data_1D31 # _entry.id 1D31 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.385 _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 1D31 pdb_00001d31 10.2210/pdb1d31/pdb RCSB UDM010 ? ? WWPDB D_1000172636 ? ? # 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 1992-04-15 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-07 # _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' # 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 # 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' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1D31 _pdbx_database_status.recvd_initial_deposition_date 1991-04-25 _pdbx_database_status.deposit_site BNL _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 'Joshua-Tor, L.' 1 'Frolow, F.' 2 'Appella, E.' 3 'Hope, H.' 4 'Rabinovich, D.' 5 'Sussman, J.L.' 6 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Three-dimensional structures of bulge-containing DNA fragments.' J.Mol.Biol. 225 397 431 1992 JMOBAK UK 0022-2836 0070 ? 1593627 '10.1016/0022-2836(92)90929-E' 1 'The Three-Dimensional Structure of a DNA Duplex Containing Looped-out Bases' Nature 334 82 84 1988 NATUAS UK 0028-0836 0006 ? ? ? 2 'Crystallization of a DNA Tridecamer d(CGCAGAATTCGCG)' J.Mol.Biol. 188 111 113 1986 JMOBAK UK 0022-2836 0070 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Joshua-Tor, L.' 1 ? primary 'Frolow, F.' 2 ? primary 'Appella, E.' 3 ? primary 'Hope, H.' 4 ? primary 'Rabinovich, D.' 5 ? primary 'Sussman, J.L.' 6 ? 1 'Joshua-Tor, L.' 7 ? 1 'Rabinovich, D.' 8 ? 1 'Hope, H.' 9 ? 1 'Frolow, F.' 10 ? 1 'Appella, E.' 11 ? 1 'Sussman, J.L.' 12 ? 2 'Saper, M.A.' 13 ? 2 'Eldar, H.' 14 ? 2 'Mizuuchi, K.' 15 ? 2 'Nickol, J.' 16 ? 2 'Appella, E.' 17 ? 2 'Sussman, J.L.' 18 ? # 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 (5'-D(*CP*GP*CP*AP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') ; 3976.599 2 ? ? ? ? 2 water nat water 18.015 23 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DC)(DA)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCAGAATTCGCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DC n 1 4 DA n 1 5 DG n 1 6 DA n 1 7 DA n 1 8 DT n 1 9 DT n 1 10 DC n 1 11 DG n 1 12 DC n 1 13 DG 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 # 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 DC 1 1 1 DC C A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 DG 5 5 5 DG G A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DA 7 7 7 DA A A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DT 9 9 9 DT T A . n A 1 10 DC 10 10 10 DC C A . n A 1 11 DG 11 11 11 DG G A . n A 1 12 DC 12 12 12 DC C A . n A 1 13 DG 13 13 13 DG G A . n B 1 1 DC 1 14 14 DC C B . n B 1 2 DG 2 15 15 DG G B . n B 1 3 DC 3 16 16 DC C B . n B 1 4 DA 4 17 17 DA A B . n B 1 5 DG 5 18 18 DG G B . n B 1 6 DA 6 19 19 DA A B . n B 1 7 DA 7 20 20 DA A B . n B 1 8 DT 8 21 21 DT T B . n B 1 9 DT 9 22 22 DT T B . n B 1 10 DC 10 23 23 DC C B . n B 1 11 DG 11 24 24 DG G B . n B 1 12 DC 12 25 25 DC C B . n B 1 13 DG 13 26 26 DG 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 HOH 1 27 27 HOH HOH A . C 2 HOH 2 30 30 HOH HOH A . C 2 HOH 3 33 33 HOH HOH A . C 2 HOH 4 34 34 HOH HOH A . C 2 HOH 5 36 36 HOH HOH A . C 2 HOH 6 37 37 HOH HOH A . C 2 HOH 7 38 38 HOH HOH A . C 2 HOH 8 39 39 HOH HOH A . C 2 HOH 9 42 42 HOH HOH A . C 2 HOH 10 43 43 HOH HOH A . C 2 HOH 11 44 44 HOH HOH A . C 2 HOH 12 48 48 HOH HOH A . D 2 HOH 1 28 28 HOH HOH B . D 2 HOH 2 29 29 HOH HOH B . D 2 HOH 3 31 31 HOH HOH B . D 2 HOH 4 32 32 HOH HOH B . D 2 HOH 5 35 35 HOH HOH B . D 2 HOH 6 40 40 HOH HOH B . D 2 HOH 7 41 41 HOH HOH B . D 2 HOH 8 45 45 HOH HOH B . D 2 HOH 9 46 46 HOH HOH B . D 2 HOH 10 47 47 HOH HOH B . D 2 HOH 11 49 49 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal NUCLSQ refinement . ? 