data_3C2J # _entry.id 3C2J # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.388 _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 3C2J pdb_00003c2j 10.2210/pdb3c2j/pdb NDB DD0090 ? ? RCSB RCSB046259 ? ? WWPDB D_1000046259 ? ? # 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 2008-06-03 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2024-03-13 # _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' Advisory 2 2 'Structure model' 'Refinement description' 3 2 'Structure model' 'Version format compliance' 4 3 'Structure model' 'Data collection' 5 3 'Structure model' 'Database references' 6 3 'Structure model' 'Derived calculations' # 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' struct_conn 5 3 '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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 3C2J _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.recvd_initial_deposition_date 2008-01-25 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Pfoh, R.' 1 'Sheldrick, G.M.' 2 # _citation.id primary _citation.title 'Crystal structure of trioxacarcin A covalently bound to DNA' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 36 _citation.page_first 3508 _citation.page_last 3514 _citation.year 2008 _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 18453630 _citation.pdbx_database_id_DOI 10.1093/nar/gkn245 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Pfoh, R.' 1 ? primary 'Laatsch, H.' 2 ? primary 'Sheldrick, G.M.' 3 ? # 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(*DAP*DAP*DCP*DCP*DGP*DGP*DTP*DT)-3') ; 2426.617 2 ? ? ? ? 2 non-polymer syn 'Trioxacarcin A' 876.850 2 ? ? ? ? 3 water nat water 18.015 21 ? ? ? ? # _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 '(DA)(DA)(DC)(DC)(DG)(DG)(DT)(DT)' _entity_poly.pdbx_seq_one_letter_code_can AACCGGTT _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'Trioxacarcin A' GGT 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DA n 1 3 DC n 1 4 DC n 1 5 DG n 1 6 DG n 1 7 DT n 1 8 DT 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' # 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 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 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 GGT non-polymer . 'Trioxacarcin A' ;(1S,2R,3aS,4S,8S,10S,13aS)-13a-[(4-C-acetyl-2,6-dideoxy-alpha-L-xylo-hexopyranosyl)oxy]-2-(dimethoxymethyl)-10,12-dihydroxy-7-methoxy-5-methyl-11-oxo-3a,8,9,10,11,13a-hexahydro-4H-spiro[2,4-epoxyfuro[3,2-b]naphtho[2,3-h]chromene-1,2'-oxiran]-8-yl 4-O-acetyl-2,6-dideoxy-3-C-methyl-alpha-L-xylo-hexopyranoside ; 'C42 H52 O20' 876.850 HOH non-polymer . WATER ? 'H2 O' 18.015 # 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 DA 1 1 1 DA A A . n A 1 2 DA 2 2 2 DA A A . n A 1 3 DC 3 3 3 DC C 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 DT 7 7 7 DT T A . n A 1 8 DT 8 8 8 DT T A . n B 1 1 DA 1 101 101 DA A B . n B 1 2 DA 2 102 102 DA A B . n B 1 3 DC 3 103 103 DC C B . n B 1 4 DC 4 104 104 DC C B . n B 1 5 DG 5 105 105 DG G B . n B 1 6 DG 6 106 106 DG G B . n B 1 7 DT 7 107 107 DT T B . n B 1 8 DT 8 108 108 DT T 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 GGT 1 9 9 GGT GT A . D 2 GGT 1 109 109 GGT GT B . E 3 HOH 1 201 201 HOH HOH A . E 3 HOH 2 202 202 HOH HOH A . E 3 HOH 3 203 203 HOH HOH A . E 3 HOH 4 205 205 HOH HOH A . E 3 HOH 