data_248D # _entry.id 248D # _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 248D pdb_0000248d 10.2210/pdb248d/pdb RCSB UHK046 ? ? WWPDB D_1000177647 ? ? # 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 1996-03-08 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2011-11-16 5 'Structure model' 1 4 2024-02-14 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Atomic model' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 5 'Structure model' chem_comp_atom 2 5 'Structure model' chem_comp_bond 3 5 'Structure model' database_2 4 5 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 248D _pdbx_database_status.recvd_initial_deposition_date 1996-02-02 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Portmann, S.' 1 'Grimm, S.' 2 'Workman, C.' 3 'Usman, N.' 4 'Egli, M.' 5 # _citation.id primary _citation.title 'Crystal structures of an A-form duplex with single-adenosine bulges and a conformational basis for site-specific RNA self-cleavage.' _citation.journal_abbrev Chem.Biol. _citation.journal_volume 3 _citation.page_first 173 _citation.page_last 184 _citation.year 1996 _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 8807843 _citation.pdbx_database_id_DOI '10.1016/S1074-5521(96)90260-4' # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Portmann, S.' 1 ? primary 'Grimm, S.' 2 ? primary 'Workman, C.' 3 ? primary 'Usman, N.' 4 ? primary 'Egli, M.' 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 ;DNA/RNA (5'-R(*GP*CP*GP*)-D(*AP*TP*AP*TP*AP*)-R(*CP*GP*C)-3'), ORTHORHOMBIC ; 3454.211 1 ? ? ? ? 2 non-polymer syn SPERMINE 202.340 2 ? ? ? ? 3 water nat water 18.015 38 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polydeoxyribonucleotide/polyribonucleotide hybrid' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code 'GCG(DA)(DT)(DA)(DT)(DA)CGC' _entity_poly.pdbx_seq_one_letter_code_can GCGATATACGC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 SPERMINE SPM 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 DA n 1 5 DT n 1 6 DA n 1 7 DT n 1 8 DA n 1 9 C n 1 10 G n 1 11 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 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 SPM non-polymer . SPERMINE ? 'C10 H26 N4' 202.340 # 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 G 3 3 3 G G A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 DT 5 5 5 DT T A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DA 8 8 8 DA A A . n A 1 9 C 9 9 9 C C A . n A 1 10 G 10 10 10 G G A . n A 1 11 C 11 11 11 C C A . 