data_4F8V # _entry.id 4F8V # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.388 _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 4F8V pdb_00004f8v 10.2210/pdb4f8v/pdb NDB NA1818 ? ? RCSB RCSB072601 ? ? WWPDB D_1000072601 ? ? # 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 2012-08-15 2 'Structure model' 1 1 2012-09-05 3 'Structure model' 1 2 2019-12-25 4 'Structure model' 1 3 2024-03-20 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Structure summary' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 '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' citation 2 4 'Structure model' chem_comp_atom 3 4 'Structure model' chem_comp_bond 4 4 'Structure model' database_2 5 4 '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' '_citation.journal_abbrev' 2 3 'Structure model' '_citation.journal_volume' 3 3 'Structure model' '_citation.page_first' 4 3 'Structure model' '_citation.page_last' 5 3 'Structure model' '_citation.pdbx_database_id_PubMed' 6 3 'Structure model' '_citation.title' 7 4 'Structure model' '_database_2.pdbx_DOI' 8 4 'Structure model' '_database_2.pdbx_database_accession' 9 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 10 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 11 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4F8V _pdbx_database_status.recvd_initial_deposition_date 2012-05-18 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 4F8U _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kondo, J.' 1 'Koganei, M.' 2 'Kasahara, T.' 3 # _citation.id primary _citation.title 'Crystal structure and specific binding mode of sisomicin to the bacterial ribosomal decoding site.' _citation.journal_abbrev 'Acs Med.Chem.Lett.' _citation.journal_volume 3 _citation.page_first 741 _citation.page_last 744 _citation.year 2012 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1948-5875 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24900542 _citation.pdbx_database_id_DOI 10.1021/ml300145y # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kondo, J.' 1 ? primary 'Koganei, M.' 2 ? primary 'Kasahara, T.' 3 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;RNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3') ; 6743.077 2 ? ? ? ? 2 non-polymer syn ;(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside ; 447.526 2 ? ? ? ? 3 water nat water 18.015 3 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GCGUCACACCGGUGAAGUCGC _entity_poly.pdbx_seq_one_letter_code_can GCGUCACACCGGUGAAGUCGC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 ;(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside ; SIS 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 C n 1 3 G n 1 4 U n 1 5 C n 1 6 A n 1 7 C n 1 8 A n 1 9 C n 1 10 C n 1 11 G n 1 12 G n 1 13 U n 1 14 G n 1 15 A n 1 16 A n 1 17 G n 1 18 U n 1 19 C n 1 20 G n 1 21 C n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 SIS non-polymer . ;(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside ; Sisomicin 'C19 H37 N5 O7' 447.526 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 G 1 3 3 G G A . n A 1 2 C 2 4 4 C C A . n A 1 3 G 3 5 5 G G A . n A 1 4 U 4 6 6 U U A . n A 1 5 C 5 7 7 C C A . n A 1 6 A 6 8 8 A A A . n A 1 7 C 7 9 9 C C