data_2ET4 # _entry.id 2ET4 # _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 2ET4 pdb_00002et4 10.2210/pdb2et4/pdb NDB DR0016 ? ? RCSB RCSB035059 ? ? WWPDB D_1000035059 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1J7T _pdbx_database_related.details 'COMPLEX BETWEEN PAROMOMYCIN AND THE 16S-RRNA A-SITE AT 2.5A RESOLUTION' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2ET4 _pdbx_database_status.recvd_initial_deposition_date 2005-10-27 _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 ? # _audit_author.name 'Westhof, E.' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title ;Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding. ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 33 _citation.page_first 5677 _citation.page_last 5690 _citation.year 2005 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16214802 _citation.pdbx_database_id_DOI 10.1093/nar/gki862 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Francois, B.' 1 ? primary 'Russell, R.J.' 2 ? primary 'Murray, J.B.' 3 ? primary 'Aboul-ela, F.' 4 ? primary 'Masquida, B.' 5 ? primary 'Vicens, Q.' 6 ? primary 'Westhof, E.' 7 ? # _cell.entry_id 2ET4 _cell.length_a 33.220 _cell.length_b 45.950 _cell.length_c 93.810 _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 2ET4 _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'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'" 7048.259 2 ? ? ? ? 2 non-polymer syn NEOMYCIN 614.644 2 ? ? ? ? 3 water nat water 18.015 48 ? ? ? ? # _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 CGCGUCACACCGGUGAAGUCGC _entity_poly.pdbx_seq_one_letter_code_can CGCGUCACACCGGUGAAGUCGC _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 C n 1 2 G n 1 3 C n 1 4 G n 1 5 U n 1 6 C n 1 7 A n 1 8 C n 1 9 A n 1 10 C n 1 11 C n 1 12 G n 1 13 G n 1 14 U n 1 15 G n 1 16 A n 1 17 A n 1 18 G n 1 19 U n 1 20 C n 1 21 G n 1 22 C n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2ET4 _struct_ref.pdbx_db_accession 2ET4 _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 2ET4 A 1 ? 22 ? 2ET4 1 ? 22 ? 1 22 2 1 2ET4 B 1 ? 22 ? 2ET4 24 ? 45 ? 24 45 # 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 HOH non-polymer . WATER ? 'H2 O' 18.015 NMY non-polymer . NEOMYCIN 'MYCIFRADIN; NEOMAS; PIMAVECORT; VONAMYCIN' 'C23 H46 N6 O13' 614.644 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.entry_id 2ET4 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.54 _exptl_crystal.density_percent_sol 51.57 _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 310 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.4 _exptl_crystal_grow.pdbx_details 'MPD, NACL, MGSO4, GLYCEROL, NA CACODYLATE, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K' _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 NACL ? ? ? 1 3 1 MGSO4 ? ? ? 1 4 1 GLYCEROL ? ? ? 1 5 1 'NA CACODYLATE' ? ? ? 1 6 1 H2O ? ? ? 1 7 2 MPD ? ? ? 1 8 2 NACL ? ? ? 1 9 2 MGSO4 ? ? ? 