data_1YB9 # _entry.id 1YB9 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.376 _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 1YB9 pdb_00001yb9 10.2210/pdb1yb9/pdb NDB AD0043 ? ? RCSB RCSB031335 ? ? WWPDB D_1000031335 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1Y7F ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-[hydroxy(methyleneamino)oxy]ethyl] Thymidine (T*) ; unspecified PDB 1Y84 ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(imidazolyl)ethyl] Thymidine (T*) ; unspecified PDB 1Y86 ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(fluoro)ethyl] Thymidine (T*) ; unspecified PDB 1Y8L ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(trifluoro)ethyl] Thymidine (T*) ; unspecified PDB 1Y8V ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-propyl Thymidine (T*) ; unspecified PDB 1WV5 ;X-RAY STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-BUTYL THYMINE IN PLACE OF T6, MG-FORM ; unspecified PDB 1WV6 ;X-RAY STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-BUTYL THYMINE IN PLACE OF T6, SR-FORM ; unspecified PDB 1Y9F ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-allyl Thymidine (T*) ; unspecified PDB 1Y9S ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-propargyl Thymidine (T*) ; unspecified PDB 1YBC ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(benzyloxy)ethyl] Thymidine (T*) ; unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1YB9 _pdbx_database_status.recvd_initial_deposition_date 2004-12-20 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _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 'Egli, M.' 1 'Minasov, G.' 2 'Tereshko, V.' 3 'Pallan, P.S.' 4 'Teplova, M.' 5 'Inamati, G.B.' 6 'Lesnik, E.A.' 7 'Owens, S.R.' 8 'Ross, B.S.' 9 'Prakash, T.P.' 10 'Manoharan, M.' 11 # _citation.id primary _citation.title ;Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of Ten 2'-O-Ribonucleic Acid Modifications. ; _citation.journal_abbrev Biochemistry _citation.journal_volume 44 _citation.page_first 9045 _citation.page_last 9057 _citation.year 2005 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15966728 _citation.pdbx_database_id_DOI 10.1021/bi050574m # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Egli, M.' 1 ? primary 'Minasov, G.' 2 ? primary 'Tereshko, V.' 3 ? primary 'Pallan, P.S.' 4 ? primary 'Teplova, M.' 5 ? primary 'Inamati, G.B.' 6 ? primary 'Lesnik, E.A.' 7 ? primary 'Owens, S.R.' 8 ? primary 'Ross, B.S.' 9 ? primary 'Prakash, T.P.' 10 ? primary 'Manoharan, M.' 11 ? # _cell.entry_id 1YB9 _cell.length_a 24.840 _cell.length_b 44.640 _cell.length_c 45.180 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YB9 _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _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*CP*GP*TP*AP*(2OT)P*AP*CP*GP*C)-3')" 3148.125 2 ? ? ? ? 2 non-polymer syn SPERMINE 202.340 1 ? ? ? ? 3 water nat water 18.015 124 ? ? ? ? # _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)(DC)(DG)(DT)(DA)(2OT)(DA)(DC)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCGTATACGC _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 DC n 1 3 DG n 1 4 DT n 1 5 DA n 1 6 2OT n 1 7 DA n 1 8 DC n 1 9 DG n 1 10 DC n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1YB9 _struct_ref.pdbx_db_accession 1YB9 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1YB9 A 1 ? 10 ? 1YB9 1 ? 10 ? 1 10 2 1 1YB9 B 1 ? 10 ? 1YB9 11 ? 20 ? 11 20 # 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 2OT 'RNA linking' n ;2'-O-[2-(N,N-DIMETHYLAMINOOXY)ETHYL] THYMIDINE-5'-MONOPHOSPHATE ; ? 