5 206 206 HOH HOH A . E 3 HOH 6 207 207 HOH HOH A . E 3 HOH 7 208 208 HOH HOH A . E 3 HOH 8 212 212 HOH HOH A . E 3 HOH 9 213 213 HOH HOH A . E 3 HOH 10 214 214 HOH HOH A . E 3 HOH 11 215 215 HOH HOH A . E 3 HOH 12 216 216 HOH HOH A . E 3 HOH 13 218 218 HOH HOH A . E 3 HOH 14 219 219 HOH HOH A . E 3 HOH 15 220 220 HOH HOH A . F 3 HOH 1 204 204 HOH HOH B . F 3 HOH 2 209 209 HOH HOH B . F 3 HOH 3 210 210 HOH HOH B . F 3 HOH 4 211 211 HOH HOH B . F 3 HOH 5 217 217 HOH HOH B . F 3 HOH 6 221 221 HOH HOH B . # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal REFMAC 5.2.0019 ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran_77 ? 1 PDB_EXTRACT 3.004 'September 10, 2007' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 2 MAR345dtb . ? ? ? ? 'data collection' ? ? ? 3 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 4 SADABS . ? ? ? ? 'data scaling' ? ? ? 5 SHELXDE . ? ? ? ? phasing ? ? ? 6 # _cell.length_a 37.600 _cell.length_b 37.600 _cell.length_c 91.620 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 3C2J _cell.pdbx_unique_axis ? _cell.Z_PDB 16 _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.space_group_name_H-M 'P 41 2 2' _symmetry.entry_id 3C2J _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 91 _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.crystals_number 1 _exptl.entry_id 3C2J _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.5 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 50.47 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'hanging drop' _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.temp 313 _exptl_crystal_grow.pdbx_details 'tri-ammoniumcitrate, DMSO, pH 7.0, hanging drop, temperature 313K' _exptl_crystal_grow.temp_details ? _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 tri-ammoniumcitrate ? ? ? 1 2 1 DMSO ? ? ? 1 3 1 HOH ? ? ? 1 4 2 tri-ammoniumcitrate ? ? ? 1 5 2 DMSO ? ? ? 1 6 2 HOH ? ? ? # _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 'MAR CCD 165 mm' _diffrn_detector.pdbx_collection_date 2007-08-08 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.monochromator 'Si 111 double crystal' _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.92039 1.0 2 0.92032 1.0 3 0.92047 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'BESSY BEAMLINE 14.2' _diffrn_source.pdbx_wavelength_list '0.92039, 0.92032, 0.92047' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site BESSY _diffrn_source.pdbx_synchrotron_beamline 14.2 # _reflns.entry_id 3C2J _reflns.observed_criterion_sigma_F 1.0 _reflns.observed_criterion_sigma_I 1.0 _reflns.d_resolution_high 1.67 _reflns.d_resolution_low 37.6 _reflns.number_all 8306 _reflns.number_obs 8225 _reflns.percent_possible_obs 99.0 _reflns.pdbx_Rmerge_I_obs 0.039 _reflns.pdbx_Rsym_value 0.021 _reflns.pdbx_netI_over_sigmaI 27.81 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 12.5 _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 1.67 _reflns_shell.d_res_low 1.76 _reflns_shell.percent_possible_obs ? _reflns_shell.percent_possible_all 94.7 _reflns_shell.Rmerge_I_obs 0.64 _reflns_shell.meanI_over_sigI_obs 2.92 _reflns_shell.pdbx_Rsym_value 0.35 _reflns_shell.pdbx_redundancy 8.98 _reflns_shell.number_unique_all ? _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 3C2J _refine.ls_d_res_high 1.780 _refine.ls_d_res_low 25.53 