1 10 2 'NA CACODYLATE' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 110 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.936 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID29' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID29 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.936 # _reflns.entry_id 2ET4 _reflns.observed_criterion_sigma_I 5 _reflns.observed_criterion_sigma_F 5 _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.3 _reflns.number_obs 7300 _reflns.number_all 7300 _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 2ET4 _refine.ls_number_reflns_obs 5398 _refine.ls_number_reflns_all 6016 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.5 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 30 _refine.ls_d_res_high 2.4 _refine.ls_percent_reflns_obs 89.7 _refine.ls_R_factor_obs 0.2085 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2085 _refine.ls_R_factor_R_free 0.2583 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free 569 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model 'PDB Entry: 1J7T' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ;G. PARKINSON, J. VOJTECHOVSKY, L. CLOWNEY,A.T. BRUNGER, H.M. BERMAN, NEW PARAMETERSFOR THE REFINEMENT OF NUCLEIC ACID CONTAINING STRUCTURES, ACTA CRYST. D, 52,57-64 (1996) ; _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_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 2ET4 _refine_analyze.Luzzati_coordinate_error_obs 0.33 _refine_analyze.Luzzati_sigma_a_obs 0.39 _refine_analyze.Luzzati_d_res_low_obs 5.0 _refine_analyze.Luzzati_coordinate_error_free 0.44 _refine_analyze.Luzzati_sigma_a_free 0.50 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_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 898 _refine_hist.pdbx_number_atoms_ligand 84 _refine_hist.number_atoms_solvent 48 _refine_hist.number_atoms_total 1030 _refine_hist.d_res_high 2.4 _refine_hist.d_res_low 30 # 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 0.0055 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d 0.9095 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 9.2824 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.2894 ? ? ? 'X-RAY DIFFRACTION' ? # _struct.entry_id 2ET4 _struct.title 'Complex Between Neomycin B and the 16S-RRNA A-Site' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2ET4 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA-AMINOGLYCOSIDE INTERACTIONS, A SITE, UOU PAIRS, AA BULGES, 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 ? D N N 2 ? E N N 3 ? F N N 3 ? # 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 2 N1 ? ? ? 1_555 B C 22 N3 ? ? A G 2 B C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 22 O2 ? ? A G 2 B C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 22 N4 ? ? A G 2 B C 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 3 N3 ? ? ? 1_555 B G 21 N1 ? ? A C 3 B G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 3 N4 ? ? ? 1_555 B G 21 O6 ? ? A C 3 B G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 3 O2 ? ? ? 1_555 B G 21 N2 ? ? A C 3 B G 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 20 N3 ? ? A G 4 B C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 20 O2 ? ? A G 4 B C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 20 N4 ? ? A G 4 B C 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 5 O4 ? ? ? 1_555 B U 19 N3 ? ? A U 5 B U 42 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog11 hydrog ? ? A C 6 N3 ? ? ? 