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 B 2 SPM 1 12 12 SPM SPM A . C 2 SPM 1 13 13 SPM SPM A . D 3 HOH 1 14 14 HOH HOH A . D 3 HOH 2 15 15 HOH HOH A . D 3 HOH 3 16 16 HOH HOH A . D 3 HOH 4 17 17 HOH HOH A . D 3 HOH 5 18 18 HOH HOH A . D 3 HOH 6 19 19 HOH HOH A . D 3 HOH 7 20 20 HOH HOH A . D 3 HOH 8 21 21 HOH HOH A . D 3 HOH 9 22 22 HOH HOH A . D 3 HOH 10 23 23 HOH HOH A . D 3 HOH 11 24 24 HOH HOH A . D 3 HOH 12 25 25 HOH HOH A . D 3 HOH 13 26 26 HOH HOH A . D 3 HOH 14 27 27 HOH HOH A . D 3 HOH 15 28 28 HOH HOH A . D 3 HOH 16 29 29 HOH HOH A . D 3 HOH 17 30 30 HOH HOH A . D 3 HOH 18 31 31 HOH HOH A . D 3 HOH 19 32 32 HOH HOH A . D 3 HOH 20 33 33 HOH HOH A . D 3 HOH 21 34 34 HOH HOH A . D 3 HOH 22 35 35 HOH HOH A . D 3 HOH 23 36 36 HOH HOH A . D 3 HOH 24 37 37 HOH HOH A . D 3 HOH 25 38 38 HOH HOH A . D 3 HOH 26 39 39 HOH HOH A . D 3 HOH 27 40 40 HOH HOH A . D 3 HOH 28 41 41 HOH HOH A . D 3 HOH 29 42 42 HOH HOH A . D 3 HOH 30 43 43 HOH HOH A . D 3 HOH 31 44 44 HOH HOH A . D 3 HOH 32 45 45 HOH HOH A . D 3 HOH 33 46 46 HOH HOH A . D 3 HOH 34 47 47 HOH HOH A . D 3 HOH 35 48 48 HOH HOH A . D 3 HOH 36 49 49 HOH HOH A . D 3 HOH 37 50 50 HOH HOH A . D 3 HOH 38 51 51 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR refinement . ? 1 R-AXIS 'data reduction' . ? 2 # _cell.entry_id 248D _cell.length_a 25.890 _cell.length_b 33.970 _cell.length_c 57.560 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 248D _symmetry.space_group_name_H-M 'C 2 2 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 # _exptl.entry_id 248D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.83 _exptl_crystal.density_percent_sol 32.86 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.40 _exptl_crystal_grow.pdbx_details 'pH 7.40, VAPOR DIFFUSION' _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 WATER ? ? ? 1 2 1 'NA CACODYLATE' ? ? ? 1 3 1 SPERMINE ? ? ? 1 4 1 MGCL2 ? ? ? 1 5 2 WATER ? ? ? 1 6 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details 'ROOM TEMPERATURE' _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS II' _diffrn_detector.pdbx_collection_date 1995-11-09 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ? _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source ? _diffrn_source.type ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 248D _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 28.780 _reflns.d_resolution_high 1.800 _reflns.number_obs 2264 _reflns.number_all 9641 _reflns.percent_possible_obs 94.000 _reflns.pdbx_Rmerge_I_obs 0.0810000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 248D _refine.ls_number_reflns_obs 2170 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.000 _refine.ls_d_res_high 1.830 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1590000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1590000 _refine.ls_R_factor_R_free 0.2360000 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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.pdbx_overall_phase_error ? _refine.overall_SU_R_Cruickshank_DPI ? _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 229 _refine_hist.pdbx_number_atoms_ligand 