data_3DVV # _entry.id 3DVV # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.380 _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 3DVV pdb_00003dvv 10.2210/pdb3dvv/pdb NDB DR0047 ? ? RCSB RCSB048553 ? ? WWPDB D_1000048553 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3C3Z _pdbx_database_related.details 'Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin (U267SeMe)' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3DVV _pdbx_database_status.recvd_initial_deposition_date 2008-07-21 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _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 'Ennifar, E.' 1 'Dumas, P.' 2 'Olieric, V.' 3 # _citation.id primary _citation.title 'A fast strategy for Selenium derivatization and phasing of RNA structures' _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 'Olieric, V.' 1 ? primary 'Rieder, U.' 2 ? primary 'Lang, K.' 3 ? primary 'Serganov, A.' 4 ? primary 'Schulze-Brise, C.' 5 ? primary 'Micura, R.' 6 ? primary 'Dumas, P.' 7 ? primary 'Ennifar, E.' 8 ? # _cell.entry_id 3DVV _cell.length_a 99.703 _cell.length_b 30.489 _cell.length_c 58.004 _cell.angle_alpha 90.00 _cell.angle_beta 122.25 _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 3DVV _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 'HIV-1 genomic RNA' 7400.499 2 ? ? ? ? 2 non-polymer syn 'POTASSIUM ION' 39.098 4 ? ? ? ? 3 non-polymer syn 'CHLORIDE ION' 35.453 1 ? ? ? ? 4 non-polymer syn RIBOSTAMYCIN 454.473 2 ? ? ? ? 5 water nat water 18.015 44 ? ? ? ? # _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 'CU(OMU)GCUGAAGUGCACACAGCAAG' _entity_poly.pdbx_seq_one_letter_code_can CUUGCUGAAGUGCACACAGCAAG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 U n 1 3 OMU n 1 4 G n 1 5 C n 1 6 U n 1 7 G n 1 8 A n 1 9 A n 1 10 G n 1 11 U n 1 12 G n 1 13 C n 1 14 A n 1 15 C n 1 16 A n 1 17 C n 1 18 A n 1 19 G n 1 20 C n 1 21 A n 1 22 A n 1 23 G n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3DVV _struct_ref.pdbx_db_accession 3DVV _struct_ref.entity_id 1 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3DVV A 1 ? 23 ? 3DVV 1 ? 23 ? 1 23 2 1 3DVV B 1 ? 23 ? 3DVV 1 ? 23 ? 1 23 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 K non-polymer . 'POTASSIUM ION' ? 'K 1' 39.098 OMU 'RNA linking' n ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; ? 'C10 H15 N2 O9 P' 338.208 RIO non-polymer . RIBOSTAMYCIN ;5-AMINO-2-AMINOMETHYL-6-[4,6-DIAMINO-2-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-3-HYDROXY-CYCLOHEXYLOXY ]-TETRAHYDRO-PYRAN-3,4-DIOL; (1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside ; 'C17 H34 N4 O10' 454.473 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _exptl.entry_id 3DVV _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.52 _exptl_crystal.density_percent_sol 51.17 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 310 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.2 _exptl_crystal_grow.pdbx_details 'MPD, cacodylate, MgCl2, KCl, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 310K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.details 1 1 1 MPD ? ? ? 1 2 1 cacodylate ? ? ? 1 3 1 MgCl2 ? ? ? 1 4 1 KCl ? ? ? 1 5 2 MPD ? ? ? 1 6 2 "cacodylate'" ? ? ? 1 7 2 MgCl2 ? ? ? 1 8 2 KCl ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 90 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2007-07-13 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.92 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID29' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID29 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.92 # _reflns.entry_id 3DVV _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 30.0 _reflns.d_resolution_high 2.0 _reflns.number_obs 9829 _reflns.number_all 10096 _reflns.percent_possible_obs 95.6 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.058 _reflns.pdbx_netI_over_sigmaI 29.0 _reflns.B_iso_Wilson_estimate 47.6 _reflns.pdbx_redundancy 8.2 _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_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.00 _reflns_shell.d_res_low 2.07 _reflns_shell.percent_possible_all 91.3 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.309 _reflns_shell.meanI_over_sigI_obs 9.8 _reflns_shell.pdbx_redundancy 8.0 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 971 _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 