1_555 B G 18 N1 ? ? A C 6 B G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 6 N4 ? ? ? 1_555 B G 18 O6 ? ? A C 6 B G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 6 O2 ? ? ? 1_555 B G 18 N2 ? ? A C 6 B G 41 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 8 N3 ? ? ? 1_555 B G 15 N1 ? ? A C 8 B G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 8 N4 ? ? ? 1_555 B G 15 O6 ? ? A C 8 B G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 8 O2 ? ? ? 1_555 B G 15 N2 ? ? A C 8 B G 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 9 N1 ? ? ? 1_555 B U 14 N3 ? ? A A 9 B U 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 9 N6 ? ? ? 1_555 B U 14 O4 ? ? A A 9 B U 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 10 N3 ? ? ? 1_555 B G 13 N1 ? ? A C 10 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 10 N4 ? ? ? 1_555 B G 13 O6 ? ? A C 10 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 10 O2 ? ? ? 1_555 B G 13 N2 ? ? A C 10 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 11 B G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 11 B G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 11 B G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 12 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 12 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 12 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 10 N3 ? ? A G 13 B C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 13 N2 ? ? ? 1_555 B C 10 O2 ? ? A G 13 B C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 13 O6 ? ? ? 1_555 B C 10 N4 ? ? A G 13 B C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A U 14 N3 ? ? ? 1_555 B A 9 N1 ? ? A U 14 B A 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A U 14 O4 ? ? ? 1_555 B A 9 N6 ? ? A U 14 B A 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 15 N1 ? ? ? 1_555 B C 8 N3 ? ? A G 15 B C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 15 N2 ? ? ? 1_555 B C 8 O2 ? ? A G 15 B C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 15 O6 ? ? ? 1_555 B C 8 N4 ? ? A G 15 B C 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 18 N1 ? ? ? 1_555 B C 6 N3 ? ? A G 18 B C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 18 N2 ? ? ? 1_555 B C 6 O2 ? ? A G 18 B C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 18 O6 ? ? ? 1_555 B C 6 N4 ? ? A G 18 B C 29 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A U 19 N3 ? ? ? 1_555 B U 5 O4 ? ? A U 19 B U 28 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog40 hydrog ? ? A C 20 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 20 B G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 20 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 20 B G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A C 20 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 20 B G 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 21 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 21 B C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 21 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 21 B C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A G 21 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 21 B C 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 22 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 22 B G 25 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? # _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 A NMY 50 ? 