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 99.820 _refine.ls_number_reflns_obs 6802 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.ls_R_factor_obs 0.222 _refine.ls_R_factor_R_work 0.220 _refine.ls_R_factor_R_free 0.265 _refine.ls_percent_reflns_R_free 4.600 _refine.ls_number_reflns_R_free 314 _refine.B_iso_mean 53.160 _refine.aniso_B[1][1] -1.010 _refine.aniso_B[2][2] -1.010 _refine.aniso_B[3][3] 2.020 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.965 _refine.correlation_coeff_Fo_to_Fc_free 0.962 _refine.pdbx_overall_ESU_R 0.127 _refine.pdbx_overall_ESU_R_Free 0.128 _refine.overall_SU_ML 0.129 _refine.overall_SU_B 8.799 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.pdbx_solvent_vdw_probe_radii 1.200 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all ? _refine.ls_R_factor_all ? _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_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_starting_model ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_data_cutoff_high_rms_absF ? _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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _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 322 _refine_hist.pdbx_number_atoms_ligand 124 _refine_hist.number_atoms_solvent 21 _refine_hist.number_atoms_total 467 _refine_hist.d_res_high 1.780 _refine_hist.d_res_low 25.53 # loop_ _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_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 500 0.016 0.021 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 180 0.002 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 780 2.490 3.000 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 468 1.566 3.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 94 0.092 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 226 0.025 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 34 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 118 0.198 0.200 ? 'X-RAY DIFFRACTION' ? r_nbd_other 227 0.246 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 244 0.257 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_other 112 0.121 0.200 ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 27 0.163 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 12 0.096 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 14 0.304 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 2 0.091 0.200 ? 'X-RAY DIFFRACTION' ? r_scbond_it 774 2.039 3.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 780 3.030 4.500 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 1.780 _refine_ls_shell.d_res_low 1.826 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 100.000 _refine_ls_shell.number_reflns_R_work 458 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.355 _refine_ls_shell.R_factor_R_free 0.415 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 30 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 488 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3C2J _struct.title 'Crystal structure analysis of trioxacarcin A covalently bound to d(AACCGGTT)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3C2J _struct_keywords.text 'DNA-drug complex, base flipping, B-DNA, DNA' _struct_keywords.pdbx_keywords 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 2 ? D N N 2 ? E N N 3 ? F N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3C2J _struct_ref.pdbx_db_accession 3C2J _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code AACCGGTT _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 3C2J A 1 ? 