data_2F4S # _entry.id 2F4S # _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 2F4S pdb_00002f4s 10.2210/pdb2f4s/pdb NDB DR0027 ? ? RCSB RCSB035452 ? ? WWPDB D_1000035452 ? ? # 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' 2 0 2020-07-29 6 'Structure model' 2 1 2024-02-14 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 5 'Structure model' repository Remediation 'Carbohydrate remediation' ? # 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' 'Atomic model' 6 5 'Structure model' 'Derived calculations' 7 5 'Structure model' 'Structure summary' 8 6 'Structure model' Advisory 9 6 'Structure model' 'Data collection' 10 6 'Structure model' 'Database references' 11 6 '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 4 'Structure model' pdbx_unobs_or_zero_occ_residues 2 4 'Structure model' software 3 5 'Structure model' atom_site 4 5 'Structure model' chem_comp 5 5 'Structure model' entity 6 5 'Structure model' pdbx_entity_nonpoly 7 5 'Structure model' struct_site 8 5 'Structure model' struct_site_gen 9 6 'Structure model' chem_comp 10 6 'Structure model' chem_comp_atom 11 6 'Structure model' chem_comp_bond 12 6 'Structure model' database_2 13 6 'Structure model' pdbx_unobs_or_zero_occ_residues # 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' '_atom_site.auth_atom_id' 11 5 'Structure model' '_atom_site.label_atom_id' 12 5 'Structure model' '_chem_comp.name' 13 5 'Structure model' '_chem_comp.pdbx_synonyms' 14 5 'Structure model' '_chem_comp.type' 15 5 'Structure model' '_entity.pdbx_description' 16 5 'Structure model' '_pdbx_entity_nonpoly.name' 17 6 'Structure model' '_chem_comp.pdbx_synonyms' 18 6 'Structure model' '_database_2.pdbx_DOI' 19 6 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.entry_id 2F4S _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 2F4T . 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(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 ? ? ? ;A-site RNA' ; 2 non-polymer syn '(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside' 322.358 1 ? ? ? ? 3 water nat water 18.015 13 ? ? ? ? # _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 '(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside' XXX 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 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 XXX D-saccharide . '(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside' ;(2R,3S,4R,5R,6R)-6-((1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYLOXY)-5-AMINO-2-(AMINOMETHYL)-TETRAHYDRO-2H-PYRA N-3,4-DIOL; NEOMYCIN A; NEAMINE; (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucoside; (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-D-glucoside; (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,6-dideoxy-glucoside ; 'C12 H26 N4 O6' 322.358 # 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 1 1 G 1 1403 1403 G G B . n B 1 2 C 2 1404 1404 C C B . n B 1 3 G 3 1405 1405 G G B . n B 1 4 U 4 1406 1406 U U B . n B 1 5 C 5 1407 1407 C C B . n B 1 6 A 6 1408 1408 A A B . n B 1 7 C 7 1409 1409 C C B . n B 1 8 A 8 1410 1410 