data_100D # _entry.id 100D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.381 _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 100D pdb_0000100d 10.2210/pdb100d/pdb RCSB AHJ060 ? ? WWPDB D_1000170001 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 100D _pdbx_database_status.recvd_initial_deposition_date 1994-12-05 _pdbx_database_status.deposit_site BNL _pdbx_database_status.process_site NDB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Ban, C.' 1 'Ramakrishnan, B.' 2 'Sundaralingam, M.' 3 # _citation.id primary _citation.title ;Crystal structure of the highly distorted chimeric decamer r(C)d(CGGCGCCG)r(G).spermine complex--spermine binding to phosphate only and minor groove tertiary base-pairing. ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 22 _citation.page_first 5466 _citation.page_last 5476 _citation.year 1994 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 7816639 _citation.pdbx_database_id_DOI 10.1093/nar/22.24.5466 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ban, C.' 1 ? primary 'Ramakrishnan, B.' 2 ? primary 'Sundaralingam, M.' 3 ? # _cell.entry_id 100D _cell.length_a 23.980 _cell.length_b 40.770 _cell.length_c 44.840 _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 100D _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 # 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(*CP*)-D(*CP*GP*GP*CP*GP*CP*CP*GP*)-R(*G)-3') ; 3078.980 2 ? ? ? ? 2 non-polymer syn SPERMINE 202.340 1 ? ? ? ? 3 water nat water 18.015 67 ? ? ? ? # _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 'C(DC)(DG)(DG)(DC)(DG)(DC)(DC)(DG)G' _entity_poly.pdbx_seq_one_letter_code_can CCGGCGCCGG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 DC n 1 3 DG n 1 4 DG n 1 5 DC n 1 6 DG n 1 7 DC n 1 8 DC n 1 9 DG n 1 10 G n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 100D _struct_ref.pdbx_db_accession 100D _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 100D A 1 ? 10 ? 100D 1 ? 10 ? 1 10 2 1 100D B 1 ? 10 ? 100D 11 ? 20 ? 11 20 # 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 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 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 # _exptl.entry_id 100D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.78 _exptl_crystal.density_percent_sol 30.89 _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 7.00 _exptl_crystal_grow.pdbx_details 'pH 7.00, 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 WATER ? ? ? 1 2 1 MPD ? ? ? 1 3 1 'NA CACODYLATE' ? ? ? 1 4 1 SPERMINE_HCL ? ? ? 1 5 2 WATER ? ? ? 1 6 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 263.