'C14 H24 N3 O10 P' 425.328 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 HOH non-polymer . WATER ? 'H2 O' 18.015 SPM non-polymer . SPERMINE ? 'C10 H26 N4' 202.340 # _exptl.entry_id 1YB9 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.99 _exptl_crystal.density_percent_sol 38.17 _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 295 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pdbx_details '10%MPD, 40mM Na-Cacodilate, 12 mM Spermine, 80mM NaCL, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K' _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 MPD ? ? ? 1 2 1 Na-Cacodilate ? ? ? 1 3 1 Spermine ? ? ? 1 4 1 NaCL ? ? ? 1 5 1 H2O ? ? ? 1 6 2 MPD ? ? ? 1 7 2 Na-Cacodilate ? ? ? 1 8 2 NaCL ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 110 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IIC' _diffrn_detector.pdbx_collection_date 1999-08-03 _diffrn_detector.details Mirrors # _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 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1YB9 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I -3.0 _reflns.d_resolution_high 1.65 _reflns.d_resolution_low 20.0 _reflns.number_all 6146 _reflns.number_obs 6146 _reflns.percent_possible_obs 95.4 _reflns.pdbx_Rmerge_I_obs 0.102 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 17.4 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.5 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.65 _reflns_shell.d_res_low 1.71 _reflns_shell.percent_possible_all 70.7 _reflns_shell.Rmerge_I_obs 0.175 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 6.1 _reflns_shell.pdbx_redundancy 2.7 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 442 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1YB9 _refine.ls_d_res_high 1.65 _refine.ls_d_res_low 20.0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 6099 _refine.ls_number_reflns_obs 6099 _refine.ls_number_reflns_R_free 672 _refine.ls_percent_reflns_obs 94.9 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.1632 _refine.ls_R_factor_R_free 0.1906 _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 410D' _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details Random _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values ? _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 Isotropic _refine.B_iso_mean 19.0 _refine.aniso_B[1][1] -0.559 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][2] 1.014 _refine.aniso_B[2][3] 0.000 _refine.aniso_B[3][3] -0.456 _refine.details 'Conjugate gradient refinement using maximum likelihood target for amplitudes' _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.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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _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 1YB9 _refine_analyze.Luzzati_coordinate_error_obs 0.16 _refine_analyze.Luzzati_sigma_a_obs 0.04 _refine_analyze.Luzzati_d_res_low_obs 5.0 _refine_analyze.Luzzati_coordinate_error_free 0.19 _refine_analyze.Luzzati_sigma_a_free 0.09 _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 418 _refine_hist.pdbx_number_atoms_ligand 18 _refine_hist.number_atoms_solvent 131 _refine_hist.number_atoms_total 567 _refine_hist.d_res_high 1.65 _refine_hist.d_res_low 20.0 # 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 0.008 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.20 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 26.8 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.53 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 