3DVV _refine.ls_number_reflns_obs 9635 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 741857.93 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 18.59 _refine.ls_d_res_high 2.00 _refine.ls_percent_reflns_obs 96.2 _refine.ls_R_factor_obs 0.268 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.268 _refine.ls_R_factor_R_free 0.277 _refine.ls_R_factor_R_free_error 0.010 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 8.1 _refine.ls_number_reflns_R_free 795 _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 45.1 _refine.aniso_B[1][1] -2.14 _refine.aniso_B[2][2] 14.78 _refine.aniso_B[3][3] -12.64 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 1.36 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.358534 _refine.solvent_model_param_bsol 36.979 _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 ID 3C3Z' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model RESTRAINED _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _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 3DVV _refine_analyze.Luzzati_coordinate_error_obs 0.42 _refine_analyze.Luzzati_sigma_a_obs 0.40 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.41 _refine_analyze.Luzzati_sigma_a_free 0.43 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _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 980 _refine_hist.pdbx_number_atoms_ligand 67 _refine_hist.number_atoms_solvent 44 _refine_hist.number_atoms_total 1091 _refine_hist.d_res_high 2.00 _refine_hist.d_res_low 18.59 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function c_bond_d 0.006 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.3 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 12.1 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 5.59 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 2.00 _refine_ls_shell.d_res_low 2.13 _refine_ls_shell.number_reflns_R_work 1488 _refine_ls_shell.R_factor_R_work 0.425 _refine_ls_shell.percent_reflns_obs 96.6 _refine_ls_shell.R_factor_R_free 0.417 _refine_ls_shell.R_factor_R_free_error 0.038 _refine_ls_shell.percent_reflns_R_free 7.5 _refine_ls_shell.number_reflns_R_free 121 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id '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 water_rep.param water.top 'X-RAY DIFFRACTION' 2 luc.param dna-rna.top 'X-RAY DIFFRACTION' 3 ion.param ion.top 'X-RAY DIFFRACTION' 4 OMU_xplor.param OMU_xplor.top 'X-RAY DIFFRACTION' 5 ribostamycine.param ribostamycine.top 'X-RAY DIFFRACTION' # _struct.entry_id 3DVV _struct.title 'Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin (U267OMe)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3DVV _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'HIV-1, RNA, antibiotic, aminoglycoside' # 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 4 ? G N N 2 ? H N N 2 ? I N N 4 ? J N N 5 ? K N N 5 ? # _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 U 2 "O3'" ? ? ? 1_555 A OMU 3 P ? ? A U 2 A OMU 3 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale2 covale both ? A OMU 3 "O3'" ? ? ? 1_555 A G 4 P ? ? A OMU 3 A G 4 1_555 ? ? ? ? ? ? ? 1.612 ? ? covale3 covale both ? B U 2 "O3'" ? ? ? 1_555 B OMU 3 P ? ? B U 2 B OMU 3 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale4 covale both ? B OMU 3 "O3'" ? ? ? 1_555 B G 4 P ? ? B OMU 3 B G 4 1_555 ? ? ? ? ? ? ? 1.601 ? ? metalc1 metalc ? ? A OMU 3 O4 ? ? ? 1_555 D K . K ? ? A OMU 3 A K 25 1_555 ? ? ? ? ? ? ? 2.770 ? ? metalc2 metalc ? ? A G 4 O6 ? ? ? 1_555 D K . K ? ? A G 4 A K 25 1_555 ? ? ? ? ? ? ? 2.576 ? ? metalc3 metalc ? ? A G 10 OP1 ? ? ? 1_555 C K . K ? ? A G 10 A K 24 1_555 ? ? ? ? ? ? ? 2.769 ? ? metalc4 metalc ? ? C K . K ? ? ? 1_555 B A 8 "O2'" ? ? A K 24 B A 8 1_555 ? ? ? ? ? ? ? 2.756 ? ? metalc5 metalc ? ? C K . K ? ? ? 1_555 K HOH . O ? ? A K 24 B HOH 42 1_555 ? ? ? ? ? ? ? 2.356 ? ? metalc6 metalc ? ? B U 2 "O2'" ? ? ? 1_555 H K . K ? ? B U 2 B K 25 1_555 ? ? ? ? ? ? ? 2.987 ? ? metalc7 metalc ? ? B OMU 3 O4 ? ? ? 1_555 G K . K ? ? B OMU 3 B K 24 1_555 ? ? ? ? ? ? ? 2.828 ? ? metalc8 metalc ? ? B G 4 O6 ? ? ? 1_555 G K . K ? ? B G 4 B K 24 1_555 ? ? ? ? ? ? ? 2.987 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 B G 23 N1 ? ? A C 1 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 B G 23 O6 ? ? A C 1 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 B G 23 N2 ? ? A C 1 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 2 N3 ? ? ? 