1 X-PLOR refinement . ? 2 # _cell.entry_id 1D31 _cell.length_a 78.480 _cell.length_b 42.840 _cell.length_c 25.160 _cell.angle_alpha 90.00 _cell.angle_beta 99.36 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D31 _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 # _exptl.entry_id 1D31 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.62 _exptl_crystal.density_percent_sol 53.12 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 277.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.00 _exptl_crystal_grow.pdbx_details 'pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K' _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 SPERMINE ? ? ? 1 4 1 MGCL2 ? ? ? 1 5 1 'NA CACODYLATE' ? ? ? 1 6 2 WATER ? ? ? 1 7 2 MPD ? ? ? 1 8 2 NACL ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 120.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector DIFFRACTOMETER _diffrn_detector.type 'RIGAKU AFC-5R' _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 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type RIGAKU _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 1.5418 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1D31 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low ? _reflns.d_resolution_high 2.000 _reflns.number_obs 5530 _reflns.number_all 6792 _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 1D31 _refine.ls_number_reflns_obs 1640 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 3.000 _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 2.600 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1860000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _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 528 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 23 _refine_hist.number_atoms_total 551 _refine_hist.d_res_high 2.600 _refine_hist.d_res_low 10.000 # _database_PDB_matrix.entry_id 1D31 _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 1D31 _struct.title 'THE THREE-DIMENSIONAL STRUCTURES OF BULGE-CONTAINING DNA FRAGMENTS' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1D31 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA, DOUBLE HELIX, BULGES, FLIPPED-OUT BASE, 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 2 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1D31 _struct_ref.pdbx_db_accession 1D31 _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 1D31 A 1 ? 13 ? 1D31 1 ? 13 ? 1 13 2 1 1D31 B 1 ? 13 ? 1D31 14 ? 26 ? 