1.65 _refine_ls_shell.d_res_low 1.71 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.2042 _refine_ls_shell.percent_reflns_obs 67.46 _refine_ls_shell.R_factor_R_free 0.2389 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 55 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 1YB9 _struct.title ;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(N,N-dimethylaminooxy)ethyl] Thymidine (T*) ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1YB9 _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;A-DNA, O2'-modification, decamer, 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 3 ? E N N 3 ? # _struct_biol.id 1 _struct_biol.details 'Chains A and B form duplex' _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 DA 5 "O3'" ? ? ? 1_555 A 2OT 6 P ? ? A DA 5 A 2OT 6 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale2 covale both ? A 2OT 6 "O3'" ? ? ? 1_555 A DA 7 P ? ? A 2OT 6 A DA 7 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale3 covale both ? B DA 5 "O3'" ? ? ? 1_555 B 2OT 6 P ? ? B DA 15 B 2OT 16 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale4 covale both ? B 2OT 6 "O3'" ? ? ? 1_555 B DA 7 P ? ? B 2OT 16 B DA 17 1_555 ? ? ? ? ? ? ? 1.603 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B 2OT 6 N3 ? ? A DA 5 B 2OT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B 2OT 6 O4 ? ? A DA 5 B 2OT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A 2OT 6 N3 ? ? ? 1_555 B DA 5 N1 ? ? A 2OT 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A 2OT 6 O4 ? ? ? 1_555 B DA 5 N6 ? ? A 2OT 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id B _struct_site.pdbx_auth_comp_id SPM _struct_site.pdbx_auth_seq_id 100 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 14 _struct_site.details 'BINDING SITE FOR RESIDUE SPM B 100' # 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 DG A 9 ? DG A 9 . ? 2_555 ? 2 AC1 14 DC A 10 ? DC A 10 . ? 2_555 ? 3 AC1 14 HOH D . ? HOH A 139 . ? 1_655 ? 4 AC1 14 HOH D . ? HOH A 160 . ? 2_555 ? 5 AC1 14 HOH D . ? HOH A 167 . ? 4_556 ? 6 AC1 14 DT B 4 ? DT B 14 . ? 3_655 ? 7 AC1 14 DA B 5 ? DA B 15 . ? 3_655 ? 8 AC1 14 DG B 9 ? DG B 19 . ? 1_555 ? 9 AC1 14 DC B 10 ? DC B 20 . ? 1_555 ? 10 AC1 14 HOH E . ? HOH B 124 . ? 3_655 ? 11 AC1 14 HOH E . ? HOH B 140 . ? 1_555 ? 12 AC1 14 HOH E . ? HOH B 166 . ? 1_555 ? 13 AC1 14 HOH E . ? HOH B 187 . ? 1_555 ? 14 AC1 14 HOH E . ? HOH B 200 . ? 1_555 ? # _database_PDB_matrix.entry_id 1YB9 _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 1YB9 _atom_sites.fract_transf_matrix[1][1] 0.040258 _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] 0.022401 _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] 0.022134 _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 DG 1 1 1 DG G A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 2OT 6 6 6 2OT DMA A . n A 1 7 DA 7 7 7 DA A 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 DG 1 11 11 DG G B . n B 1 2 DC 2 12 12 DC C B . n B 1 3 DG 3 13 13 DG G B . n B 1 4 DT 4 14 14 DT T B . n B 1 5 DA 5 15 15 DA A B . n B 1 6 2OT 6 16 16 2OT DMA B . n B 1 7 DA 7 17 17 DA A B . n B 1 8 DC 8 18 18 DC C B . n B 1 9 DG 9 19 19 DG G B . n B 1 10 DC 10 20 20 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 SPM 1 100 100 SPM SPM B . D 3 HOH 1 101 101 HOH HOH A . D 3 HOH 2 102 102 HOH HOH A . D 3 HOH 3 104 104 HOH HOH A . D 3 HOH 4 107 107 HOH HOH A . D 3 HOH 5 109 109 HOH HOH A . D 3 HOH 6 110 110 HOH HOH A . D 3 HOH 7 111 111 HOH HOH A . D 3 HOH 8 116 116 HOH HOH A . D 3 HOH 9 117 117 HOH HOH A . D 3 HOH 10 118 118 HOH HOH A . D 3 HOH 11 119 119 HOH HOH A . D 3 HOH 12 121 121 HOH HOH A . D 3 HOH 13 123 123 HOH HOH A . D 3 HOH 14 125 125 HOH HOH A . D 3 HOH 15 128 128 HOH HOH A . D 3 HOH 16 132 132 HOH HOH A . D 3 HOH 17 133 133 HOH HOH A . D 3 HOH 18 134 134 HOH HOH A . D 3 HOH 19 135 135 HOH HOH A . D 3 HOH 20 136 136 HOH HOH A . D 3 HOH 21 137 137 HOH HOH A . D 3 HOH 22 139 139 HOH HOH A . D 3 HOH 23 141 141 HOH HOH A . D 3 HOH 24 142 142 HOH HOH A . D 3 HOH 25 145 145 HOH HOH A . D 3 HOH 26 146 146 HOH HOH A . D 3 HOH 27 147 147 HOH HOH A . D 3 HOH 28 149 149 HOH HOH A . D 3 HOH 29 151 151 HOH HOH A . D 3 HOH 30 152 152 HOH HOH A . D 3 HOH 31 157 157 HOH HOH A . D 3 HOH 32 158 158 HOH HOH A . D 3 HOH 33 160 160 HOH HOH A . D 3 HOH 34 164 164 HOH HOH A . D 3 HOH 35 167 167 HOH HOH A . D 3 HOH 36 168 168 HOH HOH A . D 3 HOH 37 172 172 HOH HOH A . D 3 HOH 38 173 173 HOH HOH A . D 3 HOH 39 174 174 HOH HOH A . D 3 HOH 40 176 176 HOH HOH A . D 3 HOH 41 177 177 HOH HOH A . D 3 HOH 42 178 178 HOH HOH A . D 3 HOH 43 180 180 HOH HOH A . D 3 HOH 44 183 183 HOH HOH A . D 3 HOH 45 185 185 HOH HOH A . D 3 HOH 46 186 186 HOH HOH A . D 3 HOH 47 189 189 HOH HOH A . D 3 HOH 48 190 190 HOH HOH A . D 3 HOH 49 194 194 HOH HOH A . D 3 HOH 50 196 196 HOH HOH A . D 3 HOH 51 197 197 HOH HOH A . D 3 HOH 52 198 198 HOH HOH A . D 3 HOH 53 201 201 HOH HOH A . D 3 HOH 54 204 204 HOH HOH A . D 3 HOH 55 205 205 HOH HOH A . D 3 HOH 56 207 207 HOH HOH A . D 3 HOH 57 208 208 HOH HOH A . D 3 HOH 58 209 209 HOH HOH A . D 3 HOH 59 211 211 HOH HOH A . D 3 HOH 60 212 212 HOH HOH A . D 3 HOH 61 215 215 HOH HOH A . D 3 HOH 62 216 216 HOH HOH A . D 3 HOH 63 217 217 HOH HOH A . D 3 HOH 64 218 218 HOH HOH A . D 3 HOH 65 221 221 HOH HOH A . D 3 HOH 66 223 223 HOH HOH A . D 3 HOH 67 224 224 HOH HOH A . E 3 HOH 1 103 103 HOH HOH B . E 3 HOH 2 105 105 HOH HOH B . E 3 HOH 3 106 106 HOH HOH B . E 3 HOH 4 108 108 HOH HOH B . E 3 HOH 5 112 112 HOH HOH B . E 3 HOH 6 113 113 HOH HOH B . E 3 HOH 7 114 114 HOH HOH B . E 3 HOH 8 115 115 HOH HOH B . E 3 HOH 9 120 120 HOH HOH B . E 3 HOH 10 122 122 HOH HOH B . E 3 HOH 11 124 124 HOH HOH B . E 3 HOH 12 126 126 HOH HOH B . E 3 HOH 13 127 127 HOH HOH B . E 3 HOH 14 129 129 HOH HOH B . E 3 HOH 15 130 130 HOH HOH B . E 3 HOH 16 131 131 HOH HOH B . E 3 HOH 17 138 138 HOH HOH B . E 3 HOH 18 140 140 HOH HOH B . E 3 HOH 19 143 143 HOH HOH B . E 3 HOH 20 144 144 HOH HOH B . E 3 HOH 21 148 148 HOH HOH B . E 3 HOH 22 150 150 HOH HOH B . E 3 HOH 23 153 153 HOH HOH B . E 3 HOH 24 154 154 HOH HOH B . E 3 HOH 25 155 155 HOH HOH B . E 3 HOH 26 156 156 HOH HOH B . E 3 HOH 27 159 159 HOH HOH B . E 3 HOH 28 161 161 HOH HOH B . E 3 HOH 29 162 162 HOH HOH B . E 3 HOH 30 163 163 HOH HOH B . E 3 HOH 31 165 165 HOH HOH B . E 3 HOH 32 166 166 HOH HOH B . E 3 HOH 33 169 169 HOH HOH B . E 3 HOH 34 170 170 HOH HOH B . E 3 HOH 35 171 171 HOH HOH B . E 3 HOH 36 175 175 HOH HOH B . E 3 HOH 37 179 179 HOH HOH B . E 3 HOH 38 181 181 HOH HOH B . E 3 HOH 39 182 182 HOH HOH B . E 3 HOH 40 184 184 HOH HOH B . E 3 HOH 41 187 187 HOH HOH B . E 3 HOH 42 188 188 HOH HOH B . E 3 HOH 43 191 191 HOH HOH B . E 3 HOH 44 192 192 HOH HOH B . E 3 HOH 45 193 193 HOH HOH B . E 3 HOH 46 195 195 HOH HOH B . E 3 HOH 47 199 199 HOH HOH B . E 3 HOH 48 200 200 HOH HOH B . E 3 HOH 49 202 202 HOH HOH B . E 3 HOH 50 203 203 HOH HOH B . E 3 HOH 51 206 206 HOH HOH B . E 3 HOH 52 210 210 HOH HOH B . E 3 HOH 53 213 213 HOH HOH B . E 3 HOH 54 214 214 HOH HOH B . E 3 HOH 55 219 219 HOH HOH B . E 3 HOH 56 220 220 HOH HOH B . E 3 HOH 57 222 222 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 2OT 6 A 2OT 6 ? DT ? 