data_1V3O # _entry.id 1V3O # _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 1V3O pdb_00001v3o 10.2210/pdb1v3o/pdb NDB UD0047 ? ? RCSB RCSB006165 ? ? WWPDB D_1000006165 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1V3N 'The same structure, Br-derivative' unspecified PDB 1V3P 'The same structure, I-derivative, with I-motif of G-quartet' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1V3O _pdbx_database_status.recvd_initial_deposition_date 2003-11-03 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kondo, J.' 1 'Umeda, S.' 2 'Sunami, T.' 3 'Takenaka, A.' 4 # _citation.id primary _citation.title ;Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 32 _citation.page_first 2541 _citation.page_last 2549 _citation.year 2004 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15133122 _citation.pdbx_database_id_DOI 10.1093/nar/gkh575 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kondo, J.' 1 ? primary 'Adachi, W.' 2 ? primary 'Umeda, S.' 3 ? primary 'Sunami, T.' 4 ? primary 'Takenaka, A.' 5 ? # _cell.entry_id 1V3O _cell.length_a 34.650 _cell.length_b 42.490 _cell.length_c 64.080 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _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 1V3O _symmetry.space_group_name_H-M 'I 2 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _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 "5'-D(*GP*(C38)P*GP*AP*GP*AP*GP*C)-3'" 2602.540 2 ? ? ? ? 2 non-polymer syn 'POTASSIUM ION' 39.098 1 ? ? ? ? 3 water nat water 18.015 87 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DG)(C38)(DG)(DA)(DG)(DA)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCGAGAGC _entity_poly.pdbx_strand_id A,B _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 DG n 1 2 C38 n 1 3 DG n 1 4 DA n 1 5 DG n 1 6 DA n 1 7 DG n 1 8 DC n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1V3O _struct_ref.pdbx_db_accession 1V3O _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 1V3O A 1 ? 8 ? 1V3O 1 ? 8 ? 1 8 2 1 1V3O B 1 ? 8 ? 1V3O 9 ? 16 ? 9 16 # 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 C38 'DNA linking' n "5-IODO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 I N3 O7 P' 433.094 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 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 K non-polymer . 'POTASSIUM ION' ? 'K 1' 39.098 # _exptl.entry_id 1V3O _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.17 _exptl_crystal.density_percent_sol 43.37 _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 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;2-methyl-2,4-pentanediol, spermine tetrahydrochloride, sodium chloride, potassium chloride, sodium cacodylate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K ; _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 2-methyl-2,4-pentanediol ? ? ? 1 2 1 'spermine tetrahydrochloride' ? ? ? 1 3 1 'sodium chloride' ? ? ? 1 4 1 'potassium chloride' ? ? ? 1 5 1 'sodium cacodylate' ? ? ? 1 6 2 'sodium chloride' ? ? ? 1 7 2 'potassium chloride' ? ? ? 