1_555 B A 22 N1 ? ? A U 2 B A 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A U 2 O4 ? ? ? 1_555 B A 22 N6 ? ? A U 2 B A 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A OMU 3 N3 ? ? ? 1_555 B A 21 N1 ? ? A OMU 3 B A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A OMU 3 O4 ? ? ? 1_555 B A 21 N6 ? ? A OMU 3 B A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 20 N3 ? ? A G 4 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 20 O2 ? ? A G 4 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 20 N4 ? ? A G 4 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 N3 ? ? ? 1_555 B G 19 N1 ? ? A C 5 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N4 ? ? ? 1_555 B G 19 O6 ? ? A C 5 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 O2 ? ? ? 1_555 B G 19 N2 ? ? A C 5 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 6 N3 ? ? ? 1_555 B A 18 N1 ? ? A U 6 B A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 6 O4 ? ? ? 1_555 B A 18 N6 ? ? A U 6 B A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 7 N1 ? ? ? 1_555 B C 17 N3 ? ? A G 7 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 7 N2 ? ? ? 1_555 B C 17 O2 ? ? A G 7 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 7 O6 ? ? ? 1_555 B C 17 N4 ? ? A G 7 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 10 N1 ? ? ? 1_555 B C 15 N3 ? ? A G 10 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 10 N2 ? ? ? 1_555 B C 15 O2 ? ? A G 10 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 10 O6 ? ? ? 1_555 B C 15 N4 ? ? A G 10 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A U 11 N3 ? ? ? 1_555 B A 14 N1 ? ? A U 11 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A U 11 O4 ? ? ? 1_555 B A 14 N6 ? ? A U 11 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 13 N3 ? ? A G 12 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 13 O2 ? ? A G 12 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 13 N4 ? ? A G 12 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 13 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 13 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 13 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 13 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 13 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 13 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A A 14 N1 ? ? ? 1_555 B U 11 N3 ? ? A A 14 B U 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A A 14 N6 ? ? ? 1_555 B U 11 O4 ? ? A A 14 B U 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 15 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 15 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 15 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 15 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 15 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 15 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 17 N3 ? ? ? 1_555 B G 7 N1 ? ? A C 17 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A C 17 N4 ? ? ? 1_555 B G 7 O6 ? ? A C 17 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A C 17 O2 ? ? ? 1_555 B G 7 N2 ? ? A C 17 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A A 18 N1 ? ? ? 1_555 B U 6 N3 ? ? A A 18 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A A 18 N6 ? ? ? 1_555 B U 6 O4 ? ? A A 18 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A G 19 N1 ? ? ? 1_555 B C 5 N3 ? ? A G 19 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A G 19 N2 ? ? ? 1_555 B C 5 O2 ? ? A G 19 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 19 O6 ? ? ? 1_555 B C 5 N4 ? ? A G 19 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A C 20 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 20 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 20 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 20 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 20 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 20 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A A 21 N1 ? ? ? 1_555 B OMU 3 N3 ? ? A A 21 B OMU 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A A 21 N6 ? ? ? 1_555 B OMU 3 O4 ? ? A A 21 B OMU 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A A 22 N1 ? ? ? 1_555 B U 2 N3 ? ? A A 22 B U 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A A 22 N6 ? ? ? 