11 'BINDING SITE FOR RESIDUE NMY A 50' AC2 Software B NMY 51 ? 14 'BINDING SITE FOR RESIDUE NMY B 51' 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 11 G A 15 ? G A 15 . ? 1_555 ? 2 AC1 11 A A 16 ? A A 16 . ? 1_555 ? 3 AC1 11 A A 17 ? A A 17 . ? 1_555 ? 4 AC1 11 G A 18 ? G A 18 . ? 1_555 ? 5 AC1 11 U A 19 ? U A 19 . ? 1_555 ? 6 AC1 11 HOH E . ? HOH A 203 . ? 1_555 ? 7 AC1 11 HOH E . ? HOH A 219 . ? 1_555 ? 8 AC1 11 HOH E . ? HOH A 246 . ? 1_555 ? 9 AC1 11 G B 4 ? G B 27 . ? 1_555 ? 10 AC1 11 C B 6 ? C B 29 . ? 1_555 ? 11 AC1 11 A B 7 ? A B 30 . ? 1_555 ? 12 AC2 14 G A 4 ? G A 4 . ? 1_555 ? 13 AC2 14 U A 5 ? U A 5 . ? 1_555 ? 14 AC2 14 C A 6 ? C A 6 . ? 1_555 ? 15 AC2 14 A A 7 ? A A 7 . ? 1_555 ? 16 AC2 14 C A 8 ? C A 8 . ? 1_555 ? 17 AC2 14 HOH E . ? HOH A 240 . ? 1_555 ? 18 AC2 14 G B 15 ? G B 38 . ? 1_555 ? 19 AC2 14 A B 16 ? A B 39 . ? 1_555 ? 20 AC2 14 A B 17 ? A B 40 . ? 1_555 ? 21 AC2 14 G B 18 ? G B 41 . ? 1_555 ? 22 AC2 14 U B 19 ? U B 42 . ? 1_555 ? 23 AC2 14 HOH F . ? HOH B 202 . ? 1_555 ? 24 AC2 14 HOH F . ? HOH B 213 . ? 1_555 ? 25 AC2 14 HOH F . ? HOH B 214 . ? 1_555 ? # _database_PDB_matrix.entry_id 2ET4 _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 2ET4 _atom_sites.fract_transf_matrix[1][1] 0.030102 _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] 0.021763 _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] 0.010660 _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 C 1 1 ? ? ? A . n A 1 2 G 2 2 2 G G A . n A 1 3 C 3 3 3 C C A . n A 1 4 G 4 4 4 G G A . n A 1 5 U 5 5 5 U U A . n A 1 6 C 6 6 6 C C A . n A 1 7 A 7 7 7 A A A . n A 1 8 C 8 8 8 C C A . n A 1 9 A 9 9 9 A A A . n A 1 10 C 10 10 10 C C A . n A 1 11 C 11 11 11 C C A . n A 1 12 G 12 12 12 G G A . n A 1 13 G 13 13 13 G G A . n A 1 14 U 14 14 14 U U A . n A 1 15 G 15 15 15 G G A . n A 1 16 A 16 16 16 A A A . n A 1 17 A 17 17 17 A A A . n A 1 18 G 18 18 18 G G A . n A 1 19 U 19 19 19 U U A . n A 1 20 C 20 20 20 C C A . n A 1 21 G 21 21 21 G G A . n A 1 22 C 22 22 22 C C A . n B 1 1 C 1 24 ? ? ? B . n B 1 2 G 2 25 25 G G B . n B 1 3 C 3 26 26 C C B . n B 1 4 G 4 27 27 G G B . n B 1 5 U 5 28 28 U U B . n B 1 6 C 6 29 29 C C B . n B 1 7 A 7 30 30 A A B . n B 1 8 C 8 31 31 C C B . n B 1 9 A 9 32 32 A A B . n B 1 10 C 10 33 33 C C B . n B 1 11 C 11 34 34 C C B . n B 1 12 G 12 35 35 G G B . n B 1 13 G 13 36 36 G G B . n B 1 14 U 14 37 37 U U B . n B 1 15 G 15 38 38 G G B . n B 1 16 A 16 39 39 A A B . n B 1 17 A 17 40 40 A A B . n B 1 18 G 18 41 41 G G B . n B 1 19 U 19 42 42 U U B . n B 1 20 C 20 43 43 C C B . n B 1 21 G 21 44 44 G G B . n B 1 22 C 22 45 45 C 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 NMY 1 50 50 NMY NMY A . D 2 NMY 1 51 51 NMY NMY B . E 3 HOH 1 203 203 HOH HOH A . E 3 HOH 2 205 205 HOH HOH A . E 3 HOH 3 206 206 HOH HOH A . E 3 HOH 4 210 210 HOH HOH A . E 3 HOH 5 211 