data_2O3X # _entry.id 2O3X # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.377 _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 2O3X pdb_00002o3x 10.2210/pdb2o3x/pdb NDB DR0039 ? ? RCSB RCSB040655 ? ? WWPDB D_1000040655 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2O3V 'Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with paromamine derivative NB33' unspecified PDB 2O3W 'Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site in presence of paromomycin' unspecified PDB 2O3Y 'Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site in Presence of Paromamine Derivative NB30' unspecified # _pdbx_database_status.entry_id 2O3X _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2006-12-02 _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 'Kondo, J.' 1 'Hainrichson, M.' 2 'Nudelman, I.' 3 'Shallom-Shezifi, D.' 4 'Baasov, T.' 5 'Westhof, E.' 6 # _citation.id primary _citation.title 'Differential Selectivity of Natural and Synthetic Aminoglycosides towards the Eukaryotic and Prokaryotic Decoding A Sites.' _citation.journal_abbrev Chembiochem _citation.journal_volume 8 _citation.page_first 1700 _citation.page_last 1709 _citation.year 2007 _citation.journal_id_ASTM ? _citation.country GE _citation.journal_id_ISSN 1439-4227 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 17705310 _citation.pdbx_database_id_DOI 10.1002/cbic.200700271 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kondo, J.' 1 ? primary 'Hainrichson, M.' 2 ? primary 'Nudelman, I.' 3 ? primary 'Shallom-Shezifi, D.' 4 ? primary 'Barbieri, C.M.' 5 ? primary 'Pilch, D.S.' 6 ? primary 'Westhof, E.' 7 ? primary 'Baasov, T.' 8 ? # _cell.length_a 33.140 _cell.length_b 46.830 _cell.length_c 85.720 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 2O3X _cell.pdbx_unique_axis ? _cell.Z_PDB 8 _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 21 21 21' _symmetry.entry_id 2O3X _symmetry.Int_Tables_number 19 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _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 ;RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3') ; 7355.409 2 ? ? ? ? 2 non-polymer syn ;(1R,2R,3S,4R,6S)-4,6-DIAMINO-2-[(5-AMINO-5-DEOXY-BETA-D-RIBOFURANOSYL)OXY]-3-HYDROXYCYCLOHEXYL 2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSIDE ; 454.473 1 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code UUGCGUCACACCGGUGAAGUCGC _entity_poly.pdbx_seq_one_letter_code_can UUGCGUCACACCGGUGAAGUCGC _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 U n 1 2 U n 1 3 G n 1 4 C n 1 5 G n 1 6 U n 1 7 C n 1 8 A n 1 9 C n 1 10 A n 1 11 C n 1 12 C n 1 13 G n 1 14 G n 1 15 U n 1 16 G n 1 17 A n 1 18 A n 1 19 G n 1 20 U n 1 21 C n 1 22 G n 1 23 C n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'Chemically synthesized' # _struct_ref.id 1 _struct_ref.db_code 2O3X _struct_ref.db_name PDB _struct_ref.entity_id 1 _struct_ref.pdbx_db_accession 2O3X _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code UUGCGUCACACCGGUGAAGUCGC _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 2O3X A 1 ? 23 ? 2O3X 1 ? 23 ? 1 23 2 1 2O3X B 1 ? 23 ? 2O3X 24 ? 