8 ? 3C2J 1 ? 8 ? 1 8 2 1 3C2J B 1 ? 8 ? 3C2J 101 ? 108 ? 101 108 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _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 # _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 # _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 covale1 covale none ? A DG 6 N7 ? ? ? 1_555 C GGT . C17 ? ? A DG 6 A GGT 9 1_555 ? ? ? ? ? ? ? 1.447 ? ? covale2 covale none ? B DG 6 N7 ? ? ? 1_555 D GGT . C17 ? ? B DG 106 B GGT 109 1_555 ? ? ? ? ? ? ? 1.424 ? ? hydrog1 hydrog ? ? A DA 2 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 2 B DT 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DA 2 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 2 B DT 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 3 B DG 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 3 B DG 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 3 B DG 106 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B DG 5 N1 ? ? A DC 4 B DG 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DG 5 O6 ? ? A DC 4 B DG 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 5 N2 ? ? A DC 4 B DG 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 5 B DC 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 5 B DC 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 5 B DC 104 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 6 B DC 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 6 B DC 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 6 B DC 103 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 2 N1 ? ? A DT 8 B DA 102 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 2 N6 ? ? A DT 8 B DA 102 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A GGT 9 ? 14 'BINDING SITE FOR RESIDUE GGT A 9' AC2 Software B GGT 109 ? 11 'BINDING SITE FOR RESIDUE GGT B 109' 1 ? ? ? ? ? ? ? # 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 14 DA A 1 ? DA A 1 . ? 4_574 ? 2 AC1 14 DG A 5 ? DG A 5 . ? 1_555 ? 3 AC1 14 DG A 6 ? DG A 6 . ? 1_555 ? 4 AC1 14 DT A 7 ? DT A 7 . ? 1_555 ? 5 AC1 14 DT A 8 ? DT A 8 . ? 1_555 ? 6 AC1 14 HOH E . ? HOH A 201 . ? 1_555 ? 7 AC1 14 HOH E . ? HOH A 202 . ? 1_555 ? 8 AC1 14 HOH E . ? HOH A 208 . ? 1_555 ? 9 AC1 14 HOH E . ? HOH A 215 . ? 1_555 ? 10 AC1 14 DA B 1 ? DA B 101 . ? 1_555 ? 11 AC1 14 DA B 2 ? DA B 102 . ? 1_555 ? 12 AC1 14 DC B 3 ? DC B 103 . ? 1_555 ? 13 AC1 14 DC B 4 ? DC B 104 . ? 1_555 ? 14 AC1 14 HOH F . ? HOH B 217 . ? 1_555 ? 15 AC2 11 DA A 1 ? DA A 1 . ? 6_565 ? 16 AC2 11 DA A 2 ? DA A 2 . ? 1_555 ? 17 AC2 11 DC A 3 ? DC A 3 . ? 1_555 ? 18 AC2 11 DC A 4 ? DC A 4 . ? 1_555 ? 19 AC2 11 HOH E . ? HOH A 213 . ? 8_765 ? 20 AC2 11 DG B 5 ? DG B 105 . ? 1_555 ? 21 AC2 11 DG B 6 ? DG B 106 . ? 1_555 ? 22 AC2 11 DT B 7 ? DT B 107 . ? 1_555 ? 23 AC2 11 DT B 8 ? DT B 108 . ? 1_555 ? 24 AC2 11 HOH F . ? HOH B 210 . ? 1_555 ? 25 AC2 11 HOH F . ? HOH B 211 . ? 1_555 ? # 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 N3 A DA 1 ? ? C4 A DA 1 ? ? 1.394 1.344 0.050 0.006 N 2 1 "O3'" B DG 106 ? ? "C3'" B DG 106 ? ? 1.376 1.419 -0.043 0.006 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 N1 A DA 1 ? ? C2 A DA 1 ? ? N3 A DA 1 ? ? 