data_410D # _entry.id 410D # _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 410D pdb_0000410d 10.2210/pdb410d/pdb RCSB AH0002 ? ? WWPDB D_1000179210 ? ? # 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 1998-07-17 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' struct_conn 5 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 410D _pdbx_database_status.recvd_initial_deposition_date 1998-06-30 _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 'Tereshko, V.' 1 'Portmann, S.' 2 'Tay, E.C.' 3 'Martin, P.' 4 'Natt, F.' 5 'Altmann, K.H.' 6 'Egli, M.' 7 # _citation.id primary _citation.title ;Correlating structure and stability of DNA duplexes with incorporated 2'-O-modified RNA analogues. ; _citation.journal_abbrev Biochemistry _citation.journal_volume 37 _citation.page_first 10626 _citation.page_last 10634 _citation.year 1998 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9692952 _citation.pdbx_database_id_DOI 10.1021/bi980392a # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Tereshko, V.' 1 ? primary 'Portmann, S.' 2 ? primary 'Tay, E.C.' 3 ? primary 'Martin, P.' 4 ? primary 'Natt, F.' 5 ? primary 'Altmann, K.H.' 6 ? primary 'Egli, M.' 7 ? # 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 man ;DNA (5'-D(*GP*CP*GP*TP*AP*(T38)P*AP*CP*GP*C)-3') ; 3119.084 2 ? ? ? ? 2 non-polymer syn SPERMINE 202.340 1 ? ? ? ? 3 water nat water 18.015 140 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DG)(DC)(DG)(DT)(DA)(T38)(DA)(DC)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCGTATACGC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 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 DG n 1 2 DC n 1 3 DG n 1 4 DT n 1 5 DA n 1 6 T38 n 1 7 DA n 1 8 DC n 1 9 DG n 1 10 DC 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 SPM non-polymer . SPERMINE ? 'C10 H26 N4' 202.340 T38 'RNA linking' n ;2'-O-ETHOXYMETHYLENE THYMIDINE 5'-MONOPHOSPHATE ; ? 'C13 H21 N2 O10 P' 396.287 # 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 DG 1 1 1 DG G A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 T38 6 6 6 T38 +T A . n A 1 7 DA 7 7 7 DA A A . n A 1 8 DC 8 8 8 DC C A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DC 10 10 10 DC C A . n B 1 1 DG 1 11 11 DG G B . n B 1 2 DC 2 12 12 DC C B . n B 1 3 DG 3 13 13 DG G B . n B 1 4 DT 4 14 14 DT T B . n B 1 5 DA 5 15 15 DA A B . n B 1 6 T38 6 16 16 T38 +T B . n B 1 7 DA 7 17 17 DA A B . n B 1 8 DC 8 18 18 DC C B . n B 1 9 DG 9 19 19 DG G B . n B 1 10 DC 10 20 20 DC C B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 SPM 1 21 21 SPM SPM B . D 3 HOH 1 101 101 HOH HOH A . D 3 HOH 2 102 102 HOH HOH A . D 3 HOH 3 103 103 HOH HOH A . D 3 HOH 4 104 104 HOH HOH A . D 3 HOH 5 106 106 HOH HOH A . D 3 HOH 6 108 108 HOH HOH A . D 3 HOH 7 109 109 HOH HOH A . D 3 HOH 8 