data_2F4T # _entry.id 2F4T # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 2F4T pdb_00002f4t 10.2210/pdb2f4t/pdb NDB DR0028 ? ? RCSB RCSB035453 ? ? WWPDB D_1000035453 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2006-05-02 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-18 5 'Structure model' 1 4 2024-02-14 # _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' 'Version format compliance' 3 4 'Structure model' Advisory 4 4 'Structure model' 'Refinement description' 5 5 'Structure model' Advisory 6 5 'Structure model' 'Data collection' 7 5 'Structure model' 'Database references' 8 5 '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 4 'Structure model' pdbx_unobs_or_zero_occ_atoms 2 4 'Structure model' software 3 5 'Structure model' chem_comp_atom 4 5 'Structure model' chem_comp_bond 5 5 'Structure model' database_2 6 5 'Structure model' pdbx_unobs_or_zero_occ_atoms 7 5 '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 4 'Structure model' '_software.classification' 2 4 'Structure model' '_software.contact_author' 3 4 'Structure model' '_software.contact_author_email' 4 4 'Structure model' '_software.date' 5 4 'Structure model' '_software.language' 6 4 'Structure model' '_software.location' 7 4 'Structure model' '_software.name' 8 4 'Structure model' '_software.type' 9 4 'Structure model' '_software.version' 10 5 'Structure model' '_database_2.pdbx_DOI' 11 5 'Structure model' '_database_2.pdbx_database_accession' 12 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 13 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 14 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 2F4T _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2005-11-24 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _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.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2F4S . unspecified PDB 2F4U . unspecified PDB 2F4V . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Murray, J.B.' 1 'Meroueh, S.O.' 2 'Russell, R.J.' 3 'Lentzen, G.' 4 'Haddad, J.' 5 'Mobashery, S.' 6 # _citation.id primary _citation.title 'Interactions of designer antibiotics and the bacterial ribosomal aminoacyl-tRNA site' _citation.journal_abbrev Chem.Biol. _citation.journal_volume 13 _citation.page_first 129 _citation.page_last 138 _citation.year 2006 _citation.journal_id_ASTM CBOLE2 _citation.country UK _citation.journal_id_ISSN 1074-5521 _citation.journal_id_CSD 2050 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 16492561 _citation.pdbx_database_id_DOI 10.1016/j.chembiol.2005.11.004 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Murray, J.B.' 1 ? primary 'Meroueh, S.O.' 2 ? primary 'Russell, R.J.' 3 ? primary 'Lentzen, G.' 4 ? primary 'Haddad, J.' 5 ? primary 'Mobashery, S.' 6 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-R(*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'" 6743.077 1 ? ? ? 'A-site RNA' 2 polymer syn "5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)-3'" 7355.409 1 ? ? ? 'A-site RNA' 3 non-polymer syn ;(2R)-4-AMINO-N-{(1R,2S,3R,4R,5S)-5-AMINO-2-{2-[(2-AMINOETHYL)AMINO]ETHOXY}-4-[(2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-3-HYDROXYCYCLOHEXYL}-2-HYDROXYBUTANAMIDE ; 509.598 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polyribonucleotide no no GCGUCACACCGGUGAAGUCGC GCGUCACACCGGUGAAGUCGC A ? 