data_2PN3 # _entry.id 2PN3 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 2PN3 pdb_00002pn3 10.2210/pdb2pn3/pdb NDB AR0077 ? ? RCSB RCSB042560 ? ? WWPDB D_1000042560 ? ? # 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 2008-04-01 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2024-02-21 # _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' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' struct_conn 5 3 'Structure model' struct_conn_type # 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.conn_type_id' 4 3 'Structure model' '_struct_conn.id' 5 3 'Structure model' '_struct_conn.pdbx_dist_value' 6 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 7 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 8 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 9 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 10 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 11 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 12 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 13 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 14 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 15 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 16 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 17 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 18 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 19 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 20 3 'Structure model' '_struct_conn.ptnr2_label_seq_id' 21 3 'Structure model' '_struct_conn_type.id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2PN3 _pdbx_database_status.recvd_initial_deposition_date 2007-04-23 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Zhao, Q.' 1 'Han, Q.' 2 'Kissinger, C.R.' 3 'Hermann, T.' 4 'Thompson, P.A.' 5 # _citation.id primary _citation.title 'Structure of hepatitis C virus IRES subdomain IIa.' _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 64 _citation.page_first 436 _citation.page_last 443 _citation.year 2008 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18391410 _citation.pdbx_database_id_DOI 10.1107/S0907444908002011 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zhao, Q.' 1 ? primary 'Han, Q.' 2 ? primary 'Kissinger, C.R.' 3 ? primary 'Hermann, T.' 4 ? primary 'Thompson, P.A.' 5 ? # 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*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP*AP*CP*GP*CP*C)-3'" 7644.589 1 ? 'G47C, U48G, A70C' 'HCV IRES Subdomain IIa (residue 47-70)' ? 2 polymer syn "5'-R(*GP*CP*GP*(5BU)P*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*(5BU)P*CP*CP*GP*G)-3'" 6564.623 1 ? 'A99C, A116G' 'HCV IRES Subdomain IIa (residue 98-117)' ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no no CGGAGGAACUACUGUCUUCACGCC CGGAGGAACUACUGUCUUCACGCC A ? 2 polyribonucleotide no yes 'GCG(5BU)GUCGUGCAGCC(5BU)CCGG' GCGUGUCGUGCAGCCUCCGG B ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name 'MAGNESIUM ION' _pdbx_entity_nonpoly.comp_id MG # 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 G n 1 4 A n 1 5 G n 1 6 G n 1 7 A n 1 8 A n 1 9 C n 1 10 U n 1 11 A n 1 12 C n 1 13 U n 1 14 G n 1 15 U n 1 16 C n 1 17 U n 1 18 U n 1 19 C n 1 20 A n 1 21 C n 1 22 G n 1 23 C n 1 24 C n 2 1 G n 2 2 C n 2 3 G n 2 4 5BU n 2 5 G n 2 6 U n 2 7 C n 2 8 G n 2 9 U n 2 10 G n 2 11 C n 2 12 A n 2 13 G n 2 14 C n 2 15 C n 2 16 5BU n 2 17 C n 2 18 C n 2 19 G n 2 20 G n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _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 1 1 sample ? ? ? ? ? 'This sequence occurs naturally in hepatitis C virus' 2 1 sample ? ? ? ? ? 