data_3Q5C # _entry.id 3Q5C # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.380 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3Q5C pdb_00003q5c 10.2210/pdb3q5c/pdb NDB NA0916 ? ? RCSB RCSB063213 ? ? WWPDB D_1000063213 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3Q5C _pdbx_database_status.recvd_initial_deposition_date 2010-12-28 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Venkadesh, S.' 1 'Mandal, P.K.' 2 'Gautham, N.' 3 # _citation.id primary _citation.title 'The sequence d(CGGCGGCCGC) self-assembles into a two dimensional rhombic DNA lattice' _citation.journal_abbrev Biochem.Biophys.Res.Commun. _citation.journal_volume 407 _citation.page_first 548 _citation.page_last 551 _citation.year 2011 _citation.journal_id_ASTM BBRCA9 _citation.country US _citation.journal_id_ISSN 0006-291X _citation.journal_id_CSD 0146 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21419105 _citation.pdbx_database_id_DOI 10.1016/j.bbrc.2011.03.056 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Venkadesh, S.' 1 ? primary 'Mandal, P.K.' 2 ? primary 'Gautham, N.' 3 ? # _cell.entry_id 3Q5C _cell.length_a 23.640 _cell.length_b 33.841 _cell.length_c 40.400 _cell.angle_alpha 112.77 _cell.angle_beta 90.00 _cell.angle_gamma 110.44 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3Q5C _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*CP*GP*GP*CP*GP*GP*CP*CP*GP*C)-3') ; 3046.980 4 ? ? ? ? 2 water nat water 18.015 9 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DG)(DC)(DG)(DG)(DC)(DC)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can CGGCGGCCGC _entity_poly.pdbx_strand_id A,B,C,D _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DG n 1 4 DC n 1 5 DG n 1 6 DG n 1 7 DC n 1 8 DC n 1 9 DG n 1 10 DC n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'Chemically synthesized' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3Q5C _struct_ref.pdbx_db_accession 3Q5C _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3Q5C A 1 ? 10 ? 3Q5C 1 ? 10 ? 1 10 2 1 3Q5C B 1 ? 10 ? 3Q5C 1 ? 10 ? 1 10 3 1 3Q5C C 1 ? 10 ? 3Q5C 1 ? 10 ? 1 10 4 1 3Q5C D 1 ? 10 ? 3Q5C 1 ? 10 ? 1 10 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 HOH non-polymer . WATER ? 'H2 O' 18.015 # _exptl.entry_id 3Q5C _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.26 _exptl_crystal.density_percent_sol 45.65 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;1mM DNA, 50mM Cacodylate buffer, 50mM CaCl2, 1mM spermine, 50% MPD in Reservior, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MARMOSAIC 225 mm CCD' _diffrn_detector.pdbx_collection_date 2010-07-07 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si (111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9922 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE BM14' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline BM14 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9922 # _reflns.entry_id 3Q5C _reflns.observed_criterion_sigma_I 1.0 _reflns.observed_criterion_sigma_F 