1_555 B U 2 O4 ? ? A A 22 B U 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A G 23 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 23 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A G 23 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 23 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A G 23 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 23 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A K 24 ? 4 'BINDING SITE FOR RESIDUE K A 24' AC2 Software A K 25 ? 2 'BINDING SITE FOR RESIDUE K A 25' AC3 Software A CL 26 ? 1 'BINDING SITE FOR RESIDUE CL A 26' AC4 Software B K 24 ? 2 'BINDING SITE FOR RESIDUE K B 24' AC5 Software B K 25 ? 2 'BINDING SITE FOR RESIDUE K B 25' AC6 Software A RIO 27 ? 15 'BINDING SITE FOR RESIDUE RIO A 27' AC7 Software B RIO 26 ? 14 'BINDING SITE FOR RESIDUE RIO B 26' 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 4 A A 9 ? A A 9 . ? 1_555 ? 2 AC1 4 G A 10 ? G A 10 . ? 1_555 ? 3 AC1 4 A B 8 ? A B 8 . ? 1_555 ? 4 AC1 4 HOH K . ? HOH B 42 . ? 1_555 ? 5 AC2 2 OMU A 3 ? OMU A 3 . ? 1_555 ? 6 AC2 2 G A 4 ? G A 4 . ? 1_555 ? 7 AC3 1 C A 17 ? C A 17 . ? 1_555 ? 8 AC4 2 OMU B 3 ? OMU B 3 . ? 1_555 ? 9 AC4 2 G B 4 ? G B 4 . ? 1_555 ? 10 AC5 2 U B 2 ? U B 2 . ? 1_555 ? 11 AC5 2 C B 13 ? C B 13 . ? 4_556 ? 12 AC6 15 G A 7 ? G A 7 . ? 1_555 ? 13 AC6 15 A A 8 ? A A 8 . ? 1_555 ? 14 AC6 15 A A 9 ? A A 9 . ? 1_555 ? 15 AC6 15 G A 10 ? G A 10 . ? 1_555 ? 16 AC6 15 U A 11 ? U A 11 . ? 1_555 ? 17 AC6 15 HOH J . ? HOH A 30 . ? 1_555 ? 18 AC6 15 HOH J . ? HOH A 33 . ? 1_555 ? 19 AC6 15 HOH J . ? HOH A 36 . ? 1_555 ? 20 AC6 15 HOH J . ? HOH A 37 . ? 1_555 ? 21 AC6 15 HOH J . ? HOH A 45 . ? 1_555 ? 22 AC6 15 HOH J . ? HOH A 50 . ? 1_555 ? 23 AC6 15 A B 14 ? A B 14 . ? 1_555 ? 24 AC6 15 C B 15 ? C B 15 . ? 1_555 ? 25 AC6 15 A B 16 ? A B 16 . ? 1_555 ? 26 AC6 15 HOH K . ? HOH B 27 . ? 1_555 ? 27 AC7 14 C A 13 ? C A 13 . ? 1_555 ? 28 AC7 14 A A 14 ? A A 14 . ? 1_555 ? 29 AC7 14 C A 15 ? C A 15 . ? 1_555 ? 30 AC7 14 A A 16 ? A A 16 . ? 1_555 ? 31 AC7 14 HOH J . ? HOH A 45 . ? 1_555 ? 32 AC7 14 G B 7 ? G B 7 . ? 1_555 ? 33 AC7 14 A B 8 ? A B 8 . ? 1_555 ? 34 AC7 14 A B 9 ? A B 9 . ? 1_555 ? 35 AC7 14 G B 10 ? G B 10 . ? 1_555 ? 36 AC7 14 U B 11 ? U B 11 . ? 1_555 ? 37 AC7 14 G B 12 ? G B 12 . ? 1_555 ? 38 AC7 14 HOH K . ? HOH B 28 . ? 1_555 ? 39 AC7 14 HOH K . ? HOH B 31 . ? 1_555 ? 40 AC7 14 HOH K . ? HOH B 38 . ? 1_555 ? # _database_PDB_matrix.entry_id 3DVV _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 3DVV _atom_sites.fract_transf_matrix[1][1] 0.010030 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.006330 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.032799 _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] 0.020386 _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 CL K N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 C 1 1 1 C CYT A . n A 1 2 U 2 2 2 U URI A . n A 1 3 OMU 3 3 3 OMU OMU A . n A 1 4 G 4 4 4 G GUA A . n A 1 5 C 5 5 5 C CYT A . n A 1 6 U 6 6 6 U URI A . n A 1 7 G 7 7 7 G GUA A . n A 1 8 A 8 8 8 A ADE A . n A 1 9 A 9 9 9 A ADE A . n A 1 10 G 10 10 10 G GUA A . n A 1 11 U 11 11 11 U URI A . n A 1 12 G 12 12 12 G GUA A . n A 1 13 C 13 13 13 C CYT A . n A 1 14 A 14 14 14 A ADE A . n A 1 15 C 15 15 15 C CYT A . n A 1 16 A 16 16 16 A ADE A . n A 1 17 C 17 17 17 C CYT A . n A 1 18 A 18 18 18 A ADE A . n A 1 19 G 19 19 19 G GUA A . n A 1 20 C 20 20 20 C CYT A . n A 1 21 A 21 21 21 A ADE A . n A 1 22 A 22 22 22 A ADE A . n A 1 23 G 23 23 23 G GUA A . n B 1 1 C 1 1 1 C CYT B . n B 1 2 U 2 2 2 U URI B . n B 1 3 OMU 3 3 3 OMU OMU B . n B 1 4 G 4 4 4 G GUA B . n B 1 5 C 5 5 5 C CYT B . n B 1 6 U 6 6 6 U URI B . n B 1 7 G 7 7 7 G GUA B . n B 1 8 A 8 8 8 A ADE B . n B 1 9 A 9 9 9 A ADE B . n B 1 10 G 10 10 10 G GUA B . n B 1 11 U 11 11 11 U URI B . n B 1 12 G 12 12 12 G GUA B . n B 1 13 C 13 13 13 C CYT B . n B 1 14 A 14 14 14 A ADE B . n B 1 15 C 15 15 15 C CYT B . n B 1 16 A 16 16 16 A ADE B . n B 1 17 C 17 17 17 C CYT B . n B 1 18 A 18 18 18 A ADE B . n B 1 19 G 19 19 19 G GUA B . n B 1 20 C 20 20 20 C CYT B . n B 1 21 A 21 21 21 A ADE B . n B 1 22 A 22 22 22 A ADE B . n B 1 23 G 23 23 23 G GUA 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 K 1 24 1 K K1 A . D 2 K 1 25 3 K K1 A . E 3 CL 1 26 11 CL CL1 A . F 4 RIO 1 27 24 RIO RIB A . G 2 K 1 24 2 