211 HOH HOH A . E 3 HOH 6 212 212 HOH HOH A . E 3 HOH 7 216 216 HOH HOH A . E 3 HOH 8 217 217 HOH HOH A . E 3 HOH 9 218 218 HOH HOH A . E 3 HOH 10 219 219 HOH HOH A . E 3 HOH 11 220 220 HOH HOH A . E 3 HOH 12 221 221 HOH HOH A . E 3 HOH 13 222 222 HOH HOH A . E 3 HOH 14 223 223 HOH HOH A . E 3 HOH 15 224 224 HOH HOH A . E 3 HOH 16 227 227 HOH HOH A . E 3 HOH 17 228 228 HOH HOH A . E 3 HOH 18 230 230 HOH HOH A . E 3 HOH 19 231 231 HOH HOH A . E 3 HOH 20 232 232 HOH HOH A . E 3 HOH 21 233 233 HOH HOH A . E 3 HOH 22 234 234 HOH HOH A . E 3 HOH 23 236 236 HOH HOH A . E 3 HOH 24 237 237 HOH HOH A . E 3 HOH 25 238 238 HOH HOH A . E 3 HOH 26 239 239 HOH HOH A . E 3 HOH 27 240 240 HOH HOH A . E 3 HOH 28 241 241 HOH HOH A . E 3 HOH 29 242 242 HOH HOH A . E 3 HOH 30 244 244 HOH HOH A . E 3 HOH 31 246 246 HOH HOH A . E 3 HOH 32 247 247 HOH HOH A . F 3 HOH 1 200 200 HOH HOH B . F 3 HOH 2 201 201 HOH HOH B . F 3 HOH 3 202 202 HOH HOH B . F 3 HOH 4 204 204 HOH HOH B . F 3 HOH 5 207 207 HOH HOH B . F 3 HOH 6 208 208 HOH HOH B . F 3 HOH 7 209 209 HOH HOH B . F 3 HOH 8 213 213 HOH HOH B . F 3 HOH 9 214 214 HOH HOH B . F 3 HOH 10 215 215 HOH HOH B . F 3 HOH 11 225 225 HOH HOH B . F 3 HOH 12 226 226 HOH HOH B . F 3 HOH 13 229 229 HOH HOH B . F 3 HOH 14 235 235 HOH HOH B . F 3 HOH 15 243 243 HOH HOH B . F 3 HOH 16 245 245 HOH HOH B . # _struct_site_keywords.site_id 1 _struct_site_keywords.text BIS-INTERCALATION # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # 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 2005-12-13 2 'Structure model' 1 1 2008-05-01 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_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_site.pdbx_auth_asym_id' 4 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal HKL-2000 'data collection' . ? 1 SCALEPACK 'data scaling' . ? 2 AMoRE phasing . ? 3 CNS refinement 1.1 ? 4 HKL-2000 'data reduction' . ? 5 # _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 A _pdbx_validate_planes.auth_seq_id 5 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.066 _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 C 1 ? A C 1 2 1 Y 1 B C 24 ? B C 1 # 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 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 NMY C1 C N R 114 NMY O1 O N N 115 NMY C2 C N R 116 NMY N2 N N N 117 NMY C3 C N R 118 NMY O3 O N N 119 NMY C4 C N S 120 NMY O4 O N N 121 NMY C5 C N R 122 NMY O5 O N N 123 NMY C6 C N N 124 NMY C7 C N R 125 NMY N7 N N N 126 NMY C12 C N S 127 NMY C11 C N R 128 NMY O11 O N N 129 NMY C10 C N R 130 NMY C9 C N S 131 NMY N9 N N N 132 NMY C8 C N N 133 NMY C13 C N S 134 NMY C14 C N R 135 NMY C15 C N S 136 NMY C16 C N R 137 NMY O16 O N N 138 NMY C17 C N N 139 NMY C21 C N S 140 NMY C20 C N R 141 NMY C19 C N R 142 NMY C18 C N R 143 NMY O18 O N N 144 NMY C22 C N S 145 NMY O22 O N N 146 NMY C23 C N N 147 NMY N6 N N N 148 NMY O14 O N N 149 NMY O20 O N N 150 NMY O21 O N N 151 NMY O17 O N N 152 NMY O12 O N N 153 NMY N19 N N N 154 NMY N23 N N N 155 NMY H1 H N N 156 NMY H2 H N N 157 NMY HN21 H N N 158 NMY HN22 H N N 159 NMY H3 H N N 160 NMY HO3 H N N 161 NMY H4 H N N 162 NMY HO4 H N N 163 NMY H5 H N N 164 NMY H61 H N N 165 