2.0 _reflns.d_resolution_low 36.80 _reflns.d_resolution_high 2.50 _reflns.number_obs 3490 _reflns.number_all 3708 _reflns.percent_possible_obs 94.1 _reflns.pdbx_Rmerge_I_obs 0.097 _reflns.pdbx_Rsym_value 0.130 _reflns.pdbx_netI_over_sigmaI 3.8 _reflns.B_iso_Wilson_estimate 33.8 _reflns.pdbx_redundancy 1.9 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.50 _reflns_shell.d_res_low 2.64 _reflns_shell.percent_possible_all 93.2 _reflns_shell.Rmerge_I_obs 0.278 _reflns_shell.pdbx_Rsym_value 0.393 _reflns_shell.meanI_over_sigI_obs 1.4 _reflns_shell.pdbx_redundancy 1.9 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 535 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.number_possible ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.Rmerge_I_all ? _reflns_shell.meanI_over_sigI_all ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3Q5C _refine.ls_number_reflns_obs 3449 _refine.ls_number_reflns_all 3606 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.010 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 29.3570 _refine.ls_d_res_high 2.5010 _refine.ls_percent_reflns_obs 90.42 _refine.ls_R_factor_obs 0.2425 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2407 _refine.ls_R_factor_R_free 0.2743 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.33 _refine.ls_number_reflns_R_free 145 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 51.6479 _refine.solvent_model_param_bsol 35.6020 _refine.solvent_model_param_ksol 0.3240 _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 27.9058 _refine.aniso_B[2][2] -27.2791 _refine.aniso_B[3][3] -0.6267 _refine.aniso_B[1][2] 5.2849 _refine.aniso_B[1][3] -8.3794 _refine.aniso_B[2][3] 4.1963 _refine.pdbx_ls_cross_valid_method Throught _refine.pdbx_starting_model 'PDB ENTRY 1P4Y' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.0000 _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_overall_phase_error 41.0200 _refine.details ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 808 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 9 _refine_hist.number_atoms_total 817 _refine_hist.d_res_high 2.5010 _refine_hist.d_res_low 29.3570 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' f_bond_d 904 0.016 ? ? ? 'X-RAY DIFFRACTION' f_angle_d 1388 2.739 ? ? ? 'X-RAY DIFFRACTION' f_chiral_restr 156 0.110 ? ? ? 'X-RAY DIFFRACTION' f_plane_restr 40 0.008 ? ? ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 384 36.143 ? ? ? # _struct.entry_id 3Q5C _struct.title 'Crystal structure of four-way junction with sticky end' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3Q5C _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Sticky end, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 1 ? D N N 1 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 2 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 3 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 3 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 3 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 