2 B 2OT 6 B 2OT 16 ? DT ? # _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 # _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 2005-06-28 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-08-23 # _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' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 '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 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_initial_refinement_model 5 4 'Structure model' struct_conn 6 4 '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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 AMoRE phasing . ? 3 CNS refinement . ? 4 # 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 2OT P P N N 1 2OT OP1 O N N 2 2OT OP2 O N N 3 2OT "O5'" O N N 4 2OT "C5'" C N N 5 2OT "C4'" C N R 6 2OT "O4'" O N N 7 2OT "C1'" C N R 8 2OT N1 N N N 9 2OT C6 C N N 10 2OT C2 C N N 11 2OT O2 O N N 12 2OT N3 N N N 13 2OT C4 C N N 14 2OT O4 O N N 15 2OT C5 C N N 16 2OT C5M C N N 17 2OT "C2'" C N R 18 2OT "O2'" O N N 19 2OT "CB'" C N N 20 2OT "CC'" C N N 21 2OT "OD'" O N N 22 2OT "NE'" N N N 23 2OT "CF'" C N N 24 2OT "CG'" C N N 25 2OT "C3'" C N R 26 2OT "O3'" O N N 27 2OT OP3 O N N 28 2OT HOP2 H N N 29 2OT "H5'" H N N 30 2OT "H5''" H N N 31 2OT "H4'" H N N 32 2OT "H1'" H N N 33 2OT H6 H N N 34 2OT HN3 H N N 35 2OT H71 H N N 36 2OT H72 H N N 37 2OT H73 H N N 38 2OT "H2'" H N N 39 2OT "HB'1" H N N 40 2OT "HB'2" H N N 41 2OT "HC'1" H N N 42 2OT "HC'2" H N N 43 2OT "HF'1" H N N 44 2OT "HF'2" H N N 45 2OT "HF'3" H N N 46 2OT "HG'1" H N N 47 2OT "HG'2" H N N 48 2OT "HG'3" H N N 49 2OT "H3'" H N N 50 2OT "HO3'" H N N 51 2OT HOP3 H N N 52 DA OP3 O N N 53 DA P P N N 54 DA OP1 O N N 55 DA OP2 O N N 56 DA "O5'" O N N 57 DA "C5'" C N N 58 DA "C4'" C N R 59 DA "O4'" O N N 60 DA "C3'" C N S 61 DA "O3'" O N N 62 DA "C2'" C N N 63 DA "C1'" C N R 64 DA N9 N Y N 65 DA C8 C Y N 66 DA N7 N Y N 67 DA C5 C Y N 68 DA C6 C Y N 69 DA N6 N N N 70 DA N1 N Y N 71 DA C2 C Y N 72 DA N3 N Y N 73 DA C4 C Y N 74 DA HOP3 H N N 75 DA HOP2 H N N 76 DA "H5'" H N N 77 DA "H5''" H N N 78 DA "H4'" H N N 79 DA "H3'" H N N 80 DA "HO3'" H N N 81 DA "H2'" H N N 82 DA "H2''" H N N 83 DA "H1'" H N N 84 DA H8 H N N 85 DA H61 H N N 86 DA H62 H N N 87 DA H2 H N N 88 DC OP3 O N N 89 DC P P N N 90 DC OP1 O N N 91 DC OP2 O N N 92 DC "O5'" O N N 93 DC "C5'" C N N 94 DC "C4'" C N R 95 DC "O4'" O N N 96 DC "C3'" C N S 97 DC "O3'" O N N 98 DC "C2'" C N N 99 DC "C1'" C N R 100 DC N1 N N N 101 DC C2 C N N 102 DC O2 O N N 103 DC N3 N N N 104 DC C4 C N N 105 DC N4 N N N 106 DC C5 C N N 107 DC C6 C N N 108 DC HOP3 H N N 109 DC HOP2 H N N 110 DC "H5'" H N N 111 DC "H5''" H N N 112 DC "H4'" H N N 113 DC "H3'" H N N 114 DC "HO3'" H N N 115 DC "H2'" H N N 116 DC "H2''" H N N 117 DC "H1'" H N N 118 DC H41 H N N 119 DC H42 H N N 120 DC H5 H N N 121 DC H6 H N N 122 DG OP3 O N N 123 DG P P N N 124 DG OP1 O N N 125 DG OP2 O N N 126 DG "O5'" O N N 127 DG "C5'" C N N 128 DG "C4'" C N R 129 DG "O4'" O N N 130 DG "C3'" C N S 131 DG "O3'" O N N 132 DG "C2'" C N N 133 DG "C1'" C N R 134 DG N9 N Y N 135 DG C8 C Y N 136 DG N7 N Y N 137 DG C5 C Y N 138 DG C6 C N N 139 DG O6 O N N 140 DG N1 N N N 141 DG C2 C N N 142 DG N2 N N N 143 DG N3 N N N 144 DG C4 C Y N 145 DG HOP3 H N N 146 DG HOP2 H N N 147 DG "H5'" H N N 148 DG "H5''" H N N 149 DG "H4'" H N N 150 DG "H3'" H N N 151 DG "HO3'" H N N 152 DG "H2'" H N N 153 DG "H2''" H N N 154 DG "H1'" H N N 155 DG H8 H N N 156 DG H1 H N N 157 DG H21 H N N 158 DG H22 H N N 159 DT OP3 O N N 160 DT P P N N 161 DT OP1 