28 _refine_hist.number_atoms_solvent 38 _refine_hist.number_atoms_total 295 _refine_hist.d_res_high 1.830 _refine_hist.d_res_low 10.000 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function x_bond_d 0.013 ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg 3.28 ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 248D _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 248D _struct.title 'CRYSTAL STRUCTURES OF AN A-FORM DUPLEX WITH SINGLE-ADENOSINE BULGES AND A CONFORMATIONAL BASIS FOR SITE SPECIFIC RNA SELF-CLEAVAGE' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 248D _struct_keywords.pdbx_keywords DNA/RNA _struct_keywords.text 'A-DNA/RNA, DOUBLE HELIX, BULGES, DNA-RNA complex' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 2 ? D N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 248D _struct_ref.pdbx_db_accession 248D _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 248D _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 11 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 248D _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 11 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 11 # _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 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # 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' 4_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 # _struct_biol.id 1 # 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 A C 11 N3 ? ? A G 1 A C 11 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 11 O2 ? ? A G 1 A C 11 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 11 N4 ? ? A G 1 A C 11 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 A G 10 N1 ? ? A C 2 A G 10 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 A G 10 O6 ? ? A C 2 A G 10 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 A G 10 N2 ? ? A C 2 A G 10 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 A C 9 N3 ? ? A G 3 A C 9 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 A C 9 O2 ? ? A G 3 A C 9 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 A C 9 N4 ? ? A G 3 A C 9 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N1 ? ? ? 1_555 A DT 7 N3 ? ? A DA 4 A DT 7 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 4 N6 ? ? ? 1_555 A DT 7 O4 ? ? A DA 4 A DT 7 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 5 N3 ? ? ? 1_555 A DA 6 N1 ? ? A DT 5 A DA 6 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 5 O4 ? ? ? 1_555 A DA 6 N6 ? ? A DT 5 A DA 6 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 6 N1 ? ? ? 1_555 A DT 5 N3 ? ? A DA 6 A DT 5 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N6 ? ? ? 1_555 A DT 5 O4 ? ? A DA 6 A DT 5 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 7 N3 ? ? ? 