A A B . n B 1 9 C 9 1411 1411 C C B . n B 1 10 C 10 1412 1412 C C B . n B 1 11 G 11 1488 1488 G G B . n B 1 12 G 12 1489 1489 G G B . n B 1 13 U 13 1490 1490 U U B . n B 1 14 G 14 1491 1491 G G B . n B 1 15 A 15 1492 1492 A A B . n B 1 16 A 16 1493 1493 A A B . n B 1 17 G 17 1494 1494 G G B . n B 1 18 U 18 1495 1495 U U B . n B 1 19 C 19 1496 1496 C C B . n B 1 20 G 20 1497 1497 G G B . n B 1 21 C 21 1498 1498 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 XXX 1 501 501 XXX XXX B . D 3 HOH 1 1 1 HOH TIP A . D 3 HOH 2 7 7 HOH TIP A . D 3 HOH 3 8 8 HOH TIP A . D 3 HOH 4 9 9 HOH TIP A . D 3 HOH 5 11 11 HOH TIP A . D 3 HOH 6 12 12 HOH TIP A . D 3 HOH 7 13 13 HOH TIP A . E 3 HOH 1 2 2 HOH TIP B . E 3 HOH 2 3 3 HOH TIP B . E 3 HOH 3 4 4 HOH TIP B . E 3 HOH 4 5 5 HOH TIP B . E 3 HOH 5 6 6 HOH TIP B . E 3 HOH 6 10 10 HOH TIP B . # 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 33.055 _cell.length_b 47.310 _cell.length_c 85.343 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.entry_id 2F4S _cell.pdbx_unique_axis ? _cell.Z_PDB 8 _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 21 21 21' _symmetry.entry_id 2F4S _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 19 _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.entry_id 2F4S _exptl.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.47 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 50.28 _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 2F4S _reflns.d_resolution_low 30.00 _reflns.d_resolution_high 2.80 _reflns.number_obs 3231 _reflns.percent_possible_obs 89.700 _reflns.pdbx_Rmerge_I_obs 0.079 _reflns.pdbx_chi_squared 0.784 _reflns.pdbx_redundancy 4.700 _reflns.pdbx_scaling_rejects ? _reflns.pdbx_netI_over_sigmaI 8.1 _reflns.pdbx_Rsym_value ? _reflns.observed_criterion_sigma_F 0 _reflns.observed_criterion_sigma_I 0 _reflns.number_all 3231 _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 2.90 2.80 297 85.800 0.327 0.805 4.500 ? 2.3 ? ? ? ? ? 1 3.02 2.90 316 90.500 0.232 0.635 4.600 ? ? ? ? ? ? ? 2 3.15 3.02 316 90.800 0.147 0.525 4.800 ? ? ? ? ? ? ? 3 3.32 3.15 315 90.000 0.105 0.448 5.000 ? ? ? ? ? ? ? 4 3.53 3.32 315 91.600 0.104 0.589 4.800 ? ? ? ? ? ? ? 5 3.80 3.53 326 91.300 0.084 0.788 4.900 ? ? ? ? ? ? ? 6 4.18 3.80 339 93.900 0.08 0.853 4.900 ? ? ? ? ? ? ? 7 4.78 4.18 349 94.600 0.067 0.891 4.900 ? ? ? ? ? ? ? 8 6.02 4.78 352 95.900 0.061 1.059 4.800 ? ? ? ? ? ? ? 9 30.00 6.02 306 74.600 0.057 1.312 4.100 ? ? ? ? ? ? ? 10 # _refine.ls_d_res_high 2.800 _refine.ls_d_res_low 20.000 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 90.100 _refine.ls_number_reflns_obs 3221 _refine.ls_R_factor_R_work 0.225 _refine.ls_R_factor_R_free 0.249 _refine.ls_percent_reflns_R_free 8.500 _refine.ls_number_reflns_R_free 305 _refine.B_iso_mean 59.886 _refine.solvent_model_param_bsol 39.523 _refine.aniso_B[1][1] 4.101 _refine.aniso_B[2][2] 12.914 _refine.aniso_B[3][3] -17.015 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.entry_id 2F4S _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 3221 _refine.ls_R_factor_all 0.225 _refine.ls_R_factor_obs 0.249 _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 900 _refine_hist.pdbx_number_atoms_ligand 22 _refine_hist.number_atoms_solvent 13 _refine_hist.number_atoms_total 935 _refine_hist.d_res_high 2.800 _refine_hist.d_res_low 20.000 # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 nea.par nea.top 'X-RAY DIFFRACTION' 2 CNS_TOPPAR:dna-rna_rep.