1 8 2 'sodium cacodylate' ? ? ? # _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 'OXFORD PX210' _diffrn_detector.pdbx_collection_date 2001-03-27 _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 ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.90 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SPRING-8 BEAMLINE BL44XU' _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL44XU _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.90 # _reflns.entry_id 1V3O _reflns.observed_criterion_sigma_F 0.0 _reflns.observed_criterion_sigma_I 0.0 _reflns.d_resolution_high 1.7 _reflns.d_resolution_low 35 _reflns.number_all 5463 _reflns.number_obs 5269 _reflns.percent_possible_obs 96.5 _reflns.pdbx_Rmerge_I_obs 0.096 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 4.2 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.7 _reflns_shell.d_res_low 1.76 _reflns_shell.percent_possible_all 100.0 _reflns_shell.Rmerge_I_obs 0.137 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 1.9 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 527 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 1V3O _refine.ls_d_res_high 1.7 _refine.ls_d_res_low 9.0 _refine.pdbx_ls_sigma_F 3.0 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 5414 _refine.ls_number_reflns_obs 5063 _refine.ls_number_reflns_R_free 528 _refine.ls_percent_reflns_obs 93.5 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.262 _refine.ls_R_factor_R_free 0.296 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 'PDB ENTRY 1V3N' _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values 'G. PARKINSON ET AL., (1996) ACTACRYST. D52, 57-64' _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.details ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_phase_error ? _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_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_analyze.entry_id 1V3O _refine_analyze.Luzzati_coordinate_error_obs 0.40 _refine_analyze.Luzzati_sigma_a_obs 0.60 _refine_analyze.Luzzati_d_res_low_obs 5.0 _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _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 332 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 87 _refine_hist.number_atoms_total 420 _refine_hist.d_res_high 1.7 _refine_hist.d_res_low 9.0 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.004 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 0.9 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 23.6 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 0.8 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 1.7 _refine_ls_shell.d_res_low 1.76 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.5554 _refine_ls_shell.percent_reflns_obs 90.4 _refine_ls_shell.R_factor_R_free 0.6045 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 50 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 1V3O _struct.title 'Crystal structure of d(GCGAGAGC): the DNA quadruplex structure split from the octaplex' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1V3O _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;octaplex, quadruplex, G-duet, base-intercalated duplex, base-intercalated motif, sheared G:A pair, DNA, deoxyribonucleic acid, X-ray analysis ; # 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 2 ? D N N 3 ? E N N 3 ? # _struct_biol.id 1 _struct_biol.details 'The biological assembly is a quadruplex generated from the duplex in the asymmetric unit by the operations: x, y, z and -x, y, -z.' _struct_biol.pdbx_parent_biol_id ? # 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 covale1 covale both ? A DG 1 "O3'" ? ? ? 1_555 A C38 2 P ? ? A DG 1 A C38 2 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale2 covale one ? A C38 2 "O3'" ? ? ? 