A . n A 1 8 A 8 10 10 A A A . n A 1 9 C 9 11 11 C C A . n A 1 10 C 10 12 12 C C A . n A 1 11 G 11 13 13 G G A . n A 1 12 G 12 14 14 G G A . n A 1 13 U 13 15 15 U U A . n A 1 14 G 14 16 16 G G A . n A 1 15 A 15 17 17 A A A . n A 1 16 A 16 18 18 A A A . n A 1 17 G 17 19 19 G G A . n A 1 18 U 18 20 20 U U A . n A 1 19 C 19 21 21 C C A . n A 1 20 G 20 22 22 G G A . n A 1 21 C 21 23 23 C C A . n B 1 1 G 1 26 26 G G B . n B 1 2 C 2 27 27 C C B . n B 1 3 G 3 28 28 G G B . n B 1 4 U 4 29 29 U U B . n B 1 5 C 5 30 30 C C B . n B 1 6 A 6 31 31 A A B . n B 1 7 C 7 32 32 C C B . n B 1 8 A 8 33 33 A A B . n B 1 9 C 9 34 34 C C B . n B 1 10 C 10 35 35 C C B . n B 1 11 G 11 36 36 G G B . n B 1 12 G 12 37 37 G G B . n B 1 13 U 13 38 38 U U B . n B 1 14 G 14 39 39 G G B . n B 1 15 A 15 40 40 A A B . n B 1 16 A 16 41 41 A A B . n B 1 17 G 17 42 42 G G B . n B 1 18 U 18 43 43 U U B . n B 1 19 C 19 44 44 C C B . n B 1 20 G 20 45 45 G G B . n B 1 21 C 21 46 46 C C B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 SIS 1 101 52 SIS SIS A . D 2 SIS 1 101 51 SIS SIS B . E 3 HOH 1 201 1 HOH HOH A . E 3 HOH 2 202 3 HOH HOH A . F 3 HOH 1 201 2 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal ADSC 'data collection' Quantum ? 1 PHENIX 'model building' . ? 2 CNS refinement 1.3 ? 3 CrystalClear 'data reduction' . ? 4 CrystalClear 'data scaling' . ? 5 PHENIX phasing . ? 6 # _cell.entry_id 4F8V _cell.length_a 31.650 _cell.length_b 107.650 _cell.length_c 48.860 _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 4F8V _symmetry.space_group_name_H-M 'P 21 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4F8V _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.09 _exptl_crystal.density_percent_sol 60.14 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 303 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7 _exptl_crystal_grow.pdbx_details 'Na Cacodylate, Spermine, NaCl, MPD , pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 303K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315r' _diffrn_detector.pdbx_collection_date 2011-07-13 _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 1.0 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SPRING-8 BEAMLINE BL38B1' _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL38B1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0 # _reflns.entry_id 4F8V _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 44.5 _reflns.d_resolution_high 2.8 _reflns.number_obs 4352 _reflns.number_all ? _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _refine.entry_id 4F8V _refine.ls_number_reflns_obs 4352 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 44.5 _refine.ls_d_res_high 2.8 _refine.ls_percent_reflns_obs 97.1000 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.226 _refine.ls_R_factor_R_free 0.265 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.1000 _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 100.2348 _refine.solvent_model_param_bsol 68.0444 _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -12.7420 _refine.aniso_B[2][2] 41.0710 _refine.aniso_B[3][3] -28.3300 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.B_iso_max 140.760 _refine.B_iso_min 64.140 _refine.pdbx_overall_phase_error ? _refine.occupancy_max 1.000 _refine.occupancy_min 1.000 _refine.ls_redundancy_reflns_obs ? _refine.solvent_model_details ? _refine.overall_SU_B ? _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_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 900 _refine_hist.pdbx_number_atoms_ligand 62 _refine_hist.number_atoms_solvent 3 _refine_hist.number_atoms_total 965 _refine_hist.d_res_high 2.8 _refine_hist.d_res_low 44.5 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' c_bond_d ? 0.006 ? ? ? 'X-RAY DIFFRACTION' c_angle_d ? 1.025 ? ? ? 'X-RAY DIFFRACTION' c_mcbond_it ? 0.000 1.500 ? ? 'X-RAY DIFFRACTION' c_scbond_it ? 1.490 2.000 ? ? 'X-RAY DIFFRACTION' c_mcangle_it ? 0.000 2.000 ? ? 'X-RAY DIFFRACTION' c_scangle_it ? 2.368 2.500 ? ? # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.pdbx_refine_id _refine_ls_shell.redundancy_reflns_obs 2.8000 2.9000 10 99.8000 400 . 0.5432 0.5668 . 47 . 447 . 'X-RAY DIFFRACTION' . 2.9000 3.0200 10 100.0000 366 . 0.4957 0.5097 . 51 . 417 . 'X-RAY DIFFRACTION' . 3.0200 3.1500 10 100.0000 392 . 0.3835 0.4066 . 48 . 440 . 'X-RAY DIFFRACTION' . 3.1500 3.3200 10 97.7000 371 . 0.2791 0.2818 . 50 . 421 . 'X-RAY DIFFRACTION' . 3.3200 3.5300 10 99.3000 405 . 0.2707 0.3474 . 39 . 444 . 'X-RAY DIFFRACTION' . 3.5300 3.8000 10 96.3000 378 . 0.2385 0.2728 . 43 . 421 . 'X-RAY DIFFRACTION' . 3.8000 4.1800 10 95.0000 374 . 0.2456 0.2465 . 48 . 422 . 'X-RAY DIFFRACTION' . 4.1800 4.7900 10 97.5000 398 . 0.1956 0.2507 . 34 . 432 . 'X-RAY DIFFRACTION' . 4.7900 6.0300 10 95.1000 397 . 0.1678 0.2188 . 48 . 445 . 'X-RAY DIFFRACTION' . 6.0300 100.0000 10 91.6000 417 . 0.1803 0.2089 . 43 . 460 . 'X-RAY DIFFRACTION' . # loop_ _pdbx_xplor_file.pdbx_refine_id _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file 'X-RAY DIFFRACTION' 1 sis_xplor.param ? 'X-RAY DIFFRACTION' 2 dna-rna.param ? 'X-RAY DIFFRACTION' 3 water_rep.param ? 'X-RAY DIFFRACTION' 4 ion.param ? # _database_PDB_matrix.entry_id 4F8V _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 4F8V _struct.title 'Crystal structure of the bacterial ribosomal decoding site in complex with sisomicin (P21212 form)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4F8V _struct_keywords.pdbx_keywords RNA/ANTIBIOTIC _struct_keywords.text 'decording, ribosome, RNA-ANTIBIOTIC complex' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4F8V _struct_ref.pdbx_db_accession 4F8V _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 4F8V A 1 ? 21 ? 4F8V 3 ? 23 ? 3 23 2 1 4F8V B 1 ? 21 ? 4F8V 26 ? 46 ? 26 46 # _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)' 2510 ? 1 MORE -16 ? 1 'SSA (A^2)' 8060 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 21 N3 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 21 O2 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 21 N4 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 20 N1 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 20 O6 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 20 N2 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 19 N3 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 19 O2 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 19 N4 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 4 O4 ? ? ? 