2 polyribonucleotide no no UUGCGUCACACCGGUGAAGUCGC UUGCGUCACACCGGUGAAGUCGC B ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name ;(2R)-4-AMINO-N-{(1R,2S,3R,4R,5S)-5-AMINO-2-{2-[(2-AMINOETHYL)AMINO]ETHOXY}-4-[(2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-3-HYDROXYCYCLOHEXYL}-2-HYDROXYBUTANAMIDE ; _pdbx_entity_nonpoly.comp_id AB9 # 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 2 1 U n 2 2 U n 2 3 G n 2 4 C n 2 5 G n 2 6 U n 2 7 C n 2 8 A n 2 9 C n 2 10 A n 2 11 C n 2 12 C n 2 13 G n 2 14 G n 2 15 U n 2 16 G n 2 17 A n 2 18 A n 2 19 G n 2 20 U n 2 21 C n 2 22 G n 2 23 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 AB9 non-polymer . ;(2R)-4-AMINO-N-{(1R,2S,3R,4R,5S)-5-AMINO-2-{2-[(2-AMINOETHYL)AMINO]ETHOXY}-4-[(2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-3-HYDROXYCYCLOHEXYL}-2-HYDROXYBUTANAMIDE ; ? 'C20 H43 N7 O8' 509.598 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 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 1403 1403 G G A . n A 1 2 C 2 1404 1404 C C A . n A 1 3 G 3 1405 1405 G G A . n A 1 4 U 4 1406 1406 U U A . n A 1 5 C 5 1407 1407 C C A . n A 1 6 A 6 1408 1408 A A A . n A 1 7 C 7 1409 1409 C C A . n A 1 8 A 8 1410 1410 A A A . n A 1 9 C 9 1411 1411 C C A . n A 1 10 C 10 1412 1412 C C A . n A 1 11 G 11 1488 1488 G G A . n A 1 12 G 12 1489 1489 G G A . n A 1 13 U 13 1490 1490 U U A . n A 1 14 G 14 1491 1491 G G A . n A 1 15 A 15 1492 1492 A A A . n A 1 16 A 16 1493 1493 A A A . n A 1 17 G 17 1494 1494 G G A . n A 1 18 U 18 1495 1495 U U A . n A 1 19 C 19 1496 1496 C C A . n A 1 20 G 20 1497 1497 G G A . n A 1 21 C 21 1498 1498 C C A . n B 2 1 U 1 1401 1401 U U B . n B 2 2 U 2 1402 1402 U U B . n B 2 3 G 3 1403 1403 G G B . n B 2 4 C 4 1404 1404 C C B . n B 2 5 G 5 1405 1405 G G B . n B 2 6 U 6 1406 1406 U U B . n B 2 7 C 7 1407 1407 C C B . n B 2 8 A 8 1408 1408 A A B . n B 2 9 C 9 1409 1409 C C B . n B 2 10 A 10 1410 1410 A A B . n B 2 11 C 11 1411 1411 C C B . n B 2 12 C 12 1412 1412 C C B . n B 2 13 G 13 1488 1488 G G B . n B 2 14 G 14 1489 1489 G G B . n B 2 15 U 15 1490 1490 U U B . n B 2 16 G 16 1491 1491 G G B . n B 2 17 A 17 1492 1492 A A B . n B 2 18 A 18 1493 1493 A A B . n B 2 19 G 19 1494 1494 G G B . n B 2 20 U 20 1495 1495 U U B . n B 2 21 C 21 1496 1496 C C B . n B 2 22 G 22 1497 1497 G G B . n B 2 23 C 23 1498 1498 C C B . n # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id AB9 _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 1 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id AB9 _pdbx_nonpoly_scheme.auth_mon_id AB9 _pdbx_nonpoly_scheme.pdb_strand_id B _pdbx_nonpoly_scheme.pdb_ins_code . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 0 B U 1402 ? P ? B U 2 P 2 1 Y 0 B U 1402 ? OP1 ? B U 2 OP1 3 1 Y 0 B U 1402 ? OP2 ? B U 2 OP2 # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal DENZO . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data reduction' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 1 SCALEPACK . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data scaling' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 2 CNS . ? package 'Axel T. Brunger' axel.brunger@yale.edu refinement http://cns.csb.yale.edu/v1.1/ Fortran_77 ? 3 PDB_EXTRACT 1.701 'OCT. 28, 2005' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 4 # _cell.length_a 45.976 _cell.length_b 32.926 _cell.length_c 46.414 _cell.angle_alpha 90.00 _cell.angle_beta 95.62 _cell.angle_gamma 90.00 _cell.entry_id 2F4T _cell.pdbx_unique_axis ? _cell.Z_PDB 2 _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.space_group_name_H-M 'P 1 21 1' _symmetry.entry_id 2F4T _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 4 _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.entry_id 2F4T _exptl.