46 ? 24 46 # 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 N30 non-polymer . ;(1R,2R,3S,4R,6S)-4,6-DIAMINO-2-[(5-AMINO-5-DEOXY-BETA-D-RIBOFURANOSYL)OXY]-3-HYDROXYCYCLOHEXYL 2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSIDE ; ? 'C17 H34 N4 O10' 454.473 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.crystals_number 1 _exptl.entry_id 2O3X _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.26 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 45.59 _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.pH 6.5 _exptl_crystal_grow.temp 300 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details ;Sodium Cacodylate, Potassium chloride, 2-methyl-2,4-pentanediol, spermine tetrahydrochloride, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K ; _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.conc _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.details 1 1 1 'Sodium Cacodylate' ? ? ? 1 2 1 'Potassium chloride' ? ? ? 1 3 1 2-methyl-2,4-pentanediol ? ? ? 1 4 1 'spermine tetrahydrochloride' ? ? ? 1 5 1 glycerol ? ? ? 1 6 2 'Sodium Cacodylate' ? ? ? 1 7 2 'Potassium chloride' ? ? ? 1 8 2 2-methyl-2,4-pentanediol ? ? ? 1 9 2 'spermine tetrahydrochloride' ? ? ? # _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 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2006-05-22 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator 'Si(111)' _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9737 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID29' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9737 _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID29 # _reflns.entry_id 2O3X _reflns.d_resolution_high 2.900 _reflns.d_resolution_low 42.860 _reflns.number_obs 3222 _reflns.pdbx_scaling_rejects 159 _reflns.pdbx_Rmerge_I_obs 0.163 _reflns.pdbx_netI_over_sigmaI 8.300 _reflns.pdbx_chi_squared 0.940 _reflns.pdbx_redundancy 6.530 _reflns.percent_possible_obs 99.400 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal 2.90 3.00 ? 2266 ? 0.35 3.0 ? 0.570 6.93 ? 327 100.00 ? 1 3.00 3.12 ? 2093 ? 0.289 2.5 ? 0.340 6.77 ? 309 100.00 ? 2 3.12 3.27 ? 2092 ? 0.259 3.0 ? 0.350 6.86 ? 305 100.00 ? 3 3.27 3.44 ? 2153 ? 0.244 3.8 ? 0.500 6.75 ? 319 100.00 ? 4 3.44 3.65 ? 2196 ? 0.239 5.1 ? 0.810 6.82 ? 322 100.00 ? 5 3.65 3.94 ? 2103 ? 0.249 5.5 ? 0.840 6.70 ? 314 100.00 ? 6 3.94 4.33 ? 2135 ? 0.217 6.3 ? 0.940 6.61 ? 322 99.70 ? 7 4.33 4.96 ? 2041 ? 0.174 9.2 ? 1.340 6.30 ? 322 100.00 ? 8 4.96 6.24 ? 2008 ? 0.151 14.0 ? 1.500 5.90 ? 337 100.00 ? 9 6.24 42.86 ? 2105 ? 0.071 32.9 ? 2.470 5.76 ? 345 95.30 ? 10 # _refine.entry_id 2O3X _refine.ls_d_res_high 2.900 _refine.ls_d_res_low 10.000 _refine.pdbx_ls_sigma_F 3 _refine.ls_percent_reflns_obs 93.800 _refine.ls_number_reflns_obs 2948 _refine.ls_R_factor_R_work 0.246 _refine.ls_R_factor_R_free 0.285 _refine.ls_percent_reflns_R_free 9.300 _refine.ls_number_reflns_R_free 292 _refine.B_iso_mean 76.921 _refine.solvent_model_param_bsol 47.316 _refine.aniso_B[1][1] 13.647 _refine.aniso_B[2][2] 2.852 _refine.aniso_B[3][3] -16.499 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.overall_FOM_work_R_set 