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' # _struct.entry_id 2F4S _struct.title 'A-site RNA in complex with neamine' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2F4S _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'A-site RNA, neamine, 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 1 ? C N N 2 ? D N N 3 ? E N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 2F4S _struct_ref.pdbx_db_accession 2F4S _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 2F4S A 1 ? 21 ? 2F4S 1403 ? 1498 ? 1403 1498 2 1 2F4S B 1 ? 21 ? 2F4S 1403 ? 1498 ? 1403 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,D,E # _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 21 N3 ? ? A G 1403 B C 1498 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B C 21 O2 ? ? A G 1403 B C 1498 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B C 21 N4 ? ? A G 1403 B C 1498 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 B G 20 N1 ? ? A C 1404 B G 1497 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 B G 20 O6 ? ? A C 1404 B G 1497 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 B G 20 N2 ? ? A C 1404 B G 1497 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 19 N3 ? ? A G 1405 B C 1496 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 19 O2 ? ? A G 1405 B C 1496 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 19 N4 ? ? A G 1405 B C 1496 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A C 5 N3 ? ? ? 1_555 B G 17 N1 ? ? A C 1407 B G 1494 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 N4 ? ? ? 1_555 B G 17 O6 ? ? A C 1407 B G 1494 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 O2 ? ? ? 1_555 B G 17 N2 ? ? A C 1407 B G 1494 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 14 N1 ? ? A C 1409 B G 1491 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 14 O6 ? ? A C 1409 B G 1491 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 14 N2 ? ? A C 1409 B G 1491 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 8 N1 ? ? ? 1_555 B U 13 N3 ? ? A A 1410 B U 1490 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A A 8 N6 ? ? ? 1_555 B U 13 O4 ? ? A A 1410 B U 1490 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 9 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 1411 B G 1489 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 9 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 1411 B G 1489 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 9 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 1411 B G 1489 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 10 N3 ? ? ? 1_555 B G 11 N1 ? ? A C 1412 B G 1488 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 10 N4 ? ? ? 