O N N 162 DT OP2 O N N 163 DT "O5'" O N N 164 DT "C5'" C N N 165 DT "C4'" C N R 166 DT "O4'" O N N 167 DT "C3'" C N S 168 DT "O3'" O N N 169 DT "C2'" C N N 170 DT "C1'" C N R 171 DT N1 N N N 172 DT C2 C N N 173 DT O2 O N N 174 DT N3 N N N 175 DT C4 C N N 176 DT O4 O N N 177 DT C5 C N N 178 DT C7 C N N 179 DT C6 C N N 180 DT HOP3 H N N 181 DT HOP2 H N N 182 DT "H5'" H N N 183 DT "H5''" H N N 184 DT "H4'" H N N 185 DT "H3'" H N N 186 DT "HO3'" H N N 187 DT "H2'" H N N 188 DT "H2''" H N N 189 DT "H1'" H N N 190 DT H3 H N N 191 DT H71 H N N 192 DT H72 H N N 193 DT H73 H N N 194 DT H6 H N N 195 HOH O O N N 196 HOH H1 H N N 197 HOH H2 H N N 198 SPM N1 N N N 199 SPM C2 C N N 200 SPM C3 C N N 201 SPM C4 C N N 202 SPM N5 N N N 203 SPM C6 C N N 204 SPM C7 C N N 205 SPM C8 C N N 206 SPM C9 C N N 207 SPM N10 N N N 208 SPM C11 C N N 209 SPM C12 C N N 210 SPM C13 C N N 211 SPM N14 N N N 212 SPM HN11 H N N 213 SPM HN12 H N N 214 SPM H21 H N N 215 SPM H22 H N N 216 SPM H31 H N N 217 SPM H32 H N N 218 SPM H41 H N N 219 SPM H42 H N N 220 SPM HN5 H N N 221 SPM H61 H N N 222 SPM H62 H N N 223 SPM H71 H N N 224 SPM H72 H N N 225 SPM H81 H N N 226 SPM H82 H N N 227 SPM H91 H N N 228 SPM H92 H N N 229 SPM HN0 H N N 230 SPM H111 H N N 231 SPM H112 H N N 232 SPM H121 H N N 233 SPM H122 H N N 234 SPM H131 H N N 235 SPM H132 H N N 236 SPM HN41 H N N 237 SPM HN42 H N N 238 # 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 2OT P OP1 doub N N 1 2OT P OP2 sing N N 2 2OT P "O5'" sing N N 3 2OT P OP3 sing N N 4 2OT OP2 HOP2 sing N N 5 2OT "O5'" "C5'" sing N N 6 2OT "C5'" "C4'" sing N N 7 2OT "C5'" "H5'" sing N N 8 2OT "C5'" "H5''" sing N N 9 2OT "C4'" "O4'" sing N N 10 2OT "C4'" "C3'" sing N N 11 2OT "C4'" "H4'" sing N N 12 2OT "O4'" "C1'" sing N N 13 2OT "C1'" N1 sing N N 14 2OT "C1'" "C2'" sing N N 15 2OT "C1'" "H1'" sing N N 16 2OT N1 C6 sing N N 17 2OT N1 C2 sing N N 18 2OT C6 C5 doub N N 19 2OT C6 H6 sing N N 20 2OT C2 O2 doub N N 21 2OT C2 N3 sing N N 22 2OT N3 C4 sing N N 23 2OT N3 HN3 sing N N 24 2OT C4 O4 doub N N 25 2OT C4 C5 sing N N 26 2OT C5 C5M sing N N 27 2OT C5M H71 sing N N 28 2OT C5M H72 sing N N 29 2OT C5M H73 sing N N 30 2OT "C2'" "O2'" sing N N 31 2OT "C2'" "C3'" sing N N 32 2OT "C2'" "H2'" sing N N 33 2OT "O2'" "CB'" sing N N 34 2OT "CB'" "CC'" sing N N 35 2OT "CB'" "HB'1" sing N N 36 2OT "CB'" "HB'2" sing N N 37 2OT "CC'" "OD'" sing N N 38 2OT "CC'" "HC'1" sing N N 39 2OT "CC'" "HC'2" sing N N 40 2OT "OD'" "NE'" sing N N 41 2OT "NE'" "CF'" sing N N 42 2OT "NE'" "CG'" sing N N 43 2OT "CF'" "HF'1" sing N N 44 2OT "CF'" "HF'2" sing N N 45 2OT "CF'" "HF'3" sing N N 46 2OT "CG'" "HG'1" sing N N 47 2OT "CG'" "HG'2" sing N N 48 2OT "CG'" "HG'3" sing N N 49 2OT "C3'" "O3'" sing N N 50 2OT "C3'" "H3'" sing N N 51 2OT "O3'" "HO3'" sing N N 52 2OT OP3 HOP3 sing N N 53 DA OP3 P sing N N 54 DA OP3 HOP3 sing N N 55 DA P OP1 doub N N 56 DA P OP2 sing N N 57 DA P "O5'" sing N N 58 DA OP2 HOP2 sing N N 59 DA "O5'" "C5'" sing N N 60 DA "C5'" "C4'" sing N N 61 DA "C5'" "H5'" sing N N 62 DA "C5'" "H5''" sing N N 63 DA "C4'" "O4'" sing N N 64 DA "C4'" "C3'" sing N N 65 DA "C4'" "H4'" sing N N 66 DA "O4'" "C1'" sing N N 67 DA "C3'" "O3'" sing N N 68 DA "C3'" "C2'" sing N N 69 DA "C3'" "H3'" sing N N 70 DA "O3'" "HO3'" sing N N 71 DA "C2'" "C1'" sing N N 72 DA "C2'" "H2'" sing N N 73 DA "C2'" "H2''" sing N N 74 DA "C1'" N9 sing N N 75 DA "C1'" "H1'" sing N N 76 DA N9 C8 sing Y N 77 DA N9 C4 sing Y N 78 DA C8 N7 doub Y N 79 DA C8 H8 sing N N 80 DA N7 C5 sing Y N 81 DA C5 C6 sing Y N 82 DA C5 C4 doub Y N 83 DA C6 N6 sing