'This sequence occurs naturally in hepatitis C virus' # 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 5BU 'RNA linking' n "5-BROMO-URIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O9 P' 403.077 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 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # 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 47 47 C C A . n A 1 2 G 2 48 48 G G A . n A 1 3 G 3 49 49 G G A . n A 1 4 A 4 50 50 A A A . n A 1 5 G 5 51 51 G G A . n A 1 6 G 6 52 52 G G A . n A 1 7 A 7 53 53 A A A . n A 1 8 A 8 54 54 A A A . n A 1 9 C 9 55 55 C C A . n A 1 10 U 10 56 56 U U A . n A 1 11 A 11 57 57 A A A . n A 1 12 C 12 58 58 C C A . n A 1 13 U 13 59 59 U U A . n A 1 14 G 14 60 60 G G A . n A 1 15 U 15 61 61 U U A . n A 1 16 C 16 62 62 C C A . n A 1 17 U 17 63 63 U U A . n A 1 18 U 18 64 64 U U A . n A 1 19 C 19 65 65 C C A . n A 1 20 A 20 66 66 A A A . n A 1 21 C 21 67 67 C C A . n A 1 22 G 22 68 68 G G A . n A 1 23 C 23 69 69 C C A . n A 1 24 C 24 70 70 C C A . n B 2 1 G 1 98 98 G G B . n B 2 2 C 2 99 99 C C B . n B 2 3 G 3 100 100 G G B . n B 2 4 5BU 4 101 101 5BU 5BU B . n B 2 5 G 5 102 102 G G B . n B 2 6 U 6 103 103 U U B . n B 2 7 C 7 104 104 C C B . n B 2 8 G 8 105 105 G G B . n B 2 9 U 9 106 106 U U B . n B 2 10 G 10 107 107 G G B . n B 2 11 C 11 108 108 C C B . n B 2 12 A 12 109 109 A A B . n B 2 13 G 13 110 110 G G B . n B 2 14 C 14 111 111 C C B . n B 2 15 C 15 112 112 C C B . n B 2 16 5BU 16 113 113 5BU 5BU B . n B 2 17 C 17 114 114 C C B . n B 2 18 C 18 115 115 C C B . n B 2 19 G 19 116 116 G G B . n B 2 20 G 20 117 117 G G 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 3 MG 1 1 1 MG MG A . D 3 MG 1 2 2 MG MG A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0019 ? 1 APS 'data collection' 'BioCARS developed GUI' ? 2 HKL-2000 'data reduction' . ? 3 HKL-2000 'data scaling' . ? 4 SOLVE phasing . ? 5 # _cell.entry_id 2PN3 _cell.length_a 48.945 _cell.length_b 48.945 _cell.length_c 120.942 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _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 2PN3 _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? # _exptl.entry_id 2PN3 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.55 _exptl_crystal.density_percent_sol 51.74 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method EVAPORATION _exptl_crystal_grow.temp 290.0 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.2 _exptl_crystal_grow.pdbx_details '5% MPD, 5mM MgSO4, 12.5mM NaCl, 50mM KCl, 25mM Cacodylate equilibrated with 65%MPD, pH 6.2, EVAPORATION, temperature 290.0K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 '5% MPD' ? ? ? 1 2 1 MgSO4 ? ? ? 1 3 1 NaCl ? ? ? 1 4 1 KCl ? ? ? 1 5 1 Cacodylate ? ? ? 1 6 2 '65% MPD' ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 77.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'MAR CCD 165 mm' _diffrn_detector.pdbx_collection_date 2004-10-30 _diffrn_detector.details mirrors # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'double-crystal Si 111' _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.9203 1.0 2 0.9197 1.0 3 0.90686 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 14-ID-B' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 14-ID-B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '0.9203, 0.9197, 0.90686' # _reflns.entry_id 2PN3 _reflns.observed_criterion_sigma_F 0 _reflns.observed_criterion_sigma_I 0 _reflns.d_resolution_high 2.9 _reflns.d_resolution_low 50 _reflns.number_all 3650 _reflns.number_obs 3420 _reflns.percent_possible_obs 93.7 _reflns.pdbx_Rmerge_I_obs 0.081 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 27.5 _reflns.B_iso_Wilson_estimate 55.3 _reflns.pdbx_redundancy 11.2 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.90 _reflns_shell.d_res_low 3.00 _reflns_shell.percent_possible_all 75.1 _reflns_shell.Rmerge_I_obs 0.345 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 4.6 _reflns_shell.pdbx_redundancy 8.1 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 253 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 2PN3 _refine.ls_number_reflns_obs 3202 _refine.ls_number_reflns_all 3452 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 45.00 _refine.ls_d_res_high 2.90 _refine.ls_percent_reflns_obs 92.74 _refine.ls_R_factor_obs 0.22969 _refine.ls_R_factor_all 0.23204 _refine.ls_R_factor_R_work 0.2288 _refine.ls_R_factor_R_free 0.28263 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.3 _refine.ls_number_reflns_R_free 143 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.891 _refine.correlation_coeff_Fo_to_Fc_free 0.843 _refine.B_iso_mean 44.297 _refine.aniso_B[1][1] -2.08 _refine.aniso_B[2][2] -2.08 _refine.aniso_B[3][3] 4.16 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model Isotropic _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _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 0.460 _refine.overall_SU_ML 0.349 _refine.overall_SU_B 18.570 _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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_analyze.entry_id 2PN3 _refine_analyze.Luzzati_coordinate_error_obs 0.35 _refine_analyze.Luzzati_sigma_a_obs 0.32 _refine_analyze.Luzzati_d_res_low_obs 5 _refine_analyze.Luzzati_coordinate_error_free 0.4 _refine_analyze.Luzzati_sigma_a_free 0.420 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 930 _refine_hist.pdbx_number_atoms_ligand 2 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 932 _refine_hist.d_res_high 2.90 _refine_hist.d_res_low 45.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.012 0.021 ? 1036 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.885 3.000 ? 1612 'X-RAY DIFFRACTION' ? r_chiral_restr 0.071 0.200 ? 218 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.005 0.020 ? 452 'X-RAY DIFFRACTION' ? r_nbd_refined 0.195 0.200 ? 405 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.299 0.200 ? 673 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.193 0.200 ? 33 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.172 0.200 ? 28 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.305 0.200 ? 2 'X-RAY DIFFRACTION' ? r_scbond_it 1.177 3.000 ? 1470 'X-RAY DIFFRACTION' ? r_scangle_it 2.006 4.500 ? 1612 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.9 _refine_ls_shell.d_res_low 2.977 _refine_ls_shell.number_reflns_R_work 169 _refine_ls_shell.R_factor_R_work 0.356 _refine_ls_shell.percent_reflns_obs 70.63 _refine_ls_shell.R_factor_R_free 0.421 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 9 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 253 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 2PN3 _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 # _struct.entry_id 2PN3 _struct.title 'Crystal Structure of Hepatitis C Virus IRES Subdomain IIa' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2PN3 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'HCV, IRES, Loop IIa, RNA, Magnesium, Crystallization' # 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 ? C N N 3 ? D N N 3 ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 2PN3 2PN3 1 ? CGGAGGAACUACUGUCUUCACGCC ? 2 PDB 2PN3 2PN3 2 ? GCGUGUCGUGCAGCCUCCGG ? # 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 2PN3 A 1 ? 24 ? 2PN3 47 ? 70 ? 47 70 2 2 2PN3 B 1 ? 20 ? 2PN3 98 ? 117 ? 98 117 # _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 # 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)' 3610 ? 1 MORE -23.8 ? 1 'SSA (A^2)' 7620 ? # _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 # _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_ _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 ? B G 3 "O3'" ? ? ? 1_555 B 5BU 4 P ? ? B G 100 B 5BU 101 1_555 ? ? ? ? ? ? ? 