data_4RBZ # _entry.id 4RBZ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _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 4RBZ pdb_00004rbz 10.2210/pdb4rbz/pdb NDB NA3176 ? ? RCSB RCSB087156 ? ? WWPDB D_1000087156 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4RBY . unspecified PDB 4RC0 . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4RBZ _pdbx_database_status.recvd_initial_deposition_date 2014-09-13 _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.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Pallan, P.S.' 1 'Egli, M.' 2 # _citation.id primary _citation.title 'Crystal Structure, Stability and siRNA Activity of Phosphorodithioate-Modified RNAs' _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Pallan, P.S.' 1 ? primary 'Yang, X.' 2 ? primary 'Sierant, M.' 3 ? primary 'Abeydeera, N.D.' 4 ? primary 'Hassell, T.' 5 ? primary 'Martinez, C.' 6 ? primary 'Janicka, M.' 7 ? primary 'Nawrot, B.' 8 ? primary 'Egli, M.' 9 ? # _cell.entry_id 4RBZ _cell.length_a 41.177 _cell.length_b 35.052 _cell.length_c 31.858 _cell.angle_alpha 90.00 _cell.angle_beta 128.66 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? _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.entry_id 4RBZ _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _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*(A2M)P*(ADS)P*UP*UP*AP*GP*CP*G)-3'" 3897.518 1 ? ? ? 'Adenosine phosphorodithioate RNA' 2 water nat water 18.015 82 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'CGCG(A2M)(ADS)UUAGCG' _entity_poly.pdbx_seq_one_letter_code_can CGCGAXUUAGCG _entity_poly.pdbx_strand_id A _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 A2M n 1 6 ADS n 1 7 U n 1 8 U n 1 9 A n 1 10 G n 1 11 C n 1 12 G 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 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4RBZ _struct_ref.pdbx_db_accession 4RBZ _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_seq_one_letter_code 'CGCG(A2M)(ADS)UUAGCG' _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4RBZ _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 12 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 4RBZ _struct_ref_seq.db_align_beg 101 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 112 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 101 _struct_ref_seq.pdbx_auth_seq_align_end 112 # 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 A2M 'RNA linking' n ;2'-O-methyladenosine 5'-(dihydrogen phosphate) ; ? 'C11 H16 N5 O7 P' 361.248 ADS non-polymer . "ADENOSINE-5'-(DITHIO)PHOSPHATE" ? 'C10 H14 N5 O5 P S2' 379.352 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 4RBZ _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.30 _exptl_crystal.density_percent_sol 46.59 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;20 mM sodium cacodylate, 40 mM potassium chloride, 6 mM spermine tetrahydrochloride, 5% v/v MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K ; _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 'MARMOSAIC 300 mm CCD' _diffrn_detector.pdbx_collection_date 2013-10-03 _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 