K K1 B . H 2 K 1 25 25 K K1 B . I 4 RIO 1 26 24 RIO RIB B . J 5 HOH 1 28 7 HOH TIP A . J 5 HOH 2 29 8 HOH TIP A . J 5 HOH 3 30 9 HOH TIP A . J 5 HOH 4 31 10 HOH TIP A . J 5 HOH 5 32 13 HOH TIP A . J 5 HOH 6 33 14 HOH TIP A . J 5 HOH 7 34 15 HOH TIP A . J 5 HOH 8 35 16 HOH TIP A . J 5 HOH 9 36 17 HOH TIP A . J 5 HOH 10 37 19 HOH TIP A . J 5 HOH 11 38 23 HOH TIP A . J 5 HOH 12 39 24 HOH TIP A . J 5 HOH 13 40 27 HOH TIP A . J 5 HOH 14 41 28 HOH TIP A . J 5 HOH 15 42 29 HOH TIP A . J 5 HOH 16 43 30 HOH TIP A . J 5 HOH 17 44 31 HOH TIP A . J 5 HOH 18 45 34 HOH TIP A . J 5 HOH 19 46 35 HOH TIP A . J 5 HOH 20 47 36 HOH TIP A . J 5 HOH 21 48 38 HOH TIP A . J 5 HOH 22 49 40 HOH TIP A . J 5 HOH 23 50 41 HOH TIP A . J 5 HOH 24 51 42 HOH TIP A . J 5 HOH 25 52 43 HOH TIP A . J 5 HOH 26 53 44 HOH TIP A . J 5 HOH 27 54 46 HOH TIP A . J 5 HOH 28 55 47 HOH TIP A . J 5 HOH 29 56 39 HOH TIP A . K 5 HOH 1 27 4 HOH TIP B . K 5 HOH 2 28 5 HOH TIP B . K 5 HOH 3 29 6 HOH TIP B . K 5 HOH 4 30 12 HOH TIP B . K 5 HOH 5 31 18 HOH TIP B . K 5 HOH 6 32 20 HOH TIP B . K 5 HOH 7 33 21 HOH TIP B . K 5 HOH 8 34 22 HOH TIP B . K 5 HOH 9 35 26 HOH TIP B . K 5 HOH 10 36 32 HOH TIP B . K 5 HOH 11 37 33 HOH TIP B . K 5 HOH 12 38 37 HOH TIP B . K 5 HOH 13 40 45 HOH TIP B . K 5 HOH 14 41 48 HOH TIP B . K 5 HOH 15 42 49 HOH TIP B . # 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 A OMU 3 A OMU 3 ? U ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; 2 B OMU 3 B OMU 3 ? U ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'MAJOR GROOVE BINDER' # _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 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K # 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)' 3660 ? 1 MORE 1 ? 1 'SSA (A^2)' 8360 ? # _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_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O4 ? A OMU 3 ? A OMU 3 ? 1_555 K ? D K . ? A K 25 ? 1_555 O6 ? A G 4 ? A G 4 ? 1_555 74.0 ? 2 OP1 ? A G 10 ? A G 10 ? 1_555 K ? C K . ? A K 24 ? 1_555 "O2'" ? B A 8 ? B A 8 ? 1_555 103.3 ? 3 OP1 ? A G 10 ? A G 10 ? 1_555 K ? C K . ? A K 24 ? 1_555 O ? K HOH . ? B HOH 42 ? 1_555 90.4 ? 4 "O2'" ? B A 8 ? B A 8 ? 1_555 K ? C K . ? A K 24 ? 1_555 O ? K HOH . ? B HOH 42 ? 1_555 67.5 ? 5 O4 ? B OMU 3 ? B OMU 3 ? 1_555 K ? G K . ? B K 24 ? 1_555 O6 ? B G 4 ? B G 4 ? 1_555 72.8 ? # 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 2008-08-12 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2023-11-01 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Refinement description' 6 3 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp 2 3 'Structure model' chem_comp_atom 3 3 'Structure model' chem_comp_bond 4 3 'Structure model' database_2 5 3 'Structure model' pdbx_initial_refinement_model 6 3 'Structure model' struct_conn 7 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_chem_comp.pdbx_synonyms' 2 3 'Structure model' '_database_2.pdbx_DOI' 3 3 'Structure model' '_database_2.pdbx_database_accession' 4 3 'Structure model' '_struct_conn.pdbx_dist_value' 5 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 7 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 8 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 9 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 10 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 11 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 12 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 13 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 14 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 15 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 16 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 17 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 18 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 19 3 'Structure model' '_struct_conn.ptnr2_label_seq_id' 20 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 21 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 22 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 HKL-2000 'data collection' . ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 CNS phasing . ? 