1_555 B U 18 N3 ? ? A U 6 B U 43 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog11 hydrog ? ? A C 5 N3 ? ? ? 1_555 B G 17 N1 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N4 ? ? ? 1_555 B G 17 O6 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 O2 ? ? ? 1_555 B G 17 N2 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 14 N1 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 14 O6 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 14 N2 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 8 N1 ? ? ? 1_555 B U 13 N3 ? ? A A 10 B U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 8 N6 ? ? ? 1_555 B U 13 O4 ? ? A A 10 B U 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 9 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 9 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 9 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 10 N3 ? ? ? 1_555 B G 11 N1 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 10 N4 ? ? ? 1_555 B G 11 O6 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 10 O2 ? ? ? 1_555 B G 11 N2 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 11 N1 ? ? ? 1_555 B C 10 N3 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 11 N2 ? ? ? 1_555 B C 10 O2 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 11 O6 ? ? ? 1_555 B C 10 N4 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 9 N3 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 9 O2 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 9 N4 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A U 13 N3 ? ? ? 1_555 B A 8 N1 ? ? A U 15 B A 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A U 13 O4 ? ? ? 1_555 B A 8 N6 ? ? A U 15 B A 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 14 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 14 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 14 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 17 N1 ? ? ? 1_555 B C 5 N3 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 17 N2 ? ? ? 1_555 B C 5 O2 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 17 O6 ? ? ? 1_555 B C 5 N4 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 19 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 19 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 19 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 20 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 20 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 20 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 21 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A SIS 101 ? 9 'BINDING SITE FOR RESIDUE SIS A 101' AC2 Software B SIS 101 ? 10 'BINDING SITE FOR RESIDUE SIS B 101' 1 ? ? ? ? ? ? ? # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 9 C A 2 ? C A 4 . ? 1_555 ? 2 AC1 9 G A 3 ? G A 5 . ? 1_555 ? 3 AC1 9 U A 4 ? U A 6 . ? 1_555 ? 4 AC1 9 C A 5 ? C A 7 . ? 1_555 ? 5 AC1 9 A A 6 ? A A 8 . ? 1_555 ? 6 AC1 9 G B 14 ? G B 39 . ? 1_555 ? 7 AC1 9 A B 16 ? A B 41 . ? 1_555 ? 8 AC1 9 G B 17 ? G B 42 . ? 1_555 ? 9 AC1 9 U B 18 ? U B 43 . ? 1_555 ? 10 AC2 10 G A 14 ? G A 16 . ? 1_555 ? 11 AC2 10 A A 16 ? A A 18 . ? 1_555 ? 12 AC2 10 G A 17 ? G A 19 . ? 1_555 ? 13 AC2 10 U A 18 ? U A 20 . ? 1_555 ? 