0.756 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _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_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 1J7T _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ;G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman, New Parameters for the Refinement of Nucleic Acid Containing Structures, Acta Cryst. D, 52, 57-64 (1996). ; _refine.details ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_overall_ESU_R ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_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_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 898 _refine_hist.pdbx_number_atoms_ligand 31 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 929 _refine_hist.d_res_high 2.900 _refine_hist.d_res_low 10.000 # 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 c_bond_d ? 0.007 1.500 ? 'X-RAY DIFFRACTION' ? c_angle_deg ? 1.234 2.00 ? 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id 2.900 3.030 8 . 285 . 0.367 0.456 . 32 . . 317 . 'X-RAY DIFFRACTION' 3.030 3.180 8 . 313 . 0.311 0.243 . 21 . . 334 . 'X-RAY DIFFRACTION' 3.180 3.380 8 . 320 . 0.322 0.414 . 42 . . 362 . 'X-RAY DIFFRACTION' 3.380 3.620 8 . 307 . 0.274 0.314 . 37 . . 344 . 'X-RAY DIFFRACTION' 3.620 3.970 8 . 336 . 0.285 0.375 . 46 . . 382 . 'X-RAY DIFFRACTION' 3.970 4.500 8 . 340 . 0.254 0.302 . 45 . . 385 . 'X-RAY DIFFRACTION' 4.500 5.500 8 . 370 . 0.227 0.269 . 34 . . 404 . 'X-RAY DIFFRACTION' 5.500 10.000 8 . 385 . 0.185 0.226 . 35 . . 420 . 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 dna-rna_rep.param dna-rna.top 'X-RAY DIFFRACTION' 2 nb30_xplor.param nb30_xplor.top 'X-RAY DIFFRACTION' 3 water.param water.top 'X-RAY DIFFRACTION' # _struct.entry_id 2O3X _struct.title 'Crystal Structure of the Prokaryotic Ribosomal Decoding Site Complexed with Paromamine Derivative NB30' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2O3X _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'aminoglycoside, antibiotics, ribosome, decoding site, Prokaryote, Translation inhibition, Stop codon readthrough, RNA' # 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 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 23 N3 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 23 O2 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 23 N4 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 22 N1 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 22 O6 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 22 N2 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 21 N3 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 21 O2 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 21 N4 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 19 N1 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 19 O6 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 19 N2 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 9 N3 ? ? ? 1_555 B G 16 N1 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 9 N4 ? ? ? 1_555 B G 16 O6 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 9 O2 ? ? ? 