1.598 ? ? covale2 covale both ? B 5BU 4 "O3'" ? ? ? 1_555 B G 5 P ? ? B 5BU 101 B G 102 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale3 covale both ? B C 15 "O3'" ? ? ? 1_555 B 5BU 16 P ? ? B C 112 B 5BU 113 1_555 ? ? ? ? ? ? ? 1.585 ? ? covale4 covale both ? B 5BU 16 "O3'" ? ? ? 1_555 B C 17 P ? ? B 5BU 113 B C 114 1_555 ? ? ? ? ? ? ? 1.584 ? ? metalc1 metalc ? ? D MG . MG ? ? ? 1_555 A U 15 O4 ? ? A MG 2 A U 61 1_555 ? ? ? ? ? ? ? 2.288 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 B G 19 N1 ? ? A C 47 B G 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 B G 19 O6 ? ? A C 47 B G 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 B G 19 N2 ? ? A C 47 B G 116 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B C 18 N3 ? ? A G 48 B C 115 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 B C 18 O2 ? ? A G 48 B C 115 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 B C 18 N4 ? ? A G 48 B C 115 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 17 N3 ? ? A G 49 B C 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 17 O2 ? ? A G 49 B C 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 17 N4 ? ? A G 49 B C 114 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A A 4 N1 ? ? ? 1_555 B 5BU 16 N3 ? ? A A 50 B 5BU 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A A 4 N6 ? ? ? 1_555 B 5BU 16 O4 ? ? A A 50 B 5BU 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 15 N3 ? ? A G 51 B C 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 15 O2 ? ? A G 51 B C 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 15 N4 ? ? A G 51 B C 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 6 N1 ? ? ? 1_555 B C 14 N3 ? ? A G 52 B C 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 6 N2 ? ? ? 1_555 B C 14 O2 ? ? A G 52 B C 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 6 O6 ? ? ? 1_555 B C 14 N4 ? ? A G 52 B C 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 13 N1 ? ? A C 58 B G 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 13 O6 ? ? A C 58 B G 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 13 N2 ? ? A C 58 B G 110 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A U 13 N3 ? ? ? 1_555 B A 12 N1 ? ? A U 59 B A 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A U 13 O4 ? ? ? 1_555 B A 12 N6 ? ? A U 59 B A 109 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 14 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 60 B C 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 14 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 60 B C 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 14 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 60 B C 108 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A U 15 N3 ? ? ? 1_555 B G 10 O6 ? ? A U 61 B G 107 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog27 hydrog ? ? A U 15 O2 ? ? ? 1_555 B G 10 N1 ? ? A U 61 B G 107 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog28 hydrog ? ? A C 16 N3 ? ? ? 1_555 B G 8 N1 ? ? A C 62 B G 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 16 N4 ? ? ? 1_555 B G 8 O6 ? ? A C 62 B G 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A C 16 O2 ? ? ? 1_555 B G 8 N2 ? ? A C 62 B G 105 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A U 17 N3 ? ? ? 1_555 B C 7 N3 ? ? A U 63 B C 104 1_555 ? ? ? ? ? ? TYPE_18_PAIR ? ? ? hydrog32 hydrog ? ? A U 17 O4 ? ? ? 1_555 B C 7 N4 ? ? A U 63 B C 104 1_555 ? ? ? ? ? ? TYPE_18_PAIR ? ? ? hydrog33 hydrog ? ? A U 18 N3 ? ? ? 1_555 B U 6 O2 ? ? A U 64 B U 103 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog34 hydrog ? ? A U 18 O4 ? ? ? 1_555 B U 6 N3 ? ? A U 64 B U 103 1_555 ? ? ? ? ? ? TYPE_16_PAIR ? ? ? hydrog35 hydrog ? ? A C 19 O2 ? ? ? 