data_2G5Q # _entry.id 2G5Q # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.280 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2G5Q NDB DR0031 RCSB RCSB036721 WWPDB D_1000036721 # _pdbx_database_PDB_obs_spr.id OBSLTE _pdbx_database_PDB_obs_spr.date 2014-05-07 _pdbx_database_PDB_obs_spr.pdb_id 4P20 _pdbx_database_PDB_obs_spr.replace_pdb_id 2G5Q _pdbx_database_PDB_obs_spr.details ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 2G5K _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.entry_id 2G5Q _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2006-02-23 _pdbx_database_status.status_code OBS _pdbx_database_status.status_code_sf OBS _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kondo, J.' 1 'Francois, B.' 2 'Russell, R.J.M.' 3 'Murray, J.B.' 4 'Westhof, E.' 5 # _citation.id primary _citation.title ;Crystal structure of the bacterial ribosomal decoding site complexed with amikacin containing the gamma-amino-alpha-hydroxybutyryl (haba) group. ; _citation.journal_abbrev Biochimie _citation.journal_volume 88 _citation.page_first 1027 _citation.page_last 1031 _citation.year 2006 _citation.journal_id_ASTM BICMBE _citation.country FR _citation.journal_id_ISSN 0300-9084 _citation.journal_id_CSD 0466 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16806634 _citation.pdbx_database_id_DOI 10.1016/j.biochi.2006.05.017 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Kondo, J.' 1 primary 'Russell, R.J.M.' 2 primary 'Murray, J.B.' 3 primary 'Westhof, E.' 4 # _cell.length_a 47.550 _cell.length_b 32.820 _cell.length_c 52.660 _cell.angle_alpha 90.00 _cell.angle_beta 108.71 _cell.angle_gamma 90.00 _cell.entry_id 2G5Q _cell.pdbx_unique_axis ? _cell.Z_PDB 4 _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 1 21 1' _symmetry.entry_id 2G5Q _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 4 _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 "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 ;(2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide ; 585.603 2 ? ? ? ? 3 water nat water 18.015 76 ? ? ? ? # _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 # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2G5Q _struct_ref.pdbx_db_accession 2G5Q _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _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 2G5Q A 1 ? 23 ? 2G5Q 0 ? 22 ? 0 22 2 1 2G5Q B 1 ? 23 ? 2G5Q 22 ? 44 ? 22 44 # 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 AKN non-polymer . ;(2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide ; AMIKACIN 'C22 H43 N5 O13' 585.603 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 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.entry_id 2G5Q _exptl.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.65 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 53.51 _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 6.4 _exptl_crystal_grow.temp 310 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details 'pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 310K' _exptl_crystal_grow.pdbx_pH_range . # _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 4' _diffrn_detector.pdbx_collection_date 2004-06-26 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator Diamond _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 0.9357 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID14-4' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9357 _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID14-4 # _reflns.entry_id 2G5Q _reflns.d_resolution_high 2.700 _reflns.d_resolution_low 32.820 _reflns.number_obs 4398 _reflns.pdbx_scaling_rejects 120 _reflns.pdbx_Rmerge_I_obs 0.16 _reflns.pdbx_netI_over_sigmaI 4.800 _reflns.pdbx_chi_squared 0.960 _reflns.pdbx_redundancy 3.590 _reflns.percent_possible_obs 100.000 _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_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.70 _reflns_shell.d_res_low 2.80 _reflns_shell.number_measured_obs ? _reflns_shell.number_measured_all 1607 _reflns_shell.number_unique_obs 445 _reflns_shell.Rmerge_I_obs 0.432 _reflns_shell.meanI_over_sigI_obs 2.0 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_chi_squared 0.590 _reflns_shell.pdbx_redundancy 3.61 _reflns_shell.percent_possible_obs 100.00 _reflns_shell.number_unique_all ? _reflns_shell.percent_possible_all ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.ls_d_res_high 2.700 _refine.ls_d_res_low 10.000 _refine.pdbx_ls_sigma_F 3 _refine.ls_percent_reflns_obs 95.700 _refine.ls_number_reflns_obs 4118 _refine.ls_R_factor_R_work 0.214 _refine.ls_R_factor_R_free 0.271 _refine.ls_percent_reflns_R_free 9.900 _refine.ls_number_reflns_R_free 425 _refine.B_iso_mean 48.391 _refine.solvent_model_param_bsol 59.847 _refine.aniso_B[1][1] 3.781 _refine.aniso_B[2][2] 0.851 _refine.aniso_B[3][3] -4.632 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] -14.368 _refine.aniso_B[2][3] 0.000 _refine.overall_FOM_work_R_set 0.790 _refine.entry_id 2G5Q _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 'pdb entry 1J7T' _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details random _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_overall_phase_error ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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 80 _refine_hist.number_atoms_solvent 76 _refine_hist.number_atoms_total 1054 _refine_hist.d_res_high 2.700 _refine_hist.d_res_low 10.000 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.006 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.0 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 1.4 ? ? ? '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 2.700 2.820 8 . 443 . 0.374 0.411 . 46 . . 489 . 'X-RAY DIFFRACTION' 2.820 2.970 8 . 447 . 0.309 0.407 . 50 . . 497 . 'X-RAY DIFFRACTION' 2.970 3.150 8 . 449 . 0.255 0.369 . 52 . . 501 . 'X-RAY DIFFRACTION' 3.150 3.380 8 . 466 . 0.191 0.283 . 56 . . 522 . 'X-RAY DIFFRACTION' 3.380 3.700 8 . 466 . 0.218 0.285 . 45 . . 511 . 'X-RAY DIFFRACTION' 3.700 4.200 8 . 470 . 0.214 0.272 . 60 . . 530 . 'X-RAY DIFFRACTION' 4.200 5.170 8 . 469 . 0.184 0.271 . 60 . . 529 . 'X-RAY DIFFRACTION' 5.170 10.000 8 . 483 . 0.171 0.171 . 56 . . 539 . '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 CNS_TOPPAR:water_rep.param CNS_TOPPAR:water.top 'X-RAY DIFFRACTION' 3 amikacin3.param amikacin3.top 'X-RAY DIFFRACTION' # _struct.entry_id 2G5Q _struct.title 'Crystal structures of the bacterial ribosomal decoding site complexed with amikacin.' _struct.pdbx_descriptor ;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', amikacin ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2G5Q _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'aminoglycoside, haba group, ribosomal decoding site, X-ray analysis, RNA, amikacin' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 3 ? # _struct_biol.id 1 # 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 hydrog1 