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'AREA DETECTOR' _diffrn_detector.type SIEMENS-NICOLET _diffrn_detector.pdbx_collection_date ? _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 'ROTATING ANODE' _diffrn_source.type MACSCIENCE _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 100D _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low ? _reflns.d_resolution_high 1.900 _reflns.number_obs 2365 _reflns.number_all 9305 _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _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 100D _refine.ls_number_reflns_obs 2314 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.000 _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 1.900 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1450000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1450000 _refine.ls_R_factor_R_free ? _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 408 _refine_hist.pdbx_number_atoms_ligand 14 _refine_hist.number_atoms_solvent 67 _refine_hist.number_atoms_total 489 _refine_hist.d_res_high 1.900 _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 0.015 ? ? ? '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 3.80 ? ? ? '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' ? # _struct.entry_id 100D _struct.title ;CRYSTAL STRUCTURE OF THE HIGHLY DISTORTED CHIMERIC DECAMER R(C)D(CGGCGCCG)R(G)-SPERMINE COMPLEX-SPERMINE BINDING TO PHOSPHATE ONLY AND MINOR GROOVE TERTIARY BASE-PAIRING ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 100D _struct_keywords.pdbx_keywords 'DNA-RNA HYBRID' _struct_keywords.text 'A-DNA/RNA, DOUBLE HELIX, DNA-RNA HYBRID' # 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_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 C 1 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 1 B G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 1 B G 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 1 B G 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 DG 4 N1 ? ? ? 1_555 B DC 7 N3 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 7 O2 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 7 N4 ? ? A DG 4 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 5 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 6 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 6 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 6 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 7 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 7 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 7 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 7 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 7 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 7 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 10 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 10 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 10 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 10 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 10 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 10 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _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 13 _struct_site.details 'BINDING SITE FOR RESIDUE SPM A 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 13 DC A 5 ? DC A 5 . ? 