1_555 B G 5 N1 ? ? A C 65 B G 102 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog36 hydrog ? ? A A 20 N1 ? ? ? 1_555 B 5BU 4 N3 ? ? A A 66 B 5BU 101 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A A 20 N6 ? ? ? 1_555 B 5BU 4 O4 ? ? A A 66 B 5BU 101 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A C 21 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 67 B G 100 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 21 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 67 B G 100 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 21 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 67 B G 100 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A G 22 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 68 B C 99 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 22 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 68 B C 99 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 22 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 68 B C 99 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 23 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 69 B G 98 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 23 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 69 B G 98 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 23 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 69 B G 98 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # 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 "O5'" A C 55 ? ? "C5'" A C 55 ? ? "C4'" A C 55 ? ? 102.54 109.40 -6.86 0.80 N 2 1 "O4'" A U 56 ? ? "C1'" A U 56 ? ? N1 A U 56 ? ? 114.17 108.50 5.67 0.70 N 3 1 "O4'" A G 60 ? ? "C4'" A G 60 ? ? "C3'" A G 60 ? ? 97.33 104.00 -6.67 1.00 N 4 1 "C4'" A C 70 ? ? "C3'" A C 70 ? ? "C2'" A C 70 ? ? 95.44 102.60 -7.16 1.00 N 5 1 "C3'" B G 105 ? ? "O3'" B G 105 ? ? P B U 106 ? ? 127.78 119.70 8.08 1.20 Y 6 1 "O5'" B G 110 ? ? "C5'" B G 110 ? ? "C4'" B G 110 ? ? 103.61 109.40 -5.79 0.80 N 7 1 "O4'" B C 111 ? ? "C1'" B C 111 ? ? N1 B C 111 ? ? 113.45 108.50 4.95 0.70 N # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 B 5BU 4 B 5BU 101 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 2 B 5BU 16 B 5BU 113 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" # 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 5BU P P N N 1 5BU OP1 O N N 2 5BU OP2 O N N 3 5BU OP3 O N N 4 5BU "O5'" O N N 5 5BU "C5'" C N N 6 5BU "C4'" C N R 7 5BU "O4'" O N N 8 5BU "C3'" C N S 9 5BU "O3'" O N N 10 5BU "C2'" C N R 11 5BU "O2'" O N N 12 5BU "C1'" C N R 13 5BU N1 N N N 14 5BU C2 C N N 15 5BU O2 O N N 16 5BU N3 N N N 17 5BU C4 C N N 18 5BU O4 O N N 19 5BU C5 C N N 20 5BU C6 C N N 21 5BU BR BR N N 22 5BU HOP2 H N N 23 5BU HOP3 H N N 24 5BU "H5'" H N N 25 5BU "H5''" H N N 26 5BU "H4'" H N N 27 5BU "H3'" H N N 28 5BU "HO3'" H N N 29 5BU "H2'" H N N 30 5BU "HO2'" H N N 31 5BU "H1'" H N N 32 5BU H3 H N N 33 5BU H6 H N N 34 A OP3 O N N 35 A P P N N 36 A OP1 O N N 37 A OP2 O N N 38 A "O5'" O N N 39 A "C5'" C N N 40 A "C4'" C N R 41 A "O4'" O N N 42 A "C3'" C N S 43 A "O3'" O N N 44 A "C2'" C N R 45 A "O2'" O N N 46 A "C1'" C N R 47 A N9 N Y N 48 A C8 C Y N 49 A N7 N Y N 50 A C5 C Y N 51 A C6 C Y N 52 A N6 N N N 53 A N1 N Y N 54 A C2 C Y N 55 A N3 N Y N 56 A C4 C Y N 57 A HOP3 H N N 58 A HOP2 H N N 59 A "H5'" H N N 60 A "H5''" H N N 61 A "H4'" H N N 62 A "H3'" H N N 63 A "HO3'" H N N 64 A "H2'" H N N 65 A "HO2'" H N N 66 A "H1'" H N N 67 A H8 H N N 68 A H61 H N N 69 A H62 H N N 70 A H2 H N N 71 C OP3 O N N 72 C P P N N 73 C OP1 O N N 74 C OP2 O N N 75 C "O5'" O N N 76 C "C5'" C N N 77 C "C4'" C N R 78 C "O4'" O N N 79 C "C3'" C N S 80 C "O3'" O N N 81 C "C2'" C N R 82 C "O2'" O N N 83 C "C1'" C N R 84 C N1 N N N 85 C C2 C N N 86 C O2 O N N 87 C N3 N N N 88 C C4 C N N 89 C N4 N N N 90 C C5 C N N 91 C C6 C N N 92 