'diamond(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97857 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 21-ID-G' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 21-ID-G _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.97857 # _reflns.entry_id 4RBZ _reflns.observed_criterion_sigma_I 5 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50 _reflns.d_resolution_high 1.18 _reflns.number_obs 11706 _reflns.number_all 11727 _reflns.percent_possible_obs 99.82 _reflns.pdbx_Rmerge_I_obs 0.074 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 45.69 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 5.9 _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.18 _reflns_shell.d_res_low 1.22 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.180 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 7.81 _reflns_shell.pdbx_redundancy 2.90 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 1159 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 4RBZ _refine.ls_number_reflns_obs 11706 _refine.ls_number_reflns_all 11727 _refine.pdbx_ls_sigma_I 5 _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 50 _refine.ls_d_res_high 1.18 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.154 _refine.ls_R_factor_R_free 0.190 _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 561 _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 THROUGHOUT _refine.details ? _refine.pdbx_starting_model 'PDB ENTRY 2Q1R' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _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.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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 256 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 82 _refine_hist.number_atoms_total 338 _refine_hist.d_res_high 1.18 _refine_hist.d_res_low 50 # 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_restraint_function _refine_ls_restr.pdbx_refine_id s_bond_d 0.010 ? ? ? ? 'X-RAY DIFFRACTION' s_angle_d 0.028 ? ? ? ? 'X-RAY DIFFRACTION' # _pdbx_refine.entry_id 4RBZ _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.R_factor_obs_no_cutoff 0.154 _pdbx_refine.free_R_factor_no_cutoff 0.190 _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.free_R_error_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff ? _pdbx_refine.free_R_val_test_set_ct_no_cutoff ? _pdbx_refine.R_factor_all_4sig_cutoff ? _pdbx_refine.R_factor_obs_4sig_cutoff ? _pdbx_refine.free_R_factor_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff ? _pdbx_refine.number_reflns_obs_4sig_cutoff ? # _struct.entry_id 4RBZ _struct.title 'X-ray structure of RNA containing adenosine phosphorodithioate' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4RBZ _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'phosphorodithioate RNA, adenosine phosphorodithioate, phosphorothioate, adenosine analogue, hydrophobic, backbone, 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 2 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A G 4 "O3'" ? ? ? 1_555 A A2M 5 P ? ? A G 104 A A2M 105 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale2 covale none ? A A2M 5 "O3'" ? ? ? 