NMY H62 H N N 166 NMY H7 H N N 167 NMY H71 H N N 168 NMY H72 H N N 169 NMY H12 H N N 170 NMY H11 H N N 171 NMY H10 H N N 172 NMY H9 H N N 173 NMY H91 H N N 174 NMY H92 H N N 175 NMY H81 H N N 176 NMY H82 H N N 177 NMY H13 H N N 178 NMY H14 H N N 179 NMY H15 H N N 180 NMY H16 H N N 181 NMY H171 H N N 182 NMY H172 H N N 183 NMY H21 H N N 184 NMY H20 H N N 185 NMY H19 H N N 186 NMY H18 H N N 187 NMY H22 H N N 188 NMY H231 H N N 189 NMY H232 H N N 190 NMY HN61 H N N 191 NMY HN62 H N N 192 NMY HO41 H N N 193 NMY HO22 H N N 194 NMY HO21 H N N 195 NMY H17 H N N 196 NMY HO12 H N N 197 NMY H191 H N N 198 NMY H192 H N N 199 NMY HN31 H N N 200 NMY HN32 H N N 201 U OP3 O N N 202 U P P N N 203 U OP1 O N N 204 U OP2 O N N 205 U "O5'" O N N 206 U "C5'" C N N 207 U "C4'" C N R 208 U "O4'" O N N 209 U "C3'" C N S 210 U "O3'" O N N 211 U "C2'" C N R 212 U "O2'" O N N 213 U "C1'" C N R 214 U N1 N N N 215 U C2 C N N 216 U O2 O N N 217 U N3 N N N 218 U C4 C N N 219 U O4 O N N 220 U C5 C N N 221 U C6 C N N 222 U HOP3 H N N 223 U HOP2 H N N 224 U "H5'" H N N 225 U "H5''" H N N 226 U "H4'" H N N 227 U "H3'" H N N 228 U "HO3'" H N N 229 U "H2'" H N N 230 U "HO2'" H N N 231 U "H1'" H N N 232 U H3 H N N 233 U H5 H N N 234 U H6 H N N 235 # 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 HOH O H1 sing N N 116 HOH O H2 sing N N 117 NMY C1 O5 sing N N 118 NMY C1 O1 sing N N 119 NMY C1 C2 sing N N 120 NMY C1 H1 sing N N 121 NMY O1 C10 sing N N 122 NMY C2 N2 sing N N 123 NMY C2 C3 sing N N 124 NMY C2 H2 sing N N 125 NMY N2 HN21 sing N N 126 NMY N2 HN22 sing N N 127 NMY C3 C4 sing N N 128 NMY C3 O3 sing N N 129 NMY C3 H3 sing N N 130 NMY O3 HO3 sing N N 131 NMY C4 C5 sing N N 132 NMY C4 O4 sing N N 133 NMY C4 H4 sing N N 134 NMY O4 HO4 sing N N 135 NMY C5 O5 sing N N 136 NMY C5 C6 sing N N 137 NMY C5 H5 sing N N 138 NMY C6 N6 sing N N 139 NMY C6 H61 sing N N 140 NMY C6 H62 sing N N 141 NMY C7 N7 sing N N 142 NMY C7 C12 sing N N 143 NMY C7 C8 sing N N 144 NMY C7 H7 sing N N 145 NMY N7 H71 sing N N 146 NMY N7 H72 sing N N 147 NMY C12 O12 sing N N 148 NMY C12 C11 sing N N 149 NMY C12 H12 sing N N 150 NMY C11 O11 sing N N 151 NMY C11 C10 sing N N 152 NMY C11 H11 sing N N 153 NMY O11 C13 sing N N 154 NMY C10 C9 sing N N 155 NMY C10 H10 sing N N 156 NMY C9 C8 sing N N 157 NMY C9 N9 sing N N 158 NMY C9 H9 sing N N 159 NMY N9 H91 sing N N 160 NMY N9 H92 sing N N 161 NMY C8 H81 sing N N 162 NMY C8 H82 sing N N 163 NMY C13 C14 sing N N 164 NMY C13 O16 sing N N 165 NMY C13 H13 sing N N 166 NMY C14 O14 sing N N 167 NMY C14 C15 sing N N 168 NMY C14 H14 sing N N 169 NMY C15 O18 sing N N 170 NMY C15 C16 sing N N 171 NMY C15 H15 sing N N 172 NMY C16 O16 sing N N 173 NMY C16 C17 sing N N 174 NMY C16 H16 sing N N 175 NMY C17 O17 sing N N 176 NMY C17 H171 sing N N 177 NMY C17 H172 sing N N 178 NMY C21 C20 sing N N 179 NMY C21 C22 sing N N 180 NMY C21 O21 sing N N 181 NMY C21 H21 sing N N 182 NMY C20 C19 sing N N 183 NMY C20 O20 sing N N 184 NMY C20 H20 sing N N 185 NMY C19 N23 sing N N 186 NMY C19 C18 sing N N 187 NMY C19 H19 sing N N 188 NMY C18 O22 sing N N 189 NMY C18 O18 sing N N 190 NMY C18 H18 sing N N 191 NMY C22 O22 sing N N 192 NMY C22 C23 sing