111 111 HOH HOH A . D 3 HOH 9 113 113 HOH HOH A . D 3 HOH 10 117 117 HOH HOH A . D 3 HOH 11 118 118 HOH HOH A . D 3 HOH 12 120 120 HOH HOH A . D 3 HOH 13 123 123 HOH HOH A . D 3 HOH 14 125 125 HOH HOH A . D 3 HOH 15 126 126 HOH HOH A . D 3 HOH 16 130 130 HOH HOH A . D 3 HOH 17 131 131 HOH HOH A . D 3 HOH 18 132 132 HOH HOH A . D 3 HOH 19 135 135 HOH HOH A . D 3 HOH 20 136 136 HOH HOH A . D 3 HOH 21 137 137 HOH HOH A . D 3 HOH 22 138 138 HOH HOH A . D 3 HOH 23 141 141 HOH HOH A . D 3 HOH 24 142 142 HOH HOH A . D 3 HOH 25 143 143 HOH HOH A . D 3 HOH 26 145 145 HOH HOH A . D 3 HOH 27 147 147 HOH HOH A . D 3 HOH 28 149 149 HOH HOH A . D 3 HOH 29 152 152 HOH HOH A . D 3 HOH 30 153 153 HOH HOH A . D 3 HOH 31 155 155 HOH HOH A . D 3 HOH 32 156 156 HOH HOH A . D 3 HOH 33 157 157 HOH HOH A . D 3 HOH 34 158 158 HOH HOH A . D 3 HOH 35 160 160 HOH HOH A . D 3 HOH 36 161 161 HOH HOH A . D 3 HOH 37 162 162 HOH HOH A . D 3 HOH 38 163 163 HOH HOH A . D 3 HOH 39 165 165 HOH HOH A . D 3 HOH 40 169 169 HOH HOH A . D 3 HOH 41 173 173 HOH HOH A . D 3 HOH 42 178 178 HOH HOH A . D 3 HOH 43 179 179 HOH HOH A . D 3 HOH 44 182 182 HOH HOH A . D 3 HOH 45 184 184 HOH HOH A . D 3 HOH 46 186 186 HOH HOH A . D 3 HOH 47 188 188 HOH HOH A . D 3 HOH 48 190 190 HOH HOH A . D 3 HOH 49 192 192 HOH HOH A . D 3 HOH 50 193 193 HOH HOH A . D 3 HOH 51 197 197 HOH HOH A . D 3 HOH 52 201 201 HOH HOH A . D 3 HOH 53 204 204 HOH HOH A . D 3 HOH 54 205 205 HOH HOH A . D 3 HOH 55 206 206 HOH HOH A . D 3 HOH 56 207 207 HOH HOH A . D 3 HOH 57 209 209 HOH HOH A . D 3 HOH 58 210 210 HOH HOH A . D 3 HOH 59 212 212 HOH HOH A . D 3 HOH 60 214 214 HOH HOH A . D 3 HOH 61 215 215 HOH HOH A . D 3 HOH 62 216 216 HOH HOH A . D 3 HOH 63 218 218 HOH HOH A . D 3 HOH 64 220 220 HOH HOH A . D 3 HOH 65 221 221 HOH HOH A . D 3 HOH 66 222 222 HOH HOH A . D 3 HOH 67 224 224 HOH HOH A . D 3 HOH 68 226 226 HOH HOH A . D 3 HOH 69 229 229 HOH HOH A . D 3 HOH 70 232 232 HOH HOH A . D 3 HOH 71 235 235 HOH HOH A . D 3 HOH 72 236 236 HOH HOH A . E 3 HOH 1 105 105 HOH HOH B . E 3 HOH 2 107 107 HOH HOH B . E 3 HOH 3 110 110 HOH HOH B . E 3 HOH 4 112 112 HOH HOH B . E 3 HOH 5 114 114 HOH HOH B . E 3 HOH 6 115 115 HOH HOH B . E 3 HOH 7 116 116 HOH HOH B . E 3 HOH 8 119 119 HOH HOH B . E 3 HOH 9 121 121 HOH HOH B . E 3 HOH 10 122 122 HOH HOH B . E 3 HOH 11 124 124 HOH HOH B . E 3 HOH 12 127 127 HOH HOH B . E 3 HOH 13 128 128 HOH HOH B . E 3 HOH 14 129 129 HOH HOH B . E 3 HOH 15 133 133 HOH HOH B . E 3 HOH 16 134 134 HOH HOH B . E 3 HOH 17 139 139 HOH HOH B . E 3 HOH 18 140 140 HOH HOH B . E 3 HOH 19 144 144 HOH HOH B . E 3 HOH 20 146 146 HOH HOH B . E 3 HOH 21 148 148 HOH HOH B . E 3 HOH 22 150 150 HOH HOH B . E 3 HOH 23 151 151 HOH HOH B . E 3 HOH 24 154 154 HOH HOH B . E 3 HOH 25 159 159 HOH HOH B . E 3 HOH 26 164 164 HOH HOH