1_555 B G 11 O6 ? ? A C 1412 B G 1488 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 10 O2 ? ? ? 1_555 B G 11 N2 ? ? A C 1412 B G 1488 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 11 N1 ? ? ? 1_555 B C 10 N3 ? ? A G 1488 B C 1412 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 11 N2 ? ? ? 1_555 B C 10 O2 ? ? A G 1488 B C 1412 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 11 O6 ? ? ? 1_555 B C 10 N4 ? ? A G 1488 B C 1412 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 9 N3 ? ? A G 1489 B C 1411 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 9 O2 ? ? A G 1489 B C 1411 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 9 N4 ? ? A G 1489 B C 1411 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A U 13 N3 ? ? ? 1_555 B A 8 N1 ? ? A U 1490 B A 1410 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A U 13 O4 ? ? ? 1_555 B A 8 N6 ? ? A U 1490 B A 1410 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 14 O6 ? ? ? 1_555 B A 6 N6 ? ? A G 1491 B A 1408 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog33 hydrog ? ? A G 14 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 1491 B C 1409 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 14 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 1491 B C 1409 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 14 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 1491 B C 1409 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 17 N1 ? ? ? 1_555 B C 5 N3 ? ? A G 1494 B C 1407 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 17 N2 ? ? ? 1_555 B C 5 O2 ? ? A G 1494 B C 1407 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 17 O6 ? ? ? 1_555 B C 5 N4 ? ? A G 1494 B C 1407 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A U 18 O4 ? ? ? 1_555 B U 4 N3 ? ? A U 1495 B U 1406 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog40 hydrog ? ? A C 19 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 1496 B G 1405 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 19 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 1496 B G 1405 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A C 19 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 1496 B G 1405 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 20 N1 ? ? ? 1_555 B C 2 N3 ? ? A G 1497 B C 1404 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 20 N2 ? ? ? 1_555 B C 2 O2 ? ? A G 1497 B C 1404 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A G 20 O6 ? ? ? 1_555 B C 2 N4 ? ? A G 1497 B C 1404 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 21 N3 ? ? ? 1_555 B G 1 N1 ? ? A C 1498 B G 1403 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 21 N4 ? ? ? 1_555 B G 1 O6 ? ? A C 1498 B G 1403 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A C 21 O2 ? ? ? 1_555 B G 1 N2 ? ? A C 1498 B G 1403 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_site.id 1 _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 ? # 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 1403 ? ? OP3 A G 1403 ? ? 1.522 1.607 -0.085 0.012 N 2 1 P B G 1403 ? ? OP3 B G 1403 ? ? 