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 23 N3 ? ? A G 2 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 23 O2 ? ? A G 2 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 23 N4 ? ? A G 2 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 22 N1 ? ? A C 3 B G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 22 O6 ? ? A C 3 B G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 22 N2 ? ? A C 3 B G 43 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 21 N3 ? ? A G 4 B C 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 21 O2 ? ? A G 4 B C 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 21 N4 ? ? A G 4 B C 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A U 6 O4 ? ? ? 1_555 B U 20 N3 ? ? A U 5 B U 41 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? hydrog11 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 19 N1 ? ? A C 6 B G 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 19 O6 ? ? A C 6 B G 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 19 N2 ? ? A C 6 B G 40 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A C 9 N3 ? ? ? 1_555 B G 16 N1 ? ? A C 8 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A C 9 N4 ? ? ? 1_555 B G 16 O6 ? ? A C 8 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? A C 9 O2 ? ? ? 1_555 B G 16 N2 ? ? A C 8 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A A 10 N1 ? ? ? 1_555 B U 15 N3 ? ? A A 9 B U 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A A 10 N6 ? ? ? 1_555 B U 15 O4 ? ? A A 9 B U 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 14 N1 ? ? A C 10 B G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 14 O6 ? ? A C 10 B G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog21 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 14 N2 ? ? A C 10 B G 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog22 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 13 N1 ? ? A C 11 B G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog23 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 13 O6 ? ? A C 11 B G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog24 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 13 N2 ? ? A C 11 B G 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog25 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 12 B C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog26 hydrog ? ? A G 13 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 12 B C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog27 hydrog ? ? A G 13 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 12 B C 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog28 hydrog ? ? A G 14 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 13 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog29 hydrog ? ? A G 14 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 13 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog30 hydrog ? ? A G 14 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 13 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog31 hydrog ? ? A U 15 N3 ? ? ? 1_555 B A 10 N1 ? ? A U 14 B A 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog32 hydrog ? ? A U 15 O4 ? ? ? 1_555 B A 10 N6 ? ? A U 14 B A 31 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog33 hydrog ? ? A G 16 N1 ? ? ? 1_555 B C 9 N3 ? ? A G 15 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog34 hydrog ? ? A G 16 N2 ? ? ? 