14 AC2 10 C B 2 ? C B 27 . ? 1_555 ? 15 AC2 10 G B 3 ? G B 28 . ? 1_555 ? 16 AC2 10 U B 4 ? U B 29 . ? 1_555 ? 17 AC2 10 C B 5 ? C B 30 . ? 1_555 ? 18 AC2 10 A B 6 ? A B 31 . ? 1_555 ? 19 AC2 10 C B 7 ? C B 32 . ? 1_555 ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 P A G 3 ? ? OP3 A G 3 ? ? 1.519 1.607 -0.088 0.012 N 2 1 P B G 26 ? ? OP3 B G 26 ? ? 1.525 1.607 -0.082 0.012 N # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'MAJOR GROOVE BINDER' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 SIS C11 C N S 114 SIS C12 C N R 115 SIS C13 C N R 116 SIS C21 C N R 117 SIS C22 C N N 118 SIS C23 C N R 119 SIS C31 C N N 120 SIS C32 C N S 121 SIS C33 C N R 122 SIS C41 C N N 123 SIS C42 C N R 124 SIS C43 C N R 125 SIS C51 C N N 126 SIS C52 C N S 127 SIS C53 C N N 128 SIS C61 C N N 129 SIS C62 C N S 130 SIS C83 C N N 131 SIS C93 C N N 132 SIS N12 N N N 133 SIS N21 N N N 134 SIS N32 N N N 135 SIS N33 N N N 136 SIS N61 N N N 137 SIS O11 O N N 138 SIS O23 O N N 139 SIS O43 O N N 140 SIS O51 O N N 141 SIS O52 O N N 142 SIS O53 O N N 143 SIS O62 O N N 144 SIS H1 H N N 145 SIS H2 H N N 146 SIS H3 H N N 147 SIS H4 H N N 148 SIS H5 H N N 149 SIS H6 H N N 150 SIS H7 H N N 151 SIS H8 H N N 152 SIS H9 H N N 153 SIS H10 H N N 154 SIS H11 H N N 155 SIS H12 H N N 156 SIS H13 H N N 157 SIS H14 H N N 158 SIS H15 H N N 159 SIS H16 H N N 160 SIS H17 H N N 161 SIS H18 H N N 162 SIS H19 H N N 163 SIS H20 H N N 164 SIS H21 H N N 165 SIS H22 H N N 166 SIS H23 H N N 167 SIS H24 H N N 168 SIS H25 H N N 169 SIS H26 H N N 170 SIS H27 H N N 171 SIS H29 H N N 172 SIS H30 H N N 173 SIS H32 H N N 174 SIS H33 H N N 175 SIS H35 H N N 176 SIS H37 H N N 177 SIS H38 H N N 178 SIS H40 H N N 179 SIS H41 H N N 180 SIS H42 H N N 181 U OP3 O N N 182 U P P N N 183 U OP1 O N N 184 U OP2 O N N 185 U "O5'" O N N 186 U "C5'" C N N 187 U "C4'" C N R 188 U "O4'" O N N 189 U "C3'" C N S 190 U "O3'" O N N 191 U "C2'" C N R 192 U "O2'" O N N 193 U "C1'" C N R 194 U N1 N N N 195 U C2 C N N 196 U O2 O N N 197 U N3 N N N 198 U C4 C N N 199 U O4 O N N 200 U C5 C N N 201 U C6 C N N 202 U HOP3 H N N 203 U HOP2 H N N 204 U "H5'" H N N 205 U "H5''" H N N 206 U "H4'" H N N 207 U "H3'" H N N 208 U "HO3'" H N N 209 U "H2'" H N N 210 U "HO2'" H N N 211 U "H1'" H N N 212 U H3 H N N 213 U H5 H N N 214 U H6 H N N 215 # 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 SIS O43 C43 sing N N 118 SIS C83 C43 sing N N 119 SIS C43 C53 sing N N 120 SIS C43 C33 sing N N 121 SIS N33 C33 sing N N 122 SIS N33 C93 sing N N 123 SIS C53 O53 sing N N 124 SIS C33 C23 sing N N 125 SIS O53 C13 sing N N 126 SIS C23 C13 sing N N 127 SIS C23 O23 sing N N 128 SIS C13 O62 sing N N 129 SIS O62 C62 sing N N 130 SIS O52 C52 sing N N 131 SIS C62 C52 sing N N 132 SIS C62 C12 sing N N 133 SIS N12 C12 sing N N 134 SIS C52 C42 sing N N 135 SIS C12 C22 sing N N 136 SIS C42 O11 sing N N 137 SIS C42 C32 sing N N 138 SIS C22 C32 sing N N 139 SIS C11 O11 sing N N 140 SIS C11 O51 sing N N 141 SIS C11 C21 sing N N 142 SIS N21 C21 sing N N 143 SIS O51 C51 sing N N 144 SIS C32 N32 sing N N 145 SIS C21 C31 sing N N 146 SIS C51 C61 sing N N 147 SIS C51 C41 doub N N 148 SIS N61 C61 sing N N 149 SIS C31 C41 sing N N 150 SIS C11 H1 sing N N 151 SIS C12 H2 sing N N 152 SIS