4 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 4 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 4 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 5 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 5 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 5 B DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 7 N3 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 7 O2 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 7 N4 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 7 N3 ? ? ? 1_555 D DG 6 N1 ? ? A DC 7 D DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 7 N4 ? ? ? 1_555 D DG 6 O6 ? ? A DC 7 D DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 7 O2 ? ? ? 1_555 D DG 6 N2 ? ? A DC 7 D DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 8 N3 ? ? ? 1_555 D DG 5 N1 ? ? A DC 8 D DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 8 N4 ? ? ? 1_555 D DG 5 O6 ? ? A DC 8 D DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 O2 ? ? ? 1_555 D DG 5 N2 ? ? A DC 8 D DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 9 N1 ? ? ? 1_555 D DC 4 N3 ? ? A DG 9 D DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 9 N2 ? ? ? 1_555 D DC 4 O2 ? ? A DG 9 D DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 O6 ? ? ? 1_555 D DC 4 N4 ? ? A DG 9 D DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 10 N4 ? ? ? 1_555 D DG 2 O6 ? ? A DC 10 D DG 2 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog23 hydrog ? ? A DC 10 N3 ? ? ? 1_555 D DG 3 N1 ? ? A DC 10 D DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 10 N4 ? ? ? 1_555 D DG 3 O6 ? ? A DC 10 D DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 10 O2 ? ? ? 1_555 D DG 3 N2 ? ? A DC 10 D DG 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? B DG 3 N1 ? ? ? 1_555 C DC 10 N3 ? ? B DG 3 C DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? B DG 3 N2 ? ? ? 1_555 C DC 10 O2 ? ? B DG 3 C DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? B DG 3 O6 ? ? ? 1_555 C DC 10 N4 ? ? B DG 3 C DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? B DC 4 O2 ? ? ? 1_555 C DG 9 N2 ? ? B DC 4 C DG 9 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog30 hydrog ? ? B DG 5 O6 ? ? ? 1_555 C DC 7 N4 ? ? B DG 5 C DC 7 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog31 hydrog ? ? B DG 5 N1 ? ? ? 1_555 C DC 8 N3 ? ? B DG 5 C DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B DG 5 N2 ? ? ? 1_555 C DC 8 O2 ? ? B DG 5 C DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? B DG 5 O6 ? ? ? 1_555 C DC 8 N4 ? ? B DG 5 C DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? B DG 6 N1 ? ? ? 1_555 C DC 7 N3 ? ? B DG 6 C DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B DG 6 N2 ? ? ? 1_555 C DC 7 O2 ? ? B DG 6 C DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? B DG 6 O6 ? ? ? 1_555 C DC 7 N4 ? ? B DG 6 C DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? C DG 3 N1 ? ? ? 