1.519 1.607 -0.088 0.012 N # _struct_site_keywords.site_id 1 _struct_site_keywords.text intercalation # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 N 0 A HOH 8 ? D HOH ? 2 1 N 0 B HOH 10 ? E HOH ? # 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 U OP3 O N N 114 U P P N N 115 U OP1 O N N 116 U OP2 O N N 117 U "O5'" O N N 118 U "C5'" C N N 119 U "C4'" C N R 120 U "O4'" O N N 121 U "C3'" C N S 122 U "O3'" O N N 123 U "C2'" C N R 124 U "O2'" O N N 125 U "C1'" C N R 126 U N1 N N N 127 U C2 C N N 128 U O2 O N N 129 U N3 N N N 130 U C4 C N N 131 U O4 O N N 132 U C5 C N N 133 U C6 C N N 134 U HOP3 H N N 135 U HOP2 H N N 136 U "H5'" H N N 137 U "H5''" H N N 138 U "H4'" H N N 139 U "H3'" H N N 140 U "HO3'" H N N 141 U "H2'" H N N 142 U "HO2'" H N N 143 U "H1'" H N N 144 U H3 H N N 145 U H5 H N N 146 U H6 H N N 147 XXX O3A O N N 148 XXX C4A C N R 149 XXX C5A C N S 150 XXX O4A O N N 151 XXX C6A C N R 152 XXX N1 N N N 153 XXX C7 C N N 154 XXX C8 C N S 155 XXX N2 N N N 156 XXX C9 C N R 157 XXX O1 O N N 158 XXX C1 C N R 159 XXX O5 O N N 160 XXX C5 C N R 161 XXX C6 C N N 162 XXX N3 N N N 163 XXX C4 C N S 164 XXX O4 O N N 165 XXX C3 C N R 166 XXX O3 O N N 167 XXX C2 C N R 168 XXX N4 N N N 169 XXX HO3A H N N 170 XXX H4A H N N 171 XXX H5A H N N 172 XXX HO4A H N N 173 XXX H6 H N N 174 XXX HN11 H N N 175 XXX HN12 H N N 176 XXX H71 H N N 177 XXX H72 H N N 178 XXX H8 H N N 179 XXX HN21 H N N 180 XXX HN22 H N N 181 XXX H9 H N N 182 XXX H1 H N N 183 XXX H5 H N N 184 XXX H61 H N N 185 XXX H62 H N N 186 XXX HN31 H N N 187 XXX HN32 H N N 188 XXX H4 H N N 189 XXX HO4 H N N 190 XXX H3 H N N 191 XXX HO3 H N N 192 XXX H2 H N N 193 XXX HN41 H N N 194 XXX HN42 H N N 195 # 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 U OP3 P sing N N 118 U OP3 HOP3 sing N N 119 U P OP1 doub N N 120 U P OP2 sing N N 121 U P "O5'" sing N N 122 U OP2 HOP2 sing N N 123 U "O5'" "C5'" sing N N 124 U "C5'" "C4'" sing N N 125 U "C5'" "H5'" sing N N 126 U "C5'" "H5''" sing N N 127 U "C4'" "O4'" sing N N 128 U "C4'" "C3'" sing N N 129 U "C4'" "H4'" sing N N 130 U "O4'" "C1'" sing N N 131 U "C3'" "O3'" sing N N 132 U "C3'" "C2'" sing N N 133 U "C3'" "H3'" sing N N 134 U "O3'" "HO3'" sing N N 135 U "C2'" "O2'" sing N N 136 U "C2'" "C1'" sing N N 137 U "C2'" "H2'" sing N N 138 U "O2'" "HO2'" sing N N 139 U "C1'" N1 sing N N 140 U "C1'" "H1'" sing N N 141 U N1 C2 sing N N 142 U N1 C6 sing N N 143 U C2 O2 doub N N 144 U C2 N3 sing N N 145 U N3 C4 sing N N 146 U N3 H3 sing N N 147 U C4 O4 doub N N 148 U C4 C5 sing N N 149 U C5 C6 doub N N 150 U C5 H5 sing N N 151 U C6 H6 sing N N 152 XXX O3A C4A sing N N 153 XXX O3A HO3A sing N N 154 XXX C4A C5A sing N N 155 XXX C4A C9 sing N N 156 XXX C4A H4A sing N N 157 XXX C5A O4A sing N N 158 XXX C5A C6A sing N N 159 XXX C5A H5A sing N N 160 XXX O4A HO4A sing N N 161 XXX C6A N1 sing N N 162 XXX C6A C7 sing N N 163 XXX C6A H6 sing N N 164 XXX N1 HN11 sing N N 165 XXX N1 HN12 sing N N 166 XXX C7 C8 sing N N 167 XXX C7 H71 sing N N 168 XXX C7 H72 sing N N 169 XXX C8 N2 sing N N 170 XXX C8 C9 sing N N 