14 26 # _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 # _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 hydrog1 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 12 N3 ? ? A DG 2 B DC 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 12 O2 ? ? A DG 2 B DC 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 12 N4 ? ? A DG 2 B DC 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 11 N1 ? ? A DC 3 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 11 O6 ? ? A DC 3 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 11 N2 ? ? A DC 3 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 5 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 5 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 5 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 9 N3 ? ? A DA 6 B DT 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 9 O4 ? ? A DA 6 B DT 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 7 B DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 7 B DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 8 B DA 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 8 B DA 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 9 B DA 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 9 B DA 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 5 N1 ? ? A DC 10 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 5 O6 ? ? A DC 10 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 5 N2 ? ? A DC 10 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 11 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 11 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 11 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 12 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 12 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 12 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 12 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 12 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 12 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 13 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 13 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DG 13 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 13 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DG 13 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 13 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 OP2 B DT 21 ? ? O B HOH 47 ? ? 1.92 2 1 OP1 B DG 26 ? ? O B HOH 41 ? ? 2.01 3 1 OP2 A DG 11 ? ? O A HOH 33 ? ? 2.15 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O B HOH 41 ? ? 1_555 O B HOH 41 ? ? 2_555 1.24 2 1 "O5'" A DC 1 ? ? 1_555 "O4'" B DC 14 ? ? 3_444 2.15 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 "C2'" _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 DT _pdbx_validate_rmsd_bond.auth_seq_id_1 22 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 "C1'" _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 DT _pdbx_validate_rmsd_bond.auth_seq_id_2 22 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.451 _pdbx_validate_rmsd_bond.bond_target_value 1.518 _pdbx_validate_rmsd_bond.bond_deviation -0.067 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.010 _pdbx_validate_rmsd_bond.linker_flag 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 "C5'" A DC 1 ? ? "C4'" A DC 1 ? ? "C3'" A DC 1 ? ? 101.82 114.10 -12.28 1.80 N 2 1 OP1 A DG 2 ? ? P A DG 2 ? ? OP2 A DG 2 ? ? 108.41 119.60 -11.19 1.50 N 3 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 102.17 108.00 -5.83 0.70 N 4 1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 111.09 108.30 2.79 0.30 N 5 1 OP1 A DA 4 ? ? P A DA 4 ? ? OP2 A DA 4 ? ? 108.79 119.60 -10.81 1.50 N 6 1 OP1 A DG 5 ? ? P A DG 5 ? ? OP2 A DG 5 ? ? 