1_555 D DC 10 N3 ? ? C DG 3 D DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? C DG 3 N2 ? ? ? 1_555 D DC 10 O2 ? ? C DG 3 D DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? C DG 3 O6 ? ? ? 1_555 D DC 10 N4 ? ? C DG 3 D DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? C DC 4 N3 ? ? ? 1_555 D DG 9 N1 ? ? C DC 4 D DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? C DC 4 N4 ? ? ? 1_555 D DG 9 O6 ? ? C DC 4 D DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? C DC 4 O2 ? ? ? 1_555 D DG 9 N2 ? ? C DC 4 D DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? C DG 5 N1 ? ? ? 1_555 D DC 8 N3 ? ? C DG 5 D DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? C DG 5 N2 ? ? ? 1_555 D DC 8 O2 ? ? C DG 5 D DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? C DG 5 O6 ? ? ? 1_555 D DC 8 N4 ? ? C DG 5 D DC 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? C DG 6 N1 ? ? ? 1_555 D DC 7 N3 ? ? C DG 6 D DC 7 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 3Q5C _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 3Q5C _atom_sites.fract_transf_matrix[1][1] 0.042301 _atom_sites.fract_transf_matrix[1][2] 0.015768 _atom_sites.fract_transf_matrix[1][3] 0.007152 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.031536 _atom_sites.fract_transf_matrix[2][3] 0.014305 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.027180 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC C A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DC 4 4 4 DC C A . n A 1 5 DG 5 5 5 DG G A . n A 1 6 DG 6 6 6 DG G A . n A 1 7 DC 7 7 7 DC C A . n A 1 8 DC 8 8 8 DC C A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DC 10 10 10 DC C A . n B 1 1 DC 1 1 1 DC C B . n B 1 2 DG 2 2 2 DG G B . n B 1 3 DG 3 3 3 DG G B . n B 1 4 DC 4 4 4 DC C B . n B 1 5 DG 5 5 5 DG G B . n B 1 6 DG 6 6 6 DG G B . n B 1 7 DC 7 7 7 DC C B . n B 1 8 DC 8 8 8 DC C B . n B 1 9 DG 9 9 9 DG G B . n B 1 10 DC 10 10 10 DC C B . n C 1 1 DC 1 1 1 DC C C . n C 1 2 DG 2 2 2 DG G C . n C 1 3 DG 3 3 3 DG G C . n C 1 4 DC 4 4 4 DC C C . n C 1 5 DG 5 5 5 DG G C . n C 1 6 DG 6 6 6 DG G C . n C 1 7 DC 7 7 7 DC C C . n C 1 8 DC 8 8 8 DC C C . n C 1 9 DG 9 9 9 DG G C . n C 1 10 DC 10 10 10 DC C C . n D 1 1 DC 1 1 1 DC C D . n D 1 2 DG 2 2 2 DG G D . n D 1 3 DG 3 3 3 DG G D . n D 1 4 DC 4 4 4 DC C D . n D 1 5 DG 5 5 5 DG G D . n D 1 6 DG 6 6 6 DG G D . n D 1 7 DC 7 7 7 DC C D . n D 1 8 DC 8 8 8 DC C D . n D 1 9 DG 9 9 9 DG G D . n D 1 10 DC 10 10 10 DC C D . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code E 2 HOH 1 11 2 HOH HOH A . E 2 HOH 2 12 4 HOH HOH A . E 2 HOH 3 13 5 HOH HOH A . F 2 HOH 1 11 1 HOH HOH B . F 2 HOH 2 12 7 HOH HOH B . G 2 HOH 1 11 3 HOH HOH C . G 2 HOH 2 12 6 HOH HOH C . G 2 HOH 3 13 8 HOH HOH C . H 2 HOH 1 11 9 HOH HOH D . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2430 ? 1 MORE -10 ? 1 'SSA (A^2)' 7190 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2011-05-18 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2023-11-01 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MAR345dtb 'data collection' . ? 