data_4NFP # _entry.id 4NFP # _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 4NFP pdb_00004nfp 10.2210/pdb4nfp/pdb NDB NA2784 ? ? RCSB RCSB083144 ? ? WWPDB D_1000083144 ? ? # 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 2014-07-02 2 'Structure model' 1 1 2014-09-03 3 'Structure model' 1 2 2024-02-28 # _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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' struct_conn 5 3 'Structure model' struct_ncs_dom_lim 6 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 3 'Structure model' '_struct_ncs_dom_lim.beg_auth_comp_id' 5 3 'Structure model' '_struct_ncs_dom_lim.beg_label_asym_id' 6 3 'Structure model' '_struct_ncs_dom_lim.beg_label_comp_id' 7 3 'Structure model' '_struct_ncs_dom_lim.beg_label_seq_id' 8 3 'Structure model' '_struct_ncs_dom_lim.end_auth_comp_id' 9 3 'Structure model' '_struct_ncs_dom_lim.end_label_asym_id' 10 3 'Structure model' '_struct_ncs_dom_lim.end_label_comp_id' 11 3 'Structure model' '_struct_ncs_dom_lim.end_label_seq_id' 12 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 13 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 14 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4NFP _pdbx_database_status.recvd_initial_deposition_date 2013-10-31 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _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 4NFO . unspecified PDB 4NFQ . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Beal, P.A.' 1 'Fisher, A.J.' 2 'Phelps, K.J.' 3 'Ibarra-Soza, J.M.' 4 'Zheng, Y.' 5 # _citation.id primary _citation.title 'Click Modification of RNA at Adenosine: Structure and Reactivity of 7-Ethynyl- and 7-Triazolyl-8-aza-7-deazaadenosine in RNA.' _citation.journal_abbrev 'Acs Chem.Biol.' _citation.journal_volume 9 _citation.page_first 1780 _citation.page_last 1787 _citation.year 2014 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1554-8929 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 24896732 _citation.pdbx_database_id_DOI 10.1021/cb500270x # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Phelps, K.J.' 1 ? primary 'Ibarra-Soza, J.M.' 2 ? primary 'Tran, K.' 3 ? primary 'Fisher, A.J.' 4 ? primary 'Beal, P.A.' 5 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn 'GCAG(A7E)CUUAAGUCUGC' 5122.101 3 ? ? ? ? 2 non-polymer syn FORMAMIDE 45.041 3 ? ? ? ? 3 water nat water 18.015 29 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'GCAG(A7E)CUUAAGUCUGC' _entity_poly.pdbx_seq_one_letter_code_can GCAGACUUAAGUCUGC _entity_poly.pdbx_strand_id A,B,C _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 FORMAMIDE ARF 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 A n 1 4 G n 1 5 A7E n 1 6 C n 1 7 U n 1 8 U n 1 9 A n 1 10 A n 1 11 G n 1 12 U n 1 13 C n 1 14 U n 1 15 G n 1 16 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 A7E 'RNA linking' n '3-ethynyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine' '8-aza-7-deaza-7-ethynyl Adenosine' 'C12 H14 N5 O7 P' 371.243 ARF 'L-peptide NH3 amino terminus' . FORMAMIDE ? 'C H3 N O' 45.041 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 # 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 1 1 G G A . n A 1 2 C 2 2 2 C C A . n A 1 3 A 3 3 3 A A A . n A 1 4 G 4 4 4 G G A . n A 1 5 A7E 5 5 5 A7E A7E A . n A 1 6 C 6 6 6 C C A . n A 1 7 U 7 7 7 U U A . n A 1 8 U 8 8 8 U U A . n A 1 9 A 9 9 9 A A A . n A 1 10 A 10 10 10 A A A . n A 1 11 G 11 11 11 G G A . n A 1 12 U 12 12 12 U U A . n A 1 13 C 13 13 13 C C A . n A 1 14 U 14 14 14 U U A . n A 1 15 G 15 15 15 G G A . n A 1 16 C 16 16 16 C C A . n B 1 1 G 1 1 1 G G B . n B 1 2 C 2 2 2 C C B . n B 1 3 A 3 3 3 A A B . n B 1 4 G 4 4 4 G G B . n B 1 5 A7E 5 5 5 A7E A7E B . n B 1 6 C 6 6 6 C C B . n B 1 7 U 7 7 7 U U B . n B 1 8 U 8 8 8 U U B . n B 1 9 A 9 9 9 A A B . n B 1 10 A 10 10 10 A A B . n B 1 11 G 11 11 11 G G B . n B 1 12 U 12 12 12 U U B . n B 1 13 C 13 13 13 C C B . n B 1 14 U 14 14 14 U U B . n B 1 15 G 15 15 15 G G B . n B 1 16 C 16 16 16 C C B . n C 1 1 G 1 1 1 G G C . n C 1 2 C 2 2 2 C C C . n C 1 3 A 3 3 3 A A C . n C 1 4 G 4 4 4 G G C . n C 1 5 A7E 5 5 5 A7E A7E C . n C 1 6 C 6 6 6 C C C . n C 1 7 U 7 7 7 U U C . n C 1 8 U 8 8 8 U U C . n C 1 9 A 9 9 9 A A C . n C 1 10 A 10 10 10 A A C . n C 1 11 G 11 11 11 G G C . n C 1 12 U 12 12 12 U U C . n C 1 13 C 13 13 13 C C C . n C 1 14 U 14 14 14 U U C . n C 1 15 G 15 15 15 G G C . n C 1 16 C 16 16 16 C C C . 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 D 2 ARF 1 101 1 ARF ARF A . E 2 ARF 1 101 2 ARF ARF B . F 2 ARF 1 101 3 ARF ARF C . G 3 HOH 1 201 3 HOH HOH A . G 3 HOH 2 202 4 HOH HOH A . G 3 HOH 3 203 9 HOH HOH A . G 3 HOH 4 204 10 HOH HOH A . G 3 HOH 5 205 11 HOH HOH A . G 3 HOH 6 206 21 HOH HOH A . G 3 HOH 7 207 22 HOH HOH A . G 3 HOH 8 208 23 HOH HOH A . G 3 HOH 9 209 27 HOH HOH A . G 3 HOH 10 210 34 HOH HOH A . G 3 HOH 11 211 36 HOH HOH A . G 3 HOH 12 212 37 HOH HOH A . G 3 HOH 13 213 44 HOH HOH A . H 3 HOH 1 201 2 HOH HOH B . H 3 HOH 2 202 8 HOH HOH B . H 3 HOH 3 203 15 HOH HOH B . H 3 HOH 4 204 16 HOH HOH B . H 3 HOH 5 205 18 HOH HOH B . H 3 HOH 6 206 24 HOH HOH B . H 3 HOH 7 207 33 HOH HOH B . H 3 HOH 8 208 39 HOH HOH B . I 3 HOH 1 201 7 HOH HOH C . I 3 HOH 2 202 12 HOH HOH C . I 3 HOH 3 203 13 HOH HOH C . I 3 HOH 4 204 17 HOH HOH C . I 3 HOH 5 205 28 HOH HOH C . I 3 HOH 6 206 40 HOH HOH C . I 3 HOH 7 207 42 HOH HOH C . I 3 HOH 8 208 43 HOH HOH C . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal Blu-Ice 'data collection' . ? 1 PHASER phasing . ? 2 REFMAC refinement 5.7.0029 ? 3 # _cell.entry_id 4NFP _cell.length_a 74.800 _cell.length_b 43.190 _cell.length_c 48.790 _cell.angle_alpha 90.00 _cell.angle_beta 120.82 _cell.angle_gamma 90.00 _cell.Z_PDB 12 _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 4NFP _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4NFP _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.37 _exptl_crystal.density_percent_sol 48.21 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 294.15 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7 _exptl_crystal_grow.pdbx_details ;10% MPD(v/v) (Drop), 35% MPD(v/v) (reservoir), 40mM Na-cacodylate trihydrate (pH 7), 12mM spermine tetrahydrochloride, 80mM SrCl2, 20mM MgCl2 hexahydrate, VAPOR DIFFUSION, SITTING DROP, temperature 294.15K ; _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.details ? _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2012-07-27 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ;Si(111) Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg ; _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.127 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SSRL BEAMLINE BL7-1' _diffrn_source.pdbx_synchrotron_site SSRL _diffrn_source.pdbx_synchrotron_beamline BL7-1 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.127 # _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.limit_k_max ? _reflns.d_resolution_high 1.85 _reflns.observed_criterion_F_min ? _reflns.pdbx_netI_over_sigmaI 18.04 _reflns.observed_criterion_F_max ? _reflns.pdbx_Rmerge_I_obs 0.029 _reflns.limit_l_max ? _reflns.limit_k_min ? _reflns.entry_id 4NFP _reflns.B_iso_Wilson_estimate ? _reflns.percent_possible_obs 91.3 _reflns.pdbx_Rsym_value ? _reflns.observed_criterion_sigma_I 0. _reflns.observed_criterion_sigma_F 0. _reflns.limit_l_min ? _reflns.limit_h_min ? _reflns.R_free_details ? _reflns.number_all 11632 _reflns.d_resolution_low 35. _reflns.pdbx_redundancy 2.7 _reflns.number_obs 10615 _reflns.limit_h_max ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.85 _reflns_shell.d_res_low 1.90 _reflns_shell.percent_possible_all 75.4 _reflns_shell.Rmerge_I_obs 0.330 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.32 _reflns_shell.pdbx_redundancy 1.85 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 858 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.ls_percent_reflns_R_free 4.9 _refine.overall_SU_B 11.676 _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_R_Free_selection_details RANDOM _refine.overall_FOM_free_R_set ? _refine.pdbx_data_cutoff_low_absF ? _refine.entry_id 4NFP _refine.aniso_B[2][3] 0.00 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_ML 0.154 _refine.aniso_B[1][3] -1.81 _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.aniso_B[3][3] -3.65 _refine.solvent_model_param_ksol ? _refine.ls_number_restraints ? _refine.aniso_B[1][1] 2.81 _refine.pdbx_overall_ESU_R 0.182 _refine.ls_R_factor_obs 0.22364 _refine.occupancy_min ? _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_starting_model ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.occupancy_max ? _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.correlation_coeff_Fo_to_Fc 0.972 _refine.ls_number_reflns_R_free 515 _refine.correlation_coeff_Fo_to_Fc_free 0.969 _refine.pdbx_ls_sigma_F 0 _refine.ls_percent_reflns_obs 91.61 _refine.ls_R_factor_R_work 0.22222 _refine.overall_SU_R_free ? _refine.ls_d_res_high 1.85 _refine.pdbx_overall_ESU_R_Free 0.156 _refine.B_iso_min ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.B_iso_mean 51.571 _refine.pdbx_stereochem_target_val_spec_case ? _refine.ls_R_factor_all 0.22364 _refine.aniso_B[2][2] 4.53 _refine.B_iso_max ? _refine.pdbx_ls_sigma_I ? _refine.ls_d_res_low 32.17 _refine.pdbx_overall_phase_error ? _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.aniso_B[1][2] 0.00 _refine.ls_R_factor_R_free 0.24940 _refine.ls_R_factor_R_free_error ? _refine.ls_number_reflns_obs 10100 _refine.overall_FOM_work_R_set ? _refine.ls_number_parameters ? _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.ls_number_reflns_all 10615 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.solvent_model_param_bsol ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _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_analyze.entry_id 4NFP _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free 0.156 _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 1017 _refine_hist.pdbx_number_atoms_ligand 9 _refine_hist.number_atoms_solvent 29 _refine_hist.number_atoms_total 1055 _refine_hist.d_res_high 1.85 _refine_hist.d_res_low 32.17 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_restraint_function _refine_ls_restr.pdbx_refine_id r_bond_refined_d 0.007 0.012 ? 