1_555 A DA 4 N1 ? ? A DT 7 A DA 4 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 7 O4 ? ? ? 1_555 A DA 4 N6 ? ? A DT 7 A DA 4 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A C 9 N3 ? ? ? 1_555 A G 3 N1 ? ? A C 9 A G 3 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A C 9 N4 ? ? ? 1_555 A G 3 O6 ? ? A C 9 A G 3 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 3 N2 ? ? A C 9 A G 3 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 2 N3 ? ? A G 10 A C 2 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A G 10 N2 ? ? ? 1_555 A C 2 O2 ? ? A G 10 A C 2 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A G 10 O6 ? ? ? 1_555 A C 2 N4 ? ? A G 10 A C 2 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 11 N3 ? ? ? 1_555 A G 1 N1 ? ? A C 11 A G 1 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 11 N4 ? ? ? 1_555 A G 1 O6 ? ? A C 11 A G 1 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A C 11 O2 ? ? ? 1_555 A G 1 N2 ? ? A C 11 A G 1 4_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A SPM 12 ? 9 'BINDING SITE FOR RESIDUE SPM A 12' AC2 Software A SPM 13 ? 10 'BINDING SITE FOR RESIDUE SPM A 13' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 9 G A 1 ? G A 1 . ? 8_455 ? 2 AC1 9 G A 1 ? G A 1 . ? 6_554 ? 3 AC1 9 DA A 8 ? DA A 8 . ? 1_555 ? 4 AC1 9 C A 9 ? C A 9 . ? 5_455 ? 5 AC1 9 C A 9 ? C A 9 . ? 1_555 ? 6 AC1 9 G A 10 ? G A 10 . ? 5_455 ? 7 AC1 9 G A 10 ? G A 10 . ? 1_555 ? 8 AC1 9 G A 10 ? G A 10 . ? 3_554 ? 9 AC1 9 C A 11 ? C A 11 . ? 3_554 ? 10 AC2 10 C A 2 ? C A 2 . ? 4_455 ? 11 AC2 10 G A 3 ? G A 3 . ? 4_455 ? 12 AC2 10 G A 3 ? G A 3 . ? 8_455 ? 13 AC2 10 DT A 5 ? DT A 5 . ? 5_455 ? 14 AC2 10 DA A 6 ? DA A 6 . ? 5_455 ? 15 AC2 10 DT A 7 ? DT A 7 . ? 5_455 ? 16 AC2 10 DA A 8 ? DA A 8 . ? 1_555 ? 17 AC2 10 HOH D . ? HOH A 18 . ? 1_555 ? 18 AC2 10 HOH D . ? HOH A 28 . ? 1_555 ? 19 AC2 10 HOH D . ? HOH A 31 . ? 5_455 ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 111.75 108.30 3.45 0.30 N 2 1 "C4'" A DT 5 ? ? "C3'" A DT 5 ? ? "C2'" A DT 5 ? ? 96.41 102.20 -5.79 0.70 N 3 1 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 114.00 108.30 5.70 0.30 N 4 1 N3 A DT 5 ? ? C2 A DT 5 ? ? O2 A DT 5 ? ? 118.60 122.30 -3.70 0.60 N 5 1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 112.52 108.30 4.22 0.30 N 6 1 "C5'" A DT 7 ? ? "C4'" A DT 7 ? ? "O4'" A DT 7 ? ? 117.94 109.80 8.14 1.10 N 7 1 N3 A DT 7 ? ? C2 A DT 7 ? ? O2 A DT 7 ? ? 118.53 122.30 -3.77 0.60 N 8 1 "O5'" A DA 8 ? ? "C5'" A DA 8 ? ? "C4'" A DA 8 ? ? 104.47 109.40 -4.93 0.80 N 9 1 "O4'" A DA 8 ? ? "C1'" A DA 8 ? ? N9 A DA 8 ? ? 112.75 108.30 4.45 0.30 N 10 1 N1 A C 9 ? ? C2 A C 9 ? ? O2 A C 9 ? ? 