B . E 3 HOH 27 166 166 HOH HOH B . E 3 HOH 28 167 167 HOH HOH B . E 3 HOH 29 168 168 HOH HOH B . E 3 HOH 30 170 170 HOH HOH B . E 3 HOH 31 171 171 HOH HOH B . E 3 HOH 32 172 172 HOH HOH B . E 3 HOH 33 174 174 HOH HOH B . E 3 HOH 34 175 175 HOH HOH B . E 3 HOH 35 176 176 HOH HOH B . E 3 HOH 36 177 177 HOH HOH B . E 3 HOH 37 180 180 HOH HOH B . E 3 HOH 38 181 181 HOH HOH B . E 3 HOH 39 183 183 HOH HOH B . E 3 HOH 40 185 185 HOH HOH B . E 3 HOH 41 187 187 HOH HOH B . E 3 HOH 42 189 189 HOH HOH B . E 3 HOH 43 191 191 HOH HOH B . E 3 HOH 44 194 194 HOH HOH B . E 3 HOH 45 195 195 HOH HOH B . E 3 HOH 46 196 196 HOH HOH B . E 3 HOH 47 198 198 HOH HOH B . E 3 HOH 48 199 199 HOH HOH B . E 3 HOH 49 200 200 HOH HOH B . E 3 HOH 50 202 202 HOH HOH B . E 3 HOH 51 203 203 HOH HOH B . E 3 HOH 52 208 208 HOH HOH B . E 3 HOH 53 211 211 HOH HOH B . E 3 HOH 54 213 213 HOH HOH B . E 3 HOH 55 217 217 HOH HOH B . E 3 HOH 56 219 219 HOH HOH B . E 3 HOH 57 223 223 HOH HOH B . E 3 HOH 58 225 225 HOH HOH B . E 3 HOH 59 227 227 HOH HOH B . E 3 HOH 60 228 228 HOH HOH B . E 3 HOH 61 230 230 HOH HOH B . E 3 HOH 62 231 231 HOH HOH B . E 3 HOH 63 233 233 HOH HOH B . E 3 HOH 64 234 234 HOH HOH B . E 3 HOH 65 237 237 HOH HOH B . E 3 HOH 66 238 238 HOH HOH B . E 3 HOH 67 239 239 HOH HOH B . E 3 HOH 68 240 240 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR refinement 3.851 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 # _cell.entry_id 410D _cell.length_a 24.620 _cell.length_b 44.080 _cell.length_c 46.180 _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 410D _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 19 # _exptl.entry_id 410D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.01 _exptl_crystal.density_percent_sol 38.76 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.00 _exptl_crystal_grow.pdbx_details 'pH 6.00, VAPOR DIFFUSION, HANGING DROP' _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 'SODIUM CACODYLATE' ? ? ? 1 2 1 NACL ? ? ? 1 3 1 BACL2 ? ? ? 1 4 1 SPERMINE ? ? ? 1 5 1 MPD ? ? ? 1 6 2 MPD ? ? ? # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 100.00 ? 1 2 ? ? 1 3 ? ? 1 4 ? ? 1 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 'IMAGE PLATE' 'RIGAKU RAXIS II' 1997-07-14 ? 2 ? ? ? ? 3 ? ? ? ? 4 ? ? ? ? # loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.wavelength_id _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.monochromator _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.pdbx_scattering_type 1 1 M ? ? x-ray 2 2 M ? ? x-ray 3 3 M ? ? x-ray 4 4 M ? ? x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 . 1.0 2 . 1.0 3 . 1.0 4 . 1.0 # loop_ _diffrn_source.diffrn_id _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 1 'ROTATING ANODE' 'RIGAKU RU200' ? ? ? ? 2 ? ? ? ? ? ? 3 ? ? ? ? ? ? 