data_2O3W # _entry.id 2O3W # _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 2O3W pdb_00002o3w 10.2210/pdb2o3w/pdb NDB DR0038 ? ? RCSB RCSB040654 ? ? WWPDB D_1000040654 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2G5K 'Homo sapiens cytoplasmic A site complexed with apramycin (Cyto/Apramycin)' unspecified PDB 2FQN 'Homo sapiens cytoplasmic A site without any aminoglycosides (Cyto-Free)' unspecified PDB 2O3V 'Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site complexed with paromamine derivative NB33' unspecified PDB 2O3X 'Crystal Structure of the Prokaryotic Ribosomal Decoding Site Complexed with Paromamine Derivative NB30' 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 2O3W _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 47.537 _cell.length_b 50.310 _cell.length_c 57.397 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 2O3W _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 2' _symmetry.entry_id 2O3W _symmetry.Int_Tables_number 18 _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*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3') ; 7355.409 2 ? ? ? ? 2 non-polymer syn PAROMOMYCIN 615.628 1 ? ? ? ? 3 water nat water 18.015 32 ? ? ? ? # _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 UUGCGUCGCUCCGGAAAAGUCGC _entity_poly.pdbx_seq_one_letter_code_can UUGCGUCGCUCCGGAAAAGUCGC _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 G n 1 9 C n 1 10 U n 1 11 C n 1 12 C n 1 13 G n 1 14 G n 1 15 A n 1 16 A 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 2O3W _struct_ref.db_name PDB _struct_ref.entity_id 1 _struct_ref.pdbx_db_accession 2O3W _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code UUGCGUCGCUCCGGAAAAGUCGC _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 2O3W A 1 ? 23 ? 2O3W 1 ? 23 ? 1 23 2 1 2O3W B 1 ? 23 ? 2O3W 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 HOH non-polymer . WATER ? 'H2 O' 18.015 PAR non-polymer . PAROMOMYCIN 'PAROMOMYCIN I; AMMINOSIDIN; CATENULIN; CRESTOMYCIN; MONOMYCIN A; NEOMYCIN E' 'C23 H45 N5 O14' 615.628 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.crystals_number 1 _exptl.entry_id 2O3W _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.33 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 47.27 _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, hexammine cobalt chloride, spermine tetrahydrochloride, 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 'hexammine cobalt chloride' ? ? ? 1 5 1 'spermine tetrahydrochloride' ? ? ? 1 6 2 'Potassium chloride' ? ? ? 1 7 2 2-methyl-2,4-pentanediol ? ? ? 1 8 2 'hexammine cobalt chloride' ? ? ? 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 2005-11-28 _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 0.9000 _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 0.9000 _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID29 # _reflns.entry_id 2O3W _reflns.d_resolution_high 2.800 _reflns.d_resolution_low 57.397 _reflns.number_obs 3672 _reflns.pdbx_Rmerge_I_obs 0.085 _reflns.pdbx_netI_over_sigmaI 5.000 _reflns.pdbx_Rsym_value 0.085 _reflns.pdbx_redundancy 6.200 _reflns.percent_possible_obs 99.800 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _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 2.80 2.95 ? 3428 ? 0.414 1.6 0.414 ? 6.70 ? 515 100.00 ? 1 2.95 3.13 ? 3229 ? 0.177 2.1 0.177 ? 6.50 ? 496 100.00 ? 2 3.13 3.35 ? 3034 ? 0.12 3.4 0.12 ? 6.50 ? 469 100.00 ? 3 3.35 3.61 ? 2813 ? 0.108 3.5 0.108 ? 6.50 ? 435 100.00 ? 4 3.61 3.96 ? 2566 ? 0.097 4.0 0.097 ? 6.40 ? 404 100.00 ? 5 3.96 4.43 ? 