N N 193 NMY C22 H22 sing N N 194 NMY C23 N19 sing N N 195 NMY C23 H231 sing N N 196 NMY C23 H232 sing N N 197 NMY N6 HN61 sing N N 198 NMY N6 HN62 sing N N 199 NMY O14 HO41 sing N N 200 NMY O20 HO22 sing N N 201 NMY O21 HO21 sing N N 202 NMY O17 H17 sing N N 203 NMY O12 HO12 sing N N 204 NMY N19 H191 sing N N 205 NMY N19 H192 sing N N 206 NMY N23 HN31 sing N N 207 NMY N23 HN32 sing N N 208 U OP3 P sing N N 209 U OP3 HOP3 sing N N 210 U P OP1 doub N N 211 U P OP2 sing N N 212 U P "O5'" sing N N 213 U OP2 HOP2 sing N N 214 U "O5'" "C5'" sing N N 215 U "C5'" "C4'" sing N N 216 U "C5'" "H5'" sing N N 217 U "C5'" "H5''" sing N N 218 U "C4'" "O4'" sing N N 219 U "C4'" "C3'" sing N N 220 U "C4'" "H4'" sing N N 221 U "O4'" "C1'" sing N N 222 U "C3'" "O3'" sing N N 223 U "C3'" "C2'" sing N N 224 U "C3'" "H3'" sing N N 225 U "O3'" "HO3'" sing N N 226 U "C2'" "O2'" sing N N 227 U "C2'" "C1'" sing N N 228 U "C2'" "H2'" sing N N 229 U "O2'" "HO2'" sing N N 230 U "C1'" N1 sing N N 231 U "C1'" "H1'" sing N N 232 U N1 C2 sing N N 233 U N1 C6 sing N N 234 U C2 O2 doub N N 235 U C2 N3 sing N N 236 U N3 C4 sing N N 237 U N3 H3 sing N N 238 U C4 O4 doub N N 239 U C4 C5 sing N N 240 U C5 C6 doub N N 241 U C5 H5 sing N N 242 U C6 H6 sing N N 243 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2ET4 'double helix' 2ET4 'a-form double helix' 2ET4 'mismatched base pair' 2ET4 '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 2 1_555 B C 22 1_555 -0.990 -0.169 0.541 6.018 0.859 7.339 1 A_G2:C45_B A 2 ? B 45 ? 19 1 1 A C 3 1_555 B G 21 1_555 0.216 0.060 0.291 -0.579 -4.558 4.117 2 A_C3:G44_B A 3 ? B 44 ? 19 1 1 A G 4 1_555 B C 20 1_555 0.177 -0.144 0.140 2.407 -1.844 -1.543 3 A_G4:C43_B A 4 ? B 43 ? 19 1 1 A U 5 1_555 B U 19 1_555 -2.425 -0.916 -0.733 1.844 -5.400 -25.472 4 A_U5:U42_B A 5 ? B 42 ? ? ? 1 A C 6 1_555 B G 18 1_555 0.226 -0.306 -0.126 -1.970 4.723 2.458 5 A_C6:G41_B A 6 ? B 41 ? 19 1 1 A C 8 1_555 B G 15 1_555 0.171 -0.093 0.234 6.781 -24.244 2.244 6 A_C8:G38_B A 8 ? B 38 ? 19 1 1 A A 9 1_555 B U 14 1_555 0.555 -0.076 0.249 4.063 -15.230 0.783 7 A_A9:U37_B A 9 ? B 37 ? 20 1 1 A C 10 1_555 B G 13 1_555 0.443 -0.194 0.102 6.042 -16.039 3.902 8 A_C10:G36_B A 10 ? B 36 ? 19 1 1 A C 11 1_555 B G 12 1_555 -0.144 -0.156 -0.002 -0.697 -11.435 -2.686 9 A_C11:G35_B A 11 ? B 35 ? 19 1 1 A G 12 1_555 B C 11 1_555 -0.225 -0.148 0.233 0.152 -12.254 2.001 10 A_G12:C34_B A 12 ? B 34 ? 19 1 1 A G 13 1_555 B C 10 1_555 -0.412 -0.100 0.152 -2.172 -19.664 0.281 11 A_G13:C33_B A 13 ? B 33 ? 19 1 1 A U 14 1_555 B A 9 1_555 0.041 0.051 0.342 -0.575 -15.825 2.665 12 A_U14:A32_B A 14 ? B 32 ? 20 1 1 A G 15 1_555 B C 8 1_555 -0.067 -0.076 -0.037 -8.538 -18.045 5.841 13 A_G15:C31_B A 15 ? B 31 ? 19 1 1 A G 18 1_555 B C 6 1_555 -0.030 -0.087 -0.141 -5.723 0.754 -2.069 14 A_G18:C29_B A 18 ? B 29 ? 19 1 1 A U 19 1_555 B U 5 1_555 2.766 -1.367 -0.373 -3.500 -10.616 -30.547 15 A_U19:U28_B A 19 ? B 28 ? ? ? 1 A C 20 1_555 B G 4 1_555 0.369 -0.303 0.116 2.552 -7.616 1.333 16 A_C20:G27_B A 20 ? B 27 ? 19 1 1 A G 21 1_555 B C 3 1_555 0.004 -0.181 0.070 -2.290 1.085 0.652 17 A_G21:C26_B A 21 ? B 26 ? 19 1 1 A C 22 1_555 B G 2 1_555 0.196 0.249 -0.466 0.146 -1.505 12.321 18 A_C22:G25_B A 22 ? B 25 ? ? 