1 PHASER phasing . ? 2 PHENIX refinement '(phenix.refine: 1.6_289)' ? 3 iMOSFLM 'data reduction' . ? 4 SCALA 'data scaling' . ? 5 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "O3'" C DC 1 ? ? "C3'" C DC 1 ? ? 1.383 1.419 -0.036 0.006 N 2 1 "C5'" D DC 1 ? ? "C4'" D DC 1 ? ? 1.555 1.512 0.043 0.007 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 112.91 108.30 4.61 0.30 N 2 1 "C3'" A DG 5 ? ? "O3'" A DG 5 ? ? P A DG 6 ? ? 133.02 119.70 13.32 1.20 Y 3 1 "O3'" A DG 5 ? ? P A DG 6 ? ? "O5'" A DG 6 ? ? 91.21 104.00 -12.79 1.90 Y 4 1 "C5'" A DG 6 ? ? "C4'" A DG 6 ? ? "O4'" A DG 6 ? ? 116.62 109.80 6.82 1.10 N 5 1 C5 A DG 6 ? ? C6 A DG 6 ? ? O6 A DG 6 ? ? 124.69 128.60 -3.91 0.60 N 6 1 "C5'" A DC 7 ? ? "C4'" A DC 7 ? ? "O4'" A DC 7 ? ? 116.84 109.80 7.04 1.10 N 7 1 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 103.15 108.00 -4.85 0.70 N 8 1 "O4'" A DC 10 ? ? "C1'" A DC 10 ? ? N1 A DC 10 ? ? 100.29 108.00 -7.71 0.70 N 9 1 "O4'" B DC 1 ? ? "C1'" B DC 1 ? ? N1 B DC 1 ? ? 118.33 108.30 10.03 0.30 N 10 1 "C3'" B DC 1 ? ? "O3'" B DC 1 ? ? P B DG 2 ? ? 133.78 119.70 14.08 1.20 Y 11 1 P B DC 4 ? ? "O5'" B DC 4 ? ? "C5'" B DC 4 ? ? 110.99 120.90 -9.91 1.60 N 12 1 "O4'" B DC 4 ? ? "C1'" B DC 4 ? ? N1 B DC 4 ? ? 111.65 108.30 3.35 0.30 N 13 1 "O4'" B DG 5 ? ? "C1'" B DG 5 ? ? N9 B DG 5 ? ? 110.19 108.30 1.89 0.30 N 14 1 "O3'" B DG 5 ? ? P B DG 6 ? ? OP1 B DG 6 ? ? 118.73 110.50 8.23 1.10 Y 15 1 "O4'" B DG 6 ? ? "C1'" B DG 6 ? ? N9 B DG 6 ? ? 111.34 108.30 3.04 0.30 N 16 1 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? "C2'" B DC 7 ? ? 99.32 105.90 -6.58 0.80 N 17 1 N1 B DC 7 ? ? "C1'" B DC 7 ? ? "C2'" B DC 7 ? ? 122.81 114.30 8.51 1.40 N 18 1 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 102.36 108.00 -5.64 0.70 N 19 1 "O4'" B DC 8 ? ? "C4'" B DC 8 ? ? "C3'" B DC 8 ? ? 101.78 104.50 -2.72 0.40 N 20 1 "C4'" B DC 8 ? ? "C3'" B DC 8 ? ? "C2'" B DC 8 ? ? 97.20 102.20 -5.00 0.70 N 21 1 "O4'" B DG 9 ? ? "C4'" B DG 9 ? ? "C3'" B DG 9 ? ? 100.83 104.50 -3.67 0.40 N 22 1 "C4'" B DG 9 ? ? "C3'" B DG 9 ? ? "C2'" B DG 9 ? ? 97.93 102.20 -4.27 0.70 N 23 1 "C3'" B DG 9 ? ? "C2'" B DG 9 ? ? "C1'" B DG 9 ? ? 94.46 102.40 -7.94 0.80 N 24 1 "O4'" B DG 9 ? ? "C1'" B DG 9 ? ? N9 B DG 9 ? ? 110.79 108.30 2.49 0.30 N 25 1 "O4'" B DC 10 ? ? "C1'" B DC 10 ? ? N1 B DC 10 ? ? 112.29 108.30 3.99 0.30 N 26 1 "O4'" C DG 2 ? ? "C1'" C DG 2 ? ? N9 C DG 2 ? ? 112.17 108.30 3.87 0.30 N 27 1 "O4'" C DG 3 ? ? "C4'" C DG 3 ? ? "C3'" C DG 3 ? ? 101.81 104.50 -2.69 0.40 N 28 1 "O4'" C DC 4 ? ? "C1'" C DC 4 ? ? N1 C DC 4 ? ? 114.22 108.30 5.92 0.30 N 29 1 "O4'" C DG 5 ? ? "C1'" C DG 5 ? ? N9 C DG 5 ? ? 103.37 108.00 -4.63 0.70 N 30 1 C4 C DG 5 ? ? C5 C DG 5 ? ? N7 C DG 5 ? ? 108.17 110.80 -2.63 0.40 N 31 1 "O5'" C DG 6 ? ? "C5'" C DG 6 ? ? "C4'" C DG 6 ? ? 99.74 109.40 -9.66 0.80 N 32 1 "O4'" C DG 6 ? ? "C1'" C DG 6 ? ? N9 C DG 6 ? ? 112.79 108.30 4.49 0.30 N 33 1 "O4'" C DC 7 ? ? "C4'" C DC 7 ? ? "C3'" C DC 7 ? ? 