1_555 A ADS 6 P ? ? A A2M 105 A ADS 106 1_555 ? ? ? ? ? ? ? 1.596 ? ? covale3 covale one ? A ADS 6 "O3'" ? ? ? 1_555 A U 7 P ? ? A ADS 106 A U 107 1_555 ? ? ? ? ? ? ? 1.593 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 A G 12 N1 ? ? A C 101 A G 112 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 A G 12 O6 ? ? A C 101 A G 112 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 A G 12 N2 ? ? A C 101 A G 112 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 11 N3 ? ? A G 102 A C 111 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 11 O2 ? ? A G 102 A C 111 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 11 N4 ? ? A G 102 A C 111 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 10 N1 ? ? A C 103 A G 110 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 10 O6 ? ? A C 103 A G 110 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 10 N2 ? ? A C 103 A G 110 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N1 ? ? ? 1_555 A A 9 N1 A ? A G 104 A A 109 2_656 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 A A 9 N6 A ? A G 104 A A 109 2_656 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog12 hydrog ? ? A A2M 5 N1 ? ? ? 1_555 A U 8 N3 A ? A A2M 105 A U 108 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A2M 5 N6 ? ? ? 1_555 A U 8 O4 A ? A A2M 105 A U 108 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 8 N3 A ? ? 1_555 A A2M 5 N1 ? ? A U 108 A A2M 105 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 8 O4 A ? ? 1_555 A A2M 5 N6 ? ? A U 108 A A2M 105 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 9 N1 A ? ? 1_555 A G 4 N1 ? ? A A 109 A G 104 2_656 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog17 hydrog ? ? A A 9 N6 A ? ? 1_555 A G 4 O6 ? ? A A 109 A G 104 2_656 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog18 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 3 N3 ? ? A G 110 A C 103 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 3 O2 ? ? A G 110 A C 103 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 3 N4 ? ? A G 110 A C 103 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 11 N3 ? ? ? 1_555 A G 2 N1 ? ? A C 111 A G 102 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 N4 ? ? ? 1_555 A G 2 O6 ? ? A C 111 A G 102 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 11 O2 ? ? ? 1_555 A G 2 N2 ? ? A C 111 A G 102 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 N1 ? ? ? 1_555 A C 1 N3 ? ? A G 112 A C 101 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 12 N2 ? ? ? 1_555 A C 1 O2 ? ? A G 112 A C 101 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 12 O6 ? ? ? 1_555 A C 1 N4 ? ? A G 112 A C 101 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 4RBZ _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 4RBZ _atom_sites.fract_transf_matrix[1][1] 0.024285 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.019428 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.028529 _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] 0.040198 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O P S # loop_ # loop_ # 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 1 101 101 C C A . n A 1 2 G 2 102 102 G G A . n A 1 3 C 3 103 103 C C A . n A 1 4 G 4 104 104 G G A . n A 1 5 A2M 5 105 105 A2M A2M A . n A 1 6 ADS 6 106 106 ADS AUS A . n A 1 7 U 7 107 107 U U A . n A 1 8 U 8 108 108 U U A . n A 1 9 A 9 109 109 A A A . n A 1 10 G 10 110 110 G G A . n A 1 11 C 11 111 111 C C A . n A 1 12 G 12 112 112 G G A . 