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.48 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 50.40 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector ? _diffrn_detector.type ? _diffrn_detector.pdbx_collection_date 2002-06-01 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.991 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID29' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.991 _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID29 # _reflns.entry_id 2F4T _reflns.d_resolution_low 30.00 _reflns.d_resolution_high 3.00 _reflns.number_obs 2746 _reflns.percent_possible_obs 97.700 _reflns.pdbx_Rmerge_I_obs 0.078 _reflns.pdbx_chi_squared 1.016 _reflns.pdbx_redundancy ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_netI_over_sigmaI 8.0 _reflns.pdbx_Rsym_value ? _reflns.observed_criterion_sigma_F 0 _reflns.observed_criterion_sigma_I 0 _reflns.number_all 2746 _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # loop_ _reflns_shell.d_res_low _reflns_shell.d_res_high _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.number_unique_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.percent_possible_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal 3.11 3.00 272 100.000 0.206 1.503 ? ? 3.2 ? ? ? ? ? 1 3.23 3.11 277 100.000 0.135 1.267 ? ? ? ? ? ? ? ? 2 3.38 3.23 272 100.000 0.133 1.294 ? ? ? ? ? ? ? ? 3 3.56 3.38 283 99.300 0.111 1.011 ? ? ? ? ? ? ? ? 4 3.78 3.56 282 100.000 0.102 0.766 ? ? ? ? ? ? ? ? 5 4.07 3.78 278 100.000 0.081 0.941 ? ? ? ? ? ? ? ? 6 4.48 4.07 276 100.000 0.075 0.895 ? ? ? ? ? ? ? ? 7 5.12 4.48 287 99.700 0.062 0.547 ? ? ? ? ? ? ? ? 8 6.44 5.12 277 99.600 0.053 0.952 ? ? ? ? ? ? ? ? 9 30.00 6.44 242 79.900 0.04 1.076 ? ? ? ? ? ? ? ? 10 # _refine.ls_d_res_high 3.000 _refine.ls_d_res_low 15.000 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 97.600 _refine.ls_number_reflns_obs 2735 _refine.ls_R_factor_R_work 0.211 _refine.ls_R_factor_R_free 0.267 _refine.ls_percent_reflns_R_free 9.800 _refine.ls_number_reflns_R_free 280 _refine.B_iso_mean 80.240 _refine.solvent_model_param_bsol 135.759 _refine.aniso_B[1][1] 1.140 _refine.aniso_B[2][2] -5.315 _refine.aniso_B[3][3] 4.175 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] -0.612 _refine.aniso_B[2][3] 0.000 _refine.entry_id 2F4T _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 2795 _refine.ls_R_factor_all 0.211 _refine.ls_R_factor_obs 0.267 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details Random _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.details ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_overall_ESU_R ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _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 932 _refine_hist.pdbx_number_atoms_ligand 35 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 967 _refine_hist.d_res_high 3.000 _refine_hist.d_res_low 15.000 # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 CNS_TOPPAR:protein_rep.param CNS_TOPPAR:protein.top 'X-RAY DIFFRACTION' 2 dna-rna-multi-endo.param CNS_TOPPAR:dna-rna.top 'X-RAY DIFFRACTION' 3 CNS_TOPPAR:water_rep.param CNS_TOPPAR:water.top 'X-RAY DIFFRACTION' 4 CNS_TOPPAR:ion.param CNS_TOPPAR:ion.top 'X-RAY DIFFRACTION' 5 893.par 893.top 'X-RAY DIFFRACTION' # _struct.entry_id 2F4T _struct.title 'Asite RNA + designer antibiotic' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2F4T _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'Asite RNA, designer antibiotic, RNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 2F4T 2F4T ? ? ? 2 2 PDB 2F4T 2F4T ? ? ? # 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 2F4T A 1 ? 21 ? 2F4T 1403 ? 1498 ? 1403 1498 2 2 2F4T B 1 ? 23 ? 2F4T 1401 ? 1498 ? 1401 1498 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B C 23 N3 ? ? A G 1403 B C 1498 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 23 O2 ? ? A G 1403 B C 1498 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 23 N4 ? ? A G 1403 B C 1498 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 22 N1 ? ? A C 1404 B G 1497 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 22 O6 ? ? A C 1404 B G 1497 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 22 N2 ? ? A C 1404 B G 1497 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 21 N3 ? ? A G 1405 B C 1496 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 21 O2 ? ? A G 1405 B C 1496 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 21 N4 ? ? A G 1405 B C 1496 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 4 O4 ? ? ? 