100.46 104.50 -4.04 0.40 N 34 1 "C3'" C DC 7 ? ? "C2'" C DC 7 ? ? "C1'" C DC 7 ? ? 96.06 102.40 -6.34 0.80 N 35 1 "O4'" C DC 7 ? ? "C1'" C DC 7 ? ? N1 C DC 7 ? ? 113.04 108.30 4.74 0.30 N 36 1 "C3'" C DC 7 ? ? "O3'" C DC 7 ? ? P C DC 8 ? ? 130.34 119.70 10.64 1.20 Y 37 1 "O5'" C DG 9 ? ? "C5'" C DG 9 ? ? "C4'" C DG 9 ? ? 101.13 109.40 -8.27 0.80 N 38 1 "O4'" C DG 9 ? ? "C1'" C DG 9 ? ? N9 C DG 9 ? ? 113.40 108.30 5.10 0.30 N 39 1 "C1'" D DC 1 ? ? "O4'" D DC 1 ? ? "C4'" D DC 1 ? ? 103.82 110.10 -6.28 1.00 N 40 1 "C3'" D DC 1 ? ? "C2'" D DC 1 ? ? "C1'" D DC 1 ? ? 91.83 102.40 -10.57 0.80 N 41 1 "O4'" D DC 1 ? ? "C1'" D DC 1 ? ? N1 D DC 1 ? ? 113.14 108.30 4.84 0.30 N 42 1 "C3'" D DC 1 ? ? "O3'" D DC 1 ? ? P D DG 2 ? ? 131.24 119.70 11.54 1.20 Y 43 1 "O3'" D DC 1 ? ? P D DG 2 ? ? OP2 D DG 2 ? ? 117.56 110.50 7.06 1.10 Y 44 1 "O4'" D DG 2 ? ? "C1'" D DG 2 ? ? N9 D DG 2 ? ? 114.62 108.30 6.32 0.30 N 45 1 "C3'" D DG 2 ? ? "O3'" D DG 2 ? ? P D DG 3 ? ? 127.06 119.70 7.36 1.20 Y 46 1 "O4'" D DG 3 ? ? "C4'" D DG 3 ? ? "C3'" D DG 3 ? ? 100.19 104.50 -4.31 0.40 N 47 1 "C4'" D DG 3 ? ? "C3'" D DG 3 ? ? "C2'" D DG 3 ? ? 96.40 102.20 -5.80 0.70 N 48 1 "C4'" D DC 7 ? ? "C3'" D DC 7 ? ? "C2'" D DC 7 ? ? 97.37 102.20 -4.83 0.70 N 49 1 "O4'" D DG 9 ? ? "C4'" D DG 9 ? ? "C3'" D DG 9 ? ? 101.59 104.50 -2.91 0.40 N 50 1 "O4'" D DC 10 ? ? "C1'" D DC 10 ? ? N1 D DC 10 ? ? 116.82 108.30 8.52 0.30 N # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DC OP3 O N N 1 DC P P N N 2 DC OP1 O N N 3 DC OP2 O N N 4 DC "O5'" O N N 5 DC "C5'" C N N 6 DC "C4'" C N R 7 DC "O4'" O N N 8 DC "C3'" C N S 9 DC "O3'" O N N 10 DC "C2'" C N N 11 DC "C1'" C N R 12 DC N1 N N N 13 DC C2 C N N 14 DC O2 O N N 15 DC N3 N N N 16 DC C4 C N N 17 DC N4 N N N 18 DC C5 C N N 19 DC C6 C N N 20 DC HOP3 H N N 21 DC HOP2 H N N 22 DC "H5'" H N N 23 DC "H5''" H N N 24 DC "H4'" H N N 25 DC "H3'" H N N 26 DC "HO3'" H N N 27 DC "H2'" H N N 28 DC "H2''" H N N 29 DC "H1'" H N N 30 DC H41 H N N 31 DC H42 H N N 32 DC H5 H N N 33 DC H6 H N N 34 DG OP3 O N N 35 DG P P N N 36 DG OP1 O N N 37 DG OP2 O N N 38 DG "O5'" O N N 39 DG "C5'" C N N 40 DG "C4'" C N R 41 DG "O4'" O N N 42 DG "C3'" C N S 43 DG "O3'" O N N 44 DG "C2'" C N N 45 DG "C1'" C N R 46 DG N9 N Y N 47 DG C8 C Y N 48 DG N7 N Y N 49 DG C5 C Y N 50 DG C6 C N N 51 DG O6 O N N 52 DG N1 N N N 53 DG C2 C N N 54 DG N2 N N N 55 DG N3 N N N 56 DG C4 C Y N 57 DG HOP3 H N N 58 DG HOP2 H N N 59 DG "H5'" H N N 60 DG "H5''" H N N 61 DG "H4'" H N N 62 DG "H3'" H N N 63 DG "HO3'" H N N 64 DG "H2'" H N N 65 DG "H2''" H N N 66 DG "H1'" H N N 67 DG H8 H N N 68 DG H1 H N N 69 DG H21 H N N 70 DG H22 H N N 71 HOH O O N N 72 HOH H1 H N N 73 HOH H2 H N N 74 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DC OP3 P sing N N 1 DC OP3 HOP3 sing N N 2 DC P OP1 doub N N 3 DC P OP2 sing N N 4 DC P "O5'" sing N N 5 DC OP2 HOP2 sing N N 6 DC "O5'" "C5'" sing N N 7 DC "C5'" "C4'" sing N N 8 DC "C5'" "H5'" sing N N 9 DC "C5'" "H5''" sing N N 10 DC "C4'" "O4'" sing N N 11 