C HOP3 H N N 93 C HOP2 H N N 94 C "H5'" H N N 95 C "H5''" H N N 96 C "H4'" H N N 97 C "H3'" H N N 98 C "HO3'" H N N 99 C "H2'" H N N 100 C "HO2'" H N N 101 C "H1'" H N N 102 C H41 H N N 103 C H42 H N N 104 C H5 H N N 105 C H6 H N N 106 G OP3 O N N 107 G P P N N 108 G OP1 O N N 109 G OP2 O N N 110 G "O5'" O N N 111 G "C5'" C N N 112 G "C4'" C N R 113 G "O4'" O N N 114 G "C3'" C N S 115 G "O3'" O N N 116 G "C2'" C N R 117 G "O2'" O N N 118 G "C1'" C N R 119 G N9 N Y N 120 G C8 C Y N 121 G N7 N Y N 122 G C5 C Y N 123 G C6 C N N 124 G O6 O N N 125 G N1 N N N 126 G C2 C N N 127 G N2 N N N 128 G N3 N N N 129 G C4 C Y N 130 G HOP3 H N N 131 G HOP2 H N N 132 G "H5'" H N N 133 G "H5''" H N N 134 G "H4'" H N N 135 G "H3'" H N N 136 G "HO3'" H N N 137 G "H2'" H N N 138 G "HO2'" H N N 139 G "H1'" H N N 140 G H8 H N N 141 G H1 H N N 142 G H21 H N N 143 G H22 H N N 144 MG MG MG N N 145 U OP3 O N N 146 U P P N N 147 U OP1 O N N 148 U OP2 O N N 149 U "O5'" O N N 150 U "C5'" C N N 151 U "C4'" C N R 152 U "O4'" O N N 153 U "C3'" C N S 154 U "O3'" O N N 155 U "C2'" C N R 156 U "O2'" O N N 157 U "C1'" C N R 158 U N1 N N N 159 U C2 C N N 160 U O2 O N N 161 U N3 N N N 162 U C4 C N N 163 U O4 O N N 164 U C5 C N N 165 U C6 C N N 166 U HOP3 H N N 167 U HOP2 H N N 168 U "H5'" H N N 169 U "H5''" H N N 170 U "H4'" H N N 171 U "H3'" H N N 172 U "HO3'" H N N 173 U "H2'" H N N 174 U "HO2'" H N N 175 U "H1'" H N N 176 U H3 H N N 177 U H5 H N N 178 U H6 H N N 179 # 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 5BU P OP1 doub N N 1 5BU P OP2 sing N N 2 5BU P OP3 sing N N 3 5BU P "O5'" sing N N 4 5BU OP2 HOP2 sing N N 5 5BU OP3 HOP3 sing N N 6 5BU "O5'" "C5'" sing N N 7 5BU "C5'" "C4'" sing N N 8 5BU "C5'" "H5'" sing N N 9 5BU "C5'" "H5''" sing N N 10 5BU "C4'" "O4'" sing N N 11 5BU "C4'" "C3'" sing N N 12 5BU "C4'" "H4'" sing N N 13 5BU "O4'" "C1'" sing N N 14 5BU "C3'" "O3'" sing N N 15 5BU "C3'" "C2'" sing N N 16 5BU "C3'" "H3'" sing N N 17 5BU "O3'" "HO3'" sing N N 18 5BU "C2'" "O2'" sing N N 19 5BU "C2'" "C1'" sing N N 20 5BU "C2'" "H2'" sing N N 21 5BU "O2'" "HO2'" sing N N 22 5BU "C1'" N1 sing N N 23 5BU "C1'" "H1'" sing N N 24 5BU N1 C2 sing N N 25 5BU N1 C6 sing N N 26 5BU C2 O2 doub N N 27 5BU C2 N3 sing N N 28 5BU N3 C4 sing N N 29 5BU N3 H3 sing N N 30 5BU C4 O4 doub N N 31 5BU C4 C5 sing N N 32 5BU C5 C6 doub N N 33 5BU C5 BR sing N N 34 5BU C6 H6 sing N N 35 A OP3 P sing N N 36 A OP3 HOP3 sing N N 37 A P OP1 doub N N 38 A P OP2 sing N N 39 A P "O5'" sing N N 40 A OP2 HOP2 sing N N 41 A "O5'" "C5'" sing N N 42 A "C5'" "C4'" sing N N 43 A "C5'" "H5'" sing N N 44 A "C5'" "H5''" sing N N 45 A "C4'" "O4'" sing N N 46 A "C4'" "C3'" sing N N 47 A "C4'" "H4'" sing N N 48 A "O4'" "C1'" sing N N 49 A "C3'" "O3'" sing N N 50 A "C3'" "C2'" sing N N 51 A "C3'" "H3'" sing N N 52 A "O3'" "HO3'" sing N N 53 A "C2'" "O2'" sing N N 54 A "C2'" "C1'" sing N N 55 A "C2'" "H2'" sing N N 56 A "O2'" "HO2'" sing N N 57 A "C1'" N9 sing N N 58 A "C1'" "H1'" sing N N 59 A N9 C8 sing Y N 60 A N9 C4 sing Y N 61 A C8 N7 doub Y N 62 A C8 H8 sing N N 63 A N7 C5 sing Y N 64 A C5 C6 sing Y N 65 A C5 C4 doub Y N 66 A C6 N6 sing N N 67 A C6 N1 doub Y N 68 A N6 H61 sing N N 69 A N6 H62 sing N N 70 A N1 C2 sing Y N 71 A C2 N3 doub Y N 72 A C2 H2 sing N N 73 A N3 C4 sing Y N 74 C OP3 P sing N N 75 C OP3 HOP3 sing N N 76 C P OP1 doub N N 77 C P OP2 sing N N 78 C P "O5'" sing N N 79 C OP2 HOP2 sing N N 80 C "O5'" "C5'" sing N N 81 C "C5'" "C4'" sing N N 82 C "C5'" "H5'" sing N N 83 C "C5'" "H5''" sing N N 84 C "C4'" "O4'" sing N N 85 C "C4'" "C3'" sing N N 86 C "C4'" "H4'" sing N N 87 C "O4'" "C1'" sing N N 88 C "C3'" "O3'" sing N N 89 C "C3'" "C2'" sing N N 90 C "C3'" "H3'" sing N N 91 C "O3'" "HO3'" sing N N 92 C "C2'" "O2'" sing N N 93 C "C2'" "C1'" sing