1140 ? 'X-RAY DIFFRACTION' r_bond_other_d 0.009 0.020 ? 480 ? 'X-RAY DIFFRACTION' r_angle_refined_deg 1.894 1.394 ? 1764 ? 'X-RAY DIFFRACTION' r_angle_other_deg 1.549 3.000 ? 1155 ? 'X-RAY DIFFRACTION' r_chiral_restr 0.076 0.200 ? 192 ? 'X-RAY DIFFRACTION' r_gen_planes_refined 0.007 0.020 ? 579 ? 'X-RAY DIFFRACTION' r_gen_planes_other 0.002 0.020 ? 264 ? 'X-RAY DIFFRACTION' # loop_ _refine_ls_restr_ncs.dom_id _refine_ls_restr_ncs.pdbx_auth_asym_id _refine_ls_restr_ncs.pdbx_number _refine_ls_restr_ncs.rms_dev_position _refine_ls_restr_ncs.weight_position _refine_ls_restr_ncs.pdbx_type _refine_ls_restr_ncs.pdbx_ens_id _refine_ls_restr_ncs.ncs_model_details _refine_ls_restr_ncs.rms_dev_B_iso _refine_ls_restr_ncs.weight_B_iso _refine_ls_restr_ncs.pdbx_asym_id _refine_ls_restr_ncs.pdbx_rms _refine_ls_restr_ncs.pdbx_weight _refine_ls_restr_ncs.pdbx_ordinal _refine_ls_restr_ncs.pdbx_refine_id 1 A 931 0.01 0.05 'interatomic distance' 1 ? ? ? ? ? ? 1 'X-RAY DIFFRACTION' 2 B 931 0.01 0.05 'interatomic distance' 1 ? ? ? ? ? ? 2 'X-RAY DIFFRACTION' 1 A 927 0.03 0.05 'interatomic distance' 2 ? ? ? ? ? ? 3 'X-RAY DIFFRACTION' 2 C 927 0.03 0.05 'interatomic distance' 2 ? ? ? ? ? ? 4 'X-RAY DIFFRACTION' 1 B 928 0.03 0.05 'interatomic distance' 3 ? ? ? ? ? ? 5 'X-RAY DIFFRACTION' 2 C 928 0.03 0.05 'interatomic distance' 3 ? ? ? ? ? ? 6 'X-RAY DIFFRACTION' # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.850 _refine_ls_shell.d_res_low 1.898 _refine_ls_shell.number_reflns_R_work 619 _refine_ls_shell.R_factor_R_work 0.396 _refine_ls_shell.percent_reflns_obs 75.41 _refine_ls_shell.R_factor_R_free 0.429 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 22 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs 619 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _struct_ncs_dom.id _struct_ncs_dom.details _struct_ncs_dom.pdbx_ens_id 1 A 1 2 B 1 1 A 2 2 C 2 1 B 3 2 C 3 # loop_ _struct_ncs_dom_lim.pdbx_ens_id _struct_ncs_dom_lim.dom_id _struct_ncs_dom_lim.pdbx_component_id _struct_ncs_dom_lim.beg_label_asym_id _struct_ncs_dom_lim.beg_label_comp_id _struct_ncs_dom_lim.beg_label_seq_id _struct_ncs_dom_lim.beg_label_alt_id _struct_ncs_dom_lim.end_label_asym_id _struct_ncs_dom_lim.end_label_comp_id _struct_ncs_dom_lim.end_label_seq_id _struct_ncs_dom_lim.end_label_alt_id _struct_ncs_dom_lim.beg_auth_asym_id _struct_ncs_dom_lim.beg_auth_comp_id _struct_ncs_dom_lim.beg_auth_seq_id _struct_ncs_dom_lim.end_auth_asym_id _struct_ncs_dom_lim.end_auth_comp_id _struct_ncs_dom_lim.end_auth_seq_id _struct_ncs_dom_lim.pdbx_refine_code _struct_ncs_dom_lim.selection_details 1 1 0 A G 1 . A C 16 . A G 1 A C 16 0 ? 1 2 0 B G 1 . B C 16 . B G 1 B C 16 0 ? 2 1 0 A G 1 . A C 16 . A G 1 A C 16 0 ? 2 2 0 C G 1 . C C 16 . C G 1 C C 16 0 ? 3 1 0 B G 1 . B C 16 . B G 1 B C 16 0 ? 3 2 0 C G 1 . C C 16 . C G 1 C C 16 0 ? # loop_ _struct_ncs_ens.id _struct_ncs_ens.details 1 ? 2 ? 3 ? # _database_PDB_matrix.entry_id 4NFP _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 4NFP _struct.title 'Crystal Structure Analysis of the 16mer GCAGNCUUAAGUCUGC containing 8-aza-7-deaza-7-ethynyl Adenosine' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4NFP _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'RNA 16mer oligo, 8-aza-7-deaza-7-ethynyladenosine, Position 5, 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 1 ? D N N 2 ? E N N 2 ? F N N 2 ? G N N 3 ? H N N 3 ? I N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4NFP _struct_ref.pdbx_db_accession 4NFP _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 4NFP A 1 ? 16 ? 4NFP 1 ? 16 ? 1 16 2 1 4NFP B 1 ? 16 ? 4NFP 1 ? 16 ? 1 16 3 1 4NFP C 1 ? 16 ? 4NFP 1 ? 16 ? 1 16 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_and_software_defined_assembly PISA dimeric 2 2 author_and_software_defined_assembly PISA dimeric 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)' 1840 ? 1 MORE -12 ? 1 'SSA (A^2)' 5800 ? 2 'ABSA (A^2)' 1830 ? 2 MORE -12 ? 2 'SSA (A^2)' 5820 ? # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1,2 A,D,G 2 1 B,C,E,F,H,I # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_756 -x+2,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 124.6028012656 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 41.8999302557 # _struct_biol.id 1 _struct_biol.details 'Asymmetric unit contains 1.5 RNA duplexes' # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A G 4 "O3'" ? ? ? 1_555 A A7E 5 P ? ? A G 4 A A7E 5 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale2 covale both ? A A7E 5 "O3'" ? ? ? 1_555 A C 6 P ? ? A A7E 5 A C 6 1_555 ? ? ? ? ? ? ? 1.627 ? ? covale3 covale both ? B G 4 "O3'" ? ? ? 1_555 B A7E 5 P ? ? B G 4 B A7E 5 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale4 covale both ? B A7E 5 "O3'" ? ? ? 1_555 B C 6 P ? ? B A7E 5 B C 6 1_555 ? ? ? ? ? ? ? 1.633 ? ? covale5 covale both ? C G 4 "O3'" ? ? ? 1_555 C A7E 5 P ? ? C G 4 C A7E 5 1_555 ? ? ? ? ? ? ? 1.591 ? ? covale6 covale both ? C A7E 5 "O3'" ? ? ? 1_555 C C 6 P ? ? C A7E 5 C C 6 1_555 ? ? ? ? ? ? ? 