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 B 2 HOH 1 201 201 HOH HOH A . B 2 HOH 2 202 202 HOH HOH A . B 2 HOH 3 203 203 HOH HOH A . B 2 HOH 4 204 204 HOH HOH A . B 2 HOH 5 205 205 HOH HOH A . B 2 HOH 6 206 206 HOH HOH A . B 2 HOH 7 207 207 HOH HOH A . B 2 HOH 8 208 208 HOH HOH A . B 2 HOH 9 209 209 HOH HOH A . B 2 HOH 10 210 210 HOH HOH A . B 2 HOH 11 211 211 HOH HOH A . B 2 HOH 12 212 212 HOH HOH A . B 2 HOH 13 213 213 HOH HOH A . B 2 HOH 14 214 214 HOH HOH A . B 2 HOH 15 215 215 HOH HOH A . B 2 HOH 16 216 216 HOH HOH A . B 2 HOH 17 217 217 HOH HOH A . B 2 HOH 18 218 218 HOH HOH A . B 2 HOH 19 219 219 HOH HOH A . B 2 HOH 20 220 220 HOH HOH A . B 2 HOH 21 221 221 HOH HOH A . B 2 HOH 22 222 222 HOH HOH A . B 2 HOH 23 223 223 HOH HOH A . B 2 HOH 24 224 224 HOH HOH A . B 2 HOH 25 225 225 HOH HOH A . B 2 HOH 26 226 226 HOH HOH A . B 2 HOH 27 227 227 HOH HOH A . B 2 HOH 28 228 228 HOH HOH A . B 2 HOH 29 229 229 HOH HOH A . B 2 HOH 30 230 230 HOH HOH A . B 2 HOH 31 231 231 HOH HOH A . B 2 HOH 32 232 232 HOH HOH A . B 2 HOH 33 233 233 HOH HOH A . B 2 HOH 34 234 234 HOH HOH A . B 2 HOH 35 235 235 HOH HOH A . B 2 HOH 36 236 236 HOH HOH A . B 2 HOH 37 237 237 HOH HOH A . B 2 HOH 38 238 238 HOH HOH A . B 2 HOH 39 239 239 HOH HOH A . B 2 HOH 40 240 240 HOH HOH A . B 2 HOH 41 241 241 HOH HOH A . B 2 HOH 42 242 242 HOH HOH A . B 2 HOH 43 243 243 HOH HOH A . B 2 HOH 44 244 244 HOH HOH A . B 2 HOH 45 245 245 HOH HOH A . B 2 HOH 46 246 246 HOH HOH A . B 2 HOH 47 247 247 HOH HOH A . B 2 HOH 48 248 248 HOH HOH A . B 2 HOH 49 249 249 HOH HOH A . B 2 HOH 50 250 250 HOH HOH A . B 2 HOH 51 251 251 HOH HOH A . B 2 HOH 52 252 252 HOH HOH A . B 2 HOH 53 253 253 HOH HOH A . B 2 HOH 54 254 254 HOH HOH A . B 2 HOH 55 255 255 HOH HOH A . B 2 HOH 56 256 256 HOH HOH A . B 2 HOH 57 257 257 HOH HOH A . B 2 HOH 58 258 258 HOH HOH A . B 2 HOH 59 259 259 HOH HOH A . B 2 HOH 60 260 260 HOH HOH A . B 2 HOH 61 261 261 HOH HOH A . B 2 HOH 62 262 262 HOH HOH A . B 2 HOH 63 263 263 HOH HOH A . B 2 HOH 64 264 264 HOH HOH A . B 2 HOH 65 265 265 HOH HOH A . B 2 HOH 66 266 266 HOH HOH A . B 2 HOH 67 267 267 HOH HOH A . B 2 HOH 68 268 268 HOH HOH A . B 2 HOH 69 269 269 HOH HOH A . B 2 HOH 70 270 270 HOH HOH A . B 2 HOH 71 271 271 HOH HOH A . B 2 HOH 72 272 272 HOH HOH A . B 2 HOH 73 273 273 HOH HOH A . B 2 HOH 74 274 274 HOH HOH A . B 2 HOH 75 275 275 HOH HOH A . B 2 HOH 76 276 276 HOH HOH A . B 2 HOH 77 277 277 HOH HOH A . B 2 HOH 78 278 278 HOH HOH A . B 2 HOH 79 279 279 HOH HOH A . B 2 HOH 80 280 280 HOH HOH A . B 2 HOH 81 281 281 HOH HOH A . B 2 HOH 82 282 282 HOH HOH A . # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id A2M _pdbx_struct_mod_residue.label_seq_id 5 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id A2M _pdbx_struct_mod_residue.auth_seq_id 105 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id A _pdbx_struct_mod_residue.details ? # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _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 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 3070 ? 