133.00 129.30 3.70 0.50 N 2 1 C2 A DA 1 ? ? N3 A DA 1 ? ? C4 A DA 1 ? ? 105.39 110.60 -5.21 0.50 N 3 1 C5 A DA 1 ? ? N7 A DA 1 ? ? C8 A DA 1 ? ? 100.63 103.90 -3.27 0.50 N 4 1 N1 A DA 2 ? ? C6 A DA 2 ? ? N6 A DA 2 ? ? 122.40 118.60 3.80 0.60 N 5 1 N1 A DC 3 ? ? C2 A DC 3 ? ? O2 A DC 3 ? ? 122.72 118.90 3.82 0.60 N 6 1 C2 A DC 4 ? ? N3 A DC 4 ? ? C4 A DC 4 ? ? 123.25 119.90 3.35 0.50 N 7 1 N1 A DC 4 ? ? C2 A DC 4 ? ? O2 A DC 4 ? ? 123.10 118.90 4.20 0.60 N 8 1 "O5'" A DG 5 ? ? P A DG 5 ? ? OP2 A DG 5 ? ? 99.60 105.70 -6.10 0.90 N 9 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 102.86 108.00 -5.14 0.70 N 10 1 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 99.95 108.00 -8.05 0.70 N 11 1 C2 A DG 6 ? ? N3 A DG 6 ? ? C4 A DG 6 ? ? 108.77 111.90 -3.13 0.50 N 12 1 "O4'" B DA 101 ? ? "C4'" B DA 101 ? ? "C3'" B DA 101 ? ? 101.87 104.50 -2.63 0.40 N 13 1 "C1'" B DA 101 ? ? "O4'" B DA 101 ? ? "C4'" B DA 101 ? ? 99.73 110.10 -10.37 1.00 N 14 1 "O4'" B DA 101 ? ? "C1'" B DA 101 ? ? N9 B DA 101 ? ? 113.77 108.30 5.47 0.30 N 15 1 "O4'" B DA 102 ? ? "C1'" B DA 102 ? ? N9 B DA 102 ? ? 110.19 108.30 1.89 0.30 N 16 1 C5 B DA 102 ? ? C6 B DA 102 ? ? N1 B DA 102 ? ? 114.15 117.70 -3.55 0.50 N 17 1 "C3'" B DC 103 ? ? "C2'" B DC 103 ? ? "C1'" B DC 103 ? ? 97.34 102.40 -5.06 0.80 N 18 1 C2 B DG 105 ? ? N3 B DG 105 ? ? C4 B DG 105 ? ? 108.58 111.90 -3.32 0.50 N 19 1 "O4'" B DG 106 ? ? "C1'" B DG 106 ? ? N9 B DG 106 ? ? 101.38 108.00 -6.62 0.70 N # _struct_site_keywords.site_id 1 _struct_site_keywords.text bis-intercalation # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 27.8075 _pdbx_refine_tls.origin_y 26.7001 _pdbx_refine_tls.origin_z 10.8679 _pdbx_refine_tls.T[1][1] 0.0408 _pdbx_refine_tls.T[2][2] 0.0232 _pdbx_refine_tls.T[3][3] 0.0633 _pdbx_refine_tls.T[1][2] 0.0630 _pdbx_refine_tls.T[1][3] -0.0403 _pdbx_refine_tls.T[2][3] -0.0308 _pdbx_refine_tls.L[1][1] 6.0011 _pdbx_refine_tls.L[2][2] 6.9791 _pdbx_refine_tls.L[3][3] 4.5977 _pdbx_refine_tls.L[1][2] -5.6741 _pdbx_refine_tls.L[1][3] 4.8055 _pdbx_refine_tls.L[2][3] -5.6437 _pdbx_refine_tls.S[1][1] -0.0461 _pdbx_refine_tls.S[2][2] 0.0876 _pdbx_refine_tls.S[3][3] -0.0415 _pdbx_refine_tls.S[1][2] -0.1295 _pdbx_refine_tls.S[1][3] -0.0523 _pdbx_refine_tls.S[2][3] -0.0697 _pdbx_refine_tls.S[2][1] 0.0054 _pdbx_refine_tls.S[3][1] -0.0277 _pdbx_refine_tls.S[3][2] -0.1275 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 A 1 A 8 ? . . . . ? 'X-RAY DIFFRACTION' 2 1 B 102 B 108 ? . . . . ? # 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 DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 GGT O44 O N N 144 GGT C48 C N N 145 GGT C47 C N N 146 GGT C44 C N S 147 GGT O43 O N N 148 GGT C43 C N R 149 GGT O42 O N N 150 GGT C42 C N N 151 GGT C45 C N S 152 GGT C46 C N N 153 GGT O41 O N N 154 GGT C41 C N S 155 GGT O11 O N N 156 GGT C13 C N S 157 GGT C14 C N S 158 GGT C17 C N N 159 GGT O12 O N N 160 GGT C15 C N R 161 GGT O8 O N N 162 GGT C12 C N S 163 GGT C16 C N N 164 GGT O9 O N N 165 GGT C33 C N N 166 GGT O10 O N N 167 GGT C32 C N N 168 GGT O7 O N N 169 GGT C11 C N S 170 GGT C7 C Y N 171 GGT C6 C Y N 172 GGT C31 C N N 173 GGT O6 O N N 174 GGT C8 C Y N 175 GGT C25 C Y N 176 GGT C26 C Y N 177 GGT C5 C Y N 178 GGT C10 C Y N 179 GGT O4 O N N 180 GGT C30 C N N 181 GGT C28 C Y N 182 GGT C27 C Y N 183 GGT C9 C Y N 184 GGT O5 O N N 185 GGT C4 C N S 186 