N N 94 C "C2'" "H2'" sing N N 95 C "O2'" "HO2'" sing N N 96 C "C1'" N1 sing N N 97 C "C1'" "H1'" sing N N 98 C N1 C2 sing N N 99 C N1 C6 sing N N 100 C C2 O2 doub N N 101 C C2 N3 sing N N 102 C N3 C4 doub N N 103 C C4 N4 sing N N 104 C C4 C5 sing N N 105 C N4 H41 sing N N 106 C N4 H42 sing N N 107 C C5 C6 doub N N 108 C C5 H5 sing N N 109 C C6 H6 sing N N 110 G OP3 P sing N N 111 G OP3 HOP3 sing N N 112 G P OP1 doub N N 113 G P OP2 sing N N 114 G P "O5'" sing N N 115 G OP2 HOP2 sing N N 116 G "O5'" "C5'" sing N N 117 G "C5'" "C4'" sing N N 118 G "C5'" "H5'" sing N N 119 G "C5'" "H5''" sing N N 120 G "C4'" "O4'" sing N N 121 G "C4'" "C3'" sing N N 122 G "C4'" "H4'" sing N N 123 G "O4'" "C1'" sing N N 124 G "C3'" "O3'" sing N N 125 G "C3'" "C2'" sing N N 126 G "C3'" "H3'" sing N N 127 G "O3'" "HO3'" sing N N 128 G "C2'" "O2'" sing N N 129 G "C2'" "C1'" sing N N 130 G "C2'" "H2'" sing N N 131 G "O2'" "HO2'" sing N N 132 G "C1'" N9 sing N N 133 G "C1'" "H1'" sing N N 134 G N9 C8 sing Y N 135 G N9 C4 sing Y N 136 G C8 N7 doub Y N 137 G C8 H8 sing N N 138 G N7 C5 sing Y N 139 G C5 C6 sing N N 140 G C5 C4 doub Y N 141 G C6 O6 doub N N 142 G C6 N1 sing N N 143 G N1 C2 sing N N 144 G N1 H1 sing N N 145 G C2 N2 sing N N 146 G C2 N3 doub N N 147 G N2 H21 sing N N 148 G N2 H22 sing N N 149 G N3 C4 sing N N 150 U OP3 P sing N N 151 U OP3 HOP3 sing N N 152 U P OP1 doub N N 153 U P OP2 sing N N 154 U P "O5'" sing N N 155 U OP2 HOP2 sing N N 156 U "O5'" "C5'" sing N N 157 U "C5'" "C4'" sing N N 158 U "C5'" "H5'" sing N N 159 U "C5'" "H5''" sing N N 160 U "C4'" "O4'" sing N N 161 U "C4'" "C3'" sing N N 162 U "C4'" "H4'" sing N N 163 U "O4'" "C1'" sing N N 164 U "C3'" "O3'" sing N N 165 U "C3'" "C2'" sing N N 166 U "C3'" "H3'" sing N N 167 U "O3'" "HO3'" sing N N 168 U "C2'" "O2'" sing N N 169 U "C2'" "C1'" sing N N 170 U "C2'" "H2'" sing N N 171 U "O2'" "HO2'" sing N N 172 U "C1'" N1 sing N N 173 U "C1'" "H1'" sing N N 174 U N1 C2 sing N N 175 U N1 C6 sing N N 176 U C2 O2 doub N N 177 U C2 N3 sing N N 178 U N3 C4 sing N N 179 U N3 H3 sing N N 180 U C4 O4 doub N N 181 U C4 C5 sing N N 182 U C5 C6 doub N N 183 U C5 H5 sing N N 184 U C6 H6 sing N N 185 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2PN3 'double helix' 2PN3 'a-form double helix' 2PN3 'bulge loop' 2PN3 'mismatched base pair' # 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 B G 19 1_555 -0.233 -0.169 -0.010 4.306 -11.369 -0.697 1 A_C47:G116_B A 47 ? B 116 ? 19 1 1 A G 2 1_555 B C 18 1_555 0.184 0.016 -0.169 -4.972 -9.488 -2.224 2 A_G48:C115_B A 48 ? B 115 ? 19 1 1 A G 3 1_555 B C 17 1_555 -0.507 -0.321 0.254 -4.815 -14.447 2.759 3 A_G49:C114_B A 49 ? B 114 ? 19 1 1 A A 4 1_555 B 5BU 16 1_555 0.459 -0.305 -0.106 -5.076 -9.925 -4.513 4 A_A50:5BU113_B A 50 ? B 113 ? 20 1 1 A G 5 1_555 B C 15 1_555 -0.057 -0.182 0.174 -1.575 -6.053 -3.289 5 A_G51:C112_B A 51 ? B 112 ? 19 1 1 A G 6 1_555 B C 14 1_555 -0.342 -0.365 0.141 -1.544 0.538 -2.875 6 A_G52:C111_B A 52 ? B 111 ? 19 1 1 A C 12 1_555 B G 13 1_555 0.091 -0.372 -0.100 8.795 -19.974 -2.656 7 A_C58:G110_B A 58 ? B 110 ? 19 1 1 A U 13 1_555 B A 12 1_555 -0.270 -0.392 -0.110 1.685 -18.252 -4.368 8 A_U59:A109_B A 59 ? B 109 ? 20 1 1 A G 14 1_555 B C 11 1_555 -0.612 -0.083 0.583 6.527 -13.744 0.752 9 A_G60:C108_B A 60 ? B 108 ? 19 1 1 A U 15 1_555 B G 10 1_555 1.676 -0.646 0.402 5.921 -9.501 -5.273 10 A_U61:G107_B A 61 ? B 107 ? 28 1 1 A C 16 1_555 B G 8 1_555 0.612 -0.031 0.171 7.804 -14.627 1.761 11 A_C62:G105_B A 62 ? B 105 ? 19 1 1 A U 17 1_555 B C 7 1_555 0.430 -1.985 0.690 7.249 -19.408 13.310 12 A_U63:C104_B A 63 ? B 104 ? 18 1 1 A U 18 1_555 B U 6 1_555 -1.989 -2.225 0.834 -6.755 -26.358 7.788 13 A_U64:U103_B A 64 ? B 103 ? 16 1 1 A C 19 1_555 B G 5 1_555 0.834 0.033 1.034 -7.415 -21.324 8.789 14 A_C65:G102_B A 65 ? B 102 ? ? 