1_555 A DG 3 P ? ? A C38 2 A DG 3 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale3 covale both ? B DG 1 "O3'" ? ? ? 1_555 B C38 2 P ? ? B DG 9 B C38 10 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale4 covale one ? B C38 2 "O3'" ? ? ? 1_555 B DG 3 P ? ? B C38 10 B DG 11 1_555 ? ? ? ? ? ? ? 1.604 ? ? metalc1 metalc ? ? A DG 5 O6 ? ? ? 1_555 C K . K ? ? A DG 5 A K 104 1_555 ? ? ? ? ? ? ? 2.674 ? ? metalc2 metalc ? ? A DG 5 O6 ? ? ? 3_555 C K . K ? ? A DG 5 A K 104 1_555 ? ? ? ? ? ? ? 2.674 ? ? metalc3 metalc ? ? D HOH . O ? ? ? 1_555 C K . K ? ? A HOH 25 A K 104 1_555 ? ? ? ? ? ? ? 3.025 ? ? metalc4 metalc ? ? D HOH . O ? ? ? 3_555 C K . K ? ? A HOH 25 A K 104 1_555 ? ? ? ? ? ? ? 3.025 ? ? metalc5 metalc ? ? C K . K ? ? ? 1_555 B DG 5 O6 ? ? A K 104 B DG 13 1_555 ? ? ? ? ? ? ? 2.888 ? ? metalc6 metalc ? ? C K . K ? ? ? 1_555 B DG 5 O6 ? ? A K 104 B DG 13 3_555 ? ? ? ? ? ? ? 2.888 ? ? metalc7 metalc ? ? C K . K ? ? ? 1_555 E HOH . O ? ? A K 104 B HOH 97 1_555 ? ? ? ? ? ? ? 3.166 ? ? metalc8 metalc ? ? C K . K ? ? ? 1_555 E HOH . O ? ? A K 104 B HOH 97 3_555 ? ? ? ? ? ? ? 3.166 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 1 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 1 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 1 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C38 2 N3 ? ? ? 1_555 B DG 7 N1 ? ? A C38 2 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C38 2 N4 ? ? ? 1_555 B DG 7 O6 ? ? A C38 2 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C38 2 O2 ? ? ? 1_555 B DG 7 N2 ? ? A C38 2 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DA 6 N7 ? ? A DG 3 B DA 14 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog8 hydrog ? ? A DG 3 N3 ? ? ? 1_555 B DA 6 N6 ? ? A DG 3 B DA 14 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog9 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DG 3 N3 ? ? A DA 6 B DG 11 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog10 hydrog ? ? A DA 6 N7 ? ? ? 1_555 B DG 3 N2 ? ? A DA 6 B DG 11 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog11 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B C38 2 N3 ? ? A DG 7 B C38 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B C38 2 O2 ? ? A DG 7 B C38 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B C38 2 N4 ? ? A DG 7 B C38 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 8 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 8 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 8 B DG 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id K _struct_site.pdbx_auth_seq_id 104 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 6 _struct_site.details 'BINDING SITE FOR RESIDUE K A 104' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 DG A 5 ? DG A 5 . ? 3_555 ? 2 AC1 6 DG A 5 ? DG A 5 . ? 1_555 ? 3 AC1 6 HOH D . ? HOH A 25 . ? 3_555 ? 4 AC1 6 HOH D . ? HOH A 25 . ? 1_555 ? 5 AC1 6 DG B 5 ? DG B 13 . ? 1_555 ? 6 AC1 6 DG B 5 ? DG B 13 . ? 3_555 ? # _database_PDB_matrix.entry_id 1V3O _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 1V3O _atom_sites.fract_transf_matrix[1][1] 0.028860 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.023535 _atom_sites.fract_transf_matrix[2][3] 0.000000 _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] 0.015605 _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 I K 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 DG 1 1 1 DG G A . n A 1 2 C38 2 2 2 C38 CID A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 DG 5 5 5 DG G A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DG 7 7 7 DG G A . n A 1 8 DC 8 8 8 DC C A . n B 1 1 DG 1 9 9 DG G B . n B 1 2 C38 2 10 10 C38 CID B . n B 1 3 DG 3 11 11 DG G B . n B 1 4 DA 4 12 12 DA A B . n B 1 5 DG 5 13 13 DG G B . n B 1 6 DA 6 14 14 DA A B . n B 1 7 DG 7 15 15 DG G B . n B 1 8 DC 8 16 16 DC C B . 