DC "C4'" "C3'" sing N N 12 DC "C4'" "H4'" sing N N 13 DC "O4'" "C1'" sing N N 14 DC "C3'" "O3'" sing N N 15 DC "C3'" "C2'" sing N N 16 DC "C3'" "H3'" sing N N 17 DC "O3'" "HO3'" sing N N 18 DC "C2'" "C1'" sing N N 19 DC "C2'" "H2'" sing N N 20 DC "C2'" "H2''" sing N N 21 DC "C1'" N1 sing N N 22 DC "C1'" "H1'" sing N N 23 DC N1 C2 sing N N 24 DC N1 C6 sing N N 25 DC C2 O2 doub N N 26 DC C2 N3 sing N N 27 DC N3 C4 doub N N 28 DC C4 N4 sing N N 29 DC C4 C5 sing N N 30 DC N4 H41 sing N N 31 DC N4 H42 sing N N 32 DC C5 C6 doub N N 33 DC C5 H5 sing N N 34 DC C6 H6 sing N N 35 DG OP3 P sing N N 36 DG OP3 HOP3 sing N N 37 DG P OP1 doub N N 38 DG P OP2 sing N N 39 DG P "O5'" sing N N 40 DG OP2 HOP2 sing N N 41 DG "O5'" "C5'" sing N N 42 DG "C5'" "C4'" sing N N 43 DG "C5'" "H5'" sing N N 44 DG "C5'" "H5''" sing N N 45 DG "C4'" "O4'" sing N N 46 DG "C4'" "C3'" sing N N 47 DG "C4'" "H4'" sing N N 48 DG "O4'" "C1'" sing N N 49 DG "C3'" "O3'" sing N N 50 DG "C3'" "C2'" sing N N 51 DG "C3'" "H3'" sing N N 52 DG "O3'" "HO3'" sing N N 53 DG "C2'" "C1'" sing N N 54 DG "C2'" "H2'" sing N N 55 DG "C2'" "H2''" sing N N 56 DG "C1'" N9 sing N N 57 DG "C1'" "H1'" sing N N 58 DG N9 C8 sing Y N 59 DG N9 C4 sing Y N 60 DG C8 N7 doub Y N 61 DG C8 H8 sing N N 62 DG N7 C5 sing Y N 63 DG C5 C6 sing N N 64 DG C5 C4 doub Y N 65 DG C6 O6 doub N N 66 DG C6 N1 sing N N 67 DG N1 C2 sing N N 68 DG N1 H1 sing N N 69 DG C2 N2 sing N N 70 DG C2 N3 doub N N 71 DG N2 H21 sing N N 72 DG N2 H22 sing N N 73 DG N3 C4 sing N N 74 HOH O H1 sing N N 75 HOH O H2 sing N N 76 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3Q5C 'double helix' 3Q5C 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DG 3 1_555 B DC 10 1_555 -1.321 -0.283 -0.385 3.911 -8.405 11.791 1 A_DG3:DC10_B A 3 ? B 10 ? 19 1 1 A DC 4 1_555 B DG 9 1_555 0.323 -0.383 -0.881 7.719 -5.377 -3.585 2 A_DC4:DG9_B A 4 ? B 9 ? 19 1 1 A DG 5 1_555 B DC 8 1_555 -0.253 -0.548 0.068 3.439 -7.161 -3.071 3 A_DG5:DC8_B A 5 ? B 8 ? 19 1 1 A DG 6 1_555 B DC 7 1_555 1.009 -0.329 0.567 6.267 -12.032 -1.807 4 A_DG6:DC7_B A 6 ? B 7 ? 19 1 1 C DC 7 1_555 B DG 6 1_555 -0.270 -0.062 0.833 -8.052 -16.319 2.145 5 C_DC7:DG6_B C 7 ? B 6 ? 19 1 1 C DC 8 1_555 B DG 5 1_555 -0.273 -0.030 0.619 1.843 -8.952 2.023 6 C_DC8:DG5_B C 8 ? B 5 ? 19 1 1 C DG 9 1_555 B DC 4 1_555 0.383 0.291 0.120 2.896 -14.022 5.176 7 C_DG9:DC4_B C 9 ? B 4 ? ? 1 1 C DC 10 1_555 B DG 3 1_555 -0.928 -0.486 0.479 -3.581 -5.290 -3.314 8 C_DC10:DG3_B C 10 ? B 3 ? 19 1 1 C DG 3 1_555 D DC 10 1_555 -0.604 0.145 0.379 5.574 -11.851 -2.031 9 C_DG3:DC10_D C 3 ? D 10 ? 19 1 1 C DC 4 1_555 D DG 9 1_555 -0.648 0.216 0.271 0.126 -10.747 4.998 10 C_DC4:DG9_D C 4 ? D 9 ? 19 1 1 C DG 5 1_555 D DC 8 1_555 0.993 0.230 -0.333 -1.660 -7.103 -6.325 11 C_DG5:DC8_D C 5 ? D 8 ? 19 1 1 C DG 6 1_555 D DC 7 1_555 0.722 0.126 -0.131 0.502 -11.417 -12.544 12 C_DG6:DC7_D C 6 ? D 7 ? ? 1 1 A DC 7 1_555 D DG 6 1_555 0.664 -0.363 0.026 2.400 -17.079 -0.037 13 A_DC7:DG6_D A 7 ? D 6 ? 