1_555 ? 2 AC1 13 DG A 6 ? DG A 6 . ? 1_555 ? 3 AC1 13 DG A 9 ? DG A 9 . ? 3_655 ? 4 AC1 13 HOH D . ? HOH A 29 . ? 3_655 ? 5 AC1 13 HOH D . ? HOH A 46 . ? 2_555 ? 6 AC1 13 HOH D . ? HOH A 56 . ? 1_555 ? 7 AC1 13 HOH D . ? HOH A 87 . ? 1_555 ? 8 AC1 13 DG B 3 ? DG B 13 . ? 2_555 ? 9 AC1 13 DG B 4 ? DG B 14 . ? 2_555 ? 10 AC1 13 DG B 9 ? DG B 19 . ? 1_655 ? 11 AC1 13 G B 10 ? G B 20 . ? 1_655 ? 12 AC1 13 HOH E . ? HOH B 33 . ? 2_555 ? 13 AC1 13 HOH E . ? HOH B 52 . ? 2_555 ? # _database_PDB_matrix.entry_id 100D _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 # _atom_sites.entry_id 100D _atom_sites.fract_transf_matrix[1][1] 0.041701 _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] 0.024528 _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] 0.022302 _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_ _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 C 1 1 1 C C 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 DG 4 4 4 DG G A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DG 6 6 6 DG G A . n A 1 7 DC 7 7 7 DC C 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 G 10 10 10 G G A . n B 1 1 C 1 11 11 C C 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 DG 4 14 14 DG G B . n B 1 5 DC 5 15 15 DC C B . n B 1 6 DG 6 16 16 DG G B . n B 1 7 DC 7 17 17 DC C 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 G 10 20 20 G G 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 A . D 3 HOH 1 25 25 HOH HOH A . D 3 HOH 2 28 28 HOH HOH A . D 3 HOH 3 29 29 HOH HOH A . D 3 HOH 4 30 30 HOH HOH A . D 3 HOH 5 31 31 HOH HOH A . D 3 HOH 6 32 32 HOH HOH A . D 3 HOH 7 34 34 HOH HOH A . D 3 HOH 8 36 36 HOH HOH A . D 3 HOH 9 37 37 HOH HOH A . D 3 HOH 10 39 39 HOH HOH A . D 3 HOH 11 40 40 HOH HOH A . D 3 HOH 12 41 41 HOH HOH A . D 3 HOH 13 42 42 HOH HOH A . D 3 HOH 14 43 43 HOH HOH A . D 3 HOH 15 44 44 HOH HOH A . D 3 HOH 16 46 46 HOH HOH A . D 3 HOH 17 50 50 HOH HOH A . D 3 HOH 18 54 54 HOH HOH A . D 3 HOH 19 55 55 HOH HOH A . D 3 HOH 20 56 56 HOH HOH A . D 3 HOH 21 58 58 HOH HOH A . D 3 HOH 22 60 60 HOH HOH A . D 3 HOH 23 62 62 HOH HOH A . D 3 HOH 24 63 63 HOH HOH A . D 3 HOH 25 64 64 HOH HOH A . D 3 HOH 26 66 66 HOH HOH A . D 3 HOH 27 67 67 HOH HOH A . D 3 HOH 28 68 68 HOH HOH A . D 3 HOH 29 73 73 HOH HOH A . D 3 HOH 30 74 74 HOH HOH A . D 3 HOH 31 75 75 HOH HOH A . D 3 HOH 32 80 80 HOH HOH A . D 3 HOH 33 81 81 HOH HOH A . D 3 HOH 34 82 82 HOH HOH A . D 3 HOH 35 83 83 HOH HOH A . D 3 HOH 36 84 84 HOH HOH A . D 3 HOH 37 86 86 HOH HOH A . D 3 HOH 38 87 87 HOH HOH A . E 3 HOH 1 22 22 HOH HOH B . E 3 HOH 2 23 23 HOH HOH B . E 3 HOH 3 24 24 HOH HOH B . E 3 HOH 4 26 26 HOH HOH B . E 3 HOH 5 27 27 HOH HOH B . E 3 HOH 6 33 33 HOH HOH B . E 3 HOH 7 35 35 HOH HOH B . E 3 HOH 8 38 38 HOH HOH B . E 3 HOH 9 45 45 HOH HOH B . E 3 HOH 10 47 47 HOH HOH B . E 3 