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 C 2 K 1 104 104 K K A . D 3 HOH 1 17 17 HOH HOH A . D 3 HOH 2 20 20 HOH HOH A . D 3 HOH 3 21 21 HOH HOH A . D 3 HOH 4 22 22 HOH HOH A . D 3 HOH 5 25 25 HOH HOH A . D 3 HOH 6 26 26 HOH HOH A . D 3 HOH 7 30 30 HOH HOH A . D 3 HOH 8 31 31 HOH HOH A . D 3 HOH 9 32 32 HOH HOH A . D 3 HOH 10 33 33 HOH HOH A . D 3 HOH 11 36 36 HOH HOH A . D 3 HOH 12 39 39 HOH HOH A . D 3 HOH 13 41 41 HOH HOH A . D 3 HOH 14 42 42 HOH HOH A . D 3 HOH 15 43 43 HOH HOH A . D 3 HOH 16 46 46 HOH HOH A . D 3 HOH 17 47 47 HOH HOH A . D 3 HOH 18 49 49 HOH HOH A . D 3 HOH 19 51 51 HOH HOH A . D 3 HOH 20 52 52 HOH HOH A . D 3 HOH 21 53 53 HOH HOH A . D 3 HOH 22 54 54 HOH HOH A . D 3 HOH 23 55 55 HOH HOH A . D 3 HOH 24 56 56 HOH HOH A . D 3 HOH 25 58 58 HOH HOH A . D 3 HOH 26 59 59 HOH HOH A . D 3 HOH 27 62 62 HOH HOH A . D 3 HOH 28 63 63 HOH HOH A . D 3 HOH 29 66 66 HOH HOH A . D 3 HOH 30 67 67 HOH HOH A . D 3 HOH 31 68 68 HOH HOH A . D 3 HOH 32 69 69 HOH HOH A . D 3 HOH 33 70 70 HOH HOH A . D 3 HOH 34 71 71 HOH HOH A . D 3 HOH 35 72 72 HOH HOH A . D 3 HOH 36 74 74 HOH HOH A . D 3 HOH 37 76 76 HOH HOH A . D 3 HOH 38 78 78 HOH HOH A . D 3 HOH 39 79 79 HOH HOH A . D 3 HOH 40 80 80 HOH HOH A . D 3 HOH 41 83 83 HOH HOH A . D 3 HOH 42 85 85 HOH HOH A . D 3 HOH 43 87 87 HOH HOH A . D 3 HOH 44 89 89 HOH HOH A . D 3 HOH 45 91 91 HOH HOH A . D 3 HOH 46 94 94 HOH HOH A . E 3 HOH 1 18 18 HOH HOH B . E 3 HOH 2 19 19 HOH HOH B . E 3 HOH 3 23 23 HOH HOH B . E 3 HOH 4 24 24 HOH HOH B . E 3 HOH 5 27 27 HOH HOH B . E 3 HOH 6 28 28 HOH HOH B . E 3 HOH 7 29 29 HOH HOH B . E 3 HOH 8 34 34 HOH HOH B . E 3 HOH 9 35 35 HOH HOH B . E 3 HOH 10 37 37 HOH HOH B . E 3 HOH 11 38 38 HOH HOH B . E 3 HOH 12 40 40 HOH HOH B . E 3 HOH 13 44 44 HOH HOH B . E 3 HOH 14 45 45 HOH HOH B . E 3 HOH 15 48 48 HOH HOH B . E 3 HOH 16 50 50 HOH HOH B . E 3 HOH 17 57 57 HOH HOH B . E 3 HOH 18 60 60 HOH HOH B . E 3 HOH 19 61 61 HOH HOH B . E 3 HOH 20 64 64 HOH HOH B . E 3 HOH 21 65 65 HOH HOH B . E 3 HOH 22 73 73 HOH HOH B . E 3 HOH 23 75 75 HOH HOH B . E 3 HOH 24 77 77 HOH HOH B . E 3 HOH 25 81 81 HOH HOH B . E 3 HOH 26 82 82 HOH HOH B . E 3 HOH 27 84 84 HOH HOH B . E 3 HOH 28 86 86 HOH HOH B . E 3 HOH 29 88 88 HOH HOH B . E 3 HOH 30 90 90 HOH HOH B . E 3 HOH 31 92 92 HOH HOH B . E 3 HOH 32 93 93 HOH HOH B . E 3 HOH 33 95 95 HOH HOH B . E 3 HOH 34 96 96 HOH HOH B . E 3 HOH 35 97 97 HOH HOH B . E 3 HOH 36 98 98 HOH HOH B . E 3 HOH 37 99 99 HOH HOH B . E 3 HOH 38 100 100 HOH HOH B . E 3 HOH 39 101 101 HOH HOH B . E 3 HOH 40 102 102 HOH HOH B . E 3 HOH 41 103 103 HOH HOH B . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A C38 2 A C38 2 ? DC ? 2 B C38 2 B C38 10 ? DC ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _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 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 3_555 -x,y,-z -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A K 104 ? C K . 2 1 B HOH 29 ? E HOH . # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O6 ? A DG 5 ? A DG 5 ? 