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 2 1_555 B C 22 1_555 A C 3 1_555 B G 21 1_555 -0.767 -2.029 3.340 -1.964 4.999 37.307 -3.781 0.936 3.087 7.766 3.051 37.678 1 AA_G2C3:G44C45_BB A 2 ? B 45 ? A 3 ? B 44 ? 1 A C 3 1_555 B G 21 1_555 A G 4 1_555 B C 20 1_555 -0.695 -1.846 2.831 -0.420 8.939 32.646 -4.320 1.141 2.269 15.541 0.729 33.818 2 AA_C3G4:C43G44_BB A 3 ? B 44 ? A 4 ? B 43 ? 1 A G 4 1_555 B C 20 1_555 A U 5 1_555 B U 19 1_555 -1.071 -2.086 3.293 4.136 1.830 20.558 -6.442 4.581 2.830 5.048 -11.411 21.045 3 AA_G4U5:U42C43_BB A 4 ? B 43 ? A 5 ? B 42 ? 1 A U 5 1_555 B U 19 1_555 A C 6 1_555 B G 18 1_555 2.236 -2.569 3.537 -4.015 -1.112 43.773 -3.320 -3.390 3.390 -1.488 5.371 43.961 4 AA_U5C6:G41U42_BB A 5 ? B 42 ? A 6 ? B 41 ? 1 A C 6 1_555 B G 18 1_555 A C 8 1_555 B G 15 1_555 1.321 -3.645 6.199 -11.658 16.717 78.490 -3.593 -1.562 5.266 13.010 9.073 80.677 5 AA_C6C8:G38G41_BB A 6 ? B 41 ? A 8 ? B 38 ? 1 A C 8 1_555 B G 15 1_555 A A 9 1_555 B U 14 1_555 -0.311 -1.518 3.167 -1.912 10.150 35.148 -3.688 0.257 2.654 16.376 3.085 36.588 6 AA_C8A9:U37G38_BB A 8 ? B 38 ? A 9 ? B 37 ? 1 A A 9 1_555 B U 14 1_555 A C 10 1_555 B G 13 1_555 0.680 -1.674 3.181 2.321 1.228 29.294 -3.554 -0.857 3.153 2.422 -4.578 29.409 7 AA_A9C10:G36U37_BB A 9 ? B 37 ? A 10 ? B 36 ? 1 A C 10 1_555 B G 13 1_555 A C 11 1_555 B G 12 1_555 -0.691 -1.796 3.335 0.447 6.788 32.223 -4.285 1.293 2.897 12.062 -0.795 32.915 8 AA_C10C11:G35G36_BB A 10 ? B 36 ? A 11 ? B 35 ? 1 A C 11 1_555 B G 12 1_555 A G 12 1_555 B C 11 1_555 -0.157 -1.521 3.071 -2.675 11.784 28.733 -4.759 -0.144 2.290 22.529 5.114 31.121 9 AA_C11G12:C34G35_BB A 11 ? B 35 ? A 12 ? B 34 ? 1 A G 12 1_555 B C 11 1_555 A G 13 1_555 B C 10 1_555 0.046 -1.530 3.309 1.010 6.304 30.923 -3.946 0.097 2.947 11.668 -1.870 31.559 10 AA_G12G13:C33C34_BB A 12 ? B 34 ? A 13 ? B 33 ? 1 A G 13 1_555 B C 10 1_555 A U 14 1_555 B A 9 1_555 0.322 -1.122 3.184 -1.350 5.162 33.515 -2.706 -0.757 2.968 8.881 2.323 33.925 11 AA_G13U14:A32C33_BB A 13 ? B 33 ? A 14 ? B 32 ? 1 A U 14 1_555 B A 9 1_555 A G 15 1_555 B C 8 1_555 0.237 -1.508 3.240 3.739 11.531 34.005 -3.949 0.106 2.618 18.983 -6.155 36.041 12 AA_U14G15:C31A32_BB A 14 ? B 32 ? A 15 ? B 31 ? 1 A G 18 1_555 B C 6 1_555 A U 19 1_555 B U 5 1_555 -2.600 -2.567 3.318 -1.703 1.874 43.389 -3.650 3.344 3.305 2.532 2.301 43.459 13 AA_G18U19:U28C29_BB A 18 ? B 29 ? A 19 ? B 28 ? 1 A U 19 1_555 B U 5 1_555 A C 20 1_555 B G 4 1_555 0.979 -2.563 3.013 -2.239 5.340 18.860 -9.523 -3.714 2.085 15.820 6.632 19.721 14 AA_U19C20:G27U28_BB A 19 ? B 28 ? A 20 ? B 27 ? 1 A C 20 1_555 B G 4 1_555 A G 21 1_555 B C 3 1_555 0.119 -1.837 3.340 -0.730 2.865 28.942 -4.281 -0.396 3.143 5.713 1.456 29.090 15 AA_C20G21:C26G27_BB A 20 ? B 27 ? A 21 ? B 26 ? 1 A G 21 1_555 B C 3 1_555 A C 22 1_555 B G 2 1_555 1.010 -2.149 3.203 7.661 7.318 31.555 -4.912 -0.554 2.811 13.006 -13.616 33.243 16 AA_G21C22:G25C26_BB A 21 ? B 26 ? A 22 ? B 25 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 NEOMYCIN NMY 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 1J7T _pdbx_initial_refinement_model.details 'PDB Entry: 1J7T' #