123.28 118.90 4.38 0.60 N # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 14 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id D _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # loop_ _refine_B_iso.class _refine_B_iso.details _refine_B_iso.treatment _refine_B_iso.pdbx_refine_id 'ALL ATOMS' TR isotropic 'X-RAY DIFFRACTION' 'ALL WATERS' TR isotropic 'X-RAY DIFFRACTION' # loop_ _refine_occupancy.class _refine_occupancy.treatment _refine_occupancy.pdbx_refine_id 'ALL ATOMS' fix 'X-RAY DIFFRACTION' 'ALL WATERS' fix 'X-RAY DIFFRACTION' # 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 C OP3 O N N 1 C P P N N 2 C OP1 O N N 3 C OP2 O N N 4 C "O5'" O N N 5 C "C5'" C N N 6 C "C4'" C N R 7 C "O4'" O N N 8 C "C3'" C N S 9 C "O3'" O N N 10 C "C2'" C N R 11 C "O2'" O N N 12 C "C1'" C N R 13 C N1 N N N 14 C C2 C N N 15 C O2 O N N 16 C N3 N N N 17 C C4 C N N 18 C N4 N N N 19 C C5 C N N 20 C C6 C N N 21 C HOP3 H N N 22 C HOP2 H N N 23 C "H5'" H N N 24 C "H5''" H N N 25 C "H4'" H N N 26 C "H3'" H N N 27 C "HO3'" H N N 28 C "H2'" H N N 29 C "HO2'" H N N 30 C "H1'" H N N 31 C H41 H N N 32 C H42 H N N 33 C H5 H N N 34 C H6 H N N 35 DA OP3 O N N 36 DA P P N N 37 DA OP1 O N N 38 DA OP2 O N N 39 DA "O5'" O N N 40 DA "C5'" C N N 41 DA "C4'" C N R 42 DA "O4'" O N N 43 DA "C3'" C N S 44 DA "O3'" O N N 45 DA "C2'" C N N 46 DA "C1'" C N R 47 DA N9 N Y N 48 DA C8 C Y N 49 DA N7 N Y N 50 DA C5 C Y N 51 DA C6 C Y N 52 DA N6 N N N 53 DA N1 N Y N 54 DA C2 C Y N 55 DA N3 N Y N 56 DA C4 C Y N 57 DA HOP3 H N N 58 DA HOP2 H N N 59 DA "H5'" H N N 60 DA "H5''" H N N 61 DA "H4'" H N N 62 DA "H3'" H N N 63 DA "HO3'" H N N 64 DA "H2'" H N N 65 DA "H2''" H N N 66 DA "H1'" H N N 67 DA H8 H N N 68 DA H61 H N N 69 DA H62 H N N 70 DA H2 H N N 71 DT OP3 O N N 72 DT P P N N 73 DT OP1 O N N 74 DT OP2 O N N 75 DT "O5'" O N N 76 DT "C5'" C N N 77 DT "C4'" C N R 78 DT "O4'" O N N 79 DT "C3'" C N S 80 DT "O3'" O N N 81 DT "C2'" C N N 82 DT "C1'" C N R 83 DT N1 N N N 84 DT C2 C N N 85 DT O2 O N N 86 DT N3 N N N 87 DT C4 C N N 88 DT O4 O N N 89 DT C5 C N N 90 DT C7 C N N 91 DT C6 C N N 92 DT HOP3 H N N 93 DT HOP2 H N N 94 DT "H5'" H N N 95 DT "H5''" H N N 96 DT "H4'" H N N 97 DT "H3'" H N N 98 DT "HO3'" H N N 99 DT "H2'" H N N 100 DT "H2''" H N N 101 DT "H1'" H N N 102 DT H3 H N N 103 DT H71 H N N 104 DT H72 H N N 105 DT H73 H N N 106 DT H6 H N N 107 G OP3 O N N 108 G P P N N 109 G OP1 O N N 110 G OP2 O N N 111 G "O5'" O N N 112 G "C5'" C N N 113 G "C4'" C N R 114 G "O4'" O N N 115 G "C3'" C N S 116 G "O3'" O N N 117 G "C2'" C N R 118 G "O2'" O N N 119 G "C1'" C N R 120 G N9 N Y N 121 G C8 C Y N 122 G N7 N Y N 123 G C5 C Y N 124 G C6 C N N 125 G O6 O N N 126 G N1 N N N 127 G C2 C N N 128 G N2 N N N 129 G N3 N N N 130 G C4 C Y N 131 G HOP3 H N N 132 G HOP2 H N N 133 G "H5'" H N N 134 G "H5''" H N N 135 G "H4'" H N N 136 G "H3'" H N N 137 G "HO3'" H N N 138 G "H2'" H N N 139 G "HO2'" H N N 140 G "H1'" H N N 141 G H8 H N N 142 G H1 H N N 143 G H21 H N N 144 G H22 H N N 145 HOH