1_555 K ? C K . ? A K 104 ? 1_555 O6 ? A DG 5 ? A DG 5 ? 3_555 62.6 ? 2 O6 ? A DG 5 ? A DG 5 ? 1_555 K ? C K . ? A K 104 ? 1_555 O ? D HOH . ? A HOH 25 ? 1_555 78.1 ? 3 O6 ? A DG 5 ? A DG 5 ? 3_555 K ? C K . ? A K 104 ? 1_555 O ? D HOH . ? A HOH 25 ? 1_555 123.0 ? 4 O6 ? A DG 5 ? A DG 5 ? 1_555 K ? C K . ? A K 104 ? 1_555 O ? D HOH . ? A HOH 25 ? 3_555 123.0 ? 5 O6 ? A DG 5 ? A DG 5 ? 3_555 K ? C K . ? A K 104 ? 1_555 O ? D HOH . ? A HOH 25 ? 3_555 78.1 ? 6 O ? D HOH . ? A HOH 25 ? 1_555 K ? C K . ? A K 104 ? 1_555 O ? D HOH . ? A HOH 25 ? 3_555 157.1 ? 7 O6 ? A DG 5 ? A DG 5 ? 1_555 K ? C K . ? A K 104 ? 1_555 O6 ? B DG 5 ? B DG 13 ? 1_555 85.0 ? 8 O6 ? A DG 5 ? A DG 5 ? 3_555 K ? C K . ? A K 104 ? 1_555 O6 ? B DG 5 ? B DG 13 ? 1_555 72.7 ? 9 O ? D HOH . ? A HOH 25 ? 1_555 K ? C K . ? A K 104 ? 1_555 O6 ? B DG 5 ? B DG 13 ? 1_555 63.8 ? 10 O ? D HOH . ? A HOH 25 ? 3_555 K ? C K . ? A K 104 ? 1_555 O6 ? B DG 5 ? B DG 13 ? 1_555 122.0 ? 11 O6 ? A DG 5 ? A DG 5 ? 1_555 K ? C K . ? A K 104 ? 1_555 O6 ? B DG 5 ? B DG 13 ? 3_555 72.7 ? 12 O6 ? A DG 5 ? A DG 5 ? 3_555 K ? C K . ? A K 104 ? 1_555 O6 ? B DG 5 ? B DG 13 ? 3_555 85.0 ? 13 O ? D HOH . ? A HOH 25 ? 1_555 K ? C K . ? A K 104 ? 1_555 O6 ? B DG 5 ? B DG 13 ? 3_555 122.0 ? 14 O ? D HOH . ? A HOH 25 ? 3_555 K ? C K . ? A K 104 ? 1_555 O6 ? B DG 5 ? B DG 13 ? 3_555 63.8 ? 15 O6 ? B DG 5 ? B DG 13 ? 1_555 K ? C K . ? A K 104 ? 1_555 O6 ? B DG 5 ? B DG 13 ? 3_555 154.0 ? 16 O6 ? A DG 5 ? A DG 5 ? 1_555 K ? C K . ? A K 104 ? 1_555 O ? E HOH . ? B HOH 97 ? 1_555 109.7 ? 17 O6 ? A DG 5 ? A DG 5 ? 3_555 K ? C K . ? A K 104 ? 1_555 O ? E HOH . ? B HOH 97 ? 1_555 148.1 ? 18 O ? D HOH . ? A HOH 25 ? 1_555 K ? C K . ? A K 104 ? 1_555 O ? E HOH . ? B HOH 97 ? 1_555 81.7 ? 19 O ? D HOH . ? A HOH 25 ? 3_555 K ? C K . ? A K 104 ? 1_555 O ? E HOH . ? B HOH 97 ? 1_555 82.5 ? 20 O6 ? B DG 5 ? B DG 13 ? 1_555 K ? C K . ? A K 104 ? 1_555 O ? E HOH . ? B HOH 97 ? 1_555 139.2 ? 21 O6 ? B DG 5 ? B DG 13 ? 3_555 K ? C K . ? A K 104 ? 1_555 O ? E HOH . ? B HOH 97 ? 1_555 63.6 ? 22 O6 ? A DG 5 ? A DG 5 ? 1_555 K ? C K . ? A K 104 ? 1_555 O ? E HOH . ? B HOH 97 ? 3_555 148.1 ? 23 O6 ? A DG 5 ? A DG 5 ? 3_555 K ? C K . ? A K 104 ? 1_555 O ? E HOH . ? B HOH 97 ? 3_555 109.7 ? 24 O ? D HOH . ? A HOH 25 ? 1_555 K ? C K . ? A K 104 ? 1_555 O ? E HOH . ? B HOH 97 ? 3_555 82.5 ? 25 O ? D HOH . ? A HOH 25 ? 3_555 K ? C K . ? A K 104 ? 1_555 O ? E HOH . ? B HOH 97 ? 3_555 81.7 ? 26 O6 ? B DG 5 ? B DG 13 ? 1_555 K ? C K . ? A K 104 ? 1_555 O ? E HOH . ? B HOH 97 ? 3_555 63.6 ? 27 O6 ? B DG 5 ? B DG 13 ? 3_555 K ? C K . ? A K 104 ? 1_555 O ? E HOH . ? B HOH 97 ? 3_555 139.2 ? 28 O ? E HOH . ? B HOH 97 ? 1_555 K ? C K . ? A K 104 ? 1_555 O ? E HOH . ? B HOH 97 ? 3_555 92.1 ? # 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 2004-06-08 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2014-04-16 5 'Structure model' 1 4 2023-10-25 # _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' 'Version format compliance' 3 4 'Structure model' Other 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' 7 5 '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 5 'Structure model' chem_comp_atom 2 5 'Structure model' chem_comp_bond 3 5 'Structure model' database_2 4 5 'Structure model' pdbx_initial_refinement_model 5 5 'Structure model' pdbx_struct_conn_angle 6 5 'Structure model' struct_conn 7 5 'Structure model' struct_site # 