1.623 ? ? hydrog1 hydrog ? ? B G 1 N1 ? ? ? 1_555 C C 16 N3 ? ? B G 1 C C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? B G 1 N2 ? ? ? 1_555 C C 16 O2 ? ? B G 1 C C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? B G 1 O6 ? ? ? 1_555 C C 16 N4 ? ? B G 1 C C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? B C 2 N3 ? ? ? 1_555 C G 15 N1 ? ? B C 2 C G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? B C 2 N4 ? ? ? 1_555 C G 15 O6 ? ? B C 2 C G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? B C 2 O2 ? ? ? 1_555 C G 15 N2 ? ? B C 2 C G 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? B A 3 N1 ? ? ? 1_555 C U 14 N3 ? ? B A 3 C U 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? B A 3 N6 ? ? ? 1_555 C U 14 O4 ? ? B A 3 C U 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? B G 4 N1 ? ? ? 1_555 C C 13 N3 ? ? B G 4 C C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? B G 4 N2 ? ? ? 1_555 C C 13 O2 ? ? B G 4 C C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? B G 4 O6 ? ? ? 1_555 C C 13 N4 ? ? B G 4 C C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? B C 6 N3 ? ? ? 1_555 C G 11 N1 ? ? B C 6 C G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? B C 6 N4 ? ? ? 1_555 C G 11 O6 ? ? B C 6 C G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? B C 6 O2 ? ? ? 1_555 C G 11 N2 ? ? B C 6 C G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? B U 7 N3 ? ? ? 1_555 C A 10 N1 ? ? B U 7 C A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? B U 7 O4 ? ? ? 1_555 C A 10 N6 ? ? B U 7 C A 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? B U 8 N3 ? ? ? 1_555 C A 9 N1 ? ? B U 8 C A 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? B U 8 O4 ? ? ? 1_555 C A 9 N6 ? ? B U 8 C A 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? B A 9 N1 ? ? ? 1_555 C U 8 N3 ? ? B A 9 C U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? B A 9 N6 ? ? ? 1_555 C U 8 O4 ? ? B A 9 C U 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? B A 10 N1 ? ? ? 1_555 C U 7 N3 ? ? B A 10 C U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? B A 10 N6 ? ? ? 1_555 C U 7 O4 ? ? B A 10 C U 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? B G 11 N1 ? ? ? 1_555 C C 6 N3 ? ? B G 11 C C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? B G 11 N2 ? ? ? 1_555 C C 6 O2 ? ? B G 11 C C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? B G 11 O6 ? ? ? 1_555 C C 6 N4 ? ? B G 11 C C 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? B C 13 N3 ? ? ? 1_555 C G 4 N1 ? ? B C 13 C G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? B C 13 N4 ? ? ? 1_555 C G 4 O6 ? ? B C 13 C G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? B C 13 O2 ? ? ? 1_555 C G 4 N2 ? ? B C 13 C G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? B U 14 N3 ? ? ? 1_555 C A 3 N1 ? ? B U 14 C A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? B U 14 O4 ? ? ? 1_555 C A 3 N6 ? ? B U 14 C A 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B G 15 N1 ? ? ? 1_555 C C 2 N3 ? ? B G 15 C C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B G 15 N2 ? ? ? 1_555 C C 2 O2 ? ? B G 15 C C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? B G 15 O6 ? ? ? 1_555 C C 2 N4 ? ? B G 15 C C 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? B C 16 N3 ? ? ? 1_555 C G 1 N1 ? ? B C 16 C G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? B C 16 N4 ? ? ? 1_555 C G 1 O6 ? ? B C 16 C G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? B C 16 O2 ? ? ? 1_555 C G 1 N2 ? ? B C 16 C G 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 16 N3 ? ? A G 1 A C 16 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 16 O2 ? ? A G 1 A C 16 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 16 N4 ? ? A G 1 A C 16 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 2 N3 ? ? ? 1_555 A G 15 N1 ? ? A C 2 A G 15 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 2 N4 ? ? ? 1_555 A G 15 O6 ? ? A C 2 A G 15 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A C 2 O2 ? ? ? 1_555 A G 15 N2 ? ? A C 2 A G 15 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A A 3 N1 ? ? ? 1_555 A U 14 N3 ? ? A A 3 A U 14 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A A 3 N6 ? ? ? 1_555 A U 14 O4 ? ? A A 3 A U 14 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 13 N3 ? ? A G 4 A C 13 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 13 O2 ? ? A G 4 A C 13 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 13 N4 ? ? A G 4 A C 13 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A C 6 N3 ? ? ? 1_555 A G 11 N1 ? ? A C 6 A G 11 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A C 6 N4 ? ? ? 1_555 A G 11 O6 ? ? A C 6 A G 11 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A C 6 O2 ? ? ? 1_555 A G 11 N2 ? ? A C 6 A G 11 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A U 7 N3 ? ? ? 1_555 A A 10 N1 ? ? A U 7 A A 10 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A U 7 O4 ? ? ? 1_555 A A 10 N6 ? ? A U 7 A A 10 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? A U 8 N3 ? ? ? 