4 ? ? ? ? ? ? # _reflns.entry_id 410D _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F 0.000 _reflns.d_resolution_low 32.000 _reflns.d_resolution_high 1.600 _reflns.number_obs 6524 _reflns.number_all 6524 _reflns.percent_possible_obs 92.700 _reflns.pdbx_Rmerge_I_obs 0.089 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 12.70 _reflns.pdbx_diffrn_id 1,2,3,4 _reflns.pdbx_ordinal 1 # _refine.entry_id 410D _refine.ls_number_reflns_obs 6414 _refine.ls_number_reflns_all 6431 _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 8.000 _refine.ls_d_res_high 1.600 _refine.ls_percent_reflns_obs 92.000 _refine.ls_R_factor_obs 0.159 _refine.ls_R_factor_all 0.162 _refine.ls_R_factor_R_work 0.159 _refine.ls_R_factor_R_free 0.184 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.000 _refine.ls_number_reflns_R_free 641 _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 R-FREE _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 RANDOM _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 404 _refine_hist.pdbx_number_atoms_ligand 24 _refine_hist.number_atoms_solvent 140 _refine_hist.number_atoms_total 568 _refine_hist.d_res_high 1.600 _refine_hist.d_res_low 8.000 # 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 0.007 ? ? ? '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 1.21 ? ? ? '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 410D _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 410D _struct.title ;DUPLEX [5'-D(GCGTA+TACGC)]2 WITH INCORPORATED 2'-O-ETHOXYMETHYLENE RIBONUCLEOSIDE ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 410D _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;DUPLEX [5'-D(GCGTA+TACGC)]2 WITH INCORPORATED 2'-O-ETHOXYMETHYLENE RIBONUCLEOSIDE, DNA ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 410D _struct_ref.pdbx_db_accession 410D _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 410D A 1 ? 10 ? 410D 1 ? 10 ? 1 10 2 1 410D B 1 ? 10 ? 410D 11 ? 20 ? 11 20 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _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 covale1 covale both ? A DA 5 "O3'" ? ? ? 1_555 A T38 6 P ? ? A DA 5 A T38 6 1_555 ? ? ? ? ? ? ? 1.594 ? ? covale2 covale one ? A T38 6 "O3'" ? ? ? 1_555 A DA 7 P ? ? A T38 6 A DA 7 1_555 ? ? ? ? ? ? ? 1.595 ? ? covale3 covale both ? B DA 5 "O3'" ? ? ? 1_555 B T38 6 P ? ? B DA 15 B T38 16 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale4 covale one ? B T38 6 "O3'" ? ? ? 1_555 B DA 7 P ? ? B T38 16 B DA 17 1_555 ? ? ? ? ? ? ? 1.615 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B T38 6 N3 ? ? A DA 5 B T38 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B T38 6 O4 ? ? A DA 5 B T38 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A T38 6 N3 ? ? ? 1_555 B DA 5 N1 ? ? A T38 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A T38 6 O4 ? ? ? 