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- PDB-4glx: DNA ligase A in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 4glx
TitleDNA ligase A in complex with inhibitor
Components
  • DNA (26-MER)
  • DNA (5'-D(*AP*CP*AP*AP*TP*TP*GP*CP*GP*AP*CP*CP*C)-3')
  • DNA (5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*G)-3')
  • DNA ligase
KeywordsLIGASE/LIGASE INHIBITOR/DNA / DNA ligase A / inhibitor / LIGASE-LIGASE INHIBITOR-DNA complex
Function / homology
Function and homology information


DNA ligase (NAD+) / DNA ligase (NAD+) activity / base-excision repair, DNA ligation / DNA ligation / NAD+ binding / DNA replication / DNA binding / metal ion binding / cytosol
Similarity search - Function
Laminin - #30 / Laminin / Zinc-finger, NAD-dependent DNA ligase C4-type / NAD-dependent DNA ligase C4 zinc finger domain / Dna Ligase; domain 1 - #70 / NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase ...Laminin - #30 / Laminin / Zinc-finger, NAD-dependent DNA ligase C4-type / NAD-dependent DNA ligase C4 zinc finger domain / Dna Ligase; domain 1 - #70 / NAD-dependent DNA ligase, active site / NAD-dependent DNA ligase, conserved site / NAD-dependent DNA ligase signature 1. / NAD-dependent DNA ligase signature 2. / NAD-dependent DNA ligase / NAD-dependent DNA ligase, OB-fold / NAD-dependent DNA ligase, adenylation / NAD-dependent DNA ligase, N-terminal / NAD-dependent DNA ligase adenylation domain / NAD-dependent DNA ligase OB-fold domain / Ligase N family / DisA/LigA, helix-hairpin-helix motif / Helix-hairpin-helix motif / DNA ligase/mRNA capping enzyme / Helix hairpin bin / RuvA domain 2-like / Other non-globular / Helix-hairpin-helix domain / BRCA1 C Terminus (BRCT) domain / D-amino Acid Aminotransferase; Chain A, domain 1 / breast cancer carboxy-terminal domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding proteins / Dna Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / Special / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-0XS / DNA / DNA (> 10) / DNA ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPrade, L. / Lange, R. / Tidten-Luksch, N. / Chambovey, A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: Structure-guided design, synthesis and biological evaluation of novel DNA ligase inhibitors with in vitro and in vivo anti-staphylococcal activity.
Authors: Surivet, J.P. / Lange, R. / Hubschwerlen, C. / Keck, W. / Specklin, J.L. / Ritz, D. / Bur, D. / Locher, H. / Seiler, P. / Strasser, D.S. / Prade, L. / Kohl, C. / Schmitt, C. / Chapoux, G. / ...Authors: Surivet, J.P. / Lange, R. / Hubschwerlen, C. / Keck, W. / Specklin, J.L. / Ritz, D. / Bur, D. / Locher, H. / Seiler, P. / Strasser, D.S. / Prade, L. / Kohl, C. / Schmitt, C. / Chapoux, G. / Ilhan, E. / Ekambaram, N. / Athanasiou, A. / Knezevic, A. / Sabato, D. / Chambovey, A. / Gaertner, M. / Enderlin, M. / Boehme, M. / Sippel, V. / Wyss, P.
History
DepositionAug 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
B: DNA (26-MER)
C: DNA (5'-D(*AP*CP*AP*AP*TP*TP*GP*CP*GP*AP*CP*CP*C)-3')
D: DNA (5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*G)-3')
A: DNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3537
Polymers80,8564
Non-polymers4973
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-69 kcal/mol
Surface area31230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.990, 100.140, 86.570
Angle α, β, γ (deg.)90.000, 105.500, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-703-

HOH

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Components

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DNA chain , 3 types, 3 molecules BCD

#1: DNA chain DNA (26-MER)


Mass: 8034.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*AP*CP*AP*AP*TP*TP*GP*CP*GP*AP*CP*CP*C)-3')


Mass: 3920.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*G)-3')


Mass: 3975.611 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 1 molecules A

#4: Protein DNA ligase / / Polydeoxyribonucleotide synthase [NAD(+)]


Mass: 64925.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2411, dnaL, JW2403, lig, ligA, lop, pdeC / Production host: Escherichia coli (E. coli) / References: UniProt: P15042, DNA ligase (NAD+)

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Non-polymers , 4 types, 207 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-0XS / 2-amino-6-bromo-7-(trifluoromethyl)-1,8-naphthyridine-3-carboxamide


Mass: 335.080 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H6BrF3N4O
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium citrate, 25 mM sodium acetate, 24 % (w/v) PEG 4000, 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: Mar225 / Detector: CCD / Date: May 27, 2009
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→19.73 Å / % possible obs: 96.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.81 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 8.22
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.9-2.10.6492.045159318109197.4
2.1-2.70.3424.937987227317197.2
2.7-2.90.1968.51137984632196.2
2.9-3.10.14810.46105533520195.8
3.1-40.07117.23252548369194.5
4-60.04623.62156045057192.4
6-100.03725.1851151635189.4
10-19.730.02933.21350446184.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
RemDAqdata collection
INTEGRATEdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.73 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.862 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.668 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2497 2251 5 %RANDOM
Rwork0.2007 ---
all0.2032 69085 --
obs0.2032 45003 62.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.26 Å2 / Biso mean: 17.2358 Å2 / Biso min: 3.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20.42 Å2
2--0.53 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4308 1061 25 204 5598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0185645
X-RAY DIFFRACTIONr_angle_refined_deg2.091.8297908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5425572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81223.228189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58315685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9141538
X-RAY DIFFRACTIONr_chiral_restr0.130.2862
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213930
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 76 -
Rwork0.279 1432 -
all-1508 -
obs--28.81 %

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