2256 ? 0.09 6.5 0.09 ? 6.10 ? 368 100.00 ? 6 4.43 5.11 ? 1973 ? 0.078 7.7 0.078 ? 5.90 ? 333 100.00 ? 7 5.11 6.26 ? 1605 ? 0.065 8.9 0.065 ? 5.50 ? 290 100.00 ? 8 6.26 8.85 ? 1315 ? 0.048 11.0 0.048 ? 5.80 ? 228 100.00 ? 9 8.85 57.40 ? 611 ? 0.06 8.4 0.06 ? 4.60 ? 134 92.10 ? 10 # _refine.entry_id 2O3W _refine.ls_d_res_high 2.800 _refine.ls_d_res_low 57.35 _refine.pdbx_ls_sigma_F 3 _refine.ls_percent_reflns_obs 94.800 _refine.ls_number_reflns_obs 3480 _refine.ls_R_factor_R_work 0.251 _refine.ls_R_factor_R_free 0.273 _refine.ls_percent_reflns_R_free 9.500 _refine.ls_number_reflns_R_free 350 _refine.B_iso_mean 72.414 _refine.solvent_model_param_bsol 125.091 _refine.aniso_B[1][1] 4.326 _refine.aniso_B[2][2] -29.838 _refine.aniso_B[3][3] 25.512 _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 0.725 _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 2FQN _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values ;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.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _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 918 _refine_hist.pdbx_number_atoms_ligand 42 _refine_hist.number_atoms_solvent 32 _refine_hist.number_atoms_total 992 _refine_hist.d_res_high 2.800 _refine_hist.d_res_low 57.35 # 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 ? 0.006 1.500 ? 'X-RAY DIFFRACTION' ? c_angle_deg ? 0.990 2.000 ? 'X-RAY DIFFRACTION' ? c_scangle_it ? 3.113 2.500 ? '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 2.800 2.920 8 . 343 . 0.521 0.592 . 43 . . 386 . 'X-RAY DIFFRACTION' 2.920 3.070 8 . 367 . 0.316 0.348 . 37 . . 404 . 'X-RAY DIFFRACTION' 3.070 3.260 8 . 373 . 0.132 0.207 . 32 . . 405 . 'X-RAY DIFFRACTION' 3.260 3.500 8 . 371 . 0.264 0.323 . 48 . . 419 . 'X-RAY DIFFRACTION' 3.500 3.840 8 . 390 . 0.261 0.403 . 43 . . 433 . 'X-RAY DIFFRACTION' 3.840 4.350 8 . 387 . 0.235 0.342 . 45 . . 432 . 'X-RAY DIFFRACTION' 4.350 5.340 8 . 399 . 0.303 0.258 . 48 . . 447 . 'X-RAY DIFFRACTION' 5.340 10.000 8 . 436 . 0.387 0.433 . 39 . . 475 . '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 CNS_TOPPAR:dna-rna_rep.param CNS_TOPPAR:dna-rna.top 'X-RAY DIFFRACTION' 2 par_xplor.param par_xplor.top 'X-RAY DIFFRACTION' 3 CNS_TOPPAR:water_rep.param CNS_TOPPAR:water.top 'X-RAY DIFFRACTION' # _struct.entry_id 2O3W _struct.title 'Crystal Structure of the Homo sapiens Cytoplasmic Ribosomal Decoding Site in presence of paromomycin' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2O3W _struct_keywords.pdbx_keywords RNA _struct_keywords.text ;aminoglycoside, antibiotics, ribosome, decoding site, Homo sapiens, Eukaryote, cytoplasmic, Translation inhibition, Stop codon readthrough, unspecific binding, 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 3 ? E N N 3 ? # _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 U 6 N3 ? ? ? 1_555 B U 20 O4 ? ? A U 6 B U 43 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog11 hydrog ? ? A U 6 O2 ? ? ? 1_555 B U 20 N3 ? ? A U 6 B U 43 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog12 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 19 N1 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 19 O6 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 19 N2 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 9 N4 ? ? ? 1_555 B A 16 N1 ? ? A C 9 B A 39 1_555 ? ? ? ? ? ? 'C-A MISPAIR' ? ? ? hydrog16 hydrog ? ? A U 10 N3 ? ? ? 1_555 B A 15 N1 ? ? A U 10 B A 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A U 10 O4 ? ? ? 1_555 B A 15 N6 ? ? A U 10 B A 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 A 15 N1 ? ? ? 