1_555 B U 20 N3 ? ? A U 1406 B U 1495 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog11 hydrog ? ? A C 5 N3 ? ? ? 1_555 B G 19 N1 ? ? A C 1407 B G 1494 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N4 ? ? ? 1_555 B G 19 O6 ? ? A C 1407 B G 1494 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 O2 ? ? ? 1_555 B G 19 N2 ? ? A C 1407 B G 1494 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 16 N1 ? ? A C 1409 B G 1491 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 16 O6 ? ? A C 1409 B G 1491 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 16 N2 ? ? A C 1409 B G 1491 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 8 N1 ? ? ? 1_555 B U 15 N3 ? ? A A 1410 B U 1490 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A A 8 N6 ? ? ? 1_555 B U 15 O4 ? ? A A 1410 B U 1490 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 9 N3 ? ? ? 1_555 B G 14 N1 ? ? A C 1411 B G 1489 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 9 N4 ? ? ? 1_555 B G 14 O6 ? ? A C 1411 B G 1489 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 9 O2 ? ? ? 1_555 B G 14 N2 ? ? A C 1411 B G 1489 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 10 N3 ? ? ? 1_555 B G 13 N1 ? ? A C 1412 B G 1488 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 10 N4 ? ? ? 1_555 B G 13 O6 ? ? A C 1412 B G 1488 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 10 O2 ? ? ? 1_555 B G 13 N2 ? ? A C 1412 B G 1488 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 11 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 1488 B C 1412 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 11 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 1488 B C 1412 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 11 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 1488 B C 1412 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 1489 B C 1411 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 1489 B C 1411 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 1489 B C 1411 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A U 13 N3 ? ? ? 1_555 B A 10 N1 ? ? A U 1490 B A 1410 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A U 13 O4 ? ? ? 1_555 B A 10 N6 ? ? A U 1490 B A 1410 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 14 N1 ? ? ? 1_555 B C 9 N3 ? ? A G 1491 B C 1409 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 14 N2 ? ? ? 1_555 B C 9 O2 ? ? A G 1491 B C 1409 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 14 O6 ? ? ? 1_555 B C 9 N4 ? ? A G 1491 B C 1409 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 17 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 1494 B C 1407 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 17 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 1494 B C 1407 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 17 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 1494 B C 1407 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A U 18 O4 ? ? ? 