C13 H3 sing N N 153 SIS C21 H4 sing N N 154 SIS C22 H5 sing N N 155 SIS C22 H6 sing N N 156 SIS C23 H7 sing N N 157 SIS C31 H8 sing N N 158 SIS C31 H9 sing N N 159 SIS C32 H10 sing N N 160 SIS C33 H11 sing N N 161 SIS C41 H12 sing N N 162 SIS C42 H13 sing N N 163 SIS C52 H14 sing N N 164 SIS C53 H15 sing N N 165 SIS C53 H16 sing N N 166 SIS C61 H17 sing N N 167 SIS C61 H18 sing N N 168 SIS C62 H19 sing N N 169 SIS C83 H20 sing N N 170 SIS C83 H21 sing N N 171 SIS C83 H22 sing N N 172 SIS C93 H23 sing N N 173 SIS C93 H24 sing N N 174 SIS C93 H25 sing N N 175 SIS N12 H26 sing N N 176 SIS N12 H27 sing N N 177 SIS N21 H29 sing N N 178 SIS N21 H30 sing N N 179 SIS N32 H32 sing N N 180 SIS N32 H33 sing N N 181 SIS N33 H35 sing N N 182 SIS N61 H37 sing N N 183 SIS N61 H38 sing N N 184 SIS O23 H40 sing N N 185 SIS O43 H41 sing N N 186 SIS O52 H42 sing N N 187 U OP3 P sing N N 188 U OP3 HOP3 sing N N 189 U P OP1 doub N N 190 U P OP2 sing N N 191 U P "O5'" sing N N 192 U OP2 HOP2 sing N N 193 U "O5'" "C5'" sing N N 194 U "C5'" "C4'" sing N N 195 U "C5'" "H5'" sing N N 196 U "C5'" "H5''" sing N N 197 U "C4'" "O4'" sing N N 198 U "C4'" "C3'" sing N N 199 U "C4'" "H4'" sing N N 200 U "O4'" "C1'" sing N N 201 U "C3'" "O3'" sing N N 202 U "C3'" "C2'" sing N N 203 U "C3'" "H3'" sing N N 204 U "O3'" "HO3'" sing N N 205 U "C2'" "O2'" sing N N 206 U "C2'" "C1'" sing N N 207 U "C2'" "H2'" sing N N 208 U "O2'" "HO2'" sing N N 209 U "C1'" N1 sing N N 210 U "C1'" "H1'" sing N N 211 U N1 C2 sing N N 212 U N1 C6 sing N N 213 U C2 O2 doub N N 214 U C2 N3 sing N N 215 U N3 C4 sing N N 216 U N3 H3 sing N N 217 U C4 O4 doub N N 218 U C4 C5 sing N N 219 U C5 C6 doub N N 220 U C5 H5 sing N N 221 U C6 H6 sing N N 222 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4F8V 'double helix' 4F8V 'a-form double helix' 4F8V 'mismatched base pair' 4F8V 'internal loop' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A G 1 1_555 B C 21 1_555 -0.844 -0.329 -0.284 -2.062 -2.583 0.923 1 A_G3:C46_B A 3 ? B 46 ? 19 1 1 A C 2 1_555 B G 20 1_555 -0.394 -0.203 0.228 3.017 -8.325 -3.280 2 A_C4:G45_B A 4 ? B 45 ? 19 1 1 A G 3 1_555 B C 19 1_555 -1.002 -0.279 -0.265 3.320 0.264 2.982 3 A_G5:C44_B A 5 ? B 44 ? 19 1 1 A U 4 1_555 B U 18 1_555 -1.843 -1.324 -0.497 5.655 -11.694 -17.123 4 A_U6:U43_B A 6 ? B 43 ? ? ? 1 A C 5 1_555 B G 17 1_555 0.238 -0.116 0.065 -0.562 -1.833 -1.735 5 A_C7:G42_B A 7 ? B 42 ? 19 1 1 A C 7 1_555 B G 14 1_555 -0.013 0.070 -0.098 8.129 -17.910 5.587 6 A_C9:G39_B A 9 ? B 39 ? 19 1 1 A A 8 1_555 B U 13 1_555 -0.273 0.113 0.460 6.707 -14.646 -0.376 7 A_A10:U38_B A 10 ? B 38 ? 20 1 1 A C 9 1_555 B G 12 1_555 0.644 0.086 0.017 4.310 -15.619 5.676 8 A_C11:G37_B A 11 ? B 37 ? 19 1 1 A C 10 1_555 B G 11 1_555 0.060 -0.087 0.034 0.953 -4.631 -0.228 9 A_C12:G36_B A 12 ? B 36 ? 19 1 1 A G 11 1_555 B C 10 1_555 -0.156 0.037 0.305 -2.136 -12.375 3.557 10 A_G13:C35_B A 13 ? B 35 ? 19 1 1 A G 12 1_555 B C 9 1_555 -0.081 -0.146 -0.219 -5.756 -24.195 1.459 11 A_G14:C34_B A 14 ? B 34 ? 19 1 1 A U 13 1_555 B A 8 1_555 0.543 -0.347 0.337 -2.194 -17.951 6.314 12 A_U15:A33_B A 15 ? B 33 ? 20 1 1 A G 14 1_555 B C 7 1_555 -0.249 -0.384 -0.558 -7.347 -15.954 -1.122 13 A_G16:C32_B A 16 ? B 32 ? 