109.27 119.60 -10.33 1.50 N 7 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 119.72 108.30 11.42 0.30 N 8 1 C5 A DG 5 ? ? C6 A DG 5 ? ? N1 A DG 5 ? ? 114.60 111.50 3.10 0.50 N 9 1 "C3'" A DG 5 ? ? "O3'" A DG 5 ? ? P A DA 6 ? ? 111.24 119.70 -8.46 1.20 Y 10 1 OP1 A DA 6 ? ? P A DA 6 ? ? OP2 A DA 6 ? ? 107.34 119.60 -12.26 1.50 N 11 1 N1 A DA 6 ? ? C2 A DA 6 ? ? N3 A DA 6 ? ? 126.00 129.30 -3.30 0.50 N 12 1 OP1 A DA 7 ? ? P A DA 7 ? ? OP2 A DA 7 ? ? 108.65 119.60 -10.95 1.50 N 13 1 C6 A DA 7 ? ? N1 A DA 7 ? ? C2 A DA 7 ? ? 122.30 118.60 3.70 0.60 N 14 1 N1 A DA 7 ? ? C2 A DA 7 ? ? N3 A DA 7 ? ? 126.17 129.30 -3.13 0.50 N 15 1 C5 A DA 7 ? ? C6 A DA 7 ? ? N1 A DA 7 ? ? 114.09 117.70 -3.61 0.50 N 16 1 OP1 A DT 8 ? ? P A DT 8 ? ? OP2 A DT 8 ? ? 109.72 119.60 -9.88 1.50 N 17 1 "O4'" A DT 8 ? ? "C1'" A DT 8 ? ? N1 A DT 8 ? ? 112.33 108.30 4.03 0.30 N 18 1 N1 A DT 8 ? ? C2 A DT 8 ? ? N3 A DT 8 ? ? 118.77 114.60 4.17 0.60 N 19 1 C2 A DT 8 ? ? N3 A DT 8 ? ? C4 A DT 8 ? ? 121.11 127.20 -6.09 0.60 N 20 1 N3 A DT 8 ? ? C4 A DT 8 ? ? C5 A DT 8 ? ? 119.90 115.20 4.70 0.60 N 21 1 C5 A DT 8 ? ? C4 A DT 8 ? ? O4 A DT 8 ? ? 119.43 124.90 -5.47 0.70 N 22 1 OP1 A DT 9 ? ? P A DT 9 ? ? OP2 A DT 9 ? ? 105.78 119.60 -13.82 1.50 N 23 1 C2 A DT 9 ? ? N3 A DT 9 ? ? C4 A DT 9 ? ? 123.49 127.20 -3.71 0.60 N 24 1 "C3'" A DC 10 ? ? "O3'" A DC 10 ? ? P A DG 11 ? ? 133.36 119.70 13.66 1.20 Y 25 1 C6 A DG 11 ? ? N1 A DG 11 ? ? C2 A DG 11 ? ? 120.41 125.10 -4.69 0.60 N 26 1 C5 A DG 11 ? ? C6 A DG 11 ? ? N1 A DG 11 ? ? 114.85 111.50 3.35 0.50 N 27 1 "C3'" A DG 11 ? ? "O3'" A DG 11 ? ? P A DC 12 ? ? 129.33 119.70 9.63 1.20 Y 28 1 "O4'" A DC 12 ? ? "C1'" A DC 12 ? ? N1 A DC 12 ? ? 113.93 108.30 5.63 0.30 N 29 1 C2 A DC 12 ? ? N3 A DC 12 ? ? C4 A DC 12 ? ? 123.09 119.90 3.19 0.50 N 30 1 "C3'" A DC 12 ? ? "O3'" A DC 12 ? ? P A DG 13 ? ? 135.25 119.70 15.55 1.20 Y 31 1 "C5'" A DG 13 ? ? "C4'" A DG 13 ? ? "C3'" A DG 13 ? ? 102.79 114.10 -11.31 1.80 N 32 1 "C5'" B DC 14 ? ? "C4'" B DC 14 ? ? "C3'" B DC 14 ? ? 102.74 114.10 -11.36 1.80 N 33 1 "O4'" B DC 14 ? ? "C1'" B DC 14 ? ? N1 B DC 14 ? ? 112.81 108.30 4.51 0.30 N 34 1 "C5'" B DG 15 ? ? "C4'" B DG 15 ? ? "C3'" B DG 15 ? ? 101.99 114.10 -12.11 1.80 N 35 1 "O3'" B DG 15 ? ? P B DC 16 ? ? "O5'" B DC 16 ? ? 115.90 104.00 11.90 1.90 Y 36 1 OP1 B DC 16 ? ? P B DC 16 ? ? OP2 B DC 16 ? ? 107.99 119.60 -11.61 1.50 N 37 1 OP1 B DA 17 ? ? P B DA 17 ? ? OP2 B DA 17 ? ? 109.58 119.60 -10.02 1.50 N 38 1 "O4'" B DA 17 ? ? "C1'" B DA 17 ? ? N9 B DA 17 ? ? 114.23 108.30 5.93 0.30 N 39 1 C5 B DA 17 ? ? C6 B DA 17 ? ? N1 B DA 17 ? ? 114.48 117.70 -3.22 0.50 N 40 1 "C3'" B DA 17 ? ? "O3'" B DA 17 ? ? P B DG 18 ? ? 138.61 119.70 18.91 1.20 Y 41 1 OP1 B DG 18 ? ? P B DG 18 ? ? OP2 B DG 18 ? ? 103.32 119.60 -16.28 1.50 N 42 1 N9 B DG 18 ? ? "C1'" B DG 18 ? ? "C2'" B DG 18 ? ? 126.99 114.30 12.69 1.40 N 43 1 "O4'" B DG 18 ? ? "C1'" B DG 18 ? ? N9 B DG 18 ? ? 111.70 108.30 3.40 0.30 N 44 1 C8 B DG 18 ? ? N9 B DG 18 ? ? C4 B DG 18 ? ? 103.90 106.40 -2.50 0.40 N 45 1 OP1 B DA 19 ? ? P B DA 19 ? ? OP2 B DA 19 ? ? 109.94 119.60 -9.66 1.50 N 46 1 OP1 B DA 20 ? ? P B DA 20 ? ? OP2 B DA 20 ? ? 107.70 119.60 -11.90 1.50 N 47 1 OP1 B DT 21 ? ? P B DT 21 ? ? OP2 B DT 21 ? ? 108.66 119.60 -10.94 1.50 N 48 1 "O4'" B DT 21 ? ? "C1'" B DT 21 ? ? N1 B DT 21 ? ? 113.01 108.30 4.71 0.30 N 49 1 "C5'" B DT 22 ? ? "C4'" B DT 22 ? ? "C3'" B DT 22 ? ? 