1_555 B U 10 N3 ? ? A A 15 B U 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A A 15 N6 ? ? ? 1_555 B U 10 O4 ? ? A A 15 B U 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A A 17 N3 ? ? ? 1_555 B C 9 N4 ? ? A A 17 B C 32 1_555 ? ? ? ? ? ? 'A-C MISPAIR' ? ? ? hydrog33 hydrog ? ? A A 18 N7 ? ? ? 1_555 B G 8 N2 ? ? A A 18 B G 31 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog34 hydrog ? ? A G 19 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 19 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 19 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A U 20 N3 ? ? ? 1_555 B U 6 O2 ? ? A U 20 B U 29 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog38 hydrog ? ? A U 20 O4 ? ? ? 1_555 B U 6 N3 ? ? A U 20 B U 29 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog39 hydrog ? ? A C 21 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 21 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 21 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 22 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 22 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 22 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 23 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 23 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 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 PAR 101 ? 8 'BINDING SITE FOR RESIDUE PAR B 101' 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 8 G A 8 ? G A 8 . ? 1_555 ? 2 AC1 8 C A 9 ? C A 9 . ? 1_555 ? 3 AC1 8 U B 10 ? U B 33 . ? 1_555 ? 4 AC1 8 C B 11 ? C B 34 . ? 1_555 ? 5 AC1 8 G B 13 ? G B 36 . ? 1_555 ? 6 AC1 8 G B 14 ? G B 37 . ? 1_555 ? 7 AC1 8 A B 15 ? A B 38 . ? 1_555 ? 8 AC1 8 A B 16 ? A B 39 . ? 3_545 ? # _atom_sites.entry_id 2O3W _atom_sites.fract_transf_matrix[1][1] 0.021036 _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] 0.019877 _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] 0.017423 _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 2 U U 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 G 8 8 8 G G A . n A 1 9 C 9 9 9 C C A . n A 1 10 U 10 10 10 U U 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 A 15 15 15 A A 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 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 G 8 31 31 G G B . n B 1 9 C 9 32 32 C C B . n B 1 10 U 10 33 33 U U 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 A 15 38 38 A A 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 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 # 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 PAR 1 101 101 PAR PAR B . D 3 HOH 1 24 202 HOH HOH A . D 3 HOH 2 25 205 HOH HOH A . D 3 HOH 3 26 207 HOH HOH A . D 3 HOH 4 27 209 HOH HOH A . D 3 HOH 5 28 213 HOH HOH A . D 3 HOH 6 29 215 HOH HOH A . D 3 HOH 7 30 216 HOH HOH A . D 3 HOH 8 31 220 HOH HOH A . D 3 HOH 9 32 222 HOH HOH A . D 3 HOH 10 33 223 HOH HOH A . D 3 HOH 11 34 224 HOH HOH A . D 3 HOH 12 35 226 HOH HOH A . D 3 HOH 13 36 227 HOH HOH A . D 3 HOH 14 37 229 HOH HOH A . E 3 HOH 1 102 201 HOH HOH B . E 3 HOH 2 103 203 HOH HOH B . E 3 HOH 3 104 204 HOH HOH B . E 3 HOH 4 105 206 HOH HOH B . E 3 HOH 5 106 208 HOH HOH B . E 3 HOH 6 107 210 HOH HOH B . E 3 HOH 7 108 211 HOH HOH B . E 3 HOH 8 109 212 HOH HOH B . E 3 HOH 9 110 214 HOH HOH B . E 3 HOH 10 111 217 HOH HOH B . E 3 HOH 11 112 218 HOH HOH B . E 3 HOH 12 113 219 HOH HOH B . E 3 HOH 13 114 221 HOH HOH B . E 3 HOH 14 115 225 HOH HOH B . E 3 HOH 15 116 228 HOH HOH B . E 3 HOH 16 117 230 HOH HOH B . E 