19 1 1 A G 17 1_555 B C 5 1_555 -0.620 0.012 -0.409 -0.374 -2.310 -0.295 14 A_G19:C30_B A 19 ? B 30 ? 19 1 1 A C 19 1_555 B G 3 1_555 0.584 -0.359 -0.337 4.983 1.786 2.632 15 A_C21:G28_B A 21 ? B 28 ? 19 1 1 A G 20 1_555 B C 2 1_555 -0.907 -0.282 0.049 1.237 -8.765 -0.870 16 A_G22:C27_B A 22 ? B 27 ? 19 1 1 A C 21 1_555 B G 1 1_555 0.479 0.363 -0.249 4.480 4.162 6.058 17 A_C23:G26_B A 23 ? B 26 ? ? 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 B C 21 1_555 A C 2 1_555 B G 20 1_555 -0.759 -2.331 3.290 -4.071 -3.697 33.439 -3.371 0.609 3.584 -6.372 7.016 33.876 1 AA_G3C4:G45C46_BB A 3 ? B 46 ? A 4 ? B 45 ? 1 A C 2 1_555 B G 20 1_555 A G 3 1_555 B C 19 1_555 0.090 -1.569 3.133 -0.413 7.619 28.536 -4.533 -0.255 2.633 15.118 0.819 29.518 2 AA_C4G5:C44G45_BB A 4 ? B 45 ? A 5 ? B 44 ? 1 A G 3 1_555 B C 19 1_555 A U 4 1_555 B U 18 1_555 -0.883 -1.891 3.269 -2.838 1.239 29.552 -3.948 1.127 3.257 2.421 5.545 29.710 3 AA_G5U6:U43C44_BB A 5 ? B 44 ? A 6 ? B 43 ? 1 A U 4 1_555 B U 18 1_555 A C 5 1_555 B G 17 1_555 0.866 -2.226 3.586 -4.385 2.446 39.682 -3.554 -1.802 3.338 3.586 6.429 39.985 4 AA_U6C7:G42U43_BB A 6 ? B 43 ? A 7 ? B 42 ? 1 A C 7 1_555 B G 14 1_555 A A 8 1_555 B U 13 1_555 -0.339 -1.419 3.242 -6.058 11.035 32.575 -3.933 -0.294 2.656 18.819 10.332 34.861 5 AA_C9A10:U38G39_BB A 9 ? B 39 ? A 10 ? B 38 ? 1 A A 8 1_555 B U 13 1_555 A C 9 1_555 B G 12 1_555 0.782 -1.528 3.301 6.247 3.765 35.172 -3.021 -0.369 3.213 6.148 -10.202 35.897 6 AA_A10C11:G37U38_BB A 10 ? B 38 ? A 11 ? B 37 ? 1 A C 9 1_555 B G 12 1_555 A C 10 1_555 B G 11 1_555 -0.793 -1.909 3.347 -1.226 4.430 29.738 -4.572 1.280 3.066 8.566 2.370 30.083 7 AA_C11C12:G36G37_BB A 11 ? B 37 ? A 12 ? B 36 ? 1 A C 10 1_555 B G 11 1_555 A G 11 1_555 B C 10 1_555 0.306 -1.594 3.207 1.291 9.334 28.239 -4.881 -0.351 2.571 18.492 -2.558 29.740 8 AA_C12G13:C35G36_BB A 12 ? B 36 ? A 13 ? B 35 ? 1 A G 11 1_555 B C 10 1_555 A G 12 1_555 B C 9 1_555 -0.072 -1.275 3.367 3.691 10.852 33.517 -3.652 0.647 2.809 18.170 -6.180 35.369 9 AA_G13G14:C34C35_BB A 13 ? B 35 ? A 14 ? B 34 ? 1 A G 12 1_555 B C 9 1_555 A U 13 1_555 B A 8 1_555 0.768 -0.960 3.024 -3.805 6.635 36.046 -2.320 -1.675 2.719 10.575 6.065 36.822 10 AA_G14U15:A33C34_BB A 14 ? B 34 ? A 15 ? B 33 ? 1 A U 13 1_555 B A 8 1_555 A G 14 1_555 B C 7 1_555 -0.047 -1.738 3.231 6.568 19.684 26.556 -5.666 0.968 1.559 36.579 -12.205 33.587 11 AA_U15G16:C32A33_BB A 15 ? B 33 ? A 16 ? B 32 ? 1 A G 17 1_555 B C 5 1_555 A C 19 1_555 B G 3 1_555 -0.222 -3.516 6.573 0.873 4.312 68.666 -3.428 0.260 6.367 3.819 -0.773 68.790 12 AA_G19C21:G28C30_BB A 19 ? B 30 ? A 21 ? B 28 ? 1 A C 19 1_555 B G 3 1_555 A G 20 1_555 B C 2 1_555 0.591 -2.036 3.318 1.429 7.909 21.927 -7.504 -1.015 2.474 19.952 -3.604 23.336 13 AA_C21G22:C27G28_BB A 21 ? B 28 ? A 22 ? B 27 ? 1 A G 20 1_555 B C 2 1_555 A C 21 1_555 B G 1 1_555 1.031 -2.093 3.291 3.995 2.659 41.426 -3.222 -1.027 3.238 3.743 -5.625 41.691 14 AA_G22C23:G26C27_BB A 22 ? B 27 ? A 23 ? B 26 ? # _atom_sites.entry_id 4F8V _atom_sites.fract_transf_matrix[1][1] 0.031596 _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] 0.009289 _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] 0.020467 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P # loop_