1_555 B G 16 N2 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 10 N1 ? ? ? 1_555 B U 15 N3 ? ? A A 10 B U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 10 N6 ? ? ? 1_555 B U 15 O4 ? ? A A 10 B U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 14 N1 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 14 O6 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 14 N2 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 13 N1 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 13 O6 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 13 N2 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 13 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 13 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 14 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 14 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 14 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A U 15 N3 ? ? ? 1_555 B A 10 N1 ? ? A U 15 B A 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A U 15 O4 ? ? ? 1_555 B A 10 N6 ? ? A U 15 B A 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 16 N1 ? ? ? 1_555 B C 9 N3 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 16 N2 ? ? ? 1_555 B C 9 O2 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 16 O6 ? ? ? 1_555 B C 9 N4 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 19 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 19 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 19 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A U 20 N3 ? ? ? 1_555 B U 6 O2 ? ? A U 20 B U 29 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog39 hydrog ? ? A U 20 O4 ? ? ? 1_555 B U 6 N3 ? ? A U 20 B U 29 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog40 hydrog ? ? A C 21 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 21 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A C 21 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 22 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 22 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A G 22 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 23 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 23 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A C 23 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 B N30 1 ? 10 'BINDING SITE FOR RESIDUE N30 B 1' 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 10 G A 5 ? G A 5 . ? 1_555 ? 2 AC1 10 C A 7 ? C A 7 . ? 1_555 ? 3 AC1 10 A A 8 ? A A 8 . ? 1_555 ? 4 AC1 10 A A 17 ? A A 17 . ? 3_645 ? 5 AC1 10 G B 16 ? G B 39 . ? 1_555 ? 6 AC1 10 A B 17 ? A B 40 . ? 1_555 ? 7 AC1 10 A B 18 ? A B 41 . ? 1_555 ? 8 AC1 10 G B 19 ? G B 42 . ? 1_555 ? 9 AC1 10 U B 20 ? U B 43 . ? 1_555 ? 10 AC1 10 C B 21 ? C B 44 . ? 