5 # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "C2'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 A _pdbx_validate_rmsd_angle.auth_seq_id_1 8 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 "C3'" _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 A _pdbx_validate_rmsd_angle.auth_seq_id_2 8 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 "O3'" _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 A _pdbx_validate_rmsd_angle.auth_seq_id_3 8 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 126.94 _pdbx_validate_rmsd_angle.angle_target_value 113.70 _pdbx_validate_rmsd_angle.angle_deviation 13.24 _pdbx_validate_rmsd_angle.angle_standard_deviation 1.60 _pdbx_validate_rmsd_angle.linker_flag 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 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 CL CL CL N N 73 G OP3 O N N 74 G P P N N 75 G OP1 O N N 76 G OP2 O N N 77 G "O5'" O N N 78 G "C5'" C N N 79 G "C4'" C N R 80 G "O4'" O N N 81 G "C3'" C N S 82 G "O3'" O N N 83 G "C2'" C N R 84 G "O2'" O N N 85 G "C1'" C N R 86 G N9 N Y N 87 G C8 C Y N 88 G N7 N Y N 89 G C5 C Y N 90 G C6 C N N 91 G O6 O N N 92 G N1 N N N 93 G C2 C N N 94 G N2 N N N 95 G N3 N N N 96 G C4 C Y N 97 G HOP3 H N N 98 G HOP2 H N N 99 G "H5'" H N N 100 G "H5''" H N N 101 G "H4'" H N N 102 G "H3'" H N N 103 G "HO3'" H N N 104 G "H2'" H N N 105 G "HO2'" H N N 106 G "H1'" H N N 107 G H8 H N N 108 G H1 H N N 109 G H21 H N N 110 G H22 H N N 111 HOH O O N N 112 HOH H1 H N N 113 HOH H2 H N N 114 K K K N N 115 OMU N1 N N N 116 OMU C2 C N N 117 OMU N3 N N N 118 OMU C4 C N N 119 OMU C5 C N N 120 OMU C6 C N N 121 OMU O2 O N N 122 OMU O4 O N N 123 OMU "C1'" C N R 124 OMU "C2'" C N R 125 OMU "O2'" O N N 126 OMU CM2 C N N 127 OMU "C3'" C N R 128 OMU "C4'" C N R 129 OMU "O3'" O N N 130 OMU "O4'" O N N 131 OMU "C5'" C N N 132 OMU "O5'" O N N 133 OMU P P N N 134 OMU OP1 O N N 135 OMU OP2 O N N 136 OMU OP3 O N N 137 OMU HN3 H N N 138 OMU H5 H N N 139 OMU H6 H N N 140 OMU "H1'" H N N 141 OMU "H2'" H N N 142 OMU HM21 H N N 143 OMU HM22 H N N 144 OMU HM23 H N N 145 OMU "H3'" H N N 146 OMU "H4'" H N N 147 OMU "HO3'" H N N 148 OMU "H5'" H N N 149 OMU "H5''" H N N 150 OMU HOP2 H N N 151 OMU HOP3 H N N 152 RIO O1 O N N 153 RIO C1 C N N 154 RIO C2 C N R 155 RIO O2 O N N 156 RIO C3 C N S 157 RIO O3 O N N 158 RIO C4 C N R 159 RIO C5 C N S 160 RIO O4 O N N 161 RIO C6 C N R 162 RIO N1 N N N 163 RIO C7 C N N 164 RIO C8 C N S 165 RIO N2 N N N 166 RIO C9 C N R 167 RIO O5 O N N 168 RIO C10 C N R 169 RIO O6 O N N 170 RIO C11 C N R 171 RIO C12 C N N 172 RIO N3 N N N 173 RIO C13 C N S 174 RIO O7 O N N 175 RIO C14 C N R 176 RIO O8 O N N 177 RIO C15 C N R 178 RIO N4 N N N 179 RIO C16 C N R 180 RIO O9 O N N 181 RIO C17 C N S 182 RIO O10 O N N 183 RIO HO1 H N N 184 RIO H1 H N N 185 RIO H1A H N N 186 RIO H2 H N N 187 RIO H3 H N N 188 RIO H4 H N N 189 RIO H5 H N N 190 RIO HO4 H N N 191 RIO H6 H N N 192 RIO HN1 H N N 193 RIO HN1A H N N 194 RIO H7 H N N 195 RIO H7A H N N 196 RIO H8 H N N 197 RIO HN2 H N N 198 RIO HN2A H N N 199 RIO H9 H N N 200 RIO H10 H N N 201 RIO H11 H N N 202 RIO H12 H N N 203 RIO H12A H N N 204 RIO HN3 H N N 205 RIO HN3A H N N 206 RIO H13 H N N 207 RIO HO7 H N N 208 RIO H14 H N N 209 RIO HO8 H N N 210 RIO H15 H N N 211 RIO HN4 H N N 212 RIO HN4A H N N 213 RIO H16 H N N 214 RIO HO9 H N N 215 RIO H17 H N N 216 RIO HO10 H N N 217 U OP3 O N N 218 U P P N N 219 U OP1 O N N 220 U OP2 O N N 221 U "O5'" O N N 222 U "C5'" C N N 223 U "C4'" C N R 224 U "O4'" O N N 225 U "C3'" C N S 226 U "O3'" O N N 227 U "C2'" C N R 228 U "O2'" O N N 229 U "C1'" C N R 230 U N1 N N N 231 U C2 C N N 232 U O2 O N N 233 U N3 N N N 234 U C4 C N N 235 U O4 O N N 236 U C5 C N N 237 U C6 C N N 238 U HOP3 H N N 239 U HOP2 H N N 240 U "H5'" H N N 241 U "H5''" H N N 242 U "H4'" H N N 243 U "H3'" H N N 244 U "HO3'" H N N 245 U "H2'" H N N 246 U "HO2'" H N N 247 U "H1'" H N N 248 U H3 H N N 249 U H5 H N N 250 U H6 H N N 251 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 OMU N1 C2 sing N N 118 OMU N1 C6 sing N N 119 OMU N1 "C1'" sing N N 120 OMU C2 N3 sing N N 121 OMU C2 O2 doub N N 122 OMU N3 C4 sing N N 123 OMU N3 HN3 sing N N 124 OMU C4 C5 sing N N 125 OMU C4 O4 doub N N 126 OMU C5 C6 doub N N 127 OMU C5 H5 sing N N 128 OMU C6 H6 sing N N 129 OMU "C1'" "C2'" sing N N 130 OMU "C1'" "O4'" sing N N 131 OMU "C1'" "H1'" sing N N 132 OMU "C2'" "O2'" sing N N 133 OMU "C2'" "C3'" sing N N 134 OMU "C2'" "H2'" sing N N 135 OMU "O2'" CM2 sing N N 136 OMU CM2 HM21 sing N N 137 OMU CM2 HM22 sing N N 138 OMU CM2 HM23 sing N N 139 OMU "C3'" "C4'" sing N N 140 OMU "C3'" "O3'" sing N