1_555 B C 9 O2 ? ? A G 15 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog35 hydrog ? ? A G 16 O6 ? ? ? 1_555 B C 9 N4 ? ? A G 15 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog36 hydrog ? ? A G 19 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 18 B C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog37 hydrog ? ? A G 19 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 18 B C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog38 hydrog ? ? A G 19 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 18 B C 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog39 hydrog ? ? A U 20 N3 ? ? ? 1_555 B U 6 O4 ? ? A U 19 B U 27 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? hydrog40 hydrog ? ? A C 21 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 20 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog41 hydrog ? ? A C 21 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 20 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog42 hydrog ? ? A C 21 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 20 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog43 hydrog ? ? A G 22 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 21 B C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog44 hydrog ? ? A G 22 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 21 B C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog45 hydrog ? ? A G 22 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 21 B C 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog46 hydrog ? ? A C 23 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 22 B G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog47 hydrog ? ? A C 23 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 22 B G 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog48 hydrog ? ? A C 23 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 22 B G 24 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 ? ? ? ? 17 'BINDING SITE FOR RESIDUE AKN B 51' AC2 Software ? ? ? ? 15 'BINDING SITE FOR RESIDUE AKN A 52' 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 17 G A 3 ? G A 2 . ? 1_555 ? 2 AC1 17 C A 4 ? C A 3 . ? 1_555 ? 3 AC1 17 G A 5 ? G A 4 . ? 1_555 ? 4 AC1 17 U A 6 ? U A 5 . ? 1_555 ? 5 AC1 17 C A 7 ? C A 6 . ? 1_555 ? 6 AC1 17 A A 8 ? A A 7 . ? 1_555 ? 7 AC1 17 G B 16 ? G B 37 . ? 1_555 ? 8 AC1 17 A B 17 ? A B 38 . ? 1_555 ? 9 AC1 17 A B 18 ? A B 39 . ? 1_555 ? 10 AC1 17 G B 19 ? G B 40 . ? 1_555 ? 11 AC1 17 U B 20 ? U B 41 . ? 1_555 ? 12 AC1 17 C B 21 ? C B 42 . ? 1_555 ? 13 AC1 17 G B 22 ? G B 43 . ? 1_555 ? 14 AC1 17 HOH F . ? HOH B 109 . ? 1_555 ? 15 AC1 17 HOH F . ? HOH B 111 . ? 1_555 ? 16 AC1 17 HOH F . ? HOH B 117 . ? 1_555 ? 17 AC1 17 HOH F . ? HOH B 148 . ? 1_555 ? 18 AC2 15 G A 16 ? G A 15 . ? 1_555 ? 19 AC2 15 A A 17 ? A A 16 . ? 1_555 ? 20 AC2 15 A A 18 ? A A 17 . ? 1_555 ? 21 AC2 15 G A 19 ? G A 18 . ? 1_555 ? 22 AC2 15 U A 20 ? U A 19 . ? 1_555 ? 23 AC2 15 C A 21 ? C A 20 . ? 1_555 ? 24 AC2 15 G A 22 ? G A 21 . ? 1_555 ? 25 AC2 15 C A 23 ? C A 22 . ? 1_555 ? 26 AC2 15 HOH E . ? HOH A 171 . ? 1_555 ? 27 AC2 15 G B 3 ? G B 24 . ? 1_555 ? 28 AC2 15 C B 4 ? C B 25 . ? 1_555 ? 29 AC2 15 G B 5 ? G B 26 . ? 1_555 ? 30 AC2 15 U B 6 ? U B 27 . ? 1_555 ? 31 AC2 15 C B 7 ? C B 28 . ? 1_555 ? 32 AC2 15 A B 8 ? A B 29 . ? 