171 XXX C8 H8 sing N N 172 XXX N2 HN21 sing N N 173 XXX N2 HN22 sing N N 174 XXX C9 O1 sing N N 175 XXX C9 H9 sing N N 176 XXX O1 C1 sing N N 177 XXX C1 O5 sing N N 178 XXX C1 C2 sing N N 179 XXX C1 H1 sing N N 180 XXX O5 C5 sing N N 181 XXX C5 C6 sing N N 182 XXX C5 C4 sing N N 183 XXX C5 H5 sing N N 184 XXX C6 N3 sing N N 185 XXX C6 H61 sing N N 186 XXX C6 H62 sing N N 187 XXX N3 HN31 sing N N 188 XXX N3 HN32 sing N N 189 XXX C4 O4 sing N N 190 XXX C4 C3 sing N N 191 XXX C4 H4 sing N N 192 XXX O4 HO4 sing N N 193 XXX C3 O3 sing N N 194 XXX C3 C2 sing N N 195 XXX C3 H3 sing N N 196 XXX O3 HO3 sing N N 197 XXX C2 N4 sing N N 198 XXX C2 H2 sing N N 199 XXX N4 HN41 sing N N 200 XXX N4 HN42 sing N N 201 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2F4S 'double helix' 2F4S 'a-form double helix' 2F4S 'bulge loop' 2F4S 'mismatched base pair' 2F4S '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 -0.916 -0.459 -0.466 -10.072 -0.070 -2.690 1 A_G1403:C1498_B A 1403 ? B 1498 ? 19 1 1 A C 2 1_555 B G 20 1_555 -0.533 -0.063 0.030 1.142 -6.328 -4.084 2 A_C1404:G1497_B A 1404 ? B 1497 ? 19 1 1 A G 3 1_555 B C 19 1_555 0.934 -0.341 0.145 2.293 -12.051 1.893 3 A_G1405:C1496_B A 1405 ? B 1496 ? 19 1 1 A C 5 1_555 B G 17 1_555 0.046 -0.283 -0.045 -0.427 2.614 -0.851 4 A_C1407:G1494_B A 1407 ? B 1494 ? 19 1 1 A C 7 1_555 B G 14 1_555 0.553 -0.242 -0.007 8.927 -17.808 1.235 5 A_C1409:G1491_B A 1409 ? B 1491 ? 19 1 1 A A 8 1_555 B U 13 1_555 0.124 -0.241 0.417 5.953 -14.300 -2.316 6 A_A1410:U1490_B A 1410 ? B 1490 ? 20 1 1 A C 9 1_555 B G 12 1_555 0.000 0.129 0.314 5.979 -16.560 6.979 7 A_C1411:G1489_B A 1411 ? B 1489 ? 19 1 1 A C 10 1_555 B G 11 1_555 -0.176 -0.258 0.538 4.527 -7.445 -0.339 8 A_C1412:G1488_B A 1412 ? B 1488 ? 19 1 1 A G 11 1_555 B C 10 1_555 -0.277 0.018 0.083 3.644 -10.505 6.683 9 A_G1488:C1412_B A 1488 ? B 1412 ? 19 1 1 A G 12 1_555 B C 9 1_555 -0.113 -0.008 0.036 -3.939 -16.507 1.193 10 A_G1489:C1411_B A 1489 ? B 1411 ? 19 1 1 A U 13 1_555 B A 8 1_555 0.716 -0.376 0.307 -7.376 -15.129 1.855 11 A_U1490:A1410_B A 1490 ? B 1410 ? 20 1 1 A G 14 1_555 B C 7 1_555 0.475 -0.209 1.057 -4.538 -16.625 3.018 12 A_G1491:C1409_B A 1491 ? B 1409 ? 19 1 1 A G 17 1_555 B C 5 1_555 1.206 -0.038 -0.118 9.701 0.064 -10.940 13 A_G1494:C1407_B A 1494 ? B 1407 ? 19 1 1 A U 18 1_555 B U 4 1_555 -2.057 -1.843 -0.764 7.512 -22.800 -10.656 14 A_U1495:U1406_B A 1495 ? B 1406 ? ? ? 1 A C 19 1_555 B G 3 1_555 0.007 -0.296 -0.178 1.061 -10.735 5.063 15 A_C1496:G1405_B A 1496 ? B 1405 ? 19 1 1 A G 20 1_555 B C 2 1_555 -0.513 -0.308 -0.195 -3.966 -4.213 2.741 16 A_G1497:C1404_B A 1497 ? B 1404 ? 19 1 1 A C 21 1_555 B G 1 1_555 0.890 -0.549 -0.276 2.378 -0.048 0.811 17 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 21 1_555 A C 2 1_555 B G 20 1_555 -0.420 -1.787 3.192 -3.862 -0.563 30.232 -3.288 0.038 3.251 -1.074 7.367 30.477 1 AA_G1403C1404:G1497C1498_BB A 1403 ? B 1498 ? A 1404 ? B 1497 ? 1 A C 2 1_555 B G 20 1_555 A G 3 1_555 B C 19 1_555 0.153 -2.059 3.272 -0.092 9.014 36.383 -4.304 -0.250 2.703 14.170 0.144 37.447 2 AA_C1404G1405:C1496G1497_BB A 1404 ? B 1497 ? A 1405 ? B 1496 ? 