N 141 OMU "C3'" "H3'" sing N N 142 OMU "C4'" "O4'" sing N N 143 OMU "C4'" "C5'" sing N N 144 OMU "C4'" "H4'" sing N N 145 OMU "O3'" "HO3'" sing N N 146 OMU "C5'" "O5'" sing N N 147 OMU "C5'" "H5'" sing N N 148 OMU "C5'" "H5''" sing N N 149 OMU "O5'" P sing N N 150 OMU P OP1 doub N N 151 OMU P OP2 sing N N 152 OMU P OP3 sing N N 153 OMU OP2 HOP2 sing N N 154 OMU OP3 HOP3 sing N N 155 RIO O1 C1 sing N N 156 RIO C1 C2 sing N N 157 RIO C2 O2 sing N N 158 RIO C2 C17 sing N N 159 RIO O2 C3 sing N N 160 RIO C3 O3 sing N N 161 RIO C3 C16 sing N N 162 RIO O3 C4 sing N N 163 RIO C4 C5 sing N N 164 RIO C4 C9 sing N N 165 RIO C5 O4 sing N N 166 RIO C5 C6 sing N N 167 RIO C6 N1 sing N N 168 RIO C6 C7 sing N N 169 RIO C7 C8 sing N N 170 RIO C8 N2 sing N N 171 RIO C8 C9 sing N N 172 RIO C9 O5 sing N N 173 RIO O5 C10 sing N N 174 RIO C10 O6 sing N N 175 RIO C10 C15 sing N N 176 RIO O6 C11 sing N N 177 RIO C11 C12 sing N N 178 RIO C11 C13 sing N N 179 RIO C12 N3 sing N N 180 RIO C13 O7 sing N N 181 RIO C13 C14 sing N N 182 RIO C14 O8 sing N N 183 RIO C14 C15 sing N N 184 RIO C15 N4 sing N N 185 RIO C16 O9 sing N N 186 RIO C16 C17 sing N N 187 RIO C17 O10 sing N N 188 RIO O1 HO1 sing N N 189 RIO C1 H1 sing N N 190 RIO C1 H1A sing N N 191 RIO C2 H2 sing N N 192 RIO C3 H3 sing N N 193 RIO C4 H4 sing N N 194 RIO C5 H5 sing N N 195 RIO O4 HO4 sing N N 196 RIO C6 H6 sing N N 197 RIO N1 HN1 sing N N 198 RIO N1 HN1A sing N N 199 RIO C7 H7 sing N N 200 RIO C7 H7A sing N N 201 RIO C8 H8 sing N N 202 RIO N2 HN2 sing N N 203 RIO N2 HN2A sing N N 204 RIO C9 H9 sing N N 205 RIO C10 H10 sing N N 206 RIO C11 H11 sing N N 207 RIO C12 H12 sing N N 208 RIO C12 H12A sing N N 209 RIO N3 HN3 sing N N 210 RIO N3 HN3A sing N N 211 RIO C13 H13 sing N N 212 RIO O7 HO7 sing N N 213 RIO C14 H14 sing N N 214 RIO O8 HO8 sing N N 215 RIO C15 H15 sing N N 216 RIO N4 HN4 sing N N 217 RIO N4 HN4A sing N N 218 RIO C16 H16 sing N N 219 RIO O9 HO9 sing N N 220 RIO C17 H17 sing N N 221 RIO O10 HO10 sing N N 222 U OP3 P sing N N 223 U OP3 HOP3 sing N N 224 U P OP1 doub N N 225 U P OP2 sing N N 226 U P "O5'" sing N N 227 U OP2 HOP2 sing N N 228 U "O5'" "C5'" sing N N 229 U "C5'" "C4'" sing N N 230 U "C5'" "H5'" sing N N 231 U "C5'" "H5''" sing N N 232 U "C4'" "O4'" sing N N 233 U "C4'" "C3'" sing N N 234 U "C4'" "H4'" sing N N 235 U "O4'" "C1'" sing N N 236 U "C3'" "O3'" sing N N 237 U "C3'" "C2'" sing N N 238 U "C3'" "H3'" sing N N 239 U "O3'" "HO3'" sing N N 240 U "C2'" "O2'" sing N N 241 U "C2'" "C1'" sing N N 242 U "C2'" "H2'" sing N N 243 U "O2'" "HO2'" sing N N 244 U "C1'" N1 sing N N 245 U "C1'" "H1'" sing N N 246 U N1 C2 sing N N 247 U N1 C6 sing N N 248 U C2 O2 doub N N 249 U C2 N3 sing N N 250 U N3 C4 sing N N 251 U N3 H3 sing N N 252 U C4 O4 doub N N 253 U C4 C5 sing N N 254 U C5 C6 doub N N 255 U C5 H5 sing N N 256 U C6 H6 sing N N 257 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3DVV 'double helix' 3DVV 'a-form double helix' 3DVV '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 B G 23 1_555 0.351 -0.265 0.157 5.084 -20.194 1.426 1 A_C1:G23_B A 1 ? B 23 ? 19 1 1 A U 2 1_555 B A 22 1_555 0.102 -0.143 -0.150 2.279 -14.836 2.459 2 A_U2:A22_B A 2 ? B 22 ? 20 1 1 A OMU 3 1_555 B A 21 1_555 0.092 -0.075 0.140 -2.076 -11.554 -0.058 3 A_OMU3:A21_B A 3 ? B 21 ? 20 1 1 A G 4 1_555 B C 20 1_555 -0.031 -0.218 0.175 0.690 -16.672 -0.155 4 A_G4:C20_B A 4 ? B 20 ? 19 1 1 A C 5 1_555 B G 19 1_555 0.451 -0.056 0.089 1.928 -16.066 3.196 5 A_C5:G19_B A 5 ? B 19 ? 19 1 1 A U 6 1_555 B A 18 1_555 -0.091 -0.154 0.264 7.263 -14.739 2.577 6 A_U6:A18_B A 6 ? B 18 ? 20 1 1 A G 7 1_555 B C 17 1_555 -0.395 -0.103 0.066 -10.650 -23.797 1.448 7 A_G7:C17_B A 7 ? B 17 ? 19 1 1 A G 10 1_555 B C 15 1_555 -0.392 -0.235 -0.115 -2.028 -0.718 1.705 8 A_G10:C15_B A 10 ? B 15 ? 19 1 1 A U 11 1_555 B A 14 1_555 -0.239 -0.361 0.117 -1.787 -5.670 0.177 9 A_U11:A14_B A 11 ? B 14 ? 20 1 1 A G 12 1_555 B C 13 1_555 -0.241 -0.186 0.197 0.702 -8.786 3.429 10 A_G12:C13_B A 12 ? B 13 ? 19 1 1 A C 13 1_555 B G 12 1_555 0.197 -0.130 0.042 4.770 -14.772 5.867 11 A_C13:G12_B A 13 ? B 12 ? 19 1 1 A A 14 1_555 B U 11 1_555 0.194 -0.171 0.101 -1.839 -4.593 -1.687 12 A_A14:U11_B A 14 ? B 11 ? 20 1 1 A C 15 1_555 B G 10 1_555 0.483 -0.263 0.151 0.367 -2.192 0.018 13 A_C15:G10_B A 15 ? B 10 ? 19 1 1 A C 17 1_555 B G 7 1_555 0.259 -0.223 -0.113 6.979 -21.979 1.538 14 A_C17:G7_B A 17 ? B 7 ? 