1_555 ? # _atom_sites.entry_id 2G5Q _atom_sites.fract_transf_matrix[1][1] 0.021030 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.007123 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.030469 _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] 0.020049 _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 0 ? ? ? A . n A 1 2 U 2 1 ? ? ? A . n A 1 3 G 3 2 2 G G A . n A 1 4 C 4 3 3 C C A . n A 1 5 G 5 4 4 G G A . n A 1 6 U 6 5 5 U U A . n A 1 7 C 7 6 6 C C A . n A 1 8 A 8 7 7 A A A . n A 1 9 C 9 8 8 C C A . n A 1 10 A 10 9 9 A A A . n A 1 11 C 11 10 10 C C A . n A 1 12 C 12 11 11 C C A . n A 1 13 G 13 12 12 G G A . n A 1 14 G 14 13 13 G G A . n A 1 15 U 15 14 14 U U A . n A 1 16 G 16 15 15 G G A . n A 1 17 A 17 16 16 A A A . n A 1 18 A 18 17 17 A A A . n A 1 19 G 19 18 18 G G A . n A 1 20 U 20 19 19 U U A . n A 1 21 C 21 20 20 C C A . n A 1 22 G 22 21 21 G G A . n A 1 23 C 23 22 22 C C A . n B 1 1 U 1 22 ? ? ? B . n B 1 2 U 2 23 ? ? ? B . n B 1 3 G 3 24 24 G G B . n B 1 4 C 4 25 25 C C B . n B 1 5 G 5 26 26 G G B . n B 1 6 U 6 27 27 U U B . n B 1 7 C 7 28 28 C C B . n B 1 8 A 8 29 29 A A B . n B 1 9 C 9 30 30 C C B . n B 1 10 A 10 31 31 A A B . n B 1 11 C 11 32 32 C C B . n B 1 12 C 12 33 33 C C B . n B 1 13 G 13 34 34 G G B . n B 1 14 G 14 35 35 G G B . n B 1 15 U 15 36 36 U U B . n B 1 16 G 16 37 37 G G B . n B 1 17 A 17 38 38 A A B . n B 1 18 A 18 39 39 A A B . n B 1 19 G 19 40 40 G G B . n B 1 20 U 20 41 41 U U B . n B 1 21 C 21 42 42 C C B . n B 1 22 G 22 43 43 G G B . n B 1 23 C 23 44 44 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 AKN 1 52 52 AKN AKN A . D 2 AKN 1 51 51 AKN AKN B . E 3 HOH 1 102 102 HOH HOH A . E 3 HOH 2 108 108 HOH HOH A . E 3 HOH 3 110 110 HOH HOH A . E 3 HOH 4 112 112 HOH HOH A . E 3 HOH 5 113 113 HOH HOH A . E 3 HOH 6 114 114 HOH HOH A . E 3 HOH 7 115 115 HOH HOH A . E 3 HOH 8 118 118 HOH HOH A . E 3 HOH 9 119 119 HOH HOH A . E 3 HOH 10 121 121 HOH HOH A . E 3 HOH 11 122 122 HOH HOH A . E 3 HOH 12 123 123 HOH HOH A . E 3 HOH 13 124 124 HOH HOH A . E 3 HOH 14 125 125 HOH HOH A . E 3 HOH 15 126 126 HOH HOH A . E 3 HOH 16 128 128 HOH HOH A . E 3 HOH 17 129 129 HOH HOH A . E 3 HOH 18 130 130 HOH HOH A . E 3 HOH 19 131 131 HOH HOH A . E 3 HOH 20 135 135 HOH HOH A . E 3 HOH 21 136 136 HOH HOH A . E 3 HOH 22 137 137 HOH HOH A . E 3 HOH 23 139 139 HOH HOH A . E 3 HOH 24 141 141 HOH HOH A . E 3 HOH 25 143 143 HOH HOH A . E 3 HOH 26 145 145 HOH HOH A . E 3 HOH 27 149 149 HOH HOH A . E 3 HOH 28 153 153 HOH HOH A . E 3 HOH 29 154 154 HOH HOH A . E 3 HOH 30 155 155 HOH HOH A . E 3 HOH 31 158 158 HOH HOH A . E 3 HOH 32 160 160 HOH HOH A . E 3 HOH 33 162 162 HOH HOH A . E 3 HOH 34 166 166 HOH HOH A . E 3 HOH 35 168 168 HOH HOH A . E 3 HOH 36 169 169 HOH HOH A . E 3 HOH 37 170 170 HOH HOH A . E 3 HOH 38 171 171 HOH HOH A . E 3 HOH 39 172 172 HOH HOH A . E 3 HOH 40 174 174 HOH HOH A . E 3 HOH 41 175 175 HOH HOH A . E 3 HOH 42 176 176 HOH HOH A . F 3 HOH 1 101 101 HOH HOH B . F 3 HOH 2 103 103 HOH HOH B . F 3 HOH 3 104 104 HOH HOH B . F 3 HOH 4 105 105 HOH HOH B . F 3 HOH 5 106 106 HOH HOH B . F 3 HOH 6 107 107 HOH HOH B . F 3 HOH 7 109 109 HOH HOH B . F 3 HOH 8 111 111 HOH HOH B . F 3 HOH 9 116 116 HOH HOH B . F 3 HOH 10 117 117 HOH HOH B . F 3 HOH 11 120 120 HOH HOH B . F 3 HOH 12 127 127 HOH HOH B . F 3 HOH 13 132 132 HOH HOH B . F 3 HOH 14 133 133 HOH HOH B . F 3 HOH 15 134 134 HOH HOH B . F 3 HOH 16 138 138 HOH HOH B . F 3 HOH 17 140 140 HOH HOH B . F 3 HOH 18 142 142 HOH HOH B . F 3 HOH 19 144 144 HOH HOH B . F 3 HOH 20 146 146 HOH HOH B . F 3 HOH 21 147 147 HOH HOH B . F 3 HOH 22 148 148 HOH HOH B . F 3 HOH 23 150 150 HOH HOH B . F 3 HOH 24 151 151 HOH HOH B . F 3 HOH 25 