1_555 A A 9 N1 ? ? A U 8 A A 9 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? A U 8 O4 ? ? ? 1_555 A A 9 N6 ? ? A U 8 A A 9 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? A A 9 N1 ? ? ? 1_555 A U 8 N3 ? ? A A 9 A U 8 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog56 hydrog ? ? A A 9 N6 ? ? ? 1_555 A U 8 O4 ? ? A A 9 A U 8 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog57 hydrog ? ? A A 10 N1 ? ? ? 1_555 A U 7 N3 ? ? A A 10 A U 7 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog58 hydrog ? ? A A 10 N6 ? ? ? 1_555 A U 7 O4 ? ? A A 10 A U 7 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? A G 11 N1 ? ? ? 1_555 A C 6 N3 ? ? A G 11 A C 6 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? A G 11 N2 ? ? ? 1_555 A C 6 O2 ? ? A G 11 A C 6 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? A G 11 O6 ? ? ? 1_555 A C 6 N4 ? ? A G 11 A C 6 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? A C 13 N3 ? ? ? 1_555 A G 4 N1 ? ? A C 13 A G 4 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? A C 13 N4 ? ? ? 1_555 A G 4 O6 ? ? A C 13 A G 4 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog64 hydrog ? ? A C 13 O2 ? ? ? 1_555 A G 4 N2 ? ? A C 13 A G 4 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog65 hydrog ? ? A U 14 N3 ? ? ? 1_555 A A 3 N1 ? ? A U 14 A A 3 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog66 hydrog ? ? A U 14 O4 ? ? ? 1_555 A A 3 N6 ? ? A U 14 A A 3 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? A G 15 N1 ? ? ? 1_555 A C 2 N3 ? ? A G 15 A C 2 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? A G 15 N2 ? ? ? 1_555 A C 2 O2 ? ? A G 15 A C 2 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? A G 15 O6 ? ? ? 1_555 A C 2 N4 ? ? A G 15 A C 2 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? A C 16 N3 ? ? ? 1_555 A G 1 N1 ? ? A C 16 A G 1 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? A C 16 N4 ? ? ? 1_555 A G 1 O6 ? ? A C 16 A G 1 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog72 hydrog ? ? A C 16 O2 ? ? ? 1_555 A G 1 N2 ? ? A C 16 A G 1 2_756 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A ARF 101 ? 1 'BINDING SITE FOR RESIDUE ARF A 101' AC2 Software B ARF 101 ? 1 'BINDING SITE FOR RESIDUE ARF B 101' AC3 Software C ARF 101 ? 1 'BINDING SITE FOR RESIDUE ARF C 101' # 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 1 U A 12 ? U A 12 . ? 1_555 ? 2 AC2 1 U B 12 ? U B 12 . ? 1_555 ? 3 AC3 1 U C 12 ? U C 12 . ? 1_555 ? # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A A7E 5 A A7E 5 ? A ? 2 B A7E 5 B A7E 5 ? A ? 3 C A7E 5 C A7E 5 ? A ? # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] _pdbx_refine_tls.S[3][3] 'X-RAY DIFFRACTION' 1 ? refined 58.5477 21.4133 35.0206 0.0677 0.1314 0.1980 0.0068 0.0033 0.0860 5.0298 10.4131 0.8602 3.8770 1.1336 2.9811 0.1560 0.3500 0.0894 -0.0620 -0.1933 0.3775 -0.0141 -0.0614 0.0373 'X-RAY DIFFRACTION' 2 ? refined 68.7562 20.6054 24.2297 0.0702 0.0661 0.1302 0.0011 -0.0241 0.0402 5.7995 2.1056 0.5026 -1.9187 -1.0138 1.0246 0.4612 0.3605 0.2153 -0.0263 -0.3767 -0.1011 -0.0164 -0.1794 -0.0845 'X-RAY DIFFRACTION' 3 ? refined 59.1842 12.7866 14.1069 0.0651 0.0225 0.1431 -0.0124 -0.0458 -0.0043 8.6927 2.7712 3.3011 -0.8060 4.0686 1.5540 0.1384 0.3730 -0.4179 -0.0339 0.0250 0.0372 0.0242 0.2252 -0.1635 'X-RAY DIFFRACTION' 4 ? refined 58.3963 22.9786 2.9127 0.1079 0.0459 0.1411 0.0407 0.0371 -0.0301 6.2267 2.0360 2.2406 -1.1011 1.2925 1.6717 0.1838 0.2407 0.0594 -0.2354 0.0488 -0.2358 -0.1362 0.1752 -0.2326 'X-RAY DIFFRACTION' 5 ? refined 43.0058 37.5158 6.8609 0.0642 0.1146 0.1426 0.0264 0.0383 0.0607 4.2939 10.3064 2.6158 3.6749 -0.2438 0.5206 -0.0295 -0.2458 0.3283 0.1313 0.1971 0.2883 -0.0848 0.1838 -0.1676 'X-RAY DIFFRACTION' 6 ? refined 48.7801 29.1179 17.6479 0.0503 0.0773 0.0942 0.0010 0.0667 -0.0007 8.7839 5.2316 1.6474 -0.9707 3.8002 -0.5219 -0.2795 -0.4430 -0.2008 0.0696 0.3863 0.0756 -0.1247 -0.1984 -0.1068 'X-RAY DIFFRACTION' 7 ? refined 50.6349 41.3462 27.7569 0.0948 0.1175 0.1569 -0.0031 -0.0104 -0.0548 1.9498 3.9342 1.4729 -0.5642 -0.4606 2.4002 -0.3002 -0.1432 0.2457 0.2789 0.4501 -0.2461 0.1916 0.2746 -0.1499 'X-RAY DIFFRACTION' 8 ? refined 41.4510 37.0158 38.9765 0.1905 0.1853 0.1471 -0.0280 -0.1247 0.0190 4.9316 1.7994 0.2176 -2.5406 0.3617 0.1168 0.0637 -0.4487 -0.2690 0.2450 0.1145 -0.0694 0.1911 -0.0696 -0.1782 'X-RAY DIFFRACTION' 9 ? refined 46.6640 31.1269 35.0116 0.1374 0.1979 0.2441 -0.0620 0.0032 -0.0999 9.6106 3.0689 0.5379 -0.6509 -1.9619 -0.1086 0.0524 0.0058 -0.5000 -0.3002 -0.0121 -0.1471 -0.0423 0.1227 -0.0403 'X-RAY DIFFRACTION' 10 ? refined 42.3304 40.3241 24.2299 0.0407 0.0755 0.1043 -0.0350 -0.0187 -0.0324 4.5976 5.7526 4.7530 -0.2900 -2.7501 -4.0461 0.1420 -0.1561 0.0188 -0.3736 0.0762 0.2440 0.1789 0.0401 -0.2183 'X-RAY DIFFRACTION' 11 ? refined 53.8516 35.8827 14.1303 0.0373 0.0990 0.1345 -0.0130 0.0540 -0.0224 3.8353 7.4131 1.2443 -2.9511 -1.7099 2.8581 0.2462 0.0051 0.2119 -0.4065 -0.0593 -0.3742 -0.1802 -0.0471 -0.1870 'X-RAY DIFFRACTION' 12 ? refined 45.5070 30.0911 2.9008 0.0607 0.0902 0.1139 -0.0265 0.0337 0.0481 1.9337 7.6449 0.6569 -1.5458 -0.7810 -0.8501 -0.0266 0.3205 0.1700 -0.1328 0.1972 0.2170 0.0291 -0.2338 -0.1706 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection _pdbx_refine_tls_group.selection_details 'X-RAY DIFFRACTION' 1 1 A 1 ? ? A 4 ? ? ? ? 