIFFRACTIONt_gen_planes926HARMONIC5
X-RAY DIFFRACTIONt_it6346HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.75
X-RAY DIFFRACTIONt_other_torsion19.28
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion801SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6053SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.42 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2854 140 5.5 %
Rwork0.2425 2406 -
all0.2448 2546 -
Refinement TLS params.Method: refined / Origin x: -27.4669 Å / Origin y: -0.6466 Å / Origin z: -9.6652 Å
111213212223313233
T-0.1535 Å2-0.0203 Å20.0171 Å2--0.2961 Å20.0298 Å2---0.0081 Å2
L0.9962 °2-0.4932 °2-0.0273 °2-0.995 °2-0.5209 °2--2.2944 °2
S-0.0555 Å °-0.0954 Å °-0.2078 Å °0.0849 Å °0.0431 Å °0.2056 Å °-0.0328 Å °0.0446 Å °0.0124 Å °
Refinement TLS groupSelection details: (A56-A395,A402-A457, A470-A556, A563-A569, A591-A858)

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