1_555 B DA 5 N6 ? ? A T38 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id B _struct_site.pdbx_auth_comp_id SPM _struct_site.pdbx_auth_seq_id 21 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 11 _struct_site.details 'BINDING SITE FOR RESIDUE SPM B 21' # 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 11 DC A 2 ? DC A 2 . ? 1_555 ? 2 AC1 11 DG A 9 ? DG A 9 . ? 4_456 ? 3 AC1 11 HOH D . ? HOH A 117 . ? 4_456 ? 4 AC1 11 HOH D . ? HOH A 120 . ? 2_555 ? 5 AC1 11 HOH D . ? HOH A 126 . ? 2_555 ? 6 AC1 11 DG B 3 ? DG B 13 . ? 1_555 ? 7 AC1 11 DT B 4 ? DT B 14 . ? 1_555 ? 8 AC1 11 DC B 8 ? DC B 18 . ? 2_455 ? 9 AC1 11 HOH E . ? HOH B 200 . ? 1_555 ? 10 AC1 11 HOH E . ? HOH B 211 . ? 1_555 ? 11 AC1 11 HOH E . ? HOH B 219 . ? 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 T38 6 A T38 6 ? T ? 2 B T38 6 B T38 16 ? T ? # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 N 0 B HOH 238 ? E HOH ? 2 1 N 0 B HOH 240 ? E HOH ? # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 SPM N1 N N N 147 SPM C2 C N N 148 SPM C3 C N N 149 SPM C4 C N N 150 SPM N5 N N N 151 SPM C6 C N N 152 SPM C7 C N N 153 SPM C8 C N N 154 SPM C9 C N N 155 SPM N10 N N N 156 SPM C11 C N N 157 SPM C12 C N N 158 SPM C13 C N N 159 SPM N14 N N N 160 SPM HN11 H N N 161 SPM HN12 H N N 162 SPM H21 H N N 163 SPM H22 H N N 164 SPM H31 H N N 165 SPM H32 H N N 166 SPM H41 H N N 167 SPM H42 H N N 168 SPM HN5 H N N 169 SPM H61 H N N 170 SPM H62 H N N 171 SPM H71 H N N 172 SPM H72 H N N 173 SPM H81 H N N 174 SPM H82 H N N 175 SPM H91 H N N 176 SPM H92 H N N 177 SPM HN0 H N N 178 SPM H111 H N N 179 SPM H112 H N N 180 SPM H121 H N N 181 SPM H122 H N N 182 SPM H131 H N N 183 SPM H132 H N N 184 SPM HN41 H N N 185 SPM HN42 H N N 186 T38 P P N N 187 T38 O1P O N N 188 T38 O2P O N N 189 T38 O3P O N N 190 T38 "O5'" O N N 191 T38 "C5'" C N N 192 T38 "C4'" C N R 193 T38 "O4'" O N N 194 T38 "C3'" C N R 195 T38 "O3'" O N N 196 T38 "C2'" C N R 197 T38 "O2'" O N N 198 T38 "C1'" C N R 199 T38 N1 N N N 200 T38 C2 C N N 201 T38 O2 O N N 202 T38 N3 N N N 203 T38 C4 C N N 204 T38 O4 O N N 205 T38 C5 C N N 206 T38 C5M C N N 207 T38 C6 C N N 208 T38 "CA'" C N N 209 T38 "CB'" C N N 210 T38 "OC'" O N N 211 T38 "CD'" C N N 212 T38 H2P H N N 213 T38 H3P H N N 214 T38 "H5'1" H N N 215 T38 "H5'2" H N N 216 T38 "H4'" H N N 217 T38 "H3'" H N N 218 T38 HA H N N 219 T38 "H2'" H N N 220 T38 "H1'" H N N 221 T38 H3 H N N 222 T38 H5M1 H N N 223 T38 H5M2 H N N 224 T38 H5M3 H N N 225 T38 H6 H N N 226 T38 "HA'1" H N N 227 T38 "HA'2" H N N 228 T38 "HB'1" H N N 229 T38 "HB'2" H N N 230 T38 "HD'1" H N N 231 T38 "HD'2" H N N 232 T38 "HD'3" H N N 233 # 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 DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 SPM N1 C2 sing N N 