'X-RAY DIFFRACTION' 2 2 A 5 ? ? A 8 ? ? ? ? 'X-RAY DIFFRACTION' 3 3 A 9 ? ? A 12 ? ? ? ? 'X-RAY DIFFRACTION' 4 4 A 13 ? ? A 16 ? ? ? ? 'X-RAY DIFFRACTION' 5 5 B 1 ? ? B 4 ? ? ? ? 'X-RAY DIFFRACTION' 6 6 B 5 ? ? B 8 ? ? ? ? 'X-RAY DIFFRACTION' 7 7 B 9 ? ? B 12 ? ? ? ? 'X-RAY DIFFRACTION' 8 8 B 13 ? ? B 16 ? ? ? ? 'X-RAY DIFFRACTION' 9 9 C 1 ? ? C 4 ? ? ? ? 'X-RAY DIFFRACTION' 10 10 C 5 ? ? C 8 ? ? ? ? 'X-RAY DIFFRACTION' 11 11 C 9 ? ? C 12 ? ? ? ? 'X-RAY DIFFRACTION' 12 12 C 13 ? ? C 16 ? ? ? ? # 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 A7E P P N N 38 A7E OP1 O N N 39 A7E OP2 O N N 40 A7E "O5'" O N N 41 A7E "C5'" C N N 42 A7E "C4'" C N R 43 A7E "O4'" O N N 44 A7E "C1'" C N R 45 A7E N9 N Y N 46 A7E N8 N Y N 47 A7E C7 C Y N 48 A7E C24 C N N 49 A7E C25 C N N 50 A7E C5 C Y N 51 A7E C6 C Y N 52 A7E N6 N N N 53 A7E N1 N Y N 54 A7E C2 C Y N 55 A7E N3 N Y N 56 A7E C4 C Y N 57 A7E "C2'" C N R 58 A7E "O2'" O N N 59 A7E "C3'" C N S 60 A7E "O3'" O N N 61 A7E H2 H N N 62 A7E H3 H N N 63 A7E H4 H N N 64 A7E H5 H N N 65 A7E H6 H N N 66 A7E H7 H N N 67 A7E H8 H N N 68 A7E H9 H N N 69 A7E H10 H N N 70 A7E H11 H N N 71 A7E H12 H N N 72 A7E H13 H N N 73 A7E H14 H N N 74 A7E OP3 O N N 75 A7E HOP3 H N N 76 ARF N N N N 77 ARF C C N N 78 ARF O O N N 79 ARF HN1 H N N 80 ARF HN2 H N N 81 ARF H H N N 82 C OP3 O N N 83 C P P N N 84 C OP1 O N N 85 C OP2 O N N 86 C "O5'" O N N 87 C "C5'" C N N 88 C "C4'" C N R 89 C "O4'" O N N 90 C "C3'" C N S 91 C "O3'" O N N 92 C "C2'" C N R 93 C "O2'" O N N 94 C "C1'" C N R 95 C N1 N N N 96 C C2 C N N 97 C O2 O N N 98 C N3 N N N 99 C C4 C N N 100 C N4 N N N 101 C C5 C N N 102 C C6 C N N 103 C HOP3 H N N 104 C HOP2 H N N 105 C "H5'" H N N 106 C "H5''" H N N 107 C "H4'" H N N 108 C "H3'" H N N 109 C "HO3'" H N N 110 C "H2'" H N N 111 C "HO2'" H N N 112 C "H1'" H N N 113 C H41 H N N 114 C H42 H N N 115 C H5 H N N 116 C H6 H N N 117 G OP3 O N N 118 G P P N N 119 G OP1 O N N 120 G OP2 O N N 121 G "O5'" O N N 122 G "C5'" C N N 123 G "C4'" C N R 124 G "O4'" O N N 125 G "C3'" C N S 126 G "O3'" O N N 127 G "C2'" C N R 128 G "O2'" O N N 129 G "C1'" C N R 130 G N9 N Y N 131 G C8 C Y N 132 G N7 N Y N 133 G C5 C Y N 134 G C6 C N N 135 G O6 O N N 136 G N1 N N N 137 G C2 C N N 138 G N2 N N N 139 G N3 N N N 140 G C4 C Y N 141 G HOP3 H N N 142 G HOP2 H N N 143 G "H5'" H N N 144 G "H5''" H N N 145 G "H4'" H N N 146 G "H3'" H N N 147 G "HO3'" H N N 148 G "H2'" H N N 149 G "HO2'" H N N 150 G "H1'" H N N 151 G H8 H N N 152 G H1 H N N 153 G H21 H N N 154 G H22 H N N 155 HOH O O N N 156 HOH H1 H N N 157 HOH H2 H N N 158 U OP3 O N N 159 U P P N N 160 U OP1 O N N 161 U OP2 O N N 162 U "O5'" O N N 163 U "C5'" C N N 164 U "C4'" C N R 165 U "O4'" O N N 166 U "C3'" C N S 167 U "O3'" O N N 168 U "C2'" C N R 169 U "O2'" O N N 170 U "C1'" C N R 171 U N1 N N N 172 U C2 C N N 173 U O2 O N N 174 U N3 N N N 175 U C4 C N N 176 U O4 O N N 177 U C5 C N N 178 U C6 C N N 179 U HOP3 H N N 180 U HOP2 H N N 181 U "H5'" H N N 182 U "H5''" H N N 183 U "H4'" H N N 184 U "H3'" H N N 185 U "HO3'" H N N 186 U "H2'" H N N 187 U "HO2'" H N N 188 U "H1'" H N N 189 U H3 H N N 190 U H5 H N N 191 U H6 H N N 192 # 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 A7E "O3'" "C3'" sing N N 40 A7E OP2 P sing N N 41 A7E OP1 P doub N N 42 A7E "C3'" "C2'" sing N N 43 A7E "C3'" "C4'" sing N N 44 A7E P "O5'" sing N N 45 A7E "O5'" "C5'" sing N N 46 A7E "C5'" "C4'" sing N N 47 A7E "C2'" "O2'" sing N N 48 A7E "C2'" "C1'" sing N N 49 A7E "C4'" "O4'" sing N N 50 A7E C25 C24 trip N N 51 A7E C24 C7 sing N N 52 A7E N8 C7 doub Y N 53 A7E N8 N9 sing Y N 54 A7E C7 C5 sing Y N 55 A7E N9 "C1'" sing N N 56 A7E N9 C4 sing Y N 57 A7E "C1'" "O4'" sing N N 58 A7E C5 C4 doub Y N 59 A7E C5 C6 sing Y N 60 A7E N6 C6 sing N N 61 A7E C4 N3 sing Y N 62 A7E C6 N1 doub Y N 63 A7E N3 C2 doub Y N 64 A7E N1 C2 sing Y N 65 A7E OP2 H2 sing N N 66 A7E "C5'" H3 sing N N 67 A7E "C5'" H4 sing N N 68 A7E "C4'" H5 sing N N 69 A7E "C1'" H6 sing N N 70 A7E C25 H7 sing N N 71 A7E N6 H8 sing N N 72 A7E N6 H9 sing N N 73 A7E C2 H10 sing N N 74 A7E "C2'" H11 sing N N 75 A7E "O2'" H12 sing N N 76 A7E "C3'" H13 sing N N 77 A7E "O3'" H14 sing N N 78 A7E P OP3 sing N N 79 A7E OP3 HOP3 sing N N 80 ARF N C sing N N 81 ARF N HN1 sing N N 82 ARF N HN2 sing N N 83 ARF C O doub N N 84 ARF C H sing N N 85 C OP3 P sing N N 86 C OP3 HOP3 sing N N 87 C P OP1 doub N N 88 C P OP2 sing N N 89 C P "O5'" sing N N 90 C OP2 HOP2 sing N N 91 C "O5'" "C5'" sing N N 92 C "C5'" "C4'" sing N N 93 C "C5'" "H5'" sing N N 94 C "C5'" "H5''" sing N N 95 C "C4'" "O4'" sing N N 96 C "C4'" "C3'" sing N N 97 C "C4'" "H4'" sing N N 98 C "O4'" "C1'" sing N N 99 C "C3'" "O3'" sing N N 100 C "C3'" "C2'" sing N N 101 C "C3'" "H3'" sing N N 102 C "O3'" "HO3'" sing N