1_555 ? # _atom_sites.entry_id 2O3X _atom_sites.fract_transf_matrix[1][1] 0.030175 _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] 0.021354 _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] 0.011666 _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 U 1 1 ? ? ? A . n A 1 2 U 2 2 ? ? ? A . n A 1 3 G 3 3 3 G G A . n A 1 4 C 4 4 4 C C A . n A 1 5 G 5 5 5 G G A . n A 1 6 U 6 6 6 U U A . n A 1 7 C 7 7 7 C C A . n A 1 8 A 8 8 8 A A A . n A 1 9 C 9 9 9 C C A . n A 1 10 A 10 10 10 A A A . n A 1 11 C 11 11 11 C C A . n A 1 12 C 12 12 12 C C A . n A 1 13 G 13 13 13 G G A . n A 1 14 G 14 14 14 G G A . n A 1 15 U 15 15 15 U U A . n A 1 16 G 16 16 16 G G A . n A 1 17 A 17 17 17 A A A . n A 1 18 A 18 18 18 A A A . n A 1 19 G 19 19 19 G G A . n A 1 20 U 20 20 20 U U A . n A 1 21 C 21 21 21 C C A . n A 1 22 G 22 22 22 G G A . n A 1 23 C 23 23 23 C C A . n B 1 1 U 1 24 ? ? ? B . n B 1 2 U 2 25 ? ? ? B . n B 1 3 G 3 26 26 G G B . n B 1 4 C 4 27 27 C C B . n B 1 5 G 5 28 28 G G B . n B 1 6 U 6 29 29 U U B . n B 1 7 C 7 30 30 C C B . n B 1 8 A 8 31 31 A A B . n B 1 9 C 9 32 32 C C B . n B 1 10 A 10 33 33 A A B . n B 1 11 C 11 34 34 C C B . n B 1 12 C 12 35 35 C C B . n B 1 13 G 13 36 36 G G B . n B 1 14 G 14 37 37 G G B . n B 1 15 U 15 38 38 U U B . n B 1 16 G 16 39 39 G G B . n B 1 17 A 17 40 40 A A B . n B 1 18 A 18 41 41 A A B . n B 1 19 G 19 42 42 G G B . n B 1 20 U 20 43 43 U U B . n B 1 21 C 21 44 44 C C B . n B 1 22 G 22 45 45 G G B . n B 1 23 C 23 46 46 C C B . n # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id N30 _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 1 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id N30 _pdbx_nonpoly_scheme.auth_mon_id N30 _pdbx_nonpoly_scheme.pdb_strand_id B _pdbx_nonpoly_scheme.pdb_ins_code . # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'MAJOR GROOVE BINDER' # _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 # _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 2007-11-06 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2023-08-30 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_initial_refinement_model 5 3 'Structure model' struct_ref_seq 6 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_ref_seq.db_align_beg' 4 3 'Structure model' '_struct_ref_seq.db_align_end' 5 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # 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 d*TREK 9.4SSI 'Apr 27 2005' package 'Pflugrath, J.W.' jwp@RigakuMSC.com 'data processing' http://www.msc.com/protein/dtrek.html ? ? 1 CNS . ? package 'Axel T. Brunger' axel.brunger@yale.edu refinement http://cns.csb.yale.edu/v1.1/ Fortran_77 ? 2 PDB_EXTRACT 2.000 'April. 3, 2006' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 3 ADSC Quantum ? ? ? ? 'data collection' ? ? ? 4 CrystalClear . ? ? ? ? 'data reduction' ? ? ? 5 CrystalClear . ? ? ? ? 'data scaling' ? ? ? 6 AMoRE . ? ? ? ? phasing ? ? ? 7 # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id U _pdbx_validate_planes.auth_asym_id B _pdbx_validate_planes.auth_seq_id 43 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.064 _pdbx_validate_planes.type 'SIDE CHAIN' # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A U 1 ? A U 1 2 1 Y 1 A U 2 ? A U 2 3 1 Y 1 B U 24 ? B U 1 4 1 Y 1 B U 25 ? B U 2 # 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 A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 N30 C11 C N R 111 N30 O11 O N N 112 N30 C21 C N R 113 N30 N21 N N N 114 N30 C31 