101.42 114.10 -12.68 1.80 N 50 1 "O4'" B DT 22 ? ? "C1'" B DT 22 ? ? "C2'" B DT 22 ? ? 112.20 106.80 5.40 0.50 N 51 1 N1 B DT 22 ? ? "C1'" B DT 22 ? ? "C2'" B DT 22 ? ? 129.30 114.30 15.00 1.40 N 52 1 "O4'" B DT 22 ? ? "C1'" B DT 22 ? ? N1 B DT 22 ? ? 118.40 108.30 10.10 0.30 N 53 1 C6 B DT 22 ? ? N1 B DT 22 ? ? C2 B DT 22 ? ? 118.27 121.30 -3.03 0.50 N 54 1 N1 B DT 22 ? ? C2 B DT 22 ? ? N3 B DT 22 ? ? 118.39 114.60 3.79 0.60 N 55 1 C2 B DT 22 ? ? N3 B DT 22 ? ? C4 B DT 22 ? ? 123.57 127.20 -3.63 0.60 N 56 1 "C3'" B DT 22 ? ? "O3'" B DT 22 ? ? P B DC 23 ? ? 129.27 119.70 9.57 1.20 Y 57 1 OP1 B DC 23 ? ? P B DC 23 ? ? OP2 B DC 23 ? ? 108.78 119.60 -10.82 1.50 N 58 1 "C5'" B DC 23 ? ? "C4'" B DC 23 ? ? "C3'" B DC 23 ? ? 102.39 114.10 -11.71 1.80 N 59 1 C2 B DC 23 ? ? N3 B DC 23 ? ? C4 B DC 23 ? ? 123.05 119.90 3.15 0.50 N 60 1 N3 B DC 23 ? ? C4 B DC 23 ? ? C5 B DC 23 ? ? 119.35 121.90 -2.55 0.40 N 61 1 "C3'" B DC 23 ? ? "O3'" B DC 23 ? ? P B DG 24 ? ? 128.12 119.70 8.42 1.20 Y 62 1 OP1 B DG 24 ? ? P B DG 24 ? ? OP2 B DG 24 ? ? 107.94 119.60 -11.66 1.50 N 63 1 OP1 B DC 25 ? ? P B DC 25 ? ? OP2 B DC 25 ? ? 106.11 119.60 -13.49 1.50 N 64 1 "C5'" B DC 25 ? ? "C4'" B DC 25 ? ? "C3'" B DC 25 ? ? 102.02 114.10 -12.08 1.80 N 65 1 "O4'" B DC 25 ? ? "C1'" B DC 25 ? ? "C2'" B DC 25 ? ? 109.98 106.80 3.18 0.50 N 66 1 "C5'" B DG 26 ? ? "C4'" B DG 26 ? ? "C3'" B DG 26 ? ? 101.46 114.10 -12.64 1.80 N # _pdbx_validate_chiral.id 1 _pdbx_validate_chiral.PDB_model_num 1 _pdbx_validate_chiral.auth_atom_id "C1'" _pdbx_validate_chiral.label_alt_id ? _pdbx_validate_chiral.auth_asym_id B _pdbx_validate_chiral.auth_comp_id DT _pdbx_validate_chiral.auth_seq_id 22 _pdbx_validate_chiral.PDB_ins_code ? _pdbx_validate_chiral.details PLANAR _pdbx_validate_chiral.omega . # 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 DG A 2 ? ? 0.049 'SIDE CHAIN' 2 1 DC B 25 ? ? 0.069 'SIDE CHAIN' # 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 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 # 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 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1D31 'double helix' 1D31 'b-form double helix' 1D31 '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 DG 2 1_555 B DC 12 1_555 0.455 -0.598 0.794 10.293 -6.202 -4.911 1 A_DG2:DC25_B A 2 ? B 25 ? 19 1 1 A DC 3 1_555 B DG 11 1_555 -0.487 -0.417 0.440 -2.553 -12.757 1.262 2 A_DC3:DG24_B A 3 ? B 24 ? 19 1 1 A DG 5 1_555 B DC 10 1_555 0.089 -0.563 0.286 4.321 0.238 -7.225 3 A_DG5:DC23_B A 5 ? B 23 ? 19 1 1 A DA 6 1_555 B DT 9 1_555 0.926 0.136 0.058 -5.102 -7.584 -16.296 4 A_DA6:DT22_B A 6 ? B 22 ? 20 1 1 A DA 7 1_555 B DT 8 1_555 -0.019 -0.087 -0.119 5.784 -17.381 1.600 5 A_DA7:DT21_B A 7 ? B 21 ? 20 1 1 A DT 8 1_555 B DA 7 1_555 -0.351 -0.043 -0.251 -0.338 -30.836 -9.606 6 A_DT8:DA20_B A 8 ? B 20 ? 20 1 1 A DT 9 1_555 B DA 6 1_555 0.078 -0.084 -0.495 5.765 -27.698 0.038 7 A_DT9:DA19_B A 9 ? B 19 ? 20 1 1 A DC 10 1_555 B DG 5 1_555 -0.396 -0.543 0.617 -12.158 -9.813 -2.696 8 A_DC10:DG18_B A 10 ? B 18 ? 19 1 1 A DG 11 1_555 B DC 3 1_555 0.179 0.010 -0.388 -17.051 0.523 -2.057 9 A_DG11:DC16_B A 11 ? B 16 ? 19 1 1 A DC 12 1_555 B DG 2 1_555 0.791 0.060 -0.006 -11.669 -8.291 3.082 10 A_DC12:DG15_B A 12 ? B 15 ? 19 1 1 A DG 13 1_555 B DC 1 1_555 0.455 -0.099 0.574 -6.091 -1.707 7.231 