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 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 5 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 8 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 9 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 11 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 12 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 13 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 14 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 15 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 16 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 17 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 18 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 19 5 'Structure model' '_pdbx_struct_conn_angle.value' 20 5 'Structure model' '_struct_conn.conn_type_id' 21 5 'Structure model' '_struct_conn.id' 22 5 'Structure model' '_struct_conn.pdbx_dist_value' 23 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 24 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 25 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 26 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 27 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 28 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 29 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 30 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 31 5 'Structure model' '_struct_conn.ptnr1_symmetry' 32 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 33 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 34 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 35 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 36 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 37 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 38 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 39 5 'Structure model' '_struct_conn.ptnr2_symmetry' 40 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 41 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 42 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal d*TREK 'data scaling' . ? 1 SCALA 'data scaling' . ? 2 AMoRE phasing . ? 3 CNS refinement 1.0 ? 4 d*TREK 'data reduction' . ? 5 CCP4 'data scaling' '(SCALA)' ? 6 # 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 C38 O3P O N N 1 C38 P P N N 2 C38 O1P O N N 3 C38 O2P O N N 4 C38 "O5'" O N N 5 C38 "C5'" C N N 6 C38 "C4'" C N R 7 C38 "O4'" O N N 8 C38 "C3'" C N S 9 C38 "O3'" O N N 10 C38 "C2'" C N N 11 C38 "C1'" C N R 12 C38 N1 N N N 13 C38 C2 C N N 14 C38 O2 O N N 15 C38 N3 N N N 16 C38 C4 C N N 17 C38 N4 N N N 18 C38 C5 C N N 19 C38 C6 C N N 20 C38 I I N N 21 C38 H3P H N N 22 C38 H2P H N N 23 C38 "H5'1" H N N 24 C38 "H5'2" H N N 25 C38 "H4'" H N N 26 C38 "H3'" H N N 27 C38 HA H N N 28 C38 "H2'1" H N N 29 C38 "H2'2" H N N 30 C38 "H1'" H N N 31 C38 H4N1 H N N 32 C38 H4N2 H N N 33 C38 H6 H N N 34 DA OP3 O N N 35 DA P P N N 36 DA OP1 O N N 37 DA OP2 O N N 38 DA "O5'" O N N 39 DA "C5'" C N N 40 DA "C4'" C N R 41 DA "O4'" O N N 42 DA "C3'" C N S 43 DA "O3'" O N N 44 DA "C2'" C N N 45 DA "C1'" C N R 46 DA N9 N Y N 47 DA C8 C Y N 48 DA N7 N Y N 49 DA C5 C Y N 50 DA C6 C Y N 51 DA N6 N N N 52 DA N1 N Y N 53 DA C2 C Y N 54 DA N3 N Y N 55 DA C4 C Y N 56 DA HOP3 H N N 57 DA HOP2 H N N 58 DA "H5'" H N N 59 DA "H5''" H N N 60 DA "H4'" H N N 61 DA "H3'" H N N 62 DA "HO3'" H N N 63 DA "H2'" H N N 64 DA "H2''" H N N 65 DA "H1'" H N