O O N N 146 HOH H1 H N N 147 HOH H2 H N N 148 SPM N1 N N N 149 SPM C2 C N N 150 SPM C3 C N N 151 SPM C4 C N N 152 SPM N5 N N N 153 SPM C6 C N N 154 SPM C7 C N N 155 SPM C8 C N N 156 SPM C9 C N N 157 SPM N10 N N N 158 SPM C11 C N N 159 SPM C12 C N N 160 SPM C13 C N N 161 SPM N14 N N N 162 SPM HN11 H N N 163 SPM HN12 H N N 164 SPM H21 H N N 165 SPM H22 H N N 166 SPM H31 H N N 167 SPM H32 H N N 168 SPM H41 H N N 169 SPM H42 H N N 170 SPM HN5 H N N 171 SPM H61 H N N 172 SPM H62 H N N 173 SPM H71 H N N 174 SPM H72 H N N 175 SPM H81 H N N 176 SPM H82 H N N 177 SPM H91 H N N 178 SPM H92 H N N 179 SPM HN0 H N N 180 SPM H111 H N N 181 SPM H112 H N N 182 SPM H121 H N N 183 SPM H122 H N N 184 SPM H131 H N N 185 SPM H132 H N N 186 SPM HN41 H N N 187 SPM HN42 H N N 188 # 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 C OP3 P sing N N 1 C OP3 HOP3 sing N N 2 C P OP1 doub N N 3 C P OP2 sing N N 4 C P "O5'" sing N N 5 C OP2 HOP2 sing N N 6 C "O5'" "C5'" sing N N 7 C "C5'" "C4'" sing N N 8 C "C5'" "H5'" sing N N 9 C "C5'" "H5''" sing N N 10 C "C4'" "O4'" sing N N 11 C "C4'" "C3'" sing N N 12 C "C4'" "H4'" sing N N 13 C "O4'" "C1'" sing N N 14 C "C3'" "O3'" sing N N 15 C "C3'" "C2'" sing N N 16 C "C3'" "H3'" sing N N 17 C "O3'" "HO3'" sing N N 18 C "C2'" "O2'" sing N N 19 C "C2'" "C1'" sing N N 20 C "C2'" "H2'" sing N N 21 C "O2'" "HO2'" sing N N 22 C "C1'" N1 sing N N 23 C "C1'" "H1'" sing N N 24 C N1 C2 sing N N 25 C N1 C6 sing N N 26 C C2 O2 doub N N 27 C C2 N3 sing N N 28 C N3 C4 doub N N 29 C C4 N4 sing N N 30 C C4 C5 sing N N 31 C N4 H41 sing N N 32 C N4 H42 sing N N 33 C C5 C6 doub N N 34 C C5 H5 sing N N 35 C C6 H6 sing N N 36 DA OP3 P sing N N 37 DA OP3 HOP3 sing N N 38 DA P OP1 doub N N 39 DA P OP2 sing N N 40 DA P "O5'" sing N N 41 DA OP2 HOP2 sing N N 42 DA "O5'" "C5'" sing N N 43 DA "C5'" "C4'" sing N N 44 DA "C5'" "H5'" sing N N 45 DA "C5'" "H5''" sing N N 46 DA "C4'" "O4'" sing N N 47 DA "C4'" "C3'" sing N N 48 DA "C4'" "H4'" sing N N 49 DA "O4'" "C1'" sing N N 50 DA "C3'" "O3'" sing N N 51 DA "C3'" "C2'" sing N N 52 DA "C3'" "H3'" sing N N 53 DA "O3'" "HO3'" sing N N 54 DA "C2'" "C1'" sing N N 55 DA "C2'" "H2'" sing N N 56 DA "C2'" "H2''" sing N N 57 DA "C1'" N9 sing N N 58 DA "C1'" "H1'" sing N N 59 DA N9 C8 sing Y N 60 DA N9 C4 sing Y N 61 DA C8 N7 doub Y N 62 DA C8 H8 sing N N 63 DA N7 C5 sing Y N 64 DA C5 C6 sing Y N 65 DA C5 C4 doub Y N 66 DA C6 N6 sing N N 67 DA C6 N1 doub Y N 68 DA N6 H61 sing N N 69 DA N6 H62 sing N N 70 DA N1 C2 sing Y N 71 DA C2 N3 doub Y N 72 DA C2 H2 sing N N 73 DA N3 C4 sing Y N 74 DT OP3 P sing N N 75 DT OP3 HOP3 sing N N 76 DT P OP1 doub N N 77 DT P OP2 sing N N 78 DT P "O5'" sing N N 79 DT OP2 HOP2 sing N N 80 DT "O5'" "C5'" sing N N 81 DT "C5'" "C4'" sing N N 82 DT "C5'" "H5'" sing N N 83 DT "C5'" "H5''" sing N N 84 DT "C4'" "O4'" sing N N 85 DT "C4'" "C3'" sing N N 86 DT "C4'" "H4'" sing N N 87 DT "O4'" "C1'" sing N N 88 DT "C3'" "O3'" sing N N 89 DT "C3'" "C2'" sing N N 90 DT "C3'" "H3'" sing N N 91 DT "O3'" "HO3'" sing N N 92 DT "C2'" "C1'" sing N N 93 DT "C2'" "H2'" sing N N 94 DT "C2'" "H2''" sing N N 95 DT "C1'" N1 sing N N 96 DT "C1'" "H1'" sing N N 97 DT N1 C2 sing N N 98 DT N1 C6 sing N N 99 DT C2 O2 doub N N 100 DT C2 N3 sing N N 101 DT N3 C4 sing N N 102 DT N3 H3 sing N N 103 DT C4 O4 doub N N 104 DT C4 C5 sing N N 105 DT C5 C7 sing N N 106 DT C5 C6 doub N N 107 DT C7 H71 sing N N 108 DT C7 H72 sing N N 109 DT C7 H73 sing N N 110 DT C6 H6 sing N N 111 G OP3 P sing N N 112 G OP3 HOP3 sing N N 113 G P OP1 doub N N 114 G P OP2 sing N N 115 G P "O5'" sing N N 116 G OP2 HOP2 sing N N 117 G "O5'" "C5'" sing N N 118 G "C5'" "C4'" sing N N 119 G "C5'" "H5'" sing N N 120 G "C5'" "H5''" sing N N 121 G "C4'" "O4'" sing N N 122 G "C4'" "C3'" sing N N 123 G "C4'" "H4'" sing N N 124 G "O4'" "C1'" sing N N 125 G "C3'" "O3'" sing N N 126 G "C3'" "C2'" sing N N 127 G "C3'" "H3'" sing N N 128 G "O3'" "HO3'" sing N N 129 G "C2'" "O2'" sing N N 130 G "C2'" "C1'" sing N N 131 G "C2'" "H2'" sing N N 132 G "O2'" "HO2'" sing N N 133 G "C1'" N9 sing N N 134 G "C1'" "H1'" sing N N 135 G N9 C8 sing Y N 136 G N9 C4 sing Y N 137 G C8 N7 doub Y N 138 G C8 H8 sing N N 139 G N7 C5 sing Y N 140 G C5 C6 sing N N 141 G C5 C4 doub Y N 142 G C6 O6 doub N N 143 G C6 N1 sing N N 144 G N1 C2 sing N N 145 G N1 H1 sing N N 146 G C2 N2 sing N N 147 G C2 N3 doub N N 148 G N2 H21 sing N N 149 G N2 H22 sing N N 150 G N3 C4 sing N N 151 HOH O H1 sing N N 152 HOH O H2 sing N N 153 SPM N1 C2 sing N N 154 SPM N1 HN11 sing N N 155 SPM N1 HN12 sing N N 156 SPM C2 C3 sing N N 157 SPM C2 H21 sing N N 158 SPM C2 H22 sing N N 159 SPM C3 C4 sing N N 160 SPM C3 H31 sing N N 161 SPM C3 H32 sing N N 162 SPM C4 N5 sing N N 163 SPM C4 H41 sing N N 164 SPM C4 H42 sing N N 165 SPM N5 C6 sing N N 166 SPM N5 HN5 sing N N 167 SPM C6 C7 sing N N 168 SPM C6 H61 sing N N 169 SPM C6 H62 sing N N 170 SPM C7 C8 sing N N 171 SPM C7 H71 sing N N 172 SPM C7 H72 sing N N 173 SPM C8 C9 sing N N 174 SPM C8 H81 sing N N 175 SPM C8 H82 sing N N 176 SPM C9 N10 sing N N 177 SPM C9 H91 sing N N 178 SPM C9 H92 sing N N 179 SPM N10 C11 sing N N 180 SPM N10 HN0 sing N N 181 SPM C11 C12 sing N N 182 SPM C11 H111 sing N N 183 SPM C11 H112 sing N N 184 SPM C12 C13 sing N N 185 SPM C12 H121 sing N N 186 SPM C12 H122 sing N N 187 SPM C13 N14 sing N N 188 SPM C13 H131 sing N N 189 SPM C13 H132 sing N N 190 SPM N14 HN41 sing N N 191 SPM N14 HN42 sing N N 192 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 248D 'a-form double helix' 248D 'bulge 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 A C 11 4_555 -0.392 -0.215 0.152 3.844 -7.092 -2.742 1 A_G1:C11_A A 1 ? A 11 ? 