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- PDB-4cd1: RnNTPDase2 in complex with PSB-071 -

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Basic information

Entry
Database: PDB / ID: 4cd1
TitleRnNTPDase2 in complex with PSB-071
ComponentsECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 2
KeywordsHYDROLASE / APYRASE / ATPASE / PURINERGIC SIGNALLING / CD39 / DRUG DESIGN / INHIBITOR / NTPDASE
Function / homology
Function and homology information


nucleoside diphosphate catabolic process / purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / UDP phosphatase activity / nucleoside diphosphate phosphatase activity / ADP phosphatase activity / GDP phosphatase activity / cellular response to interferon-alpha / response to auditory stimulus / cell projection membrane ...nucleoside diphosphate catabolic process / purine ribonucleoside diphosphate catabolic process / Phosphate bond hydrolysis by NTPDase proteins / UDP phosphatase activity / nucleoside diphosphate phosphatase activity / ADP phosphatase activity / GDP phosphatase activity / cellular response to interferon-alpha / response to auditory stimulus / cell projection membrane / cellular response to interleukin-6 / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / basement membrane / ribonucleoside triphosphate phosphatase activity / platelet activation / cellular response to tumor necrosis factor / cell body / cellular response to lipopolysaccharide / G protein-coupled receptor signaling pathway / cell surface / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
GDA1/CD39 family of nucleoside phosphatases signature. / Exopolyphosphatase. Domain 2 / Nucleoside phosphatase GDA1/CD39 / GDA1/CD39 (nucleoside phosphatase) family / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8E9 / Ectonucleoside triphosphate diphosphohydrolase 2
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2 Å
AuthorsZebisch, M. / Schaefer, P. / Straeter, N.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Crystal Structure of Ntpdase2 in Complex with the Sulfoanthraquinone Inhibitor Psb-071.
Authors: Zebisch, M. / Baqi, Y. / Schafer, P. / Muller, C.E. / Strater, N.
History
DepositionOct 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5163
Polymers50,6991
Non-polymers8172
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.007, 68.040, 162.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 2 / NTPDASE 2 / CD39 ANTIGEN-LIKE 1 / ECTO-ATP DIPHOSPHOHYDROLASE 2 / ECTO-ATPDASE 2 / ECTO-ATPASE 2 / NTPDASE2


Mass: 50699.027 Da / Num. of mol.: 1 / Fragment: ECTODOMAIN, RESIDUES 28-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: O35795, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides, apyrase
#2: Chemical ChemComp-8E9 / 1-AMINO-4-(3-METHYLPHENYL)AMINO-9,10-DIOXO-9,10-DIHYDROANTHRACENE-2-SULFONATE


Mass: 408.427 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H16N2O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details1-AMINO-4-(3-METHYLPHENYL)AMINO-9,10-DIOXO-9, 10-DIHYDROANTHRACENE-2-SULFONATE (071): PSB-071

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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: 2.23 Å3/Da / Density % sol: 44.95 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→36.6 Å / Num. obs: 30632 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 2→36.63 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.747 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23854 1529 5 %RANDOM
Rwork0.1933 ---
obs0.19556 28777 95.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.402 Å2
Baniso -1Baniso -2Baniso -3
1--4.68 Å20 Å20 Å2
2--6.08 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 2→36.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3173 0 58 127 3358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193352
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0931.9784576
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.995404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96723.176148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.61915512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5591523
X-RAY DIFFRACTIONr_chiral_restr0.1460.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212578
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 71 -
Rwork0.255 1530 -
obs--69.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.47610.4479-1.28282.83010.44274.21460.00450.17980.3757-0.46540.0989-0.0223-0.47480.1675-0.10330.3753-0.0261-0.00240.02740.00310.154218.241.689411.2146
22.2406-0.619-1.04192.98381.84535.4550.06890.27650.0153-0.05940.006-0.3142-0.05570.4162-0.07490.2528-0.0127-0.00040.1061-0.01440.092922.104225.89.2559
34.4041-3.5608-5.16943.86584.98226.7206-0.06580.3326-0.42260.0648-0.59540.54740.0888-0.65610.66120.40080.0291-0.01490.1803-0.09780.19622.320610.5347-4.6838
42.92560.5561.20461.14930.26983.39830.0208-0.3057-0.19570.0933-0.0789-0.0810.00730.09990.05810.24250.00480.02250.05040.03150.123223.080921.688129.2963
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 162
2X-RAY DIFFRACTION1A436 - 451
3X-RAY DIFFRACTION2A163 - 179
4X-RAY DIFFRACTION2A427 - 435
5X-RAY DIFFRACTION3A180 - 195
6X-RAY DIFFRACTION4A196 - 426

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