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- PDB-1efy: CRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF POLY (ADP-RIBOSE) ... -

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Basic information

Entry
Database: PDB / ID: 1efy
TitleCRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF POLY (ADP-RIBOSE) POLYMERASE COMPLEXED WITH A BENZIMIDAZOLE INHIBITOR
ComponentsPOLY (ADP-RIBOSE) POLYMERASE
KeywordsTRANSFERASE / BENZIMIDAZOLE / INHIBITOR / CATALYTIC FRAGMENT / POLYMERASE
Function / homology
Function and homology information


NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / NAD+-protein-serine ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / ATP generation from poly-ADP-D-ribose / replication fork reversal / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation ...NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / NAD+-protein-serine ADP-ribosyltransferase activity / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / DNA ADP-ribosylation / ATP generation from poly-ADP-D-ribose / replication fork reversal / NAD+ ADP-ribosyltransferase / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / nuclear replication fork / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of double-strand break repair via homologous recombination / nucleosome binding / negative regulation of innate immune response / nucleotidyltransferase activity / NAD binding / double-strand break repair / site of double-strand break / damaged DNA binding / innate immune response / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / zinc ion binding / cytosol
Similarity search - Function
Poly(ADP-ribose) polymerase, regulatory domain / Poly(ADP-ribose) Polymerase; domain 1 / : / PADR1, N-terminal helical domain / PADR1 domain profile. / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / PADR1 domain, zinc ribbon fold / PADR1 ...Poly(ADP-ribose) polymerase, regulatory domain / Poly(ADP-ribose) Polymerase; domain 1 / : / PADR1, N-terminal helical domain / PADR1 domain profile. / Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / PADR1 domain, zinc ribbon fold / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger, PARP-type / : / WGR domain profile. / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / BRCA1 C Terminus (BRCT) domain / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-(3'-METHOXYPHENYL) BENZIMIDAZOLE-4-CARBOXAMIDE / Poly [ADP-ribose] polymerase 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsWhite, A.W. / Almassy, R. / Calvert, A.H. / Curtin, N.J. / Griffin, R.J. / Hostomsky, Z. / Maegley, K. / Newell, D.R. / Srinivasan, S. / Golding, B.T.
CitationJournal: J.Med.Chem. / Year: 2000
Title: Resistance-modifying agents. 9. Synthesis and biological properties of benzimidazole inhibitors of the DNA repair enzyme poly(ADP-ribose) polymerase.
Authors: White, A.W. / Almassy, R. / Calvert, A.H. / Curtin, N.J. / Griffin, R.J. / Hostomsky, Z. / Maegley, K. / Newell, D.R. / Srinivasan, S. / Golding, B.T.
History
DepositionFeb 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: POLY (ADP-RIBOSE) POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5952
Polymers39,3281
Non-polymers2671
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.36, 64.26, 96.98
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein POLY (ADP-RIBOSE) POLYMERASE


Mass: 39328.133 Da / Num. of mol.: 1 / Fragment: CATALYTIC FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P26446, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-BZC / 2-(3'-METHOXYPHENYL) BENZIMIDAZOLE-4-CARBOXAMIDE


Mass: 267.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 3400, isopropyl alcohol, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / Details: Jung, S., (1994) J.Mol.Biol., 244, 114.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 %(w/v)beta-OG1drop
27.5 mg/mlprotein1drop
35 mMAp4A1drop
470 mMTris1reservoir
519 %PEG34001reservoir
68 %isopropyl alcohol1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 12, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. all: 18995 / Num. obs: 18995 / % possible obs: 97.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 28.3
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.222 / Num. unique all: 1807 / % possible all: 95.5
Reflection
*PLUS
Num. measured all: 95006
Reflection shell
*PLUS
% possible obs: 95.5 % / Mean I/σ(I) obs: 9.8

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Processing

Software
NameVersionClassification
X-PLOR98refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber, CHARMM
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1756 -random
Rwork0.194 ---
all0.215 19401 --
obs0.202 17889 92.2 %-
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 20 91 2875
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.315
X-RAY DIFFRACTIONx_dihedral_angle_d23.591
X-RAY DIFFRACTIONx_improper_angle_d1.137
Software
*PLUS
Name: X-PLOR / Version: 98 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 10 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.591
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.137

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