C N R 115 N30 O31 O N N 116 N30 C41 C N S 117 N30 O41 O N N 118 N30 C51 C N R 119 N30 O51 O N N 120 N30 C61 C N N 121 N30 O61 O N N 122 N30 C12 C N R 123 N30 N12 N N N 124 N30 C22 C N N 125 N30 C32 C N S 126 N30 N32 N N N 127 N30 C42 C N R 128 N30 C52 C N R 129 N30 O52 O N N 130 N30 C62 C N S 131 N30 O62 O N N 132 N30 C13 C N S 133 N30 C23 C N R 134 N30 O23 O N N 135 N30 C33 C N S 136 N30 O33 O N N 137 N30 C43 C N R 138 N30 O43 O N N 139 N30 C53 C N N 140 N30 N53 N N N 141 N30 H11 H N N 142 N30 H21 H N N 143 N30 H211 H N N 144 N30 H212 H N N 145 N30 H31 H N N 146 N30 HO31 H N N 147 N30 H41 H N N 148 N30 HO41 H N N 149 N30 H51 H N N 150 N30 H611 H N N 151 N30 H612 H N N 152 N30 HO61 H N N 153 N30 H12 H N N 154 N30 H121 H N N 155 N30 H122 H N N 156 N30 H221 H N N 157 N30 H222 H N N 158 N30 H32 H N N 159 N30 H321 H N N 160 N30 H322 H N N 161 N30 H42 H N N 162 N30 H52 H N N 163 N30 H62 H N N 164 N30 HO62 H N N 165 N30 H13 H N N 166 N30 H23 H N N 167 N30 HO23 H N N 168 N30 H33 H N N 169 N30 HO33 H N N 170 N30 H43 H N N 171 N30 H531 H N N 172 N30 H532 H N N 173 N30 HN1 H N N 174 N30 HN2 H N N 175 U OP3 O N N 176 U P P N N 177 U OP1 O N N 178 U OP2 O N N 179 U "O5'" O N N 180 U "C5'" C N N 181 U "C4'" C N R 182 U "O4'" O N N 183 U "C3'" C N S 184 U "O3'" O N N 185 U "C2'" C N R 186 U "O2'" O N N 187 U "C1'" C N R 188 U N1 N N N 189 U C2 C N N 190 U O2 O N N 191 U N3 N N N 192 U C4 C N N 193 U O4 O N N 194 U C5 C N N 195 U C6 C N N 196 U HOP3 H N N 197 U HOP2 H N N 198 U "H5'" H N N 199 U "H5''" H N N 200 U "H4'" H N N 201 U "H3'" H N N 202 U "HO3'" H N N 203 U "H2'" H N N 204 U "HO2'" H N N 205 U "H1'" H N N 206 U H3 H N N 207 U H5 H N N 208 U H6 H N N 209 # 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 A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 N30 C11 C21 sing N N 116 N30 C11 O51 sing N N 117 N30 C11 O11 sing N N 118 N30 C11 H11 sing N N 119 N30 O11 C42 sing N N 120 N30 C21 C31 sing N N 121 N30 C21 N21 sing N N 122 N30 C21 H21 sing N N 123 N30 N21 H211 sing N N 124 N30 N21 H212 sing N N 125 N30 C31 O31 sing N N 126 N30 C31 C41 sing N N 127 N30 C31 H31 sing N N 128 N30 O31 HO31 sing N N 129 N30 C41 O41 sing N N 130 N30 C41 C51 sing N N 131 N30 C41 H41 sing N N 132 N30 O41 HO41 sing N N 133 N30 C51 C61 sing N N 134 N30 C51 O51 sing N N 135 N30 C51 H51 sing N N 136 N30 C61 O61 sing N N 137 N30 C61 H611 sing N N 138 N30 C61 H612 sing N N 139 N30 O61 HO61 sing N N 140 N30 C12 C22 sing N N 141 N30 C12 N12 sing N N 142 N30 C12 C62 sing N N 143 N30 C12 H12 sing N N 144 N30 N12 H121 sing N N 145 N30 N12 H122 sing N N 146 N30 C22 C32 sing N N 147 N30 C22 H221 sing N N 148 N30 C22 H222 sing N N 149 N30 C32 N32 sing N N 150 N30 C32 C42 sing N N 151 N30 C32 H32 sing N N 152 N30 N32 H321 sing N N 153 N30 N32 H322 sing N N 154 N30 C42 C52 sing N N 155 N30 C42 H42 sing N N 156 N30 C52 C62 sing N N 157 N30 C52 O52 sing N N 158 N30 C52 H52 sing N N 159 N30 O52 C13 sing N N 160 N30 C62 O62 sing N N 161 N30 C62 H62 sing N N 162 N30 O62 HO62 sing N N 163 N30 C13 O43 sing N N 164 N30 C13 C23 sing N N 165 N30 C13 H13 sing N N 166 N30 C23 C33 sing N N 167 N30 C23 