152 152 HOH HOH B . F 3 HOH 26 156 156 HOH HOH B . F 3 HOH 27 157 157 HOH HOH B . F 3 HOH 28 159 159 HOH HOH B . F 3 HOH 29 161 161 HOH HOH B . F 3 HOH 30 163 163 HOH HOH B . F 3 HOH 31 164 164 HOH HOH B . F 3 HOH 32 165 165 HOH HOH B . F 3 HOH 33 167 167 HOH HOH B . F 3 HOH 34 173 173 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 2006-10-03 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2014-05-07 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description 1 1 'Structure model' repository 'Initial release' ? 2 4 'Structure model' repository Obsolete ? # 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' Other # 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 8.0SSI 'Feb 4 2003' 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 1.701 'Nov. 1, 2005' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 3 CrystalClear '(MSC/RIGAKU)' ? ? ? ? 'data reduction' ? ? ? 4 CrystalClear '(MSC/RIGAKU)' ? ? ? ? 'data scaling' ? ? ? 5 AMoRE . ? ? ? ? phasing ? ? ? 6 # _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 0.071 _pdbx_validate_planes.type 'SIDE CHAIN' # loop_ _pdbx_validate_chiral.id _pdbx_validate_chiral.PDB_model_num _pdbx_validate_chiral.auth_atom_id _pdbx_validate_chiral.label_alt_id _pdbx_validate_chiral.auth_asym_id _pdbx_validate_chiral.auth_comp_id _pdbx_validate_chiral.auth_seq_id _pdbx_validate_chiral.PDB_ins_code _pdbx_validate_chiral.details _pdbx_validate_chiral.omega 1 1 C37 ? A AKN 52 ? 'WRONG HAND' . 2 1 C37 ? B AKN 51 ? 'WRONG HAND' . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 N 1 A AKN 52 ? N37 ? C AKN 1 N37 2 1 N 1 B AKN 51 ? N37 ? D AKN 1 N37 # 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 0 ? A U 1 2 1 Y 1 A U 1 ? A U 2 3 1 Y 1 B U 22 ? B U 1 4 1 Y 1 B U 23 ? B U 2 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2G5Q 'double helix' 2G5Q 'a-form double helix' 2G5Q 'mismatched base pair' 2G5Q '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 -0.192 -0.153 0.383 3.829 -7.384 1.850 1 A_G2:C44_B A 2 ? B 44 ? 19 1 1 A C 4 1_555 B G 22 1_555 0.090 -0.025 0.267 -1.454 -12.569 -1.760 2 A_C3:G43_B A 3 ? B 43 ? 19 1 1 A G 5 1_555 B C 21 1_555 -0.317 -0.010 0.040 3.609 -5.903 1.583 3 A_G4:C42_B A 4 ? B 42 ? 19 1 1 A U 6 1_555 B U 20 1_555 -2.758 -1.071 -1.270 10.070 -9.261 -27.554 4 A_U5:U41_B A 5 ? B 41 ? ? ? 1 A C 7 1_555 B G 19 1_555 0.373 -0.208 -0.196 -5.086 -0.342 -1.470 5 A_C6:G40_B A 6 ? B 40 ? 19 1 1 A C 9 1_555 B G 16 1_555 0.214 -0.132 0.011 7.101 -20.838 0.320 6 A_C8:G37_B A 8 ? B 37 ? 19 1 1 A A 10 1_555 B U 15 1_555 0.124 -0.080 -0.161 1.076 -18.388 1.939 7 A_A9:U36_B A 9 ? B 36 ? 20 1 1 A C 11 1_555 B G 14 1_555 0.296 -0.190 0.056 6.331 -18.283 -0.089 8 A_C10:G35_B A 10 ? B 35 ? 19 1 1 A C 12 1_555 B G 13 1_555 0.053 -0.122 0.442 -2.146 -4.110 2.117 9 A_C11:G34_B A 11 ? B 34 ? 19 1 1 A G 13 1_555 B C 12 1_555 -0.076 -0.109 0.319 -0.590 -9.055 -0.388 10 A_G12:C33_B A 12 ? B 33 ? 19 1 1 A G 14 1_555 B C 11 1_555 -0.049 -0.018 -0.107 -5.961 -17.569 2.168 11 A_G13:C32_B A 13 ? B 32 ? 19 1 1 A U 15 1_555 B A 10 1_555 -0.015 -0.131 -0.137 4.930 -11.392 0.705 12 A_U14:A31_B A 14 ? B 31 ? 20 1 1 A G 16 1_555 B C 9 1_555 -0.335 -0.046 -0.052 -15.766 -25.962 0.003 13 A_G15:C30_B A 15 ? B 30 ? 19 1 1 A G 19 1_555 B C 7 1_555 -0.242 -0.229 -0.233 4.399 1.924 -2.127 14 A_G18:C28_B A 18 ? B 28 ? 19 1 1 A U 20 1_555 B U 6 1_555 2.017 -1.312 -0.475 1.451 -6.581 -28.908 15 A_U19:U27_B A 19 ? B 27 ? ? ? 