1 MORE 8 ? 1 'SSA (A^2)' 4160 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_656 -x+1,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 21.2753819221 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 24.8768519287 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 220 ? B HOH . 2 1 A HOH 262 ? B HOH . # 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 2015-09-16 2 'Structure model' 1 1 2017-07-12 3 'Structure model' 1 2 2023-09-20 # _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' 'Refinement description' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' pdbx_refine 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_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MD2 'data collection' 'diffractometer software from EMBL (with LS-CAT developed extensions)' ? 1 MOLREP phasing '(CCP4)' ? 2 SHELXL-97 refinement . ? 3 HKL-2000 'data reduction' . ? 4 HKL-2000 'data scaling' . ? 5 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 C8 A G 102 ? ? N9 A G 102 ? ? C4 A G 102 ? ? 108.83 106.40 2.43 0.40 N 2 1 "O4'" A A 109 ? A "C1'" A A 109 ? A N9 A A 109 ? A 112.72 108.50 4.22 0.70 N # 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 A2M P P N N 38 A2M OP1 O N N 39 A2M OP3 O N N 40 A2M "O5'" O N N 41 A2M "C5'" C N N 42 A2M "C4'" C N R 43 A2M "O4'" O N N 44 A2M "C3'" C N R 45 A2M "O3'" O N N 46 A2M "C2'" C N R 47 A2M "O2'" O N N 48 A2M "C1'" C N R 49 A2M "CM'" C N N 50 A2M N9 N Y N 51 A2M C8 C Y N 52 A2M N7 N Y N 53 A2M C5 C Y N 54 A2M C6 C Y N 55 A2M N6 N N N 56 A2M N1 N Y N 57 A2M C2 C Y N 58 A2M N3 N Y N 59 A2M C4 C Y N 60 A2M HOP3 H N N 61 A2M "H5'" H N N 62 A2M "H5''" H N N 63 A2M "H4'" H N N 64 A2M "H3'" H N N 65 A2M "HO3'" H N N 66 A2M "H2'" H N N 67 A2M "H1'" H N N 68 A2M "HM'1" H N N 69 A2M "HM'2" H N N 70 A2M "HM'3" H N N 71 A2M H8 H N N 72 A2M H61 H N N 73 A2M H62 H N N 74 A2M H2 H N N 75 A2M OP2 O N N 76 A2M HOP2 H N N 77 ADS P P N N 78 ADS O1P O N N 79 ADS S2P S N N 80 ADS S3P S N N 81 ADS "O5'" O N N 82 ADS "C5'" C N N 83 ADS "C4'" C N R 84 ADS "O4'" O N N 85 ADS "C3'" C N S 86 ADS "O3'" O N N 87 ADS "C2'" C N R 88 ADS "O2'" O N N 89 ADS "C1'" C N R 90 ADS N9 N Y N 91 ADS C8 C Y N 92 ADS N7 N Y N 93 ADS C5 C Y N 94 ADS C6 C Y N 95 ADS N6 N N N 96 ADS N1 N Y N 97 ADS C2 C Y N 98 ADS N3 N Y N 99 ADS C4 C Y N 100 ADS HSP2 H N N 101 ADS HSP3 H N N 102 ADS "H5'1" H N N 103 ADS "H5'2" H N N 104 ADS "H4'" H N N 105 ADS "H3'" H N N 106 ADS "HO3'" H N N 107 ADS "H2'" H N N 108 ADS "HO2'" H N N 109 ADS "H1'" H N N 110 ADS H8 H N N 111 ADS HN61 H N N 112 ADS HN62 H N N 113 ADS H2 H N N 114 C OP3 O N N 115 C P P N N 116 C OP1 O N N 117 C OP2 O N N 118 C "O5'" O N N 119 C "C5'" C N N 120 C "C4'" C N R 121 C "O4'" O N N 122 C "C3'" C N S 123 C "O3'" O N N 124 C "C2'" C N R 125 C "O2'" O N N 126 C "C1'" C N R 127 C N1 N N N 128 C C2 C N N 129 C O2 O N