O23 sing N N 168 N30 C23 H23 sing N N 169 N30 O23 HO23 sing N N 170 N30 C33 C43 sing N N 171 N30 C33 O33 sing N N 172 N30 C33 H33 sing N N 173 N30 O33 HO33 sing N N 174 N30 C43 C53 sing N N 175 N30 C43 O43 sing N N 176 N30 C43 H43 sing N N 177 N30 C53 N53 sing N N 178 N30 C53 H531 sing N N 179 N30 C53 H532 sing N N 180 N30 N53 HN1 sing N N 181 N30 N53 HN2 sing N N 182 U OP3 P sing N N 183 U OP3 HOP3 sing N N 184 U P OP1 doub N N 185 U P OP2 sing N N 186 U P "O5'" sing N N 187 U OP2 HOP2 sing N N 188 U "O5'" "C5'" sing N N 189 U "C5'" "C4'" sing N N 190 U "C5'" "H5'" sing N N 191 U "C5'" "H5''" sing N N 192 U "C4'" "O4'" sing N N 193 U "C4'" "C3'" sing N N 194 U "C4'" "H4'" sing N N 195 U "O4'" "C1'" sing N N 196 U "C3'" "O3'" sing N N 197 U "C3'" "C2'" sing N N 198 U "C3'" "H3'" sing N N 199 U "O3'" "HO3'" sing N N 200 U "C2'" "O2'" sing N N 201 U "C2'" "C1'" sing N N 202 U "C2'" "H2'" sing N N 203 U "O2'" "HO2'" sing N N 204 U "C1'" N1 sing N N 205 U "C1'" "H1'" sing N N 206 U N1 C2 sing N N 207 U N1 C6 sing N N 208 U C2 O2 doub N N 209 U C2 N3 sing N N 210 U N3 C4 sing N N 211 U N3 H3 sing N N 212 U C4 O4 doub N N 213 U C4 C5 sing N N 214 U C5 C6 doub N N 215 U C5 H5 sing N N 216 U C6 H6 sing N N 217 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2O3X 'double helix' 2O3X 'a-form double helix' 2O3X 'mismatched base pair' 2O3X 'internal loop' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 3 1_555 B C 23 1_555 -0.302 -0.352 0.084 -7.606 -2.755 -2.241 1 A_G3:C46_B A 3 ? B 46 ? 19 1 1 A C 4 1_555 B G 22 1_555 -0.072 -0.041 -0.470 4.280 -5.494 -0.152 2 A_C4:G45_B A 4 ? B 45 ? 19 1 1 A G 5 1_555 B C 21 1_555 -0.014 -0.143 0.260 -2.873 -1.526 4.945 3 A_G5:C44_B A 5 ? B 44 ? 19 1 1 A C 7 1_555 B G 19 1_555 0.139 -0.100 -0.450 4.593 -8.442 0.714 4 A_C7:G42_B A 7 ? B 42 ? 19 1 1 A C 9 1_555 B G 16 1_555 0.461 0.092 0.109 5.449 -23.438 7.132 5 A_C9:G39_B A 9 ? B 39 ? 19 1 1 A A 10 1_555 B U 15 1_555 0.039 -0.220 0.254 2.117 -16.191 2.570 6 A_A10:U38_B A 10 ? B 38 ? 20 1 1 A C 11 1_555 B G 14 1_555 0.169 -0.150 -0.507 9.589 -17.260 6.308 7 A_C11:G37_B A 11 ? B 37 ? 19 1 1 A C 12 1_555 B G 13 1_555 0.003 -0.188 0.393 -0.720 -9.088 -5.142 8 A_C12:G36_B A 12 ? B 36 ? 19 1 1 A G 13 1_555 B C 12 1_555 -0.151 -0.098 -0.121 -3.676 -23.030 3.417 9 A_G13:C35_B A 13 ? B 35 ? 19 1 1 A G 14 1_555 B C 11 1_555 0.156 -0.149 0.065 -6.051 -12.800 -2.689 10 A_G14:C34_B A 14 ? B 34 ? 19 1 1 A U 15 1_555 B A 10 1_555 0.244 -0.314 -0.062 2.692 -12.792 7.230 11 A_U15:A33_B A 15 ? B 33 ? 20 1 1 A G 16 1_555 B C 9 1_555 0.689 -0.143 0.353 -6.379 -11.633 -0.099 12 A_G16:C32_B A 16 ? B 32 ? 19 1 1 A G 19 1_555 B C 7 1_555 0.037 -0.071 0.017 -0.923 -5.035 -4.056 13 A_G19:C30_B A 19 ? B 30 ? 19 1 1 A U 20 1_555 B U 6 1_555 -1.525 -1.827 0.552 -6.866 -11.753 13.635 14 A_U20:U29_B A 20 ? B 29 ? 16 1 1 A C 21 1_555 B G 5 1_555 0.183 -0.151 0.959 -14.516 -10.527 1.710 15 A_C21:G28_B A 21 ? B 28 ? 19 1 1 A G 22 1_555 B C 4 1_555 -0.222 -0.168 -0.167 -11.141 -10.368 5.228 16 A_G22:C27_B A 22 ? B 27 ? 19 1 1 A C 23 1_555 B G 3 1_555 0.281 -0.217 -0.158 -1.909 -2.984 0.916 17 A_C23:G26_B A 23 ? B 26 ? 