N N 84 DA C6 N1 doub Y N 85 DA N6 H61 sing N N 86 DA N6 H62 sing N N 87 DA N1 C2 sing Y N 88 DA C2 N3 doub Y N 89 DA C2 H2 sing N N 90 DA N3 C4 sing Y N 91 DC OP3 P sing N N 92 DC OP3 HOP3 sing N N 93 DC P OP1 doub N N 94 DC P OP2 sing N N 95 DC P "O5'" sing N N 96 DC OP2 HOP2 sing N N 97 DC "O5'" "C5'" sing N N 98 DC "C5'" "C4'" sing N N 99 DC "C5'" "H5'" sing N N 100 DC "C5'" "H5''" sing N N 101 DC "C4'" "O4'" sing N N 102 DC "C4'" "C3'" sing N N 103 DC "C4'" "H4'" sing N N 104 DC "O4'" "C1'" sing N N 105 DC "C3'" "O3'" sing N N 106 DC "C3'" "C2'" sing N N 107 DC "C3'" "H3'" sing N N 108 DC "O3'" "HO3'" sing N N 109 DC "C2'" "C1'" sing N N 110 DC "C2'" "H2'" sing N N 111 DC "C2'" "H2''" sing N N 112 DC "C1'" N1 sing N N 113 DC "C1'" "H1'" sing N N 114 DC N1 C2 sing N N 115 DC N1 C6 sing N N 116 DC C2 O2 doub N N 117 DC C2 N3 sing N N 118 DC N3 C4 doub N N 119 DC C4 N4 sing N N 120 DC C4 C5 sing N N 121 DC N4 H41 sing N N 122 DC N4 H42 sing N N 123 DC C5 C6 doub N N 124 DC C5 H5 sing N N 125 DC C6 H6 sing N N 126 DG OP3 P sing N N 127 DG OP3 HOP3 sing N N 128 DG P OP1 doub N N 129 DG P OP2 sing N N 130 DG P "O5'" sing N N 131 DG OP2 HOP2 sing N N 132 DG "O5'" "C5'" sing N N 133 DG "C5'" "C4'" sing N N 134 DG "C5'" "H5'" sing N N 135 DG "C5'" "H5''" sing N N 136 DG "C4'" "O4'" sing N N 137 DG "C4'" "C3'" sing N N 138 DG "C4'" "H4'" sing N N 139 DG "O4'" "C1'" sing N N 140 DG "C3'" "O3'" sing N N 141 DG "C3'" "C2'" sing N N 142 DG "C3'" "H3'" sing N N 143 DG "O3'" "HO3'" sing N N 144 DG "C2'" "C1'" sing N N 145 DG "C2'" "H2'" sing N N 146 DG "C2'" "H2''" sing N N 147 DG "C1'" N9 sing N N 148 DG "C1'" "H1'" sing N N 149 DG N9 C8 sing Y N 150 DG N9 C4 sing Y N 151 DG C8 N7 doub Y N 152 DG C8 H8 sing N N 153 DG N7 C5 sing Y N 154 DG C5 C6 sing N N 155 DG C5 C4 doub Y N 156 DG C6 O6 doub N N 157 DG C6 N1 sing N N 158 DG N1 C2 sing N N 159 DG N1 H1 sing N N 160 DG C2 N2 sing N N 161 DG C2 N3 doub N N 162 DG N2 H21 sing N N 163 DG N2 H22 sing N N 164 DG N3 C4 sing N N 165 DT OP3 P sing N N 166 DT OP3 HOP3 sing N N 167 DT P OP1 doub N N 168 DT P OP2 sing N N 169 DT P "O5'" sing N N 170 DT OP2 HOP2 sing N N 171 DT "O5'" "C5'" sing N N 172 DT "C5'" "C4'" sing N N 173 DT "C5'" "H5'" sing N N 174 DT "C5'" "H5''" sing N N 175 DT "C4'" "O4'" sing N N 176 DT "C4'" "C3'" sing N N 177 DT "C4'" "H4'" sing N N 178 DT "O4'" "C1'" sing N N 179 DT "C3'" "O3'" sing N N 180 DT "C3'" "C2'" sing N N 181 DT "C3'" "H3'" sing N N 182 DT "O3'" "HO3'" sing N N 183 DT "C2'" "C1'" sing N N 184 DT "C2'" "H2'" sing N N 185 DT "C2'" "H2''" sing N N 186 DT "C1'" N1 sing N N 187 DT "C1'" "H1'" sing N N 188 DT N1 C2 sing N N 189 DT N1 C6 sing N N 190 DT C2 O2 doub N N 191 DT C2 N3 sing N N 192 DT N3 C4 sing N N 193 DT N3 H3 sing N N 194 DT C4 O4 doub N N 195 DT C4 C5 sing N N 196 DT C5 C7 sing N N 197 DT C5 C6 doub N N 198 DT C7 H71 sing N N 199 DT C7 H72 sing N N 200 DT C7 H73 sing N N 201 DT C6 H6 sing N N 202 HOH O H1 sing N N 203 HOH O H2 sing N N 204 SPM N1 C2 sing N N 205 SPM N1 HN11 sing N N 206 SPM N1 HN12 sing N N 207 SPM C2 C3 sing N N 208 SPM C2 H21 sing N N 209 SPM C2 H22 sing N N 210 SPM C3 C4 sing N N 211 SPM C3 H31 sing N N 212 SPM C3 H32 sing N N 213 SPM C4 N5 sing N N 214 SPM C4 H41 sing N N 215 SPM C4 H42 sing N N 216 SPM N5 C6 sing N N 217 SPM N5 HN5 sing N N 218 SPM C6 C7 sing N N 219 SPM C6 H61 sing N N 220 SPM C6 H62 sing N N 221 SPM C7 C8 sing N N 222 SPM C7 H71 sing N N 223 SPM C7 H72 sing N N 224 SPM C8 C9 sing N N 225 SPM C8 H81 sing N N 226 SPM C8 H82 sing N N 227 SPM C9 N10 sing N N 228 SPM C9 H91 sing