HOH 11 48 48 HOH HOH B . E 3 HOH 12 49 49 HOH HOH B . E 3 HOH 13 51 51 HOH HOH B . E 3 HOH 14 52 52 HOH HOH B . E 3 HOH 15 53 53 HOH HOH B . E 3 HOH 16 57 57 HOH HOH B . E 3 HOH 17 59 59 HOH HOH B . E 3 HOH 18 61 61 HOH HOH B . E 3 HOH 19 65 65 HOH HOH B . E 3 HOH 20 69 69 HOH HOH B . E 3 HOH 21 70 70 HOH HOH B . E 3 HOH 22 71 71 HOH HOH B . E 3 HOH 23 72 72 HOH HOH B . E 3 HOH 24 76 76 HOH HOH B . E 3 HOH 25 77 77 HOH HOH B . E 3 HOH 26 78 78 HOH HOH B . E 3 HOH 27 79 79 HOH HOH B . E 3 HOH 28 85 85 HOH HOH B . E 3 HOH 29 88 88 HOH HOH B . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _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 1995-03-31 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-11-22 # _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_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_site.pdbx_auth_asym_id' 4 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 4 'Structure model' '_struct_site.pdbx_auth_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' # _software.name X-PLOR _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 P B DC 12 ? ? "O5'" B DC 12 ? ? 1.660 1.593 0.067 0.010 N 2 1 N7 B DG 19 ? ? C8 B DG 19 ? ? 1.268 1.305 -0.037 0.006 N # 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 "O3'" A C 1 ? ? P A DC 2 ? ? "O5'" A DC 2 ? ? 121.02 104.00 17.02 1.90 Y 2 1 "C4'" A DC 2 ? ? "C3'" A DC 2 ? ? "C2'" A DC 2 ? ? 97.99 102.20 -4.21 0.70 N 3 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 111.45 108.30 3.15 0.30 N 4 1 N1 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 122.88 118.90 3.98 0.60 N 5 1 "O3'" A DC 2 ? ? P A DG 3 ? ? "O5'" A DG 3 ? ? 129.62 104.00 25.62 1.90 Y 6 1 "C4'" A DG 3 ? ? "C3'" A DG 3 ? ? "C2'" A DG 3 ? ? 97.24 102.20 -4.96 0.70 N 7 1 "O4'" A DG 3 ? ? "C1'" A DG 3 ? ? N9 A DG 3 ? ? 115.16 108.30 6.86 0.30 N 8 1 "O3'" A DG 4 ? ? P A DC 5 ? ? "O5'" A DC 5 ? ? 130.22 104.00 26.22 1.90 Y 9 1 "O3'" A DG 4 ? ? P A DC 5 ? ? OP1 A DC 5 ? ? 88.83 105.20 -16.37 2.20 Y 10 1 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 110.51 108.30 2.21 0.30 N 11 1 "O3'" A DC 5 ? ? P A DG 6 ? ? OP2 A DG 6 ? ? 118.16 110.50 7.66 1.10 Y 12 1 "C4'" A DG 6 ? ? "C3'" A DG 6 ? ? "C2'" A DG 6 ? ? 97.09 102.20 -5.11 0.70 N 13 1 "O4'" A DC 7 ? ? "C1'" A DC 7 ? ? N1 A DC 7 ? ? 115.10 108.30 6.80 0.30 N 14 1 "C4'" A DC 8 ? ? "C3'" A DC 8 ? ? "C2'" A DC 8 ? ? 95.10 102.20 -7.10 0.70 N 15 1 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 110.85 108.30 2.55 0.30 N 16 1 "O3'" A DC 8 ? ? P A DG 9 ? ? OP2 A DG 9 ? ? 123.20 110.50 12.70 1.10 Y 17 1 "O3'" A DC 8 ? ? P A DG 9 ? ? OP1 A DG 9 ? ? 91.81 105.20 -13.39 2.20 Y 18 1 "O4'" A DG 9 ? ? "C4'" A DG 9 ? ? "C3'" A DG 9 ? ? 102.09 104.50 -2.41 0.40 N 19 1 "C4'" A DG 9 ? ? "C3'" A DG 9 ? ? "C2'" A DG 9 ? ? 95.69 102.20 -6.51 0.70 N 20 1 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? "C2'" A DG 9 ? ? 