N 66 DA H8 H N N 67 DA H61 H N N 68 DA H62 H N N 69 DA H2 H N N 70 DC OP3 O N N 71 DC P P N N 72 DC OP1 O N N 73 DC OP2 O N N 74 DC "O5'" O N N 75 DC "C5'" C N N 76 DC "C4'" C N R 77 DC "O4'" O N N 78 DC "C3'" C N S 79 DC "O3'" O N N 80 DC "C2'" C N N 81 DC "C1'" C N R 82 DC N1 N N N 83 DC C2 C N N 84 DC O2 O N N 85 DC N3 N N N 86 DC C4 C N N 87 DC N4 N N N 88 DC C5 C N N 89 DC C6 C N N 90 DC HOP3 H N N 91 DC HOP2 H N N 92 DC "H5'" H N N 93 DC "H5''" H N N 94 DC "H4'" H N N 95 DC "H3'" H N N 96 DC "HO3'" H N N 97 DC "H2'" H N N 98 DC "H2''" H N N 99 DC "H1'" H N N 100 DC H41 H N N 101 DC H42 H N N 102 DC H5 H N N 103 DC H6 H N N 104 DG OP3 O N N 105 DG P P N N 106 DG OP1 O N N 107 DG OP2 O N N 108 DG "O5'" O N N 109 DG "C5'" C N N 110 DG "C4'" C N R 111 DG "O4'" O N N 112 DG "C3'" C N S 113 DG "O3'" O N N 114 DG "C2'" C N N 115 DG "C1'" C N R 116 DG N9 N Y N 117 DG C8 C Y N 118 DG N7 N Y N 119 DG C5 C Y N 120 DG C6 C N N 121 DG O6 O N N 122 DG N1 N N N 123 DG C2 C N N 124 DG N2 N N N 125 DG N3 N N N 126 DG C4 C Y N 127 DG HOP3 H N N 128 DG HOP2 H N N 129 DG "H5'" H N N 130 DG "H5''" H N N 131 DG "H4'" H N N 132 DG "H3'" H N N 133 DG "HO3'" H N N 134 DG "H2'" H N N 135 DG "H2''" H N N 136 DG "H1'" H N N 137 DG H8 H N N 138 DG H1 H N N 139 DG H21 H N N 140 DG H22 H N N 141 HOH O O N N 142 HOH H1 H N N 143 HOH H2 H N N 144 K K K N N 145 # 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 C38 O3P P sing N N 1 C38 O3P H3P sing N N 2 C38 P O1P doub N N 3 C38 P O2P sing N N 4 C38 P "O5'" sing N N 5 C38 O2P H2P sing N N 6 C38 "O5'" "C5'" sing N N 7 C38 "C5'" "C4'" sing N N 8 C38 "C5'" "H5'1" sing N N 9 C38 "C5'" "H5'2" sing N N 10 C38 "C4'" "O4'" sing N N 11 C38 "C4'" "C3'" sing N N 12 C38 "C4'" "H4'" sing N N 13 C38 "O4'" "C1'" sing N N 14 C38 "C3'" "O3'" sing N N 15 C38 "C3'" "C2'" sing N N 16 C38 "C3'" "H3'" sing N N 17 C38 "O3'" HA sing N N 18 C38 "C2'" "C1'" sing N N 19 C38 "C2'" "H2'1" sing N N 20 C38 "C2'" "H2'2" sing N N 21 C38 "C1'" N1 sing N N 22 C38 "C1'" "H1'" sing N N 23 C38 N1 C2 sing N N 24 C38 N1 C6 sing N N 25 C38 C2 O2 doub N N 26 C38 C2 N3 sing N N 27 C38 N3 C4 doub N N 28 C38 C4 N4 sing N N 29 C38 C4 C5 sing N N 30 C38 N4 H4N1 sing N N 31 C38 N4 H4N2 sing N N 32 C38 C5 C6 doub N N 33 C38 C5 I sing N N 34 C38 C6 H6 sing N N 35 DA OP3 P sing N N 36 DA OP3 HOP3 sing N N 37 DA P OP1 doub N N 38 DA P OP2 sing N N 39 DA P "O5'" sing N N 40 DA OP2 HOP2 sing N N 41 DA "O5'" "C5'" sing N N 42 DA "C5'" "C4'" sing N N 43 DA "C5'" "H5'" sing N N 44 DA "C5'" "H5''" sing N N 45 DA "C4'" "O4'" sing N N 46 DA "C4'" "C3'" sing N N 47 DA "C4'" "H4'" sing N N 48 DA "O4'" "C1'" sing N N 49 DA "C3'" "O3'" sing N N 50 DA "C3'" "C2'" sing N N 51 DA "C3'" "H3'" sing N N 52 DA "O3'" "HO3'" sing N N 53 DA "C2'" "C1'" sing N N 54 DA "C2'" "H2'" sing N N 55 DA "C2'" "H2''" sing N N 56 DA "C1'" N9 sing N N 57 DA "C1'" "H1'" sing N N 58 DA N9 C8 sing Y N 59 DA N9 C4 sing Y N 60 DA C8 N7 doub Y N 61 DA C8 H8 sing N N 62 DA N7 C5 sing Y N 63 DA C5 C6 sing Y N 64 DA C5 C4 doub Y N 65 DA C6 N6 sing N N 66 DA C6 N1 doub Y N 67 DA N6 H61 sing N N 68 DA N6 H62 sing N N 69 DA N1 C2 sing Y N 70 DA C2 N3 doub Y N 71 DA C2 H2 sing N N 72 DA N3 C4 sing Y N 73 DC OP3 P sing N N 74 DC OP3 HOP3 sing N N 75 DC P OP1 doub N N 76 DC P OP2 sing N N 77 DC P "O5'" sing N N 78 DC OP2 HOP2 sing N N 79 DC "O5'" "C5'" sing N N 80 DC "C5'" "C4'" sing N N 81 DC "C5'" "H5'" sing N N 82 DC "C5'" "H5''" sing N N 83 DC "C4'" "O4'" sing N N 84 DC "C4'" "C3'" sing N N 85 DC "C4'" "H4'" sing N N 86 DC "O4'" "C1'" sing N N 87 DC "C3'" "O3'" sing N N 88 DC "C3'" "C2'" sing N N 89 DC "C3'" "H3'" sing N N 90 DC "O3'" "HO3'" sing N N 91 DC "C2'" "C1'" sing N N 92 DC "C2'" "H2'" sing N N 93 DC "C2'" "H2''" sing N N 94 DC "C1'" N1 sing N N 95 DC "C1'" "H1'" sing N N 96 DC N1 C2 sing N N 97 DC N1 C6 sing N N 98 DC C2 O2 doub N N 99 DC C2 N3 sing N N 100 DC N3 C4 doub N N 101 DC C4 N4 sing N N 102 DC C4 C5 sing N N 103 DC N4 H41 sing N N 104 DC N4 H42 sing N N 105 DC C5 C6 doub N N 106 DC C5 H5 sing N N 107 DC C6 H6 sing N N 108 DG OP3 P sing N N 109 DG OP3 HOP3 sing N N 110 DG P OP1 doub N N 111 DG P OP2 sing N N 112 DG P "O5'" sing N N 113 DG OP2 HOP2 sing N N 114 DG "O5'" "C5'" sing N N 115 DG "C5'" "C4'" sing N N 116 DG "C5'" "H5'" sing N N 117 DG "C5'" "H5''" sing N N 118 DG "C4'" "O4'" sing N N 119 DG "C4'" "C3'" sing N N 120 DG "C4'" "H4'" sing N N 121 DG "O4'" "C1'" sing N N 122 DG "C3'" "O3'" sing N N 123 DG "C3'" "C2'" sing N N 124 DG "C3'" "H3'" sing N N 125 DG "O3'" "HO3'" sing N N 126 DG "C2'" "C1'" sing N N 127 DG "C2'" "H2'" sing N N 128 DG "C2'" "H2''" sing N N 129 DG "C1'" N9 sing N N 130 DG "C1'" "H1'" sing N N 131 DG N9 C8 sing Y N 132 DG N9 C4 sing Y N 133 DG C8 N7 doub Y N 134 DG C8 H8 sing N N 135 DG N7 C5 sing Y N 136 DG C5 C6 sing N N 137 DG C5 C4 doub Y N 138 DG C6 O6 doub N N 139 DG C6 N1 sing N N 140 DG N1 C2 sing N N 141 DG N1 H1 sing N N 142 DG C2 N2 sing N N 143 DG C2 N3 doub N N 144 DG N2 H21 sing N N 145 DG N2 H22 sing N N 146 DG N3 C4 sing N N 147 HOH O H1 sing N N 148 HOH O H2 sing N N 149 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1V3O 'b-form double helix' 1V3O 'mismatched base pair' 1V3O 'internal loop' # 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 1 1_555 B DC 8 1_555 -0.406 -0.153 0.178 -2.320 3.088 1.266 1 A_DG1:DC16_B A 1 ? B 16 ? 19 1 1 A C38 2 1_555 B DG 7 1_555 0.281 -0.050 -0.137 15.778 7.229 0.948 2 A_C382:DG15_B A 2 ? B 15 ? 19 1 1 A DG 3 1_555 B DA 6 1_555 6.379 -4.123 1.365 35.446 -12.617 14.482 3 A_DG3:DA14_B A 3 ? B 14 ? 11 9 1 A DA 6 1_555 B DG 3 1_555 -6.288 -4.203 1.742 -23.704 -14.916 18.192 4 A_DA6:DG11_B A 6 ? B 11 ? 11 9 1 A DG 7 1_555 B C38 2 1_555 -0.193 -0.073 -0.293 -17.800 3.390 -0.555 5 A_DG7:C3810_B A 7 ? B 10 ? 19 1 1 A DC 8 1_555 B DG 1 1_555 -0.050 -0.199 0.161 -2.851 4.111 -1.368 6 A_DC8:DG9_B A 8 ? B 9 ? 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 1 1_555 B DC 8 1_555 A C38 2 1_555 B DG 7 1_555 0.305 -0.145 2.969 1.867 3.661 26.526 -1.169 -0.219 2.937 7.917 -4.039 26.837 1 AA_DG1C382:DG15DC16_BB A 1 ? B 16 ? A 2 ? B 15 ? 1 A C38 2 1_555 B DG 7 1_555 A DG 3 1_555 B DA 6 1_555 0.143 2.084 3.136 2.907 5.905 56.386 1.868 0.010 3.324 6.226 -3.065 56.737 2 AA_C382DG3:DA14DG15_BB A 2 ? B 15 ? A 3 ? B 14 ? 1 A DA 6 1_555 B DG 3 1_555 A DG 7 1_555 B C38 2 1_555 -1.026 1.610 3.418 1.927 10.372 54.130 1.075 1.233 3.611 11.277 -2.095 55.072 3 AA_DA6DG7:C3810DG11_BB A 6 ? B 11 ? A 7 ? B 10 ? 1 A DG 7 1_555 B C38 2 1_555 A DC 8 1_555 B DG 1 1_555 -0.522 0.048 3.000 -3.445 -0.742 29.405 0.238 0.347 3.037 -1.454 6.756 29.611 4 AA_DG7DC8:DG9C3810_BB A 7 ? B 10 ? A 8 ? B 9 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'POTASSIUM ION' K 3 water 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 1V3N _pdbx_initial_refinement_model.details 'PDB ENTRY 1V3N' #