152 SPM N1 HN11 sing N N 153 SPM N1 HN12 sing N N 154 SPM C2 C3 sing N N 155 SPM C2 H21 sing N N 156 SPM C2 H22 sing N N 157 SPM C3 C4 sing N N 158 SPM C3 H31 sing N N 159 SPM C3 H32 sing N N 160 SPM C4 N5 sing N N 161 SPM C4 H41 sing N N 162 SPM C4 H42 sing N N 163 SPM N5 C6 sing N N 164 SPM N5 HN5 sing N N 165 SPM C6 C7 sing N N 166 SPM C6 H61 sing N N 167 SPM C6 H62 sing N N 168 SPM C7 C8 sing N N 169 SPM C7 H71 sing N N 170 SPM C7 H72 sing N N 171 SPM C8 C9 sing N N 172 SPM C8 H81 sing N N 173 SPM C8 H82 sing N N 174 SPM C9 N10 sing N N 175 SPM C9 H91 sing N N 176 SPM C9 H92 sing N N 177 SPM N10 C11 sing N N 178 SPM N10 HN0 sing N N 179 SPM C11 C12 sing N N 180 SPM C11 H111 sing N N 181 SPM C11 H112 sing N N 182 SPM C12 C13 sing N N 183 SPM C12 H121 sing N N 184 SPM C12 H122 sing N N 185 SPM C13 N14 sing N N 186 SPM C13 H131 sing N N 187 SPM C13 H132 sing N N 188 SPM N14 HN41 sing N N 189 SPM N14 HN42 sing N N 190 T38 P O1P doub N N 191 T38 P O2P sing N N 192 T38 P O3P sing N N 193 T38 P "O5'" sing N N 194 T38 O2P H2P sing N N 195 T38 O3P H3P sing N N 196 T38 "O5'" "C5'" sing N N 197 T38 "C5'" "C4'" sing N N 198 T38 "C5'" "H5'1" sing N N 199 T38 "C5'" "H5'2" sing N N 200 T38 "C4'" "O4'" sing N N 201 T38 "C4'" "C3'" sing N N 202 T38 "C4'" "H4'" sing N N 203 T38 "O4'" "C1'" sing N N 204 T38 "C3'" "O3'" sing N N 205 T38 "C3'" "C2'" sing N N 206 T38 "C3'" "H3'" sing N N 207 T38 "O3'" HA sing N N 208 T38 "C2'" "O2'" sing N N 209 T38 "C2'" "C1'" sing N N 210 T38 "C2'" "H2'" sing N N 211 T38 "O2'" "CA'" sing N N 212 T38 "C1'" N1 sing N N 213 T38 "C1'" "H1'" sing N N 214 T38 N1 C2 sing N N 215 T38 N1 C6 sing N N 216 T38 C2 O2 doub N N 217 T38 C2 N3 sing N N 218 T38 N3 C4 sing N N 219 T38 N3 H3 sing N N 220 T38 C4 O4 doub N N 221 T38 C4 C5 sing N N 222 T38 C5 C5M sing N N 223 T38 C5 C6 doub N N 224 T38 C5M H5M1 sing N N 225 T38 C5M H5M2 sing N N 226 T38 C5M H5M3 sing N N 227 T38 C6 H6 sing N N 228 T38 "CA'" "OC'" sing N N 229 T38 "CA'" "HA'1" sing N N 230 T38 "CA'" "HA'2" sing N N 231 T38 "CB'" "OC'" sing N N 232 T38 "CB'" "CD'" sing N N 233 T38 "CB'" "HB'1" sing N N 234 T38 "CB'" "HB'2" sing N N 235 T38 "CD'" "HD'1" sing N N 236 T38 "CD'" "HD'2" sing N N 237 T38 "CD'" "HD'3" sing N N 238 # _ndb_struct_conf_na.entry_id 410D _ndb_struct_conf_na.feature 'a-form double helix' # 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 DG 1 1_555 B DC 10 1_555 -0.413 -0.164 0.223 4.754 -4.349 -1.011 1 A_DG1:DC20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 0.230 -0.118 0.000 6.329 -13.373 0.638 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.444 -0.180 0.235 -9.593 -18.726 0.299 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 1 A DT 4 1_555 B DA 7 1_555 -0.336 -0.088 -0.016 -5.599 -16.986 -3.878 4 A_DT4:DA17_B A 4 ? B 17 ? 