1_555 B U 6 N3 ? ? A U 1495 B U 1406 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog40 hydrog ? ? A C 19 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 1496 B G 1405 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 19 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 1496 B G 1405 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A C 19 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 1496 B G 1405 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 20 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 1497 B C 1404 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 20 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 1497 B C 1404 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A G 20 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 1497 B C 1404 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 21 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 1498 B G 1403 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 21 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 1498 B G 1403 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A C 21 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 1498 B G 1403 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software B AB9 1 ? 10 'BINDING SITE FOR RESIDUE AB9 B 1' 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 10 C A 2 ? C A 1404 . ? 1_555 ? 2 AC1 10 G A 3 ? G A 1405 . ? 1_555 ? 3 AC1 10 A A 6 ? A A 1408 . ? 1_555 ? 4 AC1 10 G B 16 ? G B 1491 . ? 1_555 ? 5 AC1 10 A B 17 ? A B 1492 . ? 1_555 ? 6 AC1 10 A B 18 ? A B 1493 . ? 1_555 ? 7 AC1 10 G B 19 ? G B 1494 . ? 1_555 ? 8 AC1 10 U B 20 ? U B 1495 . ? 1_555 ? 9 AC1 10 C B 21 ? C B 1496 . ? 1_555 ? 10 AC1 10 G B 22 ? G B 1497 . ? 1_555 ? # _struct_site_keywords.site_id 1 _struct_site_keywords.text intercalation # 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 AB9 C11 C N R 38 AB9 C12 C N R 39 AB9 C21 C N R 40 AB9 C22 C N N 41 AB9 C23 C N N 42 AB9 C24 C N R 43 AB9 C25 C N N 44 AB9 C26 C N N 45 AB9 C29 C N N 46 AB9 C30 C N N 47 AB9 C31 C N R 48 AB9 C32 C N S 49 AB9 C33 C N N 50 AB9 C35 C N N 51 AB9 O11 O N N 52 AB9 N21 N N N 53 AB9 O31 O N N 54 AB9 C41 C N S 55 AB9 O41 O N N 56 AB9 C51 C N R 57 AB9 O51 O N N 58 AB9 C61 C N N 59 AB9 N61 N N N 60 AB9 N12 N N N 61 AB9 N32 N N N 62 AB9 C42 C N R 63 AB9 C52 C N R 64 AB9 O52 O N N 65 AB9 C62 C N S 66 AB9 O62 O N N 67 AB9 N31 N N N 68 AB9 N34 N N N 69 AB9 O36 O N N 70 AB9 N27 N N N 71 AB9 O28 O N N 72 AB9 H11 H N N 73 AB9 H12 H N N 74 AB9 H21 H N N 75 AB9 H221 H N N 76 AB9 H222 H N N 77 AB9 H24 H N N 78 AB9 H251 H N N 79 AB9 H252 H N N 80 AB9 H261 H N N 81 AB9 H262 H N N 82 AB9 H291 H N N 83 AB9 H292 H N N 84 AB9 H301 H N N 85 AB9 H302 H N N 86 AB9 H3 H N N 87 AB9 H32 H N N 88 AB9 H331 H N N 89 AB9 H332 H N N 90 AB9 H351 H N N 91 AB9 H352 H N N 92 AB9 H211 H N N 93 AB9 H212 H N N 94 AB9 H4 H N N 95 AB9 H41 H N N 96 AB9 H2 H N N 97 AB9 H51 H N N 98 AB9 H611 H N N 99 AB9 H612 H N N 100 AB9 H11A H N N 101 AB9 H12A H N N 102 AB9 H5 H N N 103 AB9 H321 H N N 104 AB9 H322 H N N 105 AB9 H42 H N N 106 AB9 H52 H N N 107 AB9 H1 H N N 108 AB9 H62 H N N 109 AB9 H31 H N N 110 AB9 H341 H N N 111 AB9 H342 H N N 112 AB9 H271 H N N 113 AB9 H272 H N N 114 AB9 H28 H N N 115 C OP3 O N N 116 C P P N N 117 C OP1 O N N 118 C OP2 O N N 119 C "O5'" O N N 120 C "C5'" C N N 121 C "C4'" C N R 122 C "O4'" O N N 123 C "C3'" C N S 124 C "O3'" O N N 125 C "C2'" C N R 126 C "O2'" O N N 127 C "C1'" C N R 128 C N1 N N N 129 C C2 C N N 130 C O2 O N N 131 C N3 N N N 132 C C4 C N N 133 C N4 N N N 134 C C5 C N N 135 C C6 C N N 136 C HOP3 H N N 137 C HOP2 H N N 138 C "H5'" H N N 139 C "H5''" H N N 140 C "H4'" H N N 141 C "H3'" H N N 142 C "HO3'" H N N 143 C "H2'" H N N 144 C "HO2'" H N N 145 C "H1'" H N N 146 C H41 H N N 147 C H42 H N N 148 C H5 H N N 149 C H6 H N N 150 G OP3 O N N 151 G P P N N 152 G OP1 O N N 153 G OP2 O N N 154 G "O5'" O N N 155 G "C5'" C N N 156 G "C4'" C N R 157 G "O4'" O N N 158 G "C3'" C N S 159 G "O3'" O N N 160 G "C2'" C N R 161 G "O2'" O N N 162 G "C1'" C N R 163 G N9 N Y N 164 G C8 C Y N 165 G N7 N Y N 166 G C5 C Y N 167 G C6 C N N 168 G O6 O N N 169 G N1 N N N 170 G C2 C N N 171 G N2 N N N 172 G N3 N N N 173 G C4 C Y N 174 G HOP3 H N N 175 G HOP2 H N N 176 G "H5'" H N N 177 G "H5''" H N N 178 G "H4'" H N N 179 G "H3'" H N N 180 G "HO3'" H N N 181 G "H2'" H N N 182 G "HO2'" H N N 183 G "H1'" H N N 184 G H8 H N N 185 G H1 H N N 186 G H21 H N N 187 G H22 H N N 188 U OP3 O N N 189 U P P N N 190 U OP1 O N N 191 U OP2 O N N 192 U "O5'" O N N 193 U "C5'" C N N 194 U "C4'" C N R 195 U "O4'" O N N 196 U "C3'" C N S 197 U "O3'" O N N 198 U "C2'" C N R 199 U "O2'" O N N 200 U "C1'" C N R 201 U N1 N N N 202 U C2 C N N 203 U O2 O N N 204 U N3 N N N 205 U C4 C N N 206 U O4 O N N 207 U C5 C N N 208 U C6 C N N 209 U HOP3 H N N 210 U HOP2 H N N 211 U "H5'" H N N 212 U "H5''" H N N 213 U "H4'" H N N 214 U "H3'" H N N 215 U "HO3'" H N N 216 U "H2'" H N N 217 U "HO2'" H N N 218 U "H1'" H N N 219 U H3 H N N 220 U H5 H N N 221 U H6 H N N 222 # 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 AB9 C11 C21 sing N N 40 AB9 C11 O11 sing N N 41 AB9 C11 O51 sing N N 42 AB9 C11 H11 sing N N 43 AB9 C12 C22 sing N N 44 AB9 C12 N12 sing N N 45 AB9 C12 C62 sing N N 46 AB9 C12 H12 sing N N 47 AB9 C21 C31 sing N N 48 AB9 C21 N21 sing N N 49 AB9 C21 H21 sing N N 50 AB9 C22 C32 sing N N 51 AB9 C22 H221 sing N N 52 AB9 C22 H222 sing N N 53 AB9 C23 C24 sing N N 54 AB9 C23 N12 sing N N 55 AB9 C23 O36 doub N N 56 AB9 C24 C25 sing N N 57 AB9 C24 O28 sing N N 58 AB9 C24 H24 sing N N 59 AB9 C25 C26 sing N N 60 AB9 C25 H251 sing N N 61 AB9 C25 H252 sing N N 62 AB9 C26 N27 sing N N 63 AB9 C26 H261 sing N N 64 AB9 C26 H262 sing N N 65 AB9 C29 C30 sing N N 66 AB9 C29 O62 sing N N 67 AB9 C29 H291 sing N N 68 AB9 C29 H292 sing N N 69 AB9 C30 N31 sing N N 70 AB9 C30 H301 sing N N 71 AB9 C30 H302 sing N N 72 AB9 C31 O31 sing N N 73 AB9 C31 C41 sing N N 74 AB9 C31 H3 sing N N 75 AB9 C32 N32 sing N N 76 AB9 C32 C42 sing N N 77 AB9 C32 H32 sing N N 78 AB9 C33 C35 sing N N 79 AB9 C33 N34 sing N N 80 AB9 C33 H331 sing N N 81 AB9 C33 H332 sing N N 82 AB9 C35 N31 sing N N 83 AB9 C35 H351 sing N N 84 AB9 C35 H352 sing N N 85 AB9 O11 C42 sing N N 86 AB9 N21 H211 sing N N 87 AB9 N21 H212 sing N N 88 AB9 O31 H4 sing N N 89 AB9 C41 O41 sing N N 90 AB9 C41 C51 sing N N 91 AB9 C41 H41 sing N N 92 AB9 O41 H2 sing N N 93 AB9 C51 O51 sing N N 94 AB9 C51 C61 sing N N 95 AB9 C51 H51 sing N N 96 AB9 C61 N61 sing N N 97 AB9 C61 H611 sing N N 98 AB9 C61 H612 sing N N 99 AB9 N61 H11A sing N N 100 AB9 N61 H12A sing N N 101 AB9 N12 H5 sing N N 102 AB9 N32 H321 sing N N 103 AB9 N32 H322 sing N N 104 AB9 C42 C52 sing N N 105 AB9 C42 H42 sing N N 106 AB9 C52 O52 sing N N 107 AB9 C52 C62 sing N N 108 AB9 C52 H52 sing N N 109 AB9 O52 H1 sing N N 110 AB9 C62 O62 sing N N 111 AB9 C62 H62 sing N N 112 AB9 N31 H31 sing N N 113 AB9 N34 H341 sing N N 114 AB9 N34 H342 sing N N 115 AB9 N27 H271 sing N N 116 AB9 N27 H272 sing N N 117 AB9 O28 H28 sing N N 118 C OP3 P sing N N 119 C OP3 HOP3 sing N N 120 C P OP1 doub N N 121 C P OP2 sing N N 122 C P "O5'" sing N N 123 C OP2 HOP2 sing N N 124 C "O5'" "C5'" sing N N 125 C "C5'" "C4'" sing N N 126 C "C5'" "H5'" sing N N 127 C "C5'" "H5''" sing N N 128 C "C4'" "O4'" sing N N 129 C "C4'" "C3'" sing N N 130 C "C4'" "H4'" sing N N 131 C "O4'" "C1'" sing N N 132 C "C3'" "O3'" sing N N 133 C "C3'" "C2'" sing N N 134 C "C3'" "H3'" sing N N 135 C "O3'" "HO3'" sing N N 136 C "C2'" "O2'" sing N N 137 C "C2'" "C1'" sing N N 138 C "C2'" "H2'" sing N N 139 C "O2'" "HO2'" sing N N 140 C "C1'" N1 sing N N 141 C "C1'" "H1'" sing N N 142 C N1 C2 sing N N 143 C N1 C6 sing N N 144 C C2 O2 doub N N 145 C C2 N3 sing N N 146 C N3 C4 doub N N 147 C C4 N4 sing N N 148 C C4 C5 sing N N 149 C N4 H41 sing N N 150 C N4 H42 sing N N 151 C C5 C6 doub N N 152 C C5 H5 sing N N 153 C C6 H6 sing N N 154 G OP3 P sing N N 155 G OP3 HOP3 sing N N 156 G P OP1 doub N N 157 G P OP2 sing N N 158 G P "O5'" sing N N 159 G OP2 HOP2 sing N