GGT C3 C N N 187 GGT C2 C N S 188 GGT O2 O N N 189 GGT C1 C N N 190 GGT O3 O N N 191 GGT O1 O N N 192 GGT "C1'" C N R 193 GGT "O1'" O N N 194 GGT "C5'" C N S 195 GGT "C9'" C N N 196 GGT "C4'" C N R 197 GGT "C3'" C N R 198 GGT "O2'" O N N 199 GGT "C8'" C N N 200 GGT "C2'" C N N 201 GGT "O3'" O N N 202 GGT "C6'" C N N 203 GGT "O4'" O N N 204 GGT "C7'" C N N 205 GGT H47 H N N 206 GGT H47A H N N 207 GGT H47B H N N 208 GGT HO43 H N N 209 GGT H43 H N N 210 GGT HO42 H N N 211 GGT H42 H N N 212 GGT H42A H N N 213 GGT H45 H N N 214 GGT H46 H N N 215 GGT H46A H N N 216 GGT H46B H N N 217 GGT H41 H N N 218 GGT H17 H N N 219 GGT H17A H N N 220 GGT H12 H N N 221 GGT H16 H N N 222 GGT H33 H N N 223 GGT H33A H N N 224 GGT H33B H N N 225 GGT H32 H N N 226 GGT H32A H N N 227 GGT H32B H N N 228 GGT H11 H N N 229 GGT H31 H N N 230 GGT H31A H N N 231 GGT H31B H N N 232 GGT H5 H N N 233 GGT H30 H N N 234 GGT H30A H N N 235 GGT H30B H N N 236 GGT HO5 H N N 237 GGT H4 H N N 238 GGT H3 H N N 239 GGT H3A H N N 240 GGT H2 H N N 241 GGT HO2 H N N 242 GGT "H1'" H N N 243 GGT "H5'" H N N 244 GGT "H9'" H N N 245 GGT "H9'A" H N N 246 GGT "H9'B" H N N 247 GGT "H4'" H N N 248 GGT "HO2'" H N N 249 GGT "H8'" H N N 250 GGT "H8'A" H N N 251 GGT "H8'B" H N N 252 GGT "H2'" H N N 253 GGT "H2'A" H N N 254 GGT "H7'" H N N 255 GGT "H7'A" H N N 256 GGT "H7'B" H N N 257 HOH O O N N 258 HOH H1 H N N 259 HOH H2 H N N 260 # 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 DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 GGT O44 C48 doub N N 150 GGT C48 C47 sing N N 151 GGT C48 C44 sing N N 152 GGT C44 O43 sing N N 153 GGT C44 C43 sing N N 154 GGT C44 C45 sing N N 155 GGT C43 O42 sing N N 156 GGT C43 C42 sing N N 157 GGT C42 C41 sing N N 158 GGT C45 C46 sing N N 159 GGT C45 O41 sing N N 160 GGT O41 C41 sing N N 161 GGT C41 O11 sing N N 162 GGT O11 C13 sing N N 163 GGT C13 C14 sing N N 164 GGT C13 C12 sing N N 165 GGT C13 O6 sing N N 166 GGT C14 C17 sing N N 167 GGT C14 O12 sing N N 168 GGT C14 C15 sing N N 169 GGT C15 O8 sing N N 170 GGT C15 C16 sing N N 171 GGT C15 O7 sing N N 172 GGT O8 C12 sing N N 173 GGT C12 C11 sing N N 174 GGT C16 O9 sing N N 175 GGT C16 O10 sing N N 176 GGT O9 C33 sing N N 177 GGT O10 C32 sing N N 178 GGT O7 C11 sing N N 179 GGT C11 C7 sing N N 180 GGT C7 C6 doub Y N 181 GGT C7 C8 sing Y N 182 GGT C6 C31 sing N N 183 GGT C6 C5 sing Y N 184 GGT O6 C8 sing N N 185 GGT C8 C25 doub Y N 186 GGT C25 C26 sing Y N 187 GGT C25 C9 sing Y N 188 GGT C26 C5 doub Y N 189 GGT C26 C10 sing Y N 190 GGT C10 O4 sing N N 191 GGT C10 C28 doub Y N 192 GGT O4 C30 sing N N 193 GGT C28 C27 sing Y N 194 GGT C28 C4 sing N N 195 GGT C27 C9 doub Y N 196 GGT C27 C1 sing N N 197 GGT C9 O5 sing N N 198 GGT C4 C3 sing N N 199 GGT C4 O1 sing N N 200 GGT C3 C2 sing N N 201 GGT C2 O2 sing N N 202 GGT C2 C1 sing N N 203 GGT C1 O3 doub N N 204 GGT O1 "C1'" sing N N 205 GGT "C1'" "O1'" sing N N 206 GGT "C1'" "C2'" sing N N 207 GGT "O1'" "C5'" sing N N 208 GGT "C5'" "C9'" sing N N 209 GGT "C5'" "C4'" sing N N 210 GGT "C4'" "C3'" sing N N 211 GGT "C4'" "O3'" sing N N 212 GGT "C3'" "O2'" sing N N 213 GGT "C3'" "C8'" sing N N 214 GGT "C3'" "C2'" sing N N 215 GGT "O3'" "C6'" sing N N 216 GGT "C6'" "O4'" doub N N 217 GGT "C6'" "C7'" sing N N 218 GGT O12 C17 sing N N 219 GGT C47 H47 sing N N 220 GGT C47 H47A sing N N 221 GGT C47 H47B sing