1 A G 3 1_555 B C 19 1_555 A C 5 1_555 B G 17 1_555 0.558 -2.683 6.514 1.096 8.803 60.877 -3.429 -0.446 6.120 8.638 -1.076 61.459 3 AA_G1405C1407:G1494C1496_BB A 1405 ? B 1496 ? A 1407 ? B 1494 ? 1 A C 5 1_555 B G 17 1_555 A C 7 1_555 B G 14 1_555 1.541 -3.248 6.313 -7.486 10.015 83.148 -2.874 -1.485 5.837 7.509 5.612 83.914 4 AA_C1407C1409:G1491G1494_BB A 1407 ? B 1494 ? A 1409 ? B 1491 ? 1 A C 7 1_555 B G 14 1_555 A A 8 1_555 B U 13 1_555 -0.517 -1.743 3.090 -1.587 15.084 32.079 -4.725 0.655 2.108 25.586 2.692 35.398 5 AA_C1409A1410:U1490G1491_BB A 1409 ? B 1491 ? A 1410 ? B 1490 ? 1 A A 8 1_555 B U 13 1_555 A C 9 1_555 B G 12 1_555 1.165 -2.023 3.113 3.238 1.792 28.339 -4.486 -1.659 3.093 3.641 -6.579 28.574 6 AA_A1410C1411:G1489U1490_BB A 1410 ? B 1490 ? A 1411 ? B 1489 ? 1 A C 9 1_555 B G 12 1_555 A C 10 1_555 B G 11 1_555 -0.737 -2.131 3.247 -3.468 3.000 30.841 -4.522 0.728 3.094 5.602 6.477 31.172 7 AA_C1411C1412:G1488G1489_BB A 1411 ? B 1489 ? A 1412 ? B 1488 ? 1 A C 10 1_555 B G 11 1_555 A G 11 1_555 B C 10 1_555 0.091 -1.707 3.108 3.055 6.638 26.308 -5.089 0.485 2.600 14.238 -6.553 27.286 8 AA_C1412G1488:C1412G1488_BB A 1412 ? B 1488 ? A 1488 ? B 1412 ? 1 A G 11 1_555 B C 10 1_555 A G 12 1_555 B C 9 1_555 -0.103 -1.330 3.481 0.784 5.657 35.801 -2.959 0.280 3.237 9.130 -1.266 36.239 9 AA_G1488G1489:C1411C1412_BB A 1488 ? B 1412 ? A 1489 ? B 1411 ? 1 A G 12 1_555 B C 9 1_555 A U 13 1_555 B A 8 1_555 0.442 -1.175 3.267 2.024 8.150 34.330 -3.097 -0.440 2.941 13.557 -3.367 35.312 10 AA_G1489U1490:A1410C1411_BB A 1489 ? B 1411 ? A 1490 ? B 1410 ? 1 A U 13 1_555 B A 8 1_555 A G 14 1_555 B C 7 1_555 0.308 -1.583 2.797 0.331 12.574 32.316 -4.151 -0.478 2.059 21.597 -0.568 34.616 11 AA_U1490G1491:C1409A1410_BB A 1490 ? B 1410 ? A 1491 ? B 1409 ? 1 A G 14 1_555 B C 7 1_555 A G 17 1_555 B C 5 1_555 -1.987 -2.574 5.710 6.644 13.646 79.115 -2.596 1.832 5.136 10.624 -5.172 80.323 12 AA_G1491G1494:C1407C1409_BB A 1491 ? B 1409 ? A 1494 ? B 1407 ? 1 A G 17 1_555 B C 5 1_555 A U 18 1_555 B U 4 1_555 -0.635 -2.240 3.106 0.158 5.700 21.912 -7.496 1.667 2.447 14.678 -0.408 22.633 13 AA_G1494U1495:U1406C1407_BB A 1494 ? B 1407 ? A 1495 ? B 1406 ? 1 A U 18 1_555 B U 4 1_555 A C 19 1_555 B G 3 1_555 0.639 -1.604 3.547 -5.863 4.876 41.267 -2.772 -1.531 3.230 6.847 8.235 41.936 14 AA_U1495C1496:G1405U1406_BB A 1495 ? B 1406 ? A 1496 ? B 1405 ? 1 A C 19 1_555 B G 3 1_555 A G 20 1_555 B C 2 1_555 -0.530 -2.062 3.368 -0.512 10.831 23.259 -7.394 1.065 2.212 25.183 1.190 25.630 15 AA_C1496G1497:C1404G1405_BB A 1496 ? B 1405 ? A 1497 ? B 1404 ? 1 A G 20 1_555 B C 2 1_555 A C 21 1_555 B G 1 1_555 0.434 -1.099 3.388 0.719 -2.705 38.443 -1.315 -0.564 3.461 -4.102 -1.090 38.541 16 AA_G1497C1498:G1403C1404_BB A 1497 ? B 1404 ? A 1498 ? B 1403 ? # _atom_sites.entry_id 2F4S _atom_sites.fract_transf_matrix[1][1] 0.030253 _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] 0.021137 _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] 0.011717 _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_