N N 229 SPM C9 H92 sing N N 230 SPM N10 C11 sing N N 231 SPM N10 HN0 sing N N 232 SPM C11 C12 sing N N 233 SPM C11 H111 sing N N 234 SPM C11 H112 sing N N 235 SPM C12 C13 sing N N 236 SPM C12 H121 sing N N 237 SPM C12 H122 sing N N 238 SPM C13 N14 sing N N 239 SPM C13 H131 sing N N 240 SPM C13 H132 sing N N 241 SPM N14 HN41 sing N N 242 SPM N14 HN42 sing N N 243 # _ndb_struct_conf_na.entry_id 1YB9 _ndb_struct_conf_na.feature 'a-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 1 1_555 B DC 10 1_555 -0.255 -0.268 0.173 -0.174 -5.672 -2.453 1 A_DG1:DC20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.169 -0.056 0.074 3.416 -11.197 2.105 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.334 -0.130 -0.017 -7.807 -14.752 0.743 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 1 A DT 4 1_555 B DA 7 1_555 -0.064 -0.121 -0.018 -4.650 -17.496 1.643 4 A_DT4:DA17_B A 4 ? B 17 ? 20 1 1 A DA 5 1_555 B 2OT 6 1_555 0.262 -0.119 0.143 -3.596 -13.943 -2.569 5 A_DA5:2OT16_B A 5 ? B 16 ? 20 1 1 A 2OT 6 1_555 B DA 5 1_555 0.008 -0.095 0.207 2.616 -14.303 6.651 6 A_2OT6:DA15_B A 6 ? B 15 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 0.078 -0.158 0.097 6.225 -11.167 1.160 7 A_DA7:DT14_B A 7 ? B 14 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 0.154 -0.176 -0.097 8.021 -14.091 1.260 8 A_DC8:DG13_B A 8 ? B 13 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.109 -0.159 0.063 -7.862 -10.059 1.004 9 A_DG9:DC12_B A 9 ? B 12 ? 19 1 1 A DC 10 1_555 B DG 1 1_555 0.217 -0.107 -0.034 -2.235 5.346 0.237 10 A_DC10:DG11_B A 10 ? B 11 ? 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 10 1_555 A DC 2 1_555 B DG 9 1_555 0.282 -1.696 3.189 1.738 1.157 39.735 -2.622 -0.220 3.149 1.701 -2.554 39.788 1 AA_DG1DC2:DG19DC20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DC 2 1_555 B DG 9 1_555 A DG 3 1_555 B DC 8 1_555 0.125 -2.301 3.474 1.307 8.436 23.893 -7.552 0.073 2.529 19.592 -3.036 25.351 2 AA_DC2DG3:DC18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DG 3 1_555 B DC 8 1_555 A DT 4 1_555 B DA 7 1_555 -1.109 -1.517 3.143 -1.757 5.338 36.479 -3.073 1.529 2.948 8.465 2.786 36.895 3 AA_DG3DT4:DA17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DT 4 1_555 B DA 7 1_555 A DA 5 1_555 B 2OT 6 1_555 0.507 -1.610 3.171 1.456 19.639 26.179 -5.655 -0.695 1.625 37.363 -2.770 32.655 4 AA_DT4DA5:2OT16DA17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DA 5 1_555 B 2OT 6 1_555 A 2OT 6 1_555 B DA 5 1_555 0.627 -1.280 3.106 1.191 6.009 31.903 -3.256 -0.929 2.844 10.807 -2.142 32.471 5 AA_DA52OT6:DA152OT16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A 2OT 6 1_555 B DA 5 1_555 A DA 7 1_555 B DT 4 1_555 -0.292 -1.232 3.029 0.214 13.925 30.344 -4.118 0.539 2.260 25.014 -0.384 33.319 6 AA_2OT6DA7:DT14DA15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A DA 7 1_555 B DT 4 1_555 A DC 8 1_555 B DG 3 1_555 0.390 -1.715 3.294 1.795 2.858 31.154 -3.708 -0.388 3.145 5.302 -3.330 31.332 7 AA_DA7DC8:DG13DT14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A DC 8 1_555 B DG 3 1_555 A DG 9 1_555 B DC 2 1_555 -0.263 -1.992 3.551 -1.310 13.155 29.860 -5.761 0.249 2.485 24.099 2.400 32.595 8 AA_DC8DG9:DC12DG13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DG 9 1_555 B DC 2 1_555 A DC 10 1_555 B DG 1 1_555 0.190 -1.696 3.268 2.254 -0.270 34.026 -2.849 0.036 3.287 -0.462 -3.847 34.100 9 AA_DG9DC10:DG11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 SPERMINE SPM 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 410D _pdbx_initial_refinement_model.details 'pdb entry 410D' #