N N 222 GGT O43 HO43 sing N N 223 GGT C43 H43 sing N N 224 GGT O42 HO42 sing N N 225 GGT C42 H42 sing N N 226 GGT C42 H42A sing N N 227 GGT C45 H45 sing N N 228 GGT C46 H46 sing N N 229 GGT C46 H46A sing N N 230 GGT C46 H46B sing N N 231 GGT C41 H41 sing N N 232 GGT C17 H17 sing N N 233 GGT C17 H17A sing N N 234 GGT C12 H12 sing N N 235 GGT C16 H16 sing N N 236 GGT C33 H33 sing N N 237 GGT C33 H33A sing N N 238 GGT C33 H33B sing N N 239 GGT C32 H32 sing N N 240 GGT C32 H32A sing N N 241 GGT C32 H32B sing N N 242 GGT C11 H11 sing N N 243 GGT C31 H31 sing N N 244 GGT C31 H31A sing N N 245 GGT C31 H31B sing N N 246 GGT C5 H5 sing N N 247 GGT C30 H30 sing N N 248 GGT C30 H30A sing N N 249 GGT C30 H30B sing N N 250 GGT O5 HO5 sing N N 251 GGT C4 H4 sing N N 252 GGT C3 H3 sing N N 253 GGT C3 H3A sing N N 254 GGT C2 H2 sing N N 255 GGT O2 HO2 sing N N 256 GGT "C1'" "H1'" sing N N 257 GGT "C5'" "H5'" sing N N 258 GGT "C9'" "H9'" sing N N 259 GGT "C9'" "H9'A" sing N N 260 GGT "C9'" "H9'B" sing N N 261 GGT "C4'" "H4'" sing N N 262 GGT "O2'" "HO2'" sing N N 263 GGT "C8'" "H8'" sing N N 264 GGT "C8'" "H8'A" sing N N 265 GGT "C8'" "H8'B" sing N N 266 GGT "C2'" "H2'" sing N N 267 GGT "C2'" "H2'A" sing N N 268 GGT "C7'" "H7'" sing N N 269 GGT "C7'" "H7'A" sing N N 270 GGT "C7'" "H7'B" sing N N 271 HOH O H1 sing N N 272 HOH O H2 sing N N 273 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3C2J 'double helix' 3C2J '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 DA 2 1_555 B DT 8 1_555 -0.162 -0.118 0.192 8.648 -9.458 10.098 1 A_DA2:DT108_B A 2 ? B 108 ? 20 1 1 A DC 3 1_555 B DG 6 1_555 0.350 -0.250 -0.172 -9.736 10.585 -2.427 2 A_DC3:DG106_B A 3 ? B 106 ? 19 1 1 A DC 4 1_555 B DG 5 1_555 0.304 -0.203 0.176 -3.129 -4.271 -3.178 3 A_DC4:DG105_B A 4 ? B 105 ? 19 1 1 A DG 5 1_555 B DC 4 1_555 -0.321 -0.181 0.176 2.353 -0.923 -1.072 4 A_DG5:DC104_B A 5 ? B 104 ? 19 1 1 A DG 6 1_555 B DC 3 1_555 -0.169 -0.251 -0.012 12.481 5.469 0.076 5 A_DG6:DC103_B A 6 ? B 103 ? 19 1 1 A DT 8 1_555 B DA 2 1_555 0.106 -0.119 0.030 -6.684 -6.067 7.861 6 A_DT8:DA102_B A 8 ? B 102 ? 20 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 DA 2 1_555 B DT 8 1_555 A DC 3 1_555 B DG 6 1_555 -0.039 2.023 6.769 -11.919 7.380 45.914 1.249 -1.959 6.808 9.211 14.876 47.895 1 AA_DA2DC3:DG106DT108_BB A 2 ? B 108 ? A 3 ? B 106 ? 1 A DC 3 1_555 B DG 6 1_555 A DC 4 1_555 B DG 5 1_555 -1.019 0.768 3.290 -4.188 0.182 35.094 1.238 1.045 3.389 0.300 6.915 35.335 2 AA_DC3DC4:DG105DG106_BB A 3 ? B 106 ? A 4 ? B 105 ? 1 A DC 4 1_555 B DG 5 1_555 A DG 5 1_555 B DC 4 1_555 0.276 0.451 3.174 -0.115 0.990 39.647 0.552 -0.420 3.183 1.460 0.170 39.659 3 AA_DC4DG5:DC104DG105_BB A 4 ? B 105 ? A 5 ? B 104 ? 1 A DG 5 1_555 B DC 4 1_555 A DG 6 1_555 B DC 3 1_555 0.497 0.804 3.194 3.302 -0.018 36.648 1.276 -0.345 3.225 -0.029 -5.238 36.792 4 AA_DG5DG6:DC103DC104_BB A 5 ? B 104 ? A 6 ? B 103 ? 1 A DG 6 1_555 B DC 3 1_555 A DT 8 1_555 B DA 2 1_555 -0.032 2.245 6.904 11.810 2.131 43.044 2.541 2.352 6.768 2.839 -15.734 44.609 5 AA_DG6DT8:DA102DC103_BB A 6 ? B 103 ? A 8 ? B 102 ? # _atom_sites.entry_id 3C2J _atom_sites.fract_transf_matrix[1][1] 0.026596 _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] 0.026596 _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] 0.010915 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O P # loop_