N 160 G "O5'" "C5'" sing N N 161 G "C5'" "C4'" sing N N 162 G "C5'" "H5'" sing N N 163 G "C5'" "H5''" sing N N 164 G "C4'" "O4'" sing N N 165 G "C4'" "C3'" sing N N 166 G "C4'" "H4'" sing N N 167 G "O4'" "C1'" sing N N 168 G "C3'" "O3'" sing N N 169 G "C3'" "C2'" sing N N 170 G "C3'" "H3'" sing N N 171 G "O3'" "HO3'" sing N N 172 G "C2'" "O2'" sing N N 173 G "C2'" "C1'" sing N N 174 G "C2'" "H2'" sing N N 175 G "O2'" "HO2'" sing N N 176 G "C1'" N9 sing N N 177 G "C1'" "H1'" sing N N 178 G N9 C8 sing Y N 179 G N9 C4 sing Y N 180 G C8 N7 doub Y N 181 G C8 H8 sing N N 182 G N7 C5 sing Y N 183 G C5 C6 sing N N 184 G C5 C4 doub Y N 185 G C6 O6 doub N N 186 G C6 N1 sing N N 187 G N1 C2 sing N N 188 G N1 H1 sing N N 189 G C2 N2 sing N N 190 G C2 N3 doub N N 191 G N2 H21 sing N N 192 G N2 H22 sing N N 193 G N3 C4 sing N N 194 U OP3 P sing N N 195 U OP3 HOP3 sing N N 196 U P OP1 doub N N 197 U P OP2 sing N N 198 U P "O5'" sing N N 199 U OP2 HOP2 sing N N 200 U "O5'" "C5'" sing N N 201 U "C5'" "C4'" sing N N 202 U "C5'" "H5'" sing N N 203 U "C5'" "H5''" sing N N 204 U "C4'" "O4'" sing N N 205 U "C4'" "C3'" sing N N 206 U "C4'" "H4'" sing N N 207 U "O4'" "C1'" sing N N 208 U "C3'" "O3'" sing N N 209 U "C3'" "C2'" sing N N 210 U "C3'" "H3'" sing N N 211 U "O3'" "HO3'" sing N N 212 U "C2'" "O2'" sing N N 213 U "C2'" "C1'" sing N N 214 U "C2'" "H2'" sing N N 215 U "O2'" "HO2'" sing N N 216 U "C1'" N1 sing N N 217 U "C1'" "H1'" sing N N 218 U N1 C2 sing N N 219 U N1 C6 sing N N 220 U C2 O2 doub N N 221 U C2 N3 sing N N 222 U N3 C4 sing N N 223 U N3 H3 sing N N 224 U C4 O4 doub N N 225 U C4 C5 sing N N 226 U C5 C6 doub N N 227 U C5 H5 sing N N 228 U C6 H6 sing N N 229 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2F4T 'double helix' 2F4T 'a-form double helix' 2F4T 'mismatched base pair' 2F4T '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 23 1_555 -0.733 -0.277 -0.350 -2.953 -3.791 -11.731 1 A_G1403:C1498_B A 1403 ? B 1498 ? 19 1 1 A C 2 1_555 B G 22 1_555 0.816 -0.620 -0.026 3.369 -23.796 1.848 2 A_C1404:G1497_B A 1404 ? B 1497 ? 19 1 1 A G 3 1_555 B C 21 1_555 0.212 -0.109 -0.330 -5.403 -11.673 2.385 3 A_G1405:C1496_B A 1405 ? B 1496 ? 19 1 1 A U 4 1_555 B U 20 1_555 -2.042 -0.777 -0.108 5.078 -1.040 -18.633 4 A_U1406:U1495_B A 1406 ? B 1495 ? ? ? 1 A C 5 1_555 B G 19 1_555 -0.040 -0.478 0.265 -1.829 4.140 -6.040 5 A_C1407:G1494_B A 1407 ? B 1494 ? 19 1 1 A C 7 1_555 B G 16 1_555 0.204 0.105 -0.011 4.353 -19.813 4.100 6 A_C1409:G1491_B A 1409 ? B 1491 ? 19 1 1 A A 8 1_555 B U 15 1_555 0.536 -0.219 0.233 3.792 -12.856 2.288 7 A_A1410:U1490_B A 1410 ? B 1490 ? 20 1 1 A C 9 1_555 B G 14 1_555 -0.650 -0.256 0.138 5.089 -12.573 -0.547 8 A_C1411:G1489_B A 1411 ? B 1489 ? 19 1 1 A C 10 1_555 B G 13 1_555 0.233 -0.310 0.196 -4.089 -2.975 -5.185 9 A_C1412:G1488_B A 1412 ? B 1488 ? 19 1 1 A G 11 1_555 B C 12 1_555 0.659 0.216 0.027 -1.051 -12.131 2.917 10 A_G1488:C1412_B A 1488 ? B 1412 ? 19 1 1 A G 12 1_555 B C 11 1_555 -0.528 -0.281 -0.017 -6.655 -11.728 -7.080 11 A_G1489:C1411_B A 1489 ? B 1411 ? 19 1 1 A U 13 1_555 B A 10 1_555 1.423 -0.371 0.320 -8.508 -12.144 0.631 12 A_U1490:A1410_B A 1490 ? B 1410 ? 20 1 1 A G 14 1_555 B C 9 1_555 0.429 -0.383 0.610 7.574 -3.228 0.904 13 A_G1491:C1409_B A 1491 ? B 1409 ? 19 1 1 A G 17 1_555 B C 7 1_555 1.106 0.091 0.593 9.106 -12.344 0.471 14 A_G1494:C1407_B A 1494 ? B 1407 ? 19 1 1 A U 18 1_555 B U 6 1_555 -0.836 -1.793 0.374 10.402 -14.657 -6.107 15 A_U1495:U1406_B A 1495 ? B 1406 ? ? ? 1 A C 19 1_555 B G 5 1_555 -1.118 -0.251 0.107 0.764 -9.503 -12.524 16 A_C1496:G1405_B A 1496 ? B 1405 ? 19 1 1 A G 20 1_555 B C 4 1_555 -0.613 -0.295 -0.476 -14.824 -10.875 -10.240 17 A_G1497:C1404_B A 1497 ? B 1404 ? 