N 103 C "C2'" "O2'" sing N N 104 C "C2'" "C1'" sing N N 105 C "C2'" "H2'" sing N N 106 C "O2'" "HO2'" sing N N 107 C "C1'" N1 sing N N 108 C "C1'" "H1'" sing N N 109 C N1 C2 sing N N 110 C N1 C6 sing N N 111 C C2 O2 doub N N 112 C C2 N3 sing N N 113 C N3 C4 doub N N 114 C C4 N4 sing N N 115 C C4 C5 sing N N 116 C N4 H41 sing N N 117 C N4 H42 sing N N 118 C C5 C6 doub N N 119 C C5 H5 sing N N 120 C C6 H6 sing N N 121 G OP3 P sing N N 122 G OP3 HOP3 sing N N 123 G P OP1 doub N N 124 G P OP2 sing N N 125 G P "O5'" sing N N 126 G OP2 HOP2 sing N N 127 G "O5'" "C5'" sing N N 128 G "C5'" "C4'" sing N N 129 G "C5'" "H5'" sing N N 130 G "C5'" "H5''" sing N N 131 G "C4'" "O4'" sing N N 132 G "C4'" "C3'" sing N N 133 G "C4'" "H4'" sing N N 134 G "O4'" "C1'" sing N N 135 G "C3'" "O3'" sing N N 136 G "C3'" "C2'" sing N N 137 G "C3'" "H3'" sing N N 138 G "O3'" "HO3'" sing N N 139 G "C2'" "O2'" sing N N 140 G "C2'" "C1'" sing N N 141 G "C2'" "H2'" sing N N 142 G "O2'" "HO2'" sing N N 143 G "C1'" N9 sing N N 144 G "C1'" "H1'" sing N N 145 G N9 C8 sing Y N 146 G N9 C4 sing Y N 147 G C8 N7 doub Y N 148 G C8 H8 sing N N 149 G N7 C5 sing Y N 150 G C5 C6 sing N N 151 G C5 C4 doub Y N 152 G C6 O6 doub N N 153 G C6 N1 sing N N 154 G N1 C2 sing N N 155 G N1 H1 sing N N 156 G C2 N2 sing N N 157 G C2 N3 doub N N 158 G N2 H21 sing N N 159 G N2 H22 sing N N 160 G N3 C4 sing N N 161 HOH O H1 sing N N 162 HOH O H2 sing N N 163 U OP3 P sing N N 164 U OP3 HOP3 sing N N 165 U P OP1 doub N N 166 U P OP2 sing N N 167 U P "O5'" sing N N 168 U OP2 HOP2 sing N N 169 U "O5'" "C5'" sing N N 170 U "C5'" "C4'" sing N N 171 U "C5'" "H5'" sing N N 172 U "C5'" "H5''" sing N N 173 U "C4'" "O4'" sing N N 174 U "C4'" "C3'" sing N N 175 U "C4'" "H4'" sing N N 176 U "O4'" "C1'" sing N N 177 U "C3'" "O3'" sing N N 178 U "C3'" "C2'" sing N N 179 U "C3'" "H3'" sing N N 180 U "O3'" "HO3'" sing N N 181 U "C2'" "O2'" sing N N 182 U "C2'" "C1'" sing N N 183 U "C2'" "H2'" sing N N 184 U "O2'" "HO2'" sing N N 185 U "C1'" N1 sing N N 186 U "C1'" "H1'" sing N N 187 U N1 C2 sing N N 188 U N1 C6 sing N N 189 U C2 O2 doub N N 190 U C2 N3 sing N N 191 U N3 C4 sing N N 192 U N3 H3 sing N N 193 U C4 O4 doub N N 194 U C4 C5 sing N N 195 U C5 C6 doub N N 196 U C5 H5 sing N N 197 U C6 H6 sing N N 198 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4NFP 'double helix' 4NFP 'a-form double helix' 4NFP 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 B G 1 1_555 C C 16 1_555 -0.479 -0.194 0.177 -2.132 -11.391 0.061 1 B_G1:C16_C B 1 ? C 16 ? 19 1 1 B C 2 1_555 C G 15 1_555 0.499 0.043 0.207 1.172 -17.783 7.748 2 B_C2:G15_C B 2 ? C 15 ? 19 1 1 B A 3 1_555 C U 14 1_555 0.114 -0.141 0.190 1.743 -7.790 0.088 3 B_A3:U14_C B 3 ? C 14 ? 20 1 1 B G 4 1_555 C C 13 1_555 -0.092 -0.212 0.043 3.420 -10.178 2.818 4 B_G4:C13_C B 4 ? C 13 ? 19 1 1 B C 6 1_555 C G 11 1_555 0.516 -0.233 -0.001 -0.232 -13.324 0.312 5 B_C6:G11_C B 6 ? C 11 ? 19 1 1 B U 7 1_555 C A 10 1_555 0.059 -0.115 0.025 -4.953 -15.428 -0.455 6 B_U7:A10_C B 7 ? C 10 ? 20 1 1 B U 8 1_555 C A 9 1_555 0.046 -0.084 0.149 -3.061 -10.483 0.813 7 B_U8:A9_C B 8 ? C 9 ? 20 1 1 B A 9 1_555 C U 8 1_555 -0.061 -0.090 0.136 2.728 -10.584 1.062 8 B_A9:U8_C B 9 ? C 8 ? 20 1 1 B A 10 1_555 C U 7 1_555 -0.025 -0.163 0.038 4.797 -15.255 0.322 9 B_A10:U7_C B 10 ? C 7 ? 20 1 1 B G 11 1_555 C C 6 1_555 -0.508 -0.295 0.010 0.015 -13.404 1.098 10 B_G11:C6_C B 11 ? C 6 ? 19 1 1 B C 13 1_555 C G 4 1_555 0.034 -0.179 0.058 -3.128 -11.297 3.331 11 B_C13:G4_C B 13 ? C 4 ? 19 1 1 B U 14 1_555 C A 3 1_555 -0.078 -0.101 0.193 -2.173 -8.309 0.659 12 B_U14:A3_C B 14 ? C 3 ? 20 1 1 B G 15 1_555 C C 2 1_555 -0.378 0.103 0.226 -1.388 -18.293 7.731 13 B_G15:C2_C B 15 ? C 2 ? 19 1 1 B C 16 1_555 C G 1 1_555 0.625 -0.210 0.213 1.906 -11.974 0.224 14 B_C16:G1_C B 16 ? C 1 ? 19 1 1 A G 1 1_555 A C 16 2_756 -0.495 -0.196 0.159 -2.259 -11.397 0.084 15 A_G1:C16_A A 1 ? A 16 ? 19 1 1 A C 2 1_555 A G 15 2_756 0.519 0.027 0.184 1.169 -17.872 7.162 16 A_C2:G15_A A 2 ? A 15 ? 19 1 1 A A 3 1_555 A U 14 2_756 -0.052 -0.133 0.204 1.975 -7.986 1.420 17 A_A3:U14_A A 3 ? A 14 ? 20 1 1 A G 4 1_555 A C 13 2_756 -0.135 -0.184 0.062 3.628 -10.546 3.401 18 A_G4:C13_A A 4 ? A 13 ? 19 1 1 A C 6 1_555 A G 11 2_756 0.435 -0.182 -0.012 0.179 -12.924 0.384 19 A_C6:G11_A A 6 ? A 11 ? 19 1 1 A U 7 1_555 A A 10 2_756 0.080 -0.034 0.049 -5.281 -15.219 -0.501 20 A_U7:A10_A A 7 ? A 10 ? 20 1 1 A U 8 1_555 A A 9 2_756 0.004 0.016 0.136 -2.932 -10.672 -0.619 21 A_U8:A9_A A 8 ? A 9 ? 20 1 1 A A 9 1_555 A U 8 2_756 -0.004 0.016 0.136 2.932 -10.672 -0.619 22 A_A9:U8_A A 9 ? A 8 ? 20 1 1 A A 10 1_555 A U 7 2_756 -0.080 -0.034 0.049 5.281 -15.219 -0.501 23 A_A10:U7_A A 10 ? A 7 ? 20 1 1 A G 11 1_555 A C 6 2_756 -0.435 -0.182 -0.012 -0.179 -12.924 0.384 24 A_G11:C6_A A 11 ? A 6 ? 19 1 1 A C 13 1_555 A G 4 2_756 0.135 -0.184 0.062 -3.628 -10.546 3.401 25 A_C13:G4_A A 13 ? A 4 ? 19 1 1 A U 14 1_555 A A 3 2_756 0.052 -0.133 0.204 -1.975 -7.986 1.420 26 A_U14:A3_A A 14 ? A 3 ? 20 1 1 A G 15 1_555 A C 2 2_756 -0.519 0.027 0.184 -1.169 -17.872 7.162 27 A_G15:C2_A A 15 ? A 2 ? 