99.35 105.90 -6.55 0.80 N 21 1 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 113.89 108.30 5.59 0.30 N 22 1 C8 A DG 9 ? ? N9 A DG 9 ? ? C4 A DG 9 ? ? 103.40 106.40 -3.00 0.40 N 23 1 "O3'" A DG 9 ? ? P A G 10 ? ? "O5'" A G 10 ? ? 85.49 104.00 -18.51 1.90 Y 24 1 "O3'" A DG 9 ? ? P A G 10 ? ? OP2 A G 10 ? ? 138.90 110.50 28.40 1.10 Y 25 1 "O3'" A DG 9 ? ? P A G 10 ? ? OP1 A G 10 ? ? 88.74 105.20 -16.46 2.20 Y 26 1 "O3'" B C 11 ? ? P B DC 12 ? ? OP2 B DC 12 ? ? 133.47 110.50 22.97 1.10 Y 27 1 "O3'" B C 11 ? ? P B DC 12 ? ? OP1 B DC 12 ? ? 85.11 105.20 -20.09 2.20 Y 28 1 "O4'" B DC 12 ? ? "C1'" B DC 12 ? ? N1 B DC 12 ? ? 112.79 108.30 4.49 0.30 N 29 1 N1 B DC 12 ? ? C2 B DC 12 ? ? O2 B DC 12 ? ? 123.33 118.90 4.43 0.60 N 30 1 "O3'" B DC 12 ? ? P B DG 13 ? ? "O5'" B DG 13 ? ? 121.89 104.00 17.89 1.90 Y 31 1 "O4'" B DG 13 ? ? "C1'" B DG 13 ? ? N9 B DG 13 ? ? 110.28 108.30 1.98 0.30 N 32 1 "O3'" B DG 13 ? ? P B DG 14 ? ? OP2 B DG 14 ? ? 117.30 110.50 6.80 1.10 Y 33 1 "C4'" B DG 14 ? ? "C3'" B DG 14 ? ? "C2'" B DG 14 ? ? 97.53 102.20 -4.67 0.70 N 34 1 "O3'" B DG 14 ? ? P B DC 15 ? ? OP2 B DC 15 ? ? 120.78 110.50 10.28 1.10 Y 35 1 "O4'" B DC 15 ? ? "C1'" B DC 15 ? ? N1 B DC 15 ? ? 112.55 108.30 4.25 0.30 N 36 1 N1 B DC 15 ? ? C2 B DC 15 ? ? O2 B DC 15 ? ? 122.87 118.90 3.97 0.60 N 37 1 "C3'" B DC 15 ? ? "O3'" B DC 15 ? ? P B DG 16 ? ? 110.86 119.70 -8.84 1.20 Y 38 1 "O3'" B DC 15 ? ? P B DG 16 ? ? "O5'" B DG 16 ? ? 135.42 104.00 31.42 1.90 Y 39 1 "O3'" B DC 15 ? ? P B DG 16 ? ? OP1 B DG 16 ? ? 86.77 105.20 -18.43 2.20 Y 40 1 "C4'" B DG 16 ? ? "C3'" B DG 16 ? ? "C2'" B DG 16 ? ? 94.16 102.20 -8.04 0.70 N 41 1 "O3'" B DG 16 ? ? P B DC 17 ? ? OP1 B DC 17 ? ? 81.47 105.20 -23.73 2.20 Y 42 1 "O4'" B DC 17 ? ? "C1'" B DC 17 ? ? N1 B DC 17 ? ? 113.05 108.30 4.75 0.30 N 43 1 "O3'" B DC 17 ? ? P B DC 18 ? ? OP2 B DC 18 ? ? 122.55 110.50 12.05 1.10 Y 44 1 N1 B DC 18 ? ? C2 B DC 18 ? ? O2 B DC 18 ? ? 123.42 118.90 4.52 0.60 N 45 1 "O3'" B DC 18 ? ? P B DG 19 ? ? OP1 B DG 19 ? ? 86.66 105.20 -18.54 2.20 Y 46 1 "O4'" B DG 19 ? ? "C4'" B DG 19 ? ? "C3'" B DG 19 ? ? 102.00 104.50 -2.50 0.40 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 C A 1 ? ? 0.067 'SIDE CHAIN' 2 1 DG A 3 ? ? 0.099 'SIDE CHAIN' 3 1 DG A 4 ? ? 0.081 'SIDE CHAIN' 4 1 DG A 6 ? ? 0.066 'SIDE CHAIN' 5 1 C B 11 ? ? 0.073 'SIDE CHAIN' 6 1 DG B 14 ? ? 0.093 'SIDE CHAIN' 7 1 DC B 15 ? ? 0.080 'SIDE CHAIN' # 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 DC OP3 O N N 36 DC P P N N 37 DC OP1 O N N 38 DC OP2 O N N 39 DC "O5'" O N N 40 DC "C5'" C N N 41 DC "C4'" C N R 42 DC "O4'" O N N 43 DC "C3'" C N S 44 DC "O3'" O N N 45 DC "C2'" C N N 46 DC "C1'" C N R 47 DC N1 N N N 48 DC C2 C N N 49 DC O2 O N N 50 DC N3 N N N 51 DC C4 C N N 52 DC N4 N N N 53 DC C5 C N N 54 DC C6 C N N 55 DC HOP3 H N N 56 DC HOP2 H N N 57 DC "H5'" H N N 58 DC "H5''" H N N 59 DC "H4'" H N N 60 DC "H3'" H N N 61 DC "HO3'" H N N 62 DC "H2'" H N N 63 DC "H2''" H N N 