20 1 1 A DA 5 1_555 B T38 6 1_555 0.273 -0.054 0.149 -0.049 -15.651 -4.775 5 A_DA5:T3816_B A 5 ? B 16 ? 20 1 1 A T38 6 1_555 B DA 5 1_555 -0.053 -0.096 0.314 2.424 -14.454 9.244 6 A_T386:DA15_B A 6 ? B 15 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 -0.049 -0.110 0.061 4.684 -7.432 5.622 7 A_DA7:DT14_B A 7 ? B 14 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 0.271 -0.122 -0.151 10.784 -12.445 2.219 8 A_DC8:DG13_B A 8 ? B 13 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.271 -0.186 -0.182 -6.971 -11.303 1.293 9 A_DG9:DC12_B A 9 ? B 12 ? 19 1 1 A DC 10 1_555 B DG 1 1_555 0.263 -0.131 0.146 -2.714 3.264 0.236 10 A_DC10:DG11_B A 10 ? B 11 ? 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 DG 1 1_555 B DC 10 1_555 A DC 2 1_555 B DG 9 1_555 0.279 -1.525 3.200 2.773 0.969 39.380 -2.369 -0.095 3.174 1.436 -4.108 39.485 1 AA_DG1DC2:DG19DC20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DC 2 1_555 B DG 9 1_555 A DG 3 1_555 B DC 8 1_555 0.039 -2.144 3.509 -0.365 10.927 24.584 -7.250 -0.172 2.356 24.192 0.808 26.871 2 AA_DC2DG3:DC18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DG 3 1_555 B DC 8 1_555 A DT 4 1_555 B DA 7 1_555 -1.009 -1.373 3.047 -0.490 4.484 40.120 -2.449 1.412 2.895 6.511 0.712 40.363 3 AA_DG3DT4:DA17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DT 4 1_555 B DA 7 1_555 A DA 5 1_555 B T38 6 1_555 0.278 -1.610 3.104 0.287 19.276 23.220 -6.182 -0.490 1.392 40.158 -0.598 30.095 4 AA_DT4DA5:T3816DA17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DA 5 1_555 B T38 6 1_555 A T38 6 1_555 B DA 5 1_555 1.087 -1.194 3.117 0.093 8.985 33.178 -3.298 -1.828 2.714 15.386 -0.159 34.341 5 AA_DA5T386:DA15T3816_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A T38 6 1_555 B DA 5 1_555 A DA 7 1_555 B DT 4 1_555 -0.212 -1.533 2.987 -1.028 14.492 29.632 -4.712 0.232 2.042 26.429 1.875 32.930 6 AA_T386DA7:DT14DA15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A DA 7 1_555 B DT 4 1_555 A DC 8 1_555 B DG 3 1_555 -0.297 -1.656 3.261 0.824 3.794 29.748 -3.953 0.737 3.022 7.351 -1.595 29.995 7 AA_DA7DC8:DG13DT14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A DC 8 1_555 B DG 3 1_555 A DG 9 1_555 B DC 2 1_555 -0.529 -2.032 3.647 -1.623 12.494 28.945 -6.064 0.673 2.595 23.633 3.070 31.515 8 AA_DC8DG9:DC12DG13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DG 9 1_555 B DC 2 1_555 A DC 10 1_555 B DG 1 1_555 0.176 -1.563 3.313 -0.355 2.924 36.248 -2.909 -0.331 3.179 4.690 0.570 36.364 9 AA_DG9DC10:DG11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ? # _atom_sites.entry_id 410D _atom_sites.fract_transf_matrix[1][1] 0.040617 _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] 0.022686 _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] 0.021654 _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_