1 1 A A 20 1_555 B 5BU 4 1_555 -0.098 -0.230 0.731 7.204 -10.522 -4.987 15 A_A66:5BU101_B A 66 ? B 101 ? 20 1 1 A C 21 1_555 B G 3 1_555 0.001 -0.115 0.085 2.275 -20.225 -6.980 16 A_C67:G100_B A 67 ? B 100 ? 19 1 1 A G 22 1_555 B C 2 1_555 0.042 -0.543 0.575 -1.782 -14.703 -3.216 17 A_G68:C99_B A 68 ? B 99 ? 19 1 1 A C 23 1_555 B G 1 1_555 1.242 -0.534 0.573 -10.992 -10.392 2.297 18 A_C69:G98_B A 69 ? B 98 ? 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 C 1 1_555 B G 19 1_555 A G 2 1_555 B C 18 1_555 -0.505 -1.758 3.414 -1.230 11.380 34.727 -4.325 0.642 2.738 18.456 1.995 36.510 1 AA_C47G48:C115G116_BB A 47 ? B 116 ? A 48 ? B 115 ? 1 A G 2 1_555 B C 18 1_555 A G 3 1_555 B C 17 1_555 0.384 -2.050 3.114 -3.136 6.723 28.211 -5.355 -1.361 2.512 13.499 6.297 29.151 2 AA_G48G49:C114C115_BB A 48 ? B 115 ? A 49 ? B 114 ? 1 A G 3 1_555 B C 17 1_555 A A 4 1_555 B 5BU 16 1_555 -0.744 -1.454 3.302 0.274 1.501 36.693 -2.512 1.219 3.236 2.383 -0.436 36.723 3 AA_G49A50:5BU113C114_BB A 49 ? B 114 ? A 50 ? B 113 ? 1 A A 4 1_555 B 5BU 16 1_555 A G 5 1_555 B C 15 1_555 0.813 -2.205 3.156 0.344 3.041 28.362 -5.122 -1.578 2.918 6.183 -0.699 28.523 4 AA_A50G51:C1125BU113_BB A 50 ? B 113 ? A 51 ? B 112 ? 1 A G 5 1_555 B C 15 1_555 A G 6 1_555 B C 14 1_555 0.624 -2.185 3.306 1.479 -0.218 25.197 -4.935 -0.988 3.354 -0.499 -3.386 25.240 5 AA_G51G52:C111C112_BB A 51 ? B 112 ? A 52 ? B 111 ? 1 A C 12 1_555 B G 13 1_555 A U 13 1_555 B A 12 1_555 -0.544 -1.462 3.374 -2.605 16.746 31.447 -4.667 0.536 2.358 28.458 4.427 35.622 6 AA_C58U59:A109G110_BB A 58 ? B 110 ? A 59 ? B 109 ? 1 A U 13 1_555 B A 12 1_555 A G 14 1_555 B C 11 1_555 0.456 -1.560 3.097 -4.360 2.675 26.480 -3.970 -1.995 2.818 5.771 9.407 26.961 7 AA_U59G60:C108A109_BB A 59 ? B 109 ? A 60 ? B 108 ? 1 A G 14 1_555 B C 11 1_555 A U 15 1_555 B G 10 1_555 0.614 -1.275 3.156 3.565 6.251 47.582 -2.030 -0.488 3.012 7.696 -4.389 48.092 8 AA_G60U61:G107C108_BB A 60 ? B 108 ? A 61 ? B 107 ? 1 A U 15 1_555 B G 10 1_555 A C 16 1_555 B G 8 1_555 0.423 -2.298 3.004 3.238 4.835 25.971 -6.089 -0.187 2.574 10.590 -7.092 26.604 9 AA_U61C62:G105G107_BB A 61 ? B 107 ? A 62 ? B 105 ? 1 A C 16 1_555 B G 8 1_555 A U 17 1_555 B C 7 1_555 0.428 -0.761 3.375 -9.704 9.412 30.803 -2.834 -2.306 2.775 16.744 17.264 33.573 10 AA_C62U63:C104G105_BB A 62 ? B 105 ? A 63 ? B 104 ? 1 A U 17 1_555 B C 7 1_555 A U 18 1_555 B U 6 1_555 0.471 -1.795 3.133 2.049 10.820 31.542 -4.699 -0.523 2.428 19.186 -3.634 33.363 11 AA_U63U64:U103C104_BB A 63 ? B 104 ? A 64 ? B 103 ? 1 A U 18 1_555 B U 6 1_555 A C 19 1_555 B G 5 1_555 -0.111 -1.140 3.077 -0.561 6.078 44.746 -1.985 0.098 2.907 7.940 0.733 45.139 12 AA_U64C65:G102U103_BB A 64 ? B 103 ? A 65 ? B 102 ? 1 A C 19 1_555 B G 5 1_555 A A 20 1_555 B 5BU 4 1_555 -1.049 -1.371 2.347 -0.523 11.790 24.786 -4.727 2.132 1.565 25.688 1.140 27.412 13 AA_C65A66:5BU101G102_BB A 65 ? B 102 ? A 66 ? B 101 ? 1 A A 20 1_555 B 5BU 4 1_555 A C 21 1_555 B G 3 1_555 -0.169 -2.159 3.427 2.602 1.249 33.927 -3.892 0.718 3.326 2.136 -4.449 34.046 14 AA_A66C67:G1005BU101_BB A 66 ? B 101 ? A 67 ? B 100 ? 1 A C 21 1_555 B G 3 1_555 A G 22 1_555 B C 2 1_555 -0.364 -1.804 3.061 -5.872 10.870 31.399 -4.632 -0.192 2.354 19.181 10.361 33.685 15 AA_C67G68:C99G100_BB A 67 ? B 100 ? A 68 ? B 99 ? 1 A G 22 1_555 B C 2 1_555 A C 23 1_555 B G 1 1_555 -0.293 -1.486 3.461 0.031 3.188 40.650 -2.499 0.424 3.340 4.580 -0.044 40.769 16 AA_G68C69:G98C99_BB A 68 ? B 99 ? A 69 ? B 98 ? # _atom_sites.entry_id 2PN3 _atom_sites.fract_transf_matrix[1][1] 0.020431 _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] 0.020431 _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] 0.008268 _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 BR C MG N O P # loop_