3 HOH 17 118 231 HOH HOH B . E 3 HOH 18 119 232 HOH HOH B . # _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,D,E # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 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' 6 3 'Structure model' 'Structure summary' # 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 2 3 'Structure model' chem_comp_atom 3 3 'Structure model' chem_comp_bond 4 3 'Structure model' database_2 5 3 'Structure model' pdbx_initial_refinement_model 6 3 'Structure model' struct_ref_seq 7 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' '_chem_comp.pdbx_synonyms' 2 3 'Structure model' '_database_2.pdbx_DOI' 3 3 'Structure model' '_database_2.pdbx_database_accession' 4 3 'Structure model' '_struct_ref_seq.db_align_beg' 5 3 'Structure model' '_struct_ref_seq.db_align_end' 6 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 7 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 8 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 SCALA . ? other 'Phil Evans' pre@mrc-lmb.cam.ac.uk 'data processing' http://www.ccp4.ac.uk/dist/html/INDEX.html Fortran_77 ? 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 MOSFLM . ? ? ? ? 'data reduction' ? ? ? 5 SCALA . ? ? ? ? 'data scaling' ? ? ? 6 AMoRE . ? ? ? ? phasing ? ? ? 7 # 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 B U 24 ? B U 1 3 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 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 PAR C11 C N S 114 PAR O11 O N N 115 PAR C21 C N R 116 PAR N21 N N N 117 PAR C31 C N R 118 PAR O31 O N N 119 PAR C41 C N S 120 PAR O41 O N N 121 PAR C51 C N R 122 PAR O51 O N N 123 PAR C61 C N N 124 PAR O61 O N N 125 PAR C12 C N R 126 PAR N12 N N N 127 PAR C22 C N N 128 PAR C32 C N S 129 PAR N32 N N N 130 PAR C42 C N R 131 PAR C52 C N R 132 PAR O52 O N N 133 PAR C62 C N S 134 PAR O62 O N N 135 PAR C13 C N S 136 PAR C23 C N R 137 PAR O23 O N N 138 PAR C33 C N S 139 PAR O33 O N N 140 PAR C43 C N R 141 PAR O43 O N N 142 PAR C53 C N N 143 PAR O53 O N N 144 PAR C14 C N R 145 PAR C24 C N R 146 PAR N24 N N N 147 PAR C34 C N R 148 PAR O34 O N N 149 PAR C44 C N S 150 PAR O44 O N N 151 PAR C54 C N S 152 PAR O54 O N N 153 PAR C64 C N N 154 PAR N64 N N N 155 PAR H11 H N N 156 PAR H21 H N N 157 PAR HN21 H N N 158 PAR HN22 H N N 159 PAR H31 H N N 160 PAR HO31 H N N 161 PAR H41 H N N 162 PAR HO41 H N N 163 PAR H51 H N N 164 PAR H611 H N N 165 PAR H612 H N N 166 PAR HO61 H N N 167 PAR H12 H N N 168 PAR H121 H N N 169 PAR H122 H N N 170 PAR H221 H N N 171 PAR H222 H N N 172 PAR H32 H N N 173 PAR H321 H N N 174 PAR H322 H N N 175 PAR H42 H N N 176 PAR H52 H N N 177 PAR H62 H N N 178 PAR HO62 H N N 179 PAR H13 H N N 180 PAR H23 H N N 181 PAR HO23 H N N 182 PAR H33 H N N 183 PAR H43 H N N 184 PAR H531 H N N 185 PAR H532 H N N 186 PAR HO53 H N N 187 PAR H14 H N N 188 PAR H24 H N N 189 PAR H241 H N N 190 PAR H242 H N N 191 PAR H34 H N N 192 PAR HO34 H N N 193 PAR H44 H N N 194 PAR HO44 H N N 195 PAR H54 H N N 196 PAR H641 H N N 197 PAR H642 H N N 198 PAR HN61 H N N 199 PAR HN62 H N N 200 U OP3 O N N 201 U P P N N 202 U OP1 O N N 203 U OP2 O N N 204 U "O5'" O N N 205 U "C5'" C N N 206 U "C4'" C N R 207 U "O4'" O N N 208 U "C3'" C N S 209 U "O3'" O N N 210 U "C2'" C N R 211 U "O2'" O N N 212 U "C1'" C N R 213 U N1 N N N 214 U C2 C N N 215 U O2 O N N 216 U N3 N N N 217 U C4 C N N 218 U O4 O N N 219 U C5 C N N 220 U C6 C N N 221 U HOP3 H N N 222 U HOP2 H N N 223 U "H5'" H N N 224 U "H5''" H N N 225 U "H4'" H N N 226 U "H3'" H N N 227 U "HO3'" H N N 228 U "H2'" H N N 229 U "HO2'" H