19 1 1 A C 21 1_555 B G 3 1_555 0.570 -0.433 0.129 -14.598 -4.340 -2.911 18 A_C1498:G1403_B A 1498 ? B 1403 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A G 1 1_555 B C 23 1_555 A C 2 1_555 B G 22 1_555 0.102 -1.707 3.290 -1.952 3.463 40.030 -2.869 -0.366 3.129 5.044 2.843 40.218 1 AA_G1403C1404:G1497C1498_BB A 1403 ? B 1498 ? A 1404 ? B 1497 ? 1 A C 2 1_555 B G 22 1_555 A G 3 1_555 B C 21 1_555 -0.448 -1.451 3.465 1.092 9.106 29.375 -4.509 1.057 2.878 17.430 -2.089 30.743 2 AA_C1404G1405:C1496G1497_BB A 1404 ? B 1497 ? A 1405 ? B 1496 ? 1 A G 3 1_555 B C 21 1_555 A U 4 1_555 B U 20 1_555 -0.790 -2.083 3.107 -1.824 5.367 21.679 -7.123 1.436 2.579 13.964 4.747 22.400 3 AA_G1405U1406:U1495C1496_BB A 1405 ? B 1496 ? A 1406 ? B 1495 ? 1 A U 4 1_555 B U 20 1_555 A C 5 1_555 B G 19 1_555 1.480 -2.602 3.616 -1.106 -1.204 40.161 -3.634 -2.294 3.649 -1.752 1.610 40.193 4 AA_U1406C1407:G1494U1495_BB A 1406 ? B 1495 ? A 1407 ? B 1494 ? 1 A C 5 1_555 B G 19 1_555 A C 7 1_555 B G 16 1_555 1.240 -3.561 6.209 -6.439 17.806 81.917 -3.437 -1.207 5.398 13.422 4.854 83.700 5 AA_C1407C1409:G1491G1494_BB A 1407 ? B 1494 ? A 1409 ? B 1491 ? 1 A C 7 1_555 B G 16 1_555 A A 8 1_555 B U 15 1_555 -0.247 -1.608 3.262 -3.501 9.185 31.439 -4.306 -0.122 2.709 16.454 6.272 32.903 6 AA_C1409A1410:U1490G1491_BB A 1409 ? B 1491 ? A 1410 ? B 1490 ? 1 A A 8 1_555 B U 15 1_555 A C 9 1_555 B G 14 1_555 0.898 -2.105 3.059 1.236 6.317 23.001 -6.857 -1.824 2.445 15.457 -3.025 23.873 7 AA_A1410C1411:G1489U1490_BB A 1410 ? B 1490 ? A 1411 ? B 1489 ? 1 A C 9 1_555 B G 14 1_555 A C 10 1_555 B G 13 1_555 -0.966 -2.026 3.413 -3.036 5.969 36.563 -3.981 1.109 3.123 9.416 4.790 37.151 8 AA_C1411C1412:G1488G1489_BB A 1411 ? B 1489 ? A 1412 ? B 1488 ? 1 A C 10 1_555 B G 13 1_555 A G 11 1_555 B C 12 1_555 -0.057 -1.692 3.180 1.013 7.609 31.339 -4.283 0.267 2.702 13.828 -1.841 32.242 9 AA_C1412G1488:C1412G1488_BB A 1412 ? B 1488 ? A 1488 ? B 1412 ? 1 A G 11 1_555 B C 12 1_555 A G 12 1_555 B C 11 1_555 -0.256 -1.775 3.237 -1.702 9.019 27.370 -5.390 0.170 2.546 18.416 3.475 28.840 10 AA_G1488G1489:C1411C1412_BB A 1488 ? B 1412 ? A 1489 ? B 1411 ? 1 A G 12 1_555 B C 11 1_555 A U 13 1_555 B A 10 1_555 1.028 -1.291 3.323 0.536 5.808 43.310 -2.287 -1.331 3.145 7.826 -0.722 43.682 11 AA_G1489U1490:A1410C1411_BB A 1489 ? B 1411 ? A 1490 ? B 1410 ? 1 A U 13 1_555 B A 10 1_555 A G 14 1_555 B C 9 1_555 0.160 -1.876 2.509 1.890 9.107 26.469 -5.328 -0.030 1.783 19.152 -3.974 28.028 12 AA_U1490G1491:C1409A1410_BB A 1490 ? B 1410 ? A 1491 ? B 1409 ? 1 A G 14 1_555 B C 9 1_555 A G 17 1_555 B C 7 1_555 -0.676 -1.845 6.086 5.601 16.308 69.080 -2.608 0.932 5.528 14.160 -4.863 70.939 13 AA_G1491G1494:C1407C1409_BB A 1491 ? B 1409 ? A 1494 ? B 1407 ? 1 A G 17 1_555 B C 7 1_555 A U 18 1_555 B U 6 1_555 -0.427 -1.753 2.869 -2.560 4.525 31.561 -3.874 0.383 2.625 8.249 4.667 31.975 14 AA_G1494U1495:U1406C1407_BB A 1494 ? B 1407 ? A 1495 ? B 1406 ? 1 A U 18 1_555 B U 6 1_555 A C 19 1_555 B G 5 1_555 -0.607 -1.994 3.500 1.056 3.959 32.818 -4.194 1.251 3.223 6.974 -1.859 33.066 15 AA_U1495C1496:G1405U1406_BB A 1495 ? B 1406 ? A 1496 ? B 1405 ? 1 A C 19 1_555 B G 5 1_555 A G 20 1_555 B C 4 1_555 0.409 -2.604 3.732 4.954 10.359 34.837 -5.623 0.058 2.896 16.748 -8.011 36.625 16 AA_C1496G1497:C1404G1405_BB A 1496 ? B 1405 ? A 1497 ? B 1404 ? 1 A G 20 1_555 B C 4 1_555 A C 21 1_555 B G 3 1_555 0.932 -1.730 3.294 -0.589 3.507 34.626 -3.415 -1.646 3.094 5.872 0.986 34.803 17 AA_G1497C1498:G1403C1404_BB A 1497 ? B 1404 ? A 1498 ? B 1403 ? # _atom_sites.entry_id 2F4T _atom_sites.fract_transf_matrix[1][1] 0.021750 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.002140 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.030371 _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] 0.021649 _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_