64 DC "H1'" H N N 65 DC H41 H N N 66 DC H42 H N N 67 DC H5 H N N 68 DC H6 H N N 69 DG OP3 O N N 70 DG P P N N 71 DG OP1 O N N 72 DG OP2 O N N 73 DG "O5'" O N N 74 DG "C5'" C N N 75 DG "C4'" C N R 76 DG "O4'" O N N 77 DG "C3'" C N S 78 DG "O3'" O N N 79 DG "C2'" C N N 80 DG "C1'" C N R 81 DG N9 N Y N 82 DG C8 C Y N 83 DG N7 N Y N 84 DG C5 C Y N 85 DG C6 C N N 86 DG O6 O N N 87 DG N1 N N N 88 DG C2 C N N 89 DG N2 N N N 90 DG N3 N N N 91 DG C4 C Y N 92 DG HOP3 H N N 93 DG HOP2 H N N 94 DG "H5'" H N N 95 DG "H5''" H N N 96 DG "H4'" H N N 97 DG "H3'" H N N 98 DG "HO3'" H N N 99 DG "H2'" H N N 100 DG "H2''" H N N 101 DG "H1'" H N N 102 DG H8 H N N 103 DG H1 H N N 104 DG H21 H N N 105 DG H22 H N N 106 G OP3 O N N 107 G P P N N 108 G OP1 O N N 109 G OP2 O N N 110 G "O5'" O N N 111 G "C5'" C N N 112 G "C4'" C N R 113 G "O4'" O N N 114 G "C3'" C N S 115 G "O3'" O N N 116 G "C2'" C N R 117 G "O2'" O N N 118 G "C1'" C N R 119 G N9 N Y N 120 G C8 C Y N 121 G N7 N Y N 122 G C5 C Y N 123 G C6 C N N 124 G O6 O N N 125 G N1 N N N 126 G C2 C N N 127 G N2 N N N 128 G N3 N N N 129 G C4 C Y N 130 G HOP3 H N N 131 G HOP2 H N N 132 G "H5'" H N N 133 G "H5''" H N N 134 G "H4'" H N N 135 G "H3'" H N N 136 G "HO3'" H N N 137 G "H2'" H N N 138 G "HO2'" H N N 139 G "H1'" H N N 140 G H8 H N N 141 G H1 H N N 142 G H21 H N N 143 G H22 H N N 144 HOH O O N N 145 HOH H1 H N N 146 HOH H2 H N N 147 SPM N1 N N N 148 SPM C2 C N N 149 SPM C3 C N N 150 SPM C4 C N N 151 SPM N5 N N N 152 SPM C6 C N N 153 SPM C7 C N N 154 SPM C8 C N N 155 SPM C9 C N N 156 SPM N10 N N N 157 SPM C11 C N N 158 SPM C12 C N N 159 SPM C13 C N N 160 SPM N14 N N N 161 SPM HN11 H N N 162 SPM HN12 H N N 163 SPM H21 H N N 164 SPM H22 H N N 165 SPM H31 H N N 166 SPM H32 H N N 167 SPM H41 H N N 168 SPM H42 H N N 169 SPM HN5 H N N 170 SPM H61 H N N 171 SPM H62 H N N 172 SPM H71 H N N 173 SPM H72 H N N 174 SPM H81 H N N 175 SPM H82 H N N 176 SPM H91 H N N 177 SPM H92 H N N 178 SPM HN0 H N N 179 SPM H111 H N N 180 SPM H112 H N N 181 SPM H121 H N N 182 SPM H122 H N N 183 SPM H131 H N N 184 SPM H132 H N N 185 SPM HN41 H N N 186 SPM HN42 H N N 187 # 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 DC OP3 P sing N N 37 DC OP3 HOP3 sing N N 38 DC P OP1 doub N N 39 DC P OP2 sing N N 40 DC P "O5'" sing N N 41 DC OP2 HOP2 sing N N 42 DC "O5'" "C5'" sing N N 43 DC "C5'" "C4'" sing N N 44 DC "C5'" "H5'" sing N N 45 DC "C5'" "H5''" sing N N 46 DC "C4'" "O4'" sing N N 47 DC "C4'" "C3'" sing N N 48 DC "C4'" "H4'" sing N N 49 DC "O4'" "C1'" sing N N 50 DC "C3'" "O3'" sing N N 51 DC "C3'" "C2'" sing N N 52 DC "C3'" "H3'" sing N N 53 DC "O3'" "HO3'" sing N N 54 DC "C2'" "C1'" sing N N 55 DC "C2'" "H2'" sing N N 56 DC "C2'" "H2''" sing N N 57 DC "C1'" N1 sing N N 58 DC "C1'" "H1'" sing N N 59 DC N1 C2 sing N N 60 DC N1 C6 sing N N 61 DC C2 O2 doub N N 62 DC C2 N3 sing N N 63 DC N3 C4 doub N N 64 DC C4 N4 sing N N 65 DC C4 C5 sing N N 66 DC