1 A C 21 1_555 B G 5 1_555 0.325 -0.251 -0.129 4.101 -0.051 -0.239 16 A_C20:G26_B A 20 ? B 26 ? 19 1 1 A G 22 1_555 B C 4 1_555 -0.152 -0.052 0.226 -2.854 -2.231 3.969 17 A_G21:C25_B A 21 ? B 25 ? 19 1 1 A C 23 1_555 B G 3 1_555 0.365 -0.076 0.434 -0.635 -3.250 6.447 18 A_C22:G24_B A 22 ? B 24 ? 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 -0.342 -1.866 3.416 -0.982 1.992 34.056 -3.506 0.422 3.313 3.396 1.675 34.126 1 AA_G2C3:G43C44_BB A 2 ? B 44 ? A 3 ? B 43 ? 1 A C 4 1_555 B G 22 1_555 A G 5 1_555 B C 21 1_555 -0.301 -1.947 2.969 0.498 6.366 27.571 -5.226 0.713 2.461 13.136 -1.027 28.287 2 AA_C3G4:C42G43_BB A 3 ? B 43 ? A 4 ? B 42 ? 1 A G 5 1_555 B C 21 1_555 A U 6 1_555 B U 20 1_555 -0.712 -2.139 3.212 7.205 3.628 18.480 -7.584 4.954 2.314 10.661 -21.176 20.150 3 AA_G4U5:U41C42_BB A 4 ? B 42 ? A 5 ? B 41 ? 1 A U 6 1_555 B U 20 1_555 A C 7 1_555 B G 19 1_555 2.036 -2.448 4.004 -5.027 4.448 46.687 -3.483 -3.023 3.545 5.578 6.305 47.141 4 AA_U5C6:G40U41_BB A 5 ? B 41 ? A 6 ? B 40 ? 1 A C 7 1_555 B G 19 1_555 A C 9 1_555 B G 16 1_555 1.314 -3.303 6.352 -10.294 14.274 77.339 -3.317 -1.553 5.592 11.286 8.139 79.009 5 AA_C6C8:G37G40_BB A 6 ? B 40 ? A 8 ? B 37 ? 1 A C 9 1_555 B G 16 1_555 A A 10 1_555 B U 15 1_555 -0.071 -1.563 3.340 1.036 15.652 30.404 -4.930 0.271 2.283 27.653 -1.831 34.127 6 AA_C8A9:U36G37_BB A 8 ? B 37 ? A 9 ? B 36 ? 1 A A 10 1_555 B U 15 1_555 A C 11 1_555 B G 14 1_555 0.670 -1.825 3.109 0.305 3.116 31.387 -3.894 -1.180 2.925 5.743 -0.563 31.539 7 AA_A9C10:G35U36_BB A 9 ? B 36 ? A 10 ? B 35 ? 1 A C 11 1_555 B G 14 1_555 A C 12 1_555 B G 13 1_555 -0.628 -2.050 3.496 -4.864 3.943 30.642 -4.584 0.202 3.272 7.365 9.086 31.260 8 AA_C10C11:G34G35_BB A 10 ? B 35 ? A 11 ? B 34 ? 1 A C 12 1_555 B G 13 1_555 A G 13 1_555 B C 12 1_555 -0.125 -1.656 3.072 0.295 7.040 30.429 -4.259 0.281 2.630 13.191 -0.552 31.215 9 AA_C11G12:C33G34_BB A 11 ? B 34 ? A 12 ? B 33 ? 1 A G 13 1_555 B C 12 1_555 A G 14 1_555 B C 11 1_555 0.391 -1.598 3.236 5.249 9.563 32.985 -4.049 0.096 2.710 16.297 -8.945 34.694 10 AA_G12G13:C32C33_BB A 12 ? B 33 ? A 13 ? B 32 ? 1 A G 14 1_555 B C 11 1_555 A U 15 1_555 B A 10 1_555 -0.163 -1.509 3.108 -0.267 -1.783 29.114 -2.622 0.267 3.194 -3.543 0.531 29.168 11 AA_G13U14:A31C32_BB A 13 ? B 32 ? A 14 ? B 31 ? 1 A U 15 1_555 B A 10 1_555 A G 16 1_555 B C 9 1_555 0.390 -1.453 3.559 2.059 22.078 33.941 -4.531 -0.338 2.259 33.729 -3.146 40.363 12 AA_U14G15:C30A31_BB A 14 ? B 31 ? A 15 ? B 30 ? 1 A G 16 1_555 B C 9 1_555 A G 19 1_555 B C 7 1_555 -1.554 -3.469 6.085 5.801 14.748 76.250 -3.506 1.530 5.336 11.823 -4.650 77.633 13 AA_G15G18:C28C30_BB A 15 ? B 30 ? A 18 ? B 28 ? 1 A G 19 1_555 B C 7 1_555 A U 20 1_555 B U 6 1_555 -1.645 -2.417 3.553 0.779 -1.924 45.326 -2.947 2.209 3.620 -2.495 -1.010 45.371 14 AA_G18U19:U27C28_BB A 18 ? B 28 ? A 19 ? B 27 ? 1 A U 20 1_555 B U 6 1_555 A C 21 1_555 B G 5 1_555 0.674 -2.647 3.293 -0.172 8.383 22.565 -8.680 -1.665 2.177 20.536 0.421 24.053 15 AA_U19C20:G26U27_BB A 19 ? B 27 ? A 20 ? B 26 ? 1 A C 21 1_555 B G 5 1_555 A G 22 1_555 B C 4 1_555 0.737 -1.668 3.288 -1.505 5.512 27.935 -4.585 -1.823 2.869 11.269 3.078 28.502 16 AA_C20G21:C25G26_BB A 20 ? B 26 ? A 21 ? B 25 ? 1 A G 22 1_555 B C 4 1_555 A C 23 1_555 B G 3 1_555 0.374 -2.243 3.149 0.826 -0.607 34.625 -3.676 -0.505 3.194 -1.019 -1.387 34.640 17 AA_G21C22:G24C25_BB A 21 ? B 25 ? A 22 ? B 24 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 ;(2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide ; AKN 3 water HOH #