19 1 1 A DC 8 1_555 D DG 5 1_555 0.190 0.083 -0.019 1.113 -11.424 8.385 14 A_DC8:DG5_D A 8 ? D 5 ? 19 1 1 A DG 9 1_555 D DC 4 1_555 -0.921 0.212 0.215 -4.466 -11.209 3.299 15 A_DG9:DC4_D A 9 ? D 4 ? 19 1 1 A DC 10 1_555 D DG 3 1_555 -0.070 -0.307 0.956 -9.212 -4.321 -6.305 16 A_DC10:DG3_D A 10 ? D 3 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DG 3 1_555 B DC 10 1_555 A DC 4 1_555 B DG 9 1_555 -0.205 0.940 3.049 4.473 -0.132 47.092 1.182 0.594 3.016 -0.165 -5.583 47.292 1 AA_DG3DC4:DG9DC10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A DC 4 1_555 B DG 9 1_555 A DG 5 1_555 B DC 8 1_555 -0.267 1.525 3.515 -2.587 9.253 33.051 0.931 -0.009 3.801 15.852 4.433 34.382 2 AA_DC4DG5:DC8DG9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A DG 5 1_555 B DC 8 1_555 A DG 6 1_555 B DC 7 1_555 -0.091 1.164 3.316 -3.394 -1.164 44.331 1.647 -0.196 3.284 -1.540 4.489 44.469 3 AA_DG5DG6:DC7DC8_BB A 5 ? B 8 ? A 6 ? B 7 ? 1 A DG 6 1_555 B DC 7 1_555 C DC 7 1_555 B DG 6 1_555 1.132 -0.191 3.659 4.438 -2.386 29.754 0.189 -1.140 3.787 -4.604 -8.566 30.168 4 AC_DG6DC7:DG6DC7_BB A 6 ? B 7 ? C 7 ? B 6 ? 1 C DC 7 1_555 B DG 6 1_555 C DC 8 1_555 B DG 5 1_555 -0.578 -0.242 3.174 1.673 9.962 30.180 -2.185 1.349 2.913 18.493 -3.106 31.788 5 CC_DC7DC8:DG5DG6_BB C 7 ? B 6 ? C 8 ? B 5 ? 1 C DC 8 1_555 B DG 5 1_555 C DG 9 1_555 B DC 4 1_555 0.572 0.372 3.291 4.242 6.270 34.190 -0.352 -0.294 3.350 10.505 -7.108 34.994 6 CC_DC8DG9:DC4DG5_BB C 8 ? B 5 ? C 9 ? B 4 ? 1 C DG 9 1_555 B DC 4 1_555 C DC 10 1_555 B DG 3 1_555 -0.600 0.572 3.505 -6.784 -0.436 38.653 0.909 0.013 3.549 -0.652 10.153 39.224 7 CC_DG9DC10:DG3DC4_BB C 9 ? B 4 ? C 10 ? B 3 ? 1 C DG 3 1_555 D DC 10 1_555 C DC 4 1_555 D DG 9 1_555 0.319 0.457 3.366 1.979 -0.570 32.564 0.916 -0.214 3.371 -1.015 -3.525 32.627 8 CC_DG3DC4:DG9DC10_DD C 3 ? D 10 ? C 4 ? D 9 ? 1 C DC 4 1_555 D DG 9 1_555 C DG 5 1_555 D DC 8 1_555 -0.623 2.860 3.363 2.625 -0.190 57.238 2.993 0.796 3.325 -0.198 -2.739 57.293 9 CC_DC4DG5:DC8DG9_DD C 4 ? D 9 ? C 5 ? D 8 ? 1 C DG 5 1_555 D DC 8 1_555 C DG 6 1_555 D DC 7 1_555 0.154 0.316 3.342 -3.934 10.869 21.557 -2.790 -1.645 3.069 26.727 9.675 24.428 10 CC_DG5DG6:DC7DC8_DD C 5 ? D 8 ? C 6 ? D 7 ? 1 C DG 6 1_555 D DC 7 1_555 A DC 7 1_555 D DG 6 1_555 1.175 -0.445 3.231 2.350 1.095 29.644 -1.096 -1.798 3.294 2.136 -4.581 29.754 11 CA_DG6DC7:DG6DC7_DD C 6 ? D 7 ? A 7 ? D 6 ? 1 A DC 7 1_555 D DG 6 1_555 A DC 8 1_555 D DG 5 1_555 0.278 2.420 3.397 4.192 3.895 40.461 3.007 0.098 3.614 5.598 -6.024 40.847 12 AA_DC7DC8:DG5DG6_DD A 7 ? D 6 ? A 8 ? D 5 ? 1 A DC 8 1_555 D DG 5 1_555 A DG 9 1_555 D DC 4 1_555 -0.641 1.539 3.354 -5.000 3.846 35.302 1.913 0.278 3.552 6.279 8.164 35.843 13 AA_DC8DG9:DC4DG5_DD A 8 ? D 5 ? A 9 ? D 4 ? 1 A DG 9 1_555 D DC 4 1_555 A DC 10 1_555 D DG 3 1_555 -0.693 0.431 3.738 -6.271 -2.336 42.121 0.864 0.225 3.771 -3.225 8.659 42.625 14 AA_DG9DC10:DG3DC4_DD A 9 ? D 4 ? A 10 ? D 3 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1P4Y _pdbx_initial_refinement_model.details 'PDB ENTRY 1P4Y' #