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 G 3 1_555 B C 23 1_555 A C 4 1_555 B G 22 1_555 0.101 -2.023 3.138 2.833 1.264 29.655 -4.183 0.364 3.047 2.462 -5.516 29.813 1 AA_G3C4:G45C46_BB A 3 ? B 46 ? A 4 ? B 45 ? 1 A C 4 1_555 B G 22 1_555 A G 5 1_555 B C 21 1_555 0.083 -1.707 3.499 -4.292 7.896 30.171 -4.632 -0.959 2.930 14.762 8.025 31.451 2 AA_C4G5:C44G45_BB A 4 ? B 45 ? A 5 ? B 44 ? 1 A G 5 1_555 B C 21 1_555 A C 7 1_555 B G 19 1_555 0.671 -2.913 6.212 8.663 8.721 63.757 -3.400 0.052 5.852 8.177 -8.122 64.808 3 AA_G5C7:G42C44_BB A 5 ? B 44 ? A 7 ? B 42 ? 1 A C 9 1_555 B G 16 1_555 A A 10 1_555 B U 15 1_555 -0.020 -1.699 3.161 -1.807 17.497 30.591 -4.997 -0.193 1.936 30.232 3.122 35.182 4 AA_C9A10:U38G39_BB A 9 ? B 39 ? A 10 ? B 38 ? 1 A A 10 1_555 B U 15 1_555 A C 11 1_555 B G 14 1_555 0.855 -1.449 2.976 5.740 1.371 30.541 -2.946 -0.579 3.017 2.573 -10.771 31.093 5 AA_A10C11:G37U38_BB A 10 ? B 38 ? A 11 ? B 37 ? 1 A C 11 1_555 B G 14 1_555 A C 12 1_555 B G 13 1_555 -1.077 -1.853 3.604 -8.341 6.719 32.229 -4.351 0.388 3.329 11.707 14.533 33.917 6 AA_C11C12:G36G37_BB A 11 ? B 37 ? A 12 ? B 36 ? 1 A C 12 1_555 B G 13 1_555 A G 13 1_555 B C 12 1_555 0.394 -1.798 3.265 5.304 9.132 27.293 -5.395 0.282 2.572 18.499 -10.743 29.229 7 AA_C12G13:C35G36_BB A 12 ? B 36 ? A 13 ? B 35 ? 1 A G 13 1_555 B C 12 1_555 A G 14 1_555 B C 11 1_555 -0.410 -1.602 3.262 -3.548 7.501 34.258 -3.711 0.175 2.884 12.507 5.917 35.220 8 AA_G13G14:C34C35_BB A 13 ? B 35 ? A 14 ? B 34 ? 1 A G 14 1_555 B C 11 1_555 A U 15 1_555 B A 10 1_555 0.494 -0.944 2.940 3.258 3.137 30.975 -2.278 -0.366 2.869 5.836 -6.060 31.296 9 AA_G14U15:A33C34_BB A 14 ? B 34 ? A 15 ? B 33 ? 1 A U 15 1_555 B A 10 1_555 A G 16 1_555 B C 9 1_555 0.195 -1.498 3.242 1.293 17.065 35.289 -4.078 -0.151 2.310 26.325 -1.994 39.100 10 AA_U15G16:C32A33_BB A 15 ? B 33 ? A 16 ? B 32 ? 1 A G 16 1_555 B C 9 1_555 A G 19 1_555 B C 7 1_555 -1.537 -2.579 5.931 0.844 16.685 72.037 -3.075 1.328 5.296 14.002 -0.708 73.693 11 AA_G16G19:C30C32_BB A 16 ? B 32 ? A 19 ? B 30 ? 1 A G 19 1_555 B C 7 1_555 A U 20 1_555 B U 6 1_555 0.640 -2.554 3.275 -7.882 0.091 24.477 -5.768 -3.593 2.920 0.207 18.004 25.696 12 AA_G19U20:U29C30_BB A 19 ? B 30 ? A 20 ? B 29 ? 1 A U 20 1_555 B U 6 1_555 A C 21 1_555 B G 5 1_555 -0.576 -1.436 3.548 -2.823 -2.320 42.263 -1.724 0.480 3.648 -3.211 3.906 42.414 13 AA_U20C21:G28U29_BB A 20 ? B 29 ? A 21 ? B 28 ? 1 A C 21 1_555 B G 5 1_555 A G 22 1_555 B C 4 1_555 -0.046 -2.278 2.852 7.408 9.300 31.837 -5.063 1.002 2.063 16.262 -12.953 33.931 14 AA_C21G22:C27G28_BB A 21 ? B 28 ? A 22 ? B 27 ? 1 A G 22 1_555 B C 4 1_555 A C 23 1_555 B G 3 1_555 0.206 -0.738 3.163 0.337 4.159 34.311 -1.856 -0.297 3.057 7.017 -0.568 34.556 15 AA_G22C23:G26C27_BB A 22 ? B 27 ? A 23 ? B 26 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name ;(1R,2R,3S,4R,6S)-4,6-DIAMINO-2-[(5-AMINO-5-DEOXY-BETA-D-RIBOFURANOSYL)OXY]-3-HYDROXYCYCLOHEXYL 2-AMINO-2-DEOXY-ALPHA-D-GLUCOPYRANOSIDE ; _pdbx_entity_nonpoly.comp_id N30 # _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 1J7T _pdbx_initial_refinement_model.details ? #