N N 230 U "H1'" H N N 231 U H3 H N N 232 U H5 H N N 233 U H6 H N N 234 # 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 PAR C11 O11 sing N N 118 PAR C11 C21 sing N N 119 PAR C11 O51 sing N N 120 PAR C11 H11 sing N N 121 PAR O11 C42 sing N N 122 PAR C21 N21 sing N N 123 PAR C21 C31 sing N N 124 PAR C21 H21 sing N N 125 PAR N21 HN21 sing N N 126 PAR N21 HN22 sing N N 127 PAR C31 O31 sing N N 128 PAR C31 C41 sing N N 129 PAR C31 H31 sing N N 130 PAR O31 HO31 sing N N 131 PAR C41 O41 sing N N 132 PAR C41 C51 sing N N 133 PAR C41 H41 sing N N 134 PAR O41 HO41 sing N N 135 PAR C51 O51 sing N N 136 PAR C51 C61 sing N N 137 PAR C51 H51 sing N N 138 PAR C61 O61 sing N N 139 PAR C61 H611 sing N N 140 PAR C61 H612 sing N N 141 PAR O61 HO61 sing N N 142 PAR C12 N12 sing N N 143 PAR C12 C22 sing N N 144 PAR C12 C62 sing N N 145 PAR C12 H12 sing N N 146 PAR N12 H121 sing N N 147 PAR N12 H122 sing N N 148 PAR C22 C32 sing N N 149 PAR C22 H221 sing N N 150 PAR C22 H222 sing N N 151 PAR C32 N32 sing N N 152 PAR C32 C42 sing N N 153 PAR C32 H32 sing N N 154 PAR N32 H321 sing N N 155 PAR N32 H322 sing N N 156 PAR C42 C52 sing N N 157 PAR C42 H42 sing N N 158 PAR C52 O52 sing N N 159 PAR C52 C62 sing N N 160 PAR C52 H52 sing N N 161 PAR O52 C13 sing N N 162 PAR C62 O62 sing N N 163 PAR C62 H62 sing N N 164 PAR O62 HO62 sing N N 165 PAR C13 C23 sing N N 166 PAR C13 O43 sing N N 167 PAR C13 H13 sing N N 168 PAR C23 O23 sing N N 169 PAR C23 C33 sing N N 170 PAR C23 H23 sing N N 171 PAR O23 HO23 sing N N 172 PAR C33 O33 sing N N 173 PAR C33 C43 sing N N 174 PAR C33 H33 sing N N 175 PAR O33 C14 sing N N 176 PAR C43 O43 sing N N 177 PAR C43 C53 sing N N 178 PAR C43 H43 sing N N 179 PAR C53 O53 sing N N 180 PAR C53 H531 sing N N 181 PAR C53 H532 sing N N 182 PAR O53 HO53 sing N N 183 PAR C14 C24 sing N N 184 PAR C14 O54 sing N N 185 PAR C14 H14 sing N N 186 PAR C24 N24 sing N N 187 PAR C24 C34 sing N N 188 PAR C24 H24 sing N N 189 PAR N24 H241 sing N N 190 PAR N24 H242 sing N N 191 PAR C34 O34 sing N N 192 PAR C34 C44 sing N N 193 PAR C34 H34 sing N N 194 PAR O34 HO34 sing N N 195 PAR C44 O44 sing N N 196 PAR C44 C54 sing N N 197 PAR C44 H44 sing N N 198 PAR O44 HO44 sing N N 199 PAR C54 O54 sing N N 200 PAR C54 C64 sing N N 201 PAR C54 H54 sing N N 202 PAR C64 N64 sing N N 203 PAR C64 H641 sing N N 204 PAR C64 H642 sing N N 205 PAR N64 HN61 sing N N 206 PAR N64 HN62 sing N N 207 U OP3 P sing N N 208 U OP3 HOP3 sing N N 209 U P OP1 doub N N 210 U P OP2 sing N N 211 U P "O5'" sing N N 212 U OP2 HOP2 sing N N 213 U "O5'" "C5'" sing N N 214 U "C5'" "C4'" sing N N 215 U "C5'" "H5'" sing N N 216 U "C5'" "H5''" sing N N 217 U "C4'" "O4'" sing N N 218 U "C4'" "C3'" sing N N 219 U "C4'" "H4'" sing N N 220 U "O4'" "C1'" sing N N 221 U "C3'" "O3'" sing N N 222 U "C3'" "C2'" sing N N 223 U "C3'" "H3'" sing N N 224 U "O3'" "HO3'" sing N N 225 U "C2'" "O2'" sing N N 226 U "C2'" "C1'" sing N N 227 U "C2'" "H2'" sing N N 228 U "O2'" "HO2'" sing N N 229 U "C1'" N1 sing N N 230 U "C1'" "H1'" sing N N 231 U N1 C2 sing N N 232 U N1 C6 sing N N 233 U C2 O2 doub N N 234 U C2 N3 sing N N 235 U N3 C4 sing N N 236 U N3 H3 sing N N 237 U C4 O4 doub N N 238 U C4 C5 sing N N 239 U C5 C6 doub N N 240 U C5 H5 sing N N 241 U C6 H6 sing N N 242 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2O3W 'bulge loop' 2O3W 'mismatched base pair' 2O3W 'internal loop' # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 PAROMOMYCIN PAR 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 2FQN _pdbx_initial_refinement_model.details ? #