N4 H41 sing N N 67 DC N4 H42 sing N N 68 DC C5 C6 doub N N 69 DC C5 H5 sing N N 70 DC C6 H6 sing N N 71 DG OP3 P sing N N 72 DG OP3 HOP3 sing N N 73 DG P OP1 doub N N 74 DG P OP2 sing N N 75 DG P "O5'" sing N N 76 DG OP2 HOP2 sing N N 77 DG "O5'" "C5'" sing N N 78 DG "C5'" "C4'" sing N N 79 DG "C5'" "H5'" sing N N 80 DG "C5'" "H5''" sing N N 81 DG "C4'" "O4'" sing N N 82 DG "C4'" "C3'" sing N N 83 DG "C4'" "H4'" sing N N 84 DG "O4'" "C1'" sing N N 85 DG "C3'" "O3'" sing N N 86 DG "C3'" "C2'" sing N N 87 DG "C3'" "H3'" sing N N 88 DG "O3'" "HO3'" sing N N 89 DG "C2'" "C1'" sing N N 90 DG "C2'" "H2'" sing N N 91 DG "C2'" "H2''" sing N N 92 DG "C1'" N9 sing N N 93 DG "C1'" "H1'" sing N N 94 DG N9 C8 sing Y N 95 DG N9 C4 sing Y N 96 DG C8 N7 doub Y N 97 DG C8 H8 sing N N 98 DG N7 C5 sing Y N 99 DG C5 C6 sing N N 100 DG C5 C4 doub Y N 101 DG C6 O6 doub N N 102 DG C6 N1 sing N N 103 DG N1 C2 sing N N 104 DG N1 H1 sing N N 105 DG C2 N2 sing N N 106 DG C2 N3 doub N N 107 DG N2 H21 sing N N 108 DG N2 H22 sing N N 109 DG N3 C4 sing N N 110 G OP3 P sing N N 111 G OP3 HOP3 sing N N 112 G P OP1 doub N N 113 G P OP2 sing N N 114 G P "O5'" sing N N 115 G OP2 HOP2 sing N N 116 G "O5'" "C5'" sing N N 117 G "C5'" "C4'" sing N N 118 G "C5'" "H5'" sing N N 119 G "C5'" "H5''" sing N N 120 G "C4'" "O4'" sing N N 121 G "C4'" "C3'" sing N N 122 G "C4'" "H4'" sing N N 123 G "O4'" "C1'" sing N N 124 G "C3'" "O3'" sing N N 125 G "C3'" "C2'" sing N N 126 G "C3'" "H3'" sing N N 127 G "O3'" "HO3'" sing N N 128 G "C2'" "O2'" sing N N 129 G "C2'" "C1'" sing N N 130 G "C2'" "H2'" sing N N 131 G "O2'" "HO2'" sing N N 132 G "C1'" N9 sing N N 133 G "C1'" "H1'" sing N N 134 G N9 C8 sing Y N 135 G N9 C4 sing Y N 136 G C8 N7 doub Y N 137 G C8 H8 sing N N 138 G N7 C5 sing Y N 139 G C5 C6 sing N N 140 G C5 C4 doub Y N 141 G C6 O6 doub N N 142 G C6 N1 sing N N 143 G N1 C2 sing N N 144 G N1 H1 sing N N 145 G C2 N2 sing N N 146 G C2 N3 doub N N 147 G N2 H21 sing N N 148 G N2 H22 sing N N 149 G N3 C4 sing N N 150 HOH O H1 sing N N 151 HOH O H2 sing N N 152 SPM N1 C2 sing N N 153 SPM N1 HN11 sing N N 154 SPM N1 HN12 sing N N 155 SPM C2 C3 sing N N 156 SPM C2 H21 sing N N 157 SPM C2 H22 sing N N 158 SPM C3 C4 sing N N 159 SPM C3 H31 sing N N 160 SPM C3 H32 sing N N 161 SPM C4 N5 sing N N 162 SPM C4 H41 sing N N 163 SPM C4 H42 sing N N 164 SPM N5 C6 sing N N 165 SPM N5 HN5 sing N N 166 SPM C6 C7 sing N N 167 SPM C6 H61 sing N N 168 SPM C6 H62 sing N N 169 SPM C7 C8 sing N N 170 SPM C7 H71 sing N N 171 SPM C7 H72 sing N N 172 SPM C8 C9 sing N N 173 SPM C8 H81 sing N N 174 SPM C8 H82 sing N N 175 SPM C9 N10 sing N N 176 SPM C9 H91 sing N N 177 SPM C9 H92 sing N N 178 SPM N10 C11 sing N N 179 SPM N10 HN0 sing N N 180 SPM C11 C12 sing N N 181 SPM C11 H111 sing N N 182 SPM C11 H112 sing N N 183 SPM C12 C13 sing N N 184 SPM C12 H121 sing N N 185 SPM C12 H122 sing N N 186 SPM C13 N14 sing N N 187 SPM C13 H131 sing N N 188 SPM C13 H132 sing N N 189 SPM N14 HN41 sing N N 190 SPM N14 HN42 sing N N 191 # _ndb_struct_conf_na.entry_id 100D _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 C 1 1_555 B G 10 1_555 0.068 -0.095 0.037 3.919 -8.782 -0.903 1 A_C1:G20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B DG 9 1_555 -0.021 -0.169 -0.062 4.832 -9.564 -1.893 2 A_DC2:DG19_B A 2 ? B 19 ? 