N 130 C N3 N N N 131 C C4 C N N 132 C N4 N N N 133 C C5 C N N 134 C C6 C N N 135 C HOP3 H N N 136 C HOP2 H N N 137 C "H5'" H N N 138 C "H5''" H N N 139 C "H4'" H N N 140 C "H3'" H N N 141 C "HO3'" H N N 142 C "H2'" H N N 143 C "HO2'" H N N 144 C "H1'" H N N 145 C H41 H N N 146 C H42 H N N 147 C H5 H N N 148 C H6 H N N 149 G OP3 O N N 150 G P P N N 151 G OP1 O N N 152 G OP2 O N N 153 G "O5'" O N N 154 G "C5'" C N N 155 G "C4'" C N R 156 G "O4'" O N N 157 G "C3'" C N S 158 G "O3'" O N N 159 G "C2'" C N R 160 G "O2'" O N N 161 G "C1'" C N R 162 G N9 N Y N 163 G C8 C Y N 164 G N7 N Y N 165 G C5 C Y N 166 G C6 C N N 167 G O6 O N N 168 G N1 N N N 169 G C2 C N N 170 G N2 N N N 171 G N3 N N N 172 G C4 C Y N 173 G HOP3 H N N 174 G HOP2 H N N 175 G "H5'" H N N 176 G "H5''" H N N 177 G "H4'" H N N 178 G "H3'" H N N 179 G "HO3'" H N N 180 G "H2'" H N N 181 G "HO2'" H N N 182 G "H1'" H N N 183 G H8 H N N 184 G H1 H N N 185 G H21 H N N 186 G H22 H N N 187 HOH O O N N 188 HOH H1 H N N 189 HOH H2 H N N 190 U OP3 O N N 191 U P P N N 192 U OP1 O N N 193 U OP2 O N N 194 U "O5'" O N N 195 U "C5'" C N N 196 U "C4'" C N R 197 U "O4'" O N N 198 U "C3'" C N S 199 U "O3'" O N N 200 U "C2'" C N R 201 U "O2'" O N N 202 U "C1'" C N R 203 U N1 N N N 204 U C2 C N N 205 U O2 O N N 206 U N3 N N N 207 U C4 C N N 208 U O4 O N N 209 U C5 C N N 210 U C6 C N N 211 U HOP3 H N N 212 U HOP2 H N N 213 U "H5'" H N N 214 U "H5''" H N N 215 U "H4'" H N N 216 U "H3'" H N N 217 U "HO3'" H N N 218 U "H2'" H N N 219 U "HO2'" H N N 220 U "H1'" H N N 221 U H3 H N N 222 U H5 H N N 223 U H6 H N N 224 # 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 A2M P OP1 doub N N 40 A2M P OP3 sing N N 41 A2M P "O5'" sing N N 42 A2M OP3 HOP3 sing N N 43 A2M "O5'" "C5'" sing N N 44 A2M "C5'" "C4'" sing N N 45 A2M "C5'" "H5'" sing N N 46 A2M "C5'" "H5''" sing N N 47 A2M "C4'" "O4'" sing N N 48 A2M "C4'" "C3'" sing N N 49 A2M "C4'" "H4'" sing N N 50 A2M "O4'" "C1'" sing N N 51 A2M "C3'" "O3'" sing N N 52 A2M "C3'" "C2'" sing N N 53 A2M "C3'" "H3'" sing N N 54 A2M "O3'" "HO3'" sing N N 55 A2M "C2'" "O2'" sing N N 56 A2M "C2'" "C1'" sing N N 57 A2M "C2'" "H2'" sing N N 58 A2M "O2'" "CM'" sing N N 59 A2M "C1'" N9 sing N N 60 A2M "C1'" "H1'" sing N N 61 A2M "CM'" "HM'1" sing N N 62 A2M "CM'" "HM'2" sing N N 63 A2M "CM'" "HM'3" sing N N 64 A2M N9 C8 sing Y N 65 A2M N9 C4 sing Y N 66 A2M C8 N7 doub Y N 67 A2M C8 H8 sing N N 68 A2M N7 C5 sing Y N 69 A2M C5 C6 sing Y N 70 A2M C5 C4 doub Y N 71 A2M C6 N6 sing N N 72 A2M C6 N1 doub Y N 73 A2M N6 H61 sing N N 74 A2M N6 H62 sing N N 75 A2M N1 C2 sing Y N 76 A2M C2 N3 doub Y N 77 A2M C2 H2 sing N N 78 A2M N3 C4 sing Y N 79 A2M P OP2 sing N N 80 A2M OP2 HOP2 sing N N 81 ADS P O1P doub N N 82 ADS P S2P sing N N 83 ADS P S3P sing N N 84 ADS P "O5'" sing N N 85 ADS S2P HSP2 sing N N 86 ADS S3P HSP3 sing N N 87 ADS "O5'" "C5'" sing N N 88 ADS "C5'" "C4'" sing N N 89 ADS "C5'" "H5'1" sing N N 90 ADS "C5'" "H5'2" sing N N 91 ADS "C4'" "O4'" sing N N 92 ADS "C4'" "C3'" sing N N 93 ADS "C4'" "H4'" sing N N 94 ADS "O4'" "C1'" sing N N 95 ADS "C3'" "O3'" sing N N 96 ADS "C3'" "C2'" sing N N 97 ADS "C3'" "H3'" sing