19 1 1 A A 18 1_555 B U 6 1_555 0.079 -0.176 0.220 3.293 -13.505 4.295 15 A_A18:U6_B A 18 ? B 6 ? 20 1 1 A G 19 1_555 B C 5 1_555 -0.205 -0.228 -0.093 -0.972 -13.557 1.618 16 A_G19:C5_B A 19 ? B 5 ? 19 1 1 A C 20 1_555 B G 4 1_555 0.090 -0.181 -0.014 6.350 -19.010 0.226 17 A_C20:G4_B A 20 ? B 4 ? 19 1 1 A A 21 1_555 B OMU 3 1_555 0.260 -0.106 -0.014 -1.597 -10.922 -0.535 18 A_A21:OMU3_B A 21 ? B 3 ? 20 1 1 A A 22 1_555 B U 2 1_555 0.559 -0.205 0.048 -5.629 -17.195 2.865 19 A_A22:U2_B A 22 ? B 2 ? 20 1 1 A G 23 1_555 B C 1 1_555 -0.283 -0.126 -0.133 -4.822 -20.677 2.749 20 A_G23:C1_B A 23 ? B 1 ? 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 23 1_555 A U 2 1_555 B A 22 1_555 -1.056 -1.578 3.324 -3.184 9.219 31.124 -4.363 1.348 2.844 16.675 5.758 32.580 1 AA_C1U2:A22G23_BB A 1 ? B 23 ? A 2 ? B 22 ? 1 A U 2 1_555 B A 22 1_555 A OMU 3 1_555 B A 21 1_555 -0.266 -1.167 3.384 -3.854 8.537 33.253 -3.286 -0.147 3.013 14.561 6.573 34.511 2 AA_U2OMU3:A21A22_BB A 2 ? B 22 ? A 3 ? B 21 ? 1 A OMU 3 1_555 B A 21 1_555 A G 4 1_555 B C 20 1_555 0.228 -1.497 2.926 2.235 16.639 31.298 -4.396 -0.115 1.923 28.425 -3.818 35.417 3 AA_OMU3G4:C20A21_BB A 3 ? B 21 ? A 4 ? B 20 ? 1 A G 4 1_555 B C 20 1_555 A C 5 1_555 B G 19 1_555 0.545 -1.349 3.267 1.908 4.413 33.978 -2.964 -0.631 3.097 7.505 -3.245 34.307 4 AA_G4C5:G19C20_BB A 4 ? B 20 ? A 5 ? B 19 ? 1 A C 5 1_555 B G 19 1_555 A U 6 1_555 B A 18 1_555 -0.054 -1.933 3.130 -1.526 4.790 26.031 -5.362 -0.248 2.735 10.509 3.347 26.503 5 AA_C5U6:A18G19_BB A 5 ? B 19 ? A 6 ? B 18 ? 1 A U 6 1_555 B A 18 1_555 A G 7 1_555 B C 17 1_555 -0.121 -1.555 3.440 1.602 14.762 32.685 -4.558 0.417 2.519 24.705 -2.681 35.816 6 AA_U6G7:C17A18_BB A 6 ? B 18 ? A 7 ? B 17 ? 1 A G 7 1_555 B C 17 1_555 A G 10 1_555 B C 15 1_555 -1.287 -3.922 6.130 10.298 21.593 80.653 -3.850 1.398 4.984 16.361 -7.803 83.542 7 AA_G7G10:C15C17_BB A 7 ? B 17 ? A 10 ? B 15 ? 1 A G 10 1_555 B C 15 1_555 A U 11 1_555 B A 14 1_555 -0.408 -2.660 3.263 -1.587 1.244 34.257 -4.701 0.446 3.183 2.110 2.692 34.315 8 AA_G10U11:A14C15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A U 11 1_555 B A 14 1_555 A G 12 1_555 B C 13 1_555 -0.521 -1.813 3.066 -0.113 10.042 26.455 -5.671 1.045 2.243 21.005 0.237 28.266 9 AA_U11G12:C13A14_BB A 11 ? B 14 ? A 12 ? B 13 ? 1 A G 12 1_555 B C 13 1_555 A C 13 1_555 B G 12 1_555 0.780 -1.216 3.146 2.795 8.736 35.193 -3.082 -0.889 2.826 14.153 -4.528 36.332 10 AA_G12C13:G12C13_BB A 12 ? B 13 ? A 13 ? B 12 ? 1 A C 13 1_555 B G 12 1_555 A A 14 1_555 B U 11 1_555 0.039 -1.568 3.282 0.325 11.955 31.320 -4.537 -0.019 2.531 21.201 -0.577 33.472 11 AA_C13A14:U11G12_BB A 13 ? B 12 ? A 14 ? B 11 ? 1 A A 14 1_555 B U 11 1_555 A C 15 1_555 B G 10 1_555 0.806 -2.764 3.051 1.666 4.474 29.504 -6.175 -1.260 2.653 8.714 -3.244 29.879 12 AA_A14C15:G10U11_BB A 14 ? B 11 ? A 15 ? B 10 ? 1 A C 15 1_555 B G 10 1_555 A C 17 1_555 B G 7 1_555 1.613 -4.013 6.027 -2.880 18.678 78.133 -3.974 -1.386 5.072 14.621 2.254 80.029 13 AA_C15C17:G7G10_BB A 15 ? B 10 ? A 17 ? B 7 ? 1 A C 17 1_555 B G 7 1_555 A A 18 1_555 B U 6 1_555 0.151 -1.710 3.154 -1.920 14.456 33.167 -4.512 -0.477 2.229 23.936 3.179 36.149 14 AA_C17A18:U6G7_BB A 17 ? B 7 ? A 18 ? B 6 ? 1 A A 18 1_555 B U 6 1_555 A G 19 1_555 B C 5 1_555 -0.765 -1.581 3.368 -0.293 9.841 27.433 -5.191 1.461 2.661 19.955 0.594 29.114 15 AA_A18G19:C5U6_BB A 18 ? B 6 ? A 19 ? B 5 ? 1 A G 19 1_555 B C 5 1_555 A C 20 1_555 B G 4 1_555 0.186 -1.194 2.976 -0.089 4.735 34.574 -2.628 -0.323 2.792 7.921 0.149 34.887 16 AA_G19C20:G4C5_BB A 19 ? B 5 ? A 20 ? B 4 ? 1 A C 20 1_555 B G 4 1_555 A A 21 1_555 B OMU 3 1_555 -0.322 -1.600 3.295 -0.837 15.034 32.009 -4.659 0.418 2.341 25.572 1.424 35.289 17 AA_C20A21:OMU3G4_BB A 20 ? B 4 ? A 21 ? B 3 ? 1 A A 21 1_555 B OMU 3 1_555 A A 22 1_555 B U 2 1_555 0.068 -1.313 3.300 1.830 11.314 34.948 -3.553 0.129 2.757 18.243 -2.950 36.723 18 AA_A21A22:U2OMU3_BB A 21 ? B 3 ? A 22 ? B 2 ? 1 A A 22 1_555 B U 2 1_555 A G 23 1_555 B C 1 1_555 0.680 -1.736 3.102 4.699 14.066 27.086 -5.580 -0.507 2.059 27.566 -9.210 30.814 19 AA_A22G23:C1U2_BB A 22 ? B 2 ? A 23 ? B 1 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'POTASSIUM ION' K 3 'CHLORIDE ION' CL 4 RIBOSTAMYCIN RIO 5 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 3C3Z _pdbx_initial_refinement_model.details 'PDB ID 3C3Z' #