19 1 1 A DG 3 1_555 B DC 8 1_555 -0.348 -0.155 -0.041 2.657 -10.586 1.384 3 A_DG3:DC18_B A 3 ? B 18 ? 19 1 1 A DG 4 1_555 B DC 7 1_555 -0.240 -0.199 0.090 -2.069 -10.899 0.439 4 A_DG4:DC17_B A 4 ? B 17 ? 19 1 1 A DC 5 1_555 B DG 6 1_555 0.378 -0.309 0.399 3.577 -12.554 -0.990 5 A_DC5:DG16_B A 5 ? B 16 ? 19 1 1 A DG 6 1_555 B DC 5 1_555 -0.161 0.050 0.030 -1.641 -16.837 0.002 6 A_DG6:DC15_B A 6 ? B 15 ? 19 1 1 A DC 7 1_555 B DG 4 1_555 0.418 -0.258 -0.101 2.693 -7.278 0.662 7 A_DC7:DG14_B A 7 ? B 14 ? 19 1 1 A DC 8 1_555 B DG 3 1_555 0.529 -0.125 -0.142 2.563 -6.749 2.313 8 A_DC8:DG13_B A 8 ? B 13 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.089 -0.141 -0.088 -3.824 -2.749 0.304 9 A_DG9:DC12_B A 9 ? B 12 ? 19 1 1 A G 10 1_555 B C 1 1_555 -0.264 -0.410 -0.028 -0.154 -5.956 -3.321 10 A_G10:C11_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 C 1 1_555 B G 10 1_555 A DC 2 1_555 B DG 9 1_555 0.040 -1.686 3.311 -0.715 6.534 34.027 -3.803 -0.173 2.945 11.038 1.208 34.638 1 AA_C1DC2:DG19G20_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 0.000 -1.769 3.309 -0.726 8.403 28.481 -5.108 -0.143 2.688 16.624 1.437 29.679 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 DG 4 1_555 B DC 7 1_555 -1.609 -1.437 3.251 -8.538 9.618 35.932 -3.417 1.386 3.071 15.011 13.325 38.092 3 AA_DG3DG4:DC17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DG 4 1_555 B DC 7 1_555 A DC 5 1_555 B DG 6 1_555 0.941 -0.969 3.240 -0.966 7.094 31.290 -2.972 -1.869 2.926 12.940 1.763 32.079 4 AA_DG4DC5:DG16DC17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DC 5 1_555 B DG 6 1_555 A DG 6 1_555 B DC 5 1_555 -0.884 -1.643 3.156 0.897 18.609 30.581 -4.919 1.549 1.858 31.845 -1.535 35.693 5 AA_DC5DG6:DC15DG16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A DG 6 1_555 B DC 5 1_555 A DC 7 1_555 B DG 4 1_555 0.957 -1.199 3.257 3.304 5.983 34.363 -2.875 -1.104 3.087 10.004 -5.525 35.016 6 AA_DG6DC7:DG14DC15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A DC 7 1_555 B DG 4 1_555 A DC 8 1_555 B DG 3 1_555 0.507 -1.915 3.362 0.387 4.601 28.150 -4.919 -0.943 3.024 9.380 -0.790 28.519 7 AA_DC7DC8:DG13DG14_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 -0.715 -2.331 3.651 -0.639 2.677 23.690 -6.586 1.504 3.388 6.493 1.549 23.847 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 G 10 1_555 B C 1 1_555 -0.253 -1.970 3.408 1.317 2.100 30.122 -4.213 0.758 3.253 4.033 -2.528 30.221 9 AA_DG9G10:C11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 SPERMINE SPM 3 water HOH #