19 1 1 A C 2 1_555 A G 10 4_555 0.300 -0.175 0.132 7.888 -14.138 0.424 2 A_C2:G10_A A 2 ? A 10 ? 19 1 1 A G 3 1_555 A C 9 4_555 -0.392 -0.203 -0.001 -5.512 -18.339 1.986 3 A_G3:C9_A A 3 ? A 9 ? 19 1 1 A DA 4 1_555 A DT 7 4_555 0.042 -0.179 -0.059 -7.576 -15.830 -5.096 4 A_DA4:DT7_A A 4 ? A 7 ? 20 1 1 A DT 5 1_555 A DA 6 4_555 0.002 -0.228 0.217 -0.661 -16.553 4.392 5 A_DT5:DA6_A A 5 ? A 6 ? 20 1 1 A DA 6 1_555 A DT 5 4_555 -0.002 -0.228 0.217 0.661 -16.553 4.392 6 A_DA6:DT5_A A 6 ? A 5 ? 20 1 1 A DT 7 1_555 A DA 4 4_555 -0.042 -0.179 -0.059 7.576 -15.830 -5.096 7 A_DT7:DA4_A A 7 ? A 4 ? 20 1 1 A C 9 1_555 A G 3 4_555 0.392 -0.203 -0.001 5.512 -18.339 1.986 8 A_C9:G3_A A 9 ? A 3 ? 19 1 1 A G 10 1_555 A C 2 4_555 -0.300 -0.175 0.132 -7.888 -14.138 0.424 9 A_G10:C2_A A 10 ? A 2 ? 19 1 1 A C 11 1_555 A G 1 4_555 0.392 -0.215 0.152 -3.844 -7.092 -2.742 10 A_C11:G1_A A 11 ? 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 A G 1 1_555 A C 11 4_555 A C 2 1_555 A G 10 4_555 0.288 -1.163 3.328 -1.420 0.101 37.196 -1.835 -0.642 3.312 0.159 2.225 37.222 1 AA_G1C2:G10C11_AA A 1 ? A 11 ? A 2 ? A 10 ? 1 A C 2 1_555 A G 10 4_555 A G 3 1_555 A C 9 4_555 0.396 -1.854 3.431 3.095 14.656 31.603 -5.175 -0.221 2.392 25.214 -5.325 34.891 2 AA_C2G3:C9G10_AA A 2 ? A 10 ? A 3 ? A 9 ? 1 A G 3 1_555 A C 9 4_555 A DA 4 1_555 A DT 7 4_555 -0.768 -0.566 3.426 0.070 -2.437 35.053 -0.555 1.284 3.455 -4.041 -0.116 35.135 3 AA_G3DA4:DT7C9_AA A 3 ? A 9 ? A 4 ? A 7 ? 1 A DA 4 1_555 A DT 7 4_555 A DT 5 1_555 A DA 6 4_555 1.232 -0.924 3.095 -1.141 9.468 32.717 -2.939 -2.268 2.687 16.379 1.973 34.042 4 AA_DA4DT5:DA6DT7_AA A 4 ? A 7 ? A 5 ? A 6 ? 1 A DT 5 1_555 A DA 6 4_555 A DA 6 1_555 A DT 5 4_555 0.000 -1.390 3.195 0.000 10.939 29.524 -4.417 0.000 2.532 20.596 0.000 31.443 5 AA_DT5DA6:DT5DA6_AA A 5 ? A 6 ? A 6 ? A 5 ? 1 A DA 6 1_555 A DT 5 4_555 A DT 7 1_555 A DA 4 4_555 -1.232 -0.924 3.095 1.141 9.468 32.717 -2.939 2.268 2.687 16.379 -1.973 34.042 6 AA_DA6DT7:DA4DT5_AA A 6 ? A 5 ? A 7 ? A 4 ? 1 A DT 7 1_555 A DA 4 4_555 A C 9 1_555 A G 3 4_555 0.768 -0.566 3.426 -0.070 -2.438 35.053 -0.555 -1.284 3.455 -4.041 0.116 35.135 7 AA_DT7C9:G3DA4_AA A 7 ? A 4 ? A 9 ? A 3 ? 1 A C 9 1_555 A G 3 4_555 A G 10 1_555 A C 2 4_555 -0.396 -1.854 3.431 -3.095 14.656 31.603 -5.175 0.221 2.392 25.214 5.325 34.891 8 AA_C9G10:C2G3_AA A 9 ? A 3 ? A 10 ? A 2 ? 1 A G 10 1_555 A C 2 4_555 A C 11 1_555 A G 1 4_555 -0.288 -1.163 3.328 1.420 0.101 37.196 -1.835 0.642 3.312 0.159 -2.225 37.222 9 AA_G10C11:G1C2_AA A 10 ? A 2 ? A 11 ? A 1 ? # _atom_sites.entry_id 248D _atom_sites.fract_transf_matrix[1][1] 0.038625 _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] 0.029438 _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] 0.017373 _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_