N N 98 ADS "O3'" "HO3'" sing N N 99 ADS "C2'" "O2'" sing N N 100 ADS "C2'" "C1'" sing N N 101 ADS "C2'" "H2'" sing N N 102 ADS "O2'" "HO2'" sing N N 103 ADS "C1'" N9 sing N N 104 ADS "C1'" "H1'" sing N N 105 ADS N9 C8 sing Y N 106 ADS N9 C4 sing Y N 107 ADS C8 N7 doub Y N 108 ADS C8 H8 sing N N 109 ADS N7 C5 sing Y N 110 ADS C5 C6 sing Y N 111 ADS C5 C4 doub Y N 112 ADS C6 N6 sing N N 113 ADS C6 N1 doub Y N 114 ADS N6 HN61 sing N N 115 ADS N6 HN62 sing N N 116 ADS N1 C2 sing Y N 117 ADS C2 N3 doub Y N 118 ADS C2 H2 sing N N 119 ADS N3 C4 sing Y N 120 C OP3 P sing N N 121 C OP3 HOP3 sing N N 122 C P OP1 doub N N 123 C P OP2 sing N N 124 C P "O5'" sing N N 125 C OP2 HOP2 sing N N 126 C "O5'" "C5'" sing N N 127 C "C5'" "C4'" sing N N 128 C "C5'" "H5'" sing N N 129 C "C5'" "H5''" sing N N 130 C "C4'" "O4'" sing N N 131 C "C4'" "C3'" sing N N 132 C "C4'" "H4'" sing N N 133 C "O4'" "C1'" sing N N 134 C "C3'" "O3'" sing N N 135 C "C3'" "C2'" sing N N 136 C "C3'" "H3'" sing N N 137 C "O3'" "HO3'" sing N N 138 C "C2'" "O2'" sing N N 139 C "C2'" "C1'" sing N N 140 C "C2'" "H2'" sing N N 141 C "O2'" "HO2'" sing N N 142 C "C1'" N1 sing N N 143 C "C1'" "H1'" sing N N 144 C N1 C2 sing N N 145 C N1 C6 sing N N 146 C C2 O2 doub N N 147 C C2 N3 sing N N 148 C N3 C4 doub N N 149 C C4 N4 sing N N 150 C C4 C5 sing N N 151 C N4 H41 sing N N 152 C N4 H42 sing N N 153 C C5 C6 doub N N 154 C C5 H5 sing N N 155 C C6 H6 sing N N 156 G OP3 P sing N N 157 G OP3 HOP3 sing N N 158 G P OP1 doub N N 159 G P OP2 sing N N 160 G P "O5'" sing N N 161 G OP2 HOP2 sing N N 162 G "O5'" "C5'" sing N N 163 G "C5'" "C4'" sing N N 164 G "C5'" "H5'" sing N N 165 G "C5'" "H5''" sing N N 166 G "C4'" "O4'" sing N N 167 G "C4'" "C3'" sing N N 168 G "C4'" "H4'" sing N N 169 G "O4'" "C1'" sing N N 170 G "C3'" "O3'" sing N N 171 G "C3'" "C2'" sing N N 172 G "C3'" "H3'" sing N N 173 G "O3'" "HO3'" sing N N 174 G "C2'" "O2'" sing N N 175 G "C2'" "C1'" sing N N 176 G "C2'" "H2'" sing N N 177 G "O2'" "HO2'" sing N N 178 G "C1'" N9 sing N N 179 G "C1'" "H1'" sing N N 180 G N9 C8 sing Y N 181 G N9 C4 sing Y N 182 G C8 N7 doub Y N 183 G C8 H8 sing N N 184 G N7 C5 sing Y N 185 G C5 C6 sing N N 186 G C5 C4 doub Y N 187 G C6 O6 doub N N 188 G C6 N1 sing N N 189 G N1 C2 sing N N 190 G N1 H1 sing N N 191 G C2 N2 sing N N 192 G C2 N3 doub N N 193 G N2 H21 sing N N 194 G N2 H22 sing N N 195 G N3 C4 sing N N 196 HOH O H1 sing N N 197 HOH O H2 sing N N 198 U OP3 P sing N N 199 U OP3 HOP3 sing N N 200 U P OP1 doub N N 201 U P OP2 sing N N 202 U P "O5'" sing N N 203 U OP2 HOP2 sing N N 204 U "O5'" "C5'" sing N N 205 U "C5'" "C4'" sing N N 206 U "C5'" "H5'" sing N N 207 U "C5'" "H5''" sing N N 208 U "C4'" "O4'" sing N N 209 U "C4'" "C3'" sing N N 210 U "C4'" "H4'" sing N N 211 U "O4'" "C1'" sing N N 212 U "C3'" "O3'" sing N N 213 U "C3'" "C2'" sing N N 214 U "C3'" "H3'" sing N N 215 U "O3'" "HO3'" sing N N 216 U "C2'" "O2'" sing N N 217 U "C2'" "C1'" sing N N 218 U "C2'" "H2'" sing N N 219 U "O2'" "HO2'" sing N N 220 U "C1'" N1 sing N N 221 U "C1'" "H1'" sing N N 222 U N1 C2 sing N N 223 U N1 C6 sing N N 224 U C2 O2 doub N N 225 U C2 N3 sing N N 226 U N3 C4 sing N N 227 U N3 H3 sing N N 228 U C4 O4 doub N N 229 U C4 C5 sing N N 230 U C5 C6 doub N N 231 U C5 H5 sing N N 232 U C6 H6 sing N N 233 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4RBZ 'double helix' 4RBZ 'a-form double helix' 4RBZ 'mismatched base pair' 4RBZ '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 C 1 1_555 A G 12 2_656 0.117 -0.120 -0.040 8.123 -15.710 0.069 1 A_C101:G112_A A 101 ? A 112 ? 