19 1 1 A C 16 1_555 A G 1 2_756 0.495 -0.196 0.159 2.259 -11.397 0.084 28 A_C16:G1_A A 16 ? A 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 B G 1 1_555 C C 16 1_555 B C 2 1_555 C G 15 1_555 -0.049 -1.161 3.152 0.712 1.266 38.753 -1.897 0.156 3.113 1.907 -1.072 38.779 1 BB_G1C2:G15C16_CC B 1 ? C 16 ? B 2 ? C 15 ? 1 B C 2 1_555 C G 15 1_555 B A 3 1_555 C U 14 1_555 -0.060 -1.526 3.084 0.625 8.056 31.830 -3.929 0.202 2.628 14.401 -1.117 32.813 2 BB_C2A3:U14G15_CC B 2 ? C 15 ? B 3 ? C 14 ? 1 B A 3 1_555 C U 14 1_555 B G 4 1_555 C C 13 1_555 0.321 -1.821 3.173 0.813 9.479 26.177 -5.780 -0.497 2.388 20.103 -1.724 27.824 3 BB_A3G4:C13U14_CC B 3 ? C 14 ? B 4 ? C 13 ? 1 B G 4 1_555 C C 13 1_555 B C 6 1_555 C G 11 1_555 -0.346 -2.745 6.395 -0.866 19.476 68.020 -3.657 0.243 5.539 17.056 0.758 70.434 4 BB_G4C6:G11C13_CC B 4 ? C 13 ? B 6 ? C 11 ? 1 B C 6 1_555 C G 11 1_555 B U 7 1_555 C A 10 1_555 0.210 -1.829 3.219 2.699 12.818 28.833 -5.432 0.052 2.234 24.225 -5.101 31.611 5 BB_C6U7:A10G11_CC B 6 ? C 11 ? B 7 ? C 10 ? 1 B U 7 1_555 C A 10 1_555 B U 8 1_555 C A 9 1_555 0.219 -1.583 3.255 -0.267 5.503 31.079 -3.888 -0.449 2.937 10.170 0.493 31.552 6 BB_U7U8:A9A10_CC B 7 ? C 10 ? B 8 ? C 9 ? 1 B U 8 1_555 C A 9 1_555 B A 9 1_555 C U 8 1_555 0.014 -1.446 2.983 0.053 7.464 28.940 -4.136 -0.017 2.539 14.630 -0.104 29.868 7 BB_U8A9:U8A9_CC B 8 ? C 9 ? B 9 ? C 8 ? 1 B A 9 1_555 C U 8 1_555 B A 10 1_555 C U 7 1_555 -0.206 -1.583 3.258 0.087 5.250 31.108 -3.847 0.394 2.957 9.702 -0.161 31.537 8 BB_A9A10:U7U8_CC B 9 ? C 8 ? B 10 ? C 7 ? 1 B A 10 1_555 C U 7 1_555 B G 11 1_555 C C 6 1_555 -0.216 -1.805 3.218 -2.689 12.728 28.896 -5.375 -0.040 2.253 24.028 5.076 31.633 9 BB_A10G11:C6U7_CC B 10 ? C 7 ? B 11 ? C 6 ? 1 B G 11 1_555 C C 6 1_555 B C 13 1_555 C G 4 1_555 0.325 -2.752 6.367 0.892 19.429 67.611 -3.681 -0.224 5.504 17.102 -0.785 70.032 10 BB_G11C13:G4C6_CC B 11 ? C 6 ? B 13 ? C 4 ? 1 B C 13 1_555 C G 4 1_555 B U 14 1_555 C A 3 1_555 -0.317 -1.812 3.196 -0.716 9.410 26.794 -5.619 0.499 2.439 19.552 1.489 28.378 11 BB_C13U14:A3G4_CC B 13 ? C 4 ? B 14 ? C 3 ? 1 B U 14 1_555 C A 3 1_555 B G 15 1_555 C C 2 1_555 0.095 -1.513 3.085 -0.342 8.220 31.890 -3.915 -0.219 2.624 14.658 0.609 32.908 12 BB_U14G15:C2A3_CC B 14 ? C 3 ? B 15 ? C 2 ? 1 B G 15 1_555 C C 2 1_555 B C 16 1_555 C G 1 1_555 0.056 -1.127 3.143 -0.720 1.097 39.099 -1.809 -0.166 3.110 1.638 1.076 39.120 13 BB_G15C16:G1C2_CC B 15 ? C 2 ? B 16 ? C 1 ? 1 A G 1 1_555 A C 16 2_756 A C 2 1_555 A G 15 2_756 -0.066 -1.146 3.147 0.656 1.166 39.183 -1.841 0.173 3.111 1.739 -0.978 39.205 14 AA_G1C2:G15C16_AA A 1 ? A 16 ? A 2 ? A 15 ? 1 A C 2 1_555 A G 15 2_756 A A 3 1_555 A U 14 2_756 0.047 -1.539 3.071 0.553 8.558 31.148 -4.102 0.001 2.569 15.571 -1.005 32.279 15 AA_C2A3:U14G15_AA A 2 ? A 15 ? A 3 ? A 14 ? 1 A A 3 1_555 A U 14 2_756 A G 4 1_555 A C 13 2_756 0.296 -1.826 3.182 0.594 9.398 26.713 -5.655 -0.484 2.418 19.582 -1.237 28.296 16 AA_A3G4:C13U14_AA A 3 ? A 14 ? A 4 ? A 13 ? 1 A G 4 1_555 A C 13 2_756 A C 6 1_555 A G 11 2_756 -0.376 -2.726 6.390 -0.996 19.318 67.578 -3.661 0.261 5.539 17.015 0.877 69.975 17 AA_G4C6:G11C13_AA A 4 ? A 13 ? A 6 ? A 11 ? 1 A C 6 1_555 A G 11 2_756 A U 7 1_555 A A 10 2_756 0.227 -1.840 3.243 2.525 12.893 29.361 -5.368 -0.011 2.267 23.981 -4.696 32.107 18 AA_C6U7:A10G11_AA A 6 ? A 11 ? A 7 ? A 10 ? 1 A U 7 1_555 A A 10 2_756 A U 8 1_555 A A 9 2_756 0.129 -1.610 3.236 -0.133 5.224 30.659 -3.953 -0.265 2.928 9.791 0.249 31.090 19 AA_U7U8:A9A10_AA A 7 ? A 10 ? A 8 ? A 9 ? 1 A U 8 1_555 A A 9 2_756 A A 9 1_555 A U 8 2_756 0.000 -1.447 2.995 0.000 7.634 29.640 -4.046 0.000 2.551 14.619 0.000 30.586 20 AA_U8A9:U8A9_AA A 8 ? A 9 ? A 9 ? A 8 ? 1 A A 9 1_555 A U 8 2_756 A A 10 1_555 A U 7 2_756 -0.129 -1.610 3.236 0.133 5.224 30.659 -3.953 0.265 2.928 9.791 -0.249 31.090 21 AA_A9A10:U7U8_AA A 9 ? A 8 ? A 10 ? A 7 ? 1 A A 10 1_555 A U 7 2_756 A G 11 1_555 A C 6 2_756 -0.227 -1.840 3.243 -2.525 12.893 29.361 -5.368 0.011 2.267 23.981 4.696 32.107 22 AA_A10G11:C6U7_AA A 10 ? A 7 ? A 11 ? A 6 ? 1 A G 11 1_555 A C 6 2_756 A C 13 1_555 A G 4 2_756 0.376 -2.726 6.390 0.996 19.318 67.578 -3.661 -0.261 5.539 17.015 -0.877 69.975 23 AA_G11C13:G4C6_AA A 11 ? A 6 ? A 13 ? A 4 ? 1 A C 13 1_555 A G 4 2_756 A U 14 1_555 A A 3 2_756 -0.296 -1.826 3.182 -0.594 9.398 26.713 -5.655 0.484 2.418 19.583 1.237 28.296 24 AA_C13U14:A3G4_AA A 13 ? A 4 ? A 14 ? A 3 ? 1 A U 14 1_555 A A 3 2_756 A G 15 1_555 A C 2 2_756 -0.047 -1.539 3.071 -0.553 8.558 31.148 -4.102 -0.001 2.569 15.571 1.005 32.279 25 AA_U14G15:C2A3_AA A 14 ? A 3 ? A 15 ? A 2 ? 1 A G 15 1_555 A C 2 2_756 A C 16 1_555 A G 1 2_756 0.066 -1.146 3.147 -0.656 1.166 39.183 -1.841 -0.173 3.111 1.739 0.978 39.205 26 AA_G15C16:G1C2_AA A 15 ? A 2 ? A 16 ? A 1 ? # _atom_sites.entry_id 4NFP _atom_sites.fract_transf_matrix[1][1] 0.013369 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.007977 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.023154 _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] 0.023867 _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_