19 1 1 A G 2 1_555 A C 11 2_656 -0.210 -0.133 0.034 -5.547 -18.337 0.782 2 A_G102:C111_A A 102 ? A 111 ? 19 1 1 A C 3 1_555 A G 10 2_656 0.102 -0.127 0.228 -3.929 -12.813 -2.897 3 A_C103:G110_A A 103 ? A 110 ? 19 1 1 A G 4 1_555 A A 9 2_656 -0.064 1.521 -0.302 3.237 -4.948 -18.757 4 A_G104:A109_A A 104 ? A 109 ? 8 1 1 A A2M 5 1_555 A U 8 2_656 0.230 -0.071 0.076 2.008 -12.172 -4.614 5 A_A2M105:U108_A A 105 ? A 108 ? 20 1 1 A C 1 1_555 A G 12 1_555 0.117 -0.120 -0.040 8.123 -15.710 0.069 6 A_C101:G112_A A 101 ? A 112 ? 19 1 1 A G 2 1_555 A C 11 1_555 -0.210 -0.133 0.034 -5.547 -18.337 0.783 7 A_G102:C111_A A 102 ? A 111 ? 19 1 1 A C 3 1_555 A G 10 1_555 0.102 -0.127 0.228 -3.929 -12.813 -2.897 8 A_C103:G110_A A 103 ? A 110 ? 19 1 1 A G 4 1_555 A A 9 1_555 -0.064 1.521 -0.302 3.237 -4.948 -18.757 9 A_G104:A109_A A 104 ? A 109 ? 8 1 1 A A2M 5 1_555 A U 8 1_555 0.230 -0.071 0.076 2.008 -12.172 -4.614 10 A_A2M105:U108_A A 105 ? A 108 ? 20 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 C 1 1_555 A G 12 2_656 A G 2 1_555 A C 11 2_656 -0.415 -1.746 3.441 -3.020 13.270 32.253 -4.832 0.254 2.573 22.669 5.159 34.936 1 AA_C101G102:C111G112_AA A 101 ? A 112 ? A 102 ? A 111 ? 1 A G 2 1_555 A C 11 2_656 A C 3 1_555 A G 10 2_656 -0.537 -1.305 3.187 -2.130 4.552 34.941 -2.796 0.585 3.025 7.533 3.525 35.290 2 AA_G102C103:G110C111_AA A 102 ? A 111 ? A 103 ? A 110 ? 1 A C 3 1_555 A G 10 2_656 A G 4 1_555 A A 9 2_656 -0.959 -1.275 3.135 2.757 8.300 27.668 -4.176 2.457 2.548 16.831 -5.590 28.992 3 AA_C103G104:A109G110_AA A 103 ? A 110 ? A 104 ? A 109 ? 1 A G 4 1_555 A A 9 2_656 A A2M 5 1_555 A U 8 2_656 0.441 -1.351 3.252 -2.625 11.660 31.705 -4.053 -1.147 2.566 20.455 4.605 33.829 4 AA_G104A2M105:U108A109_AA A 104 ? A 109 ? A 105 ? A 108 ? 1 A C 1 1_555 A G 12 1_555 A G 2 1_555 A C 11 1_555 -0.415 -1.746 3.441 -3.020 13.270 32.253 -4.832 0.254 2.573 22.669 5.159 34.936 5 AA_C101G102:C111G112_AA A 101 ? A 112 ? A 102 ? A 111 ? 1 A G 2 1_555 A C 11 1_555 A C 3 1_555 A G 10 1_555 -0.537 -1.305 3.187 -2.130 4.552 34.941 -2.796 0.585 3.025 7.533 3.525 35.290 6 AA_G102C103:G110C111_AA A 102 ? A 111 ? A 103 ? A 110 ? 1 A C 3 1_555 A G 10 1_555 A G 4 1_555 A A 9 1_555 -0.959 -1.275 3.135 2.757 8.300 27.668 -4.176 2.457 2.548 16.831 -5.590 28.992 7 AA_C103G104:A109G110_AA A 103 ? A 110 ? A 104 ? A 109 ? 1 A G 4 1_555 A A 9 1_555 A A2M 5 1_555 A U 8 1_555 0.441 -1.351 3.252 -2.625 11.660 31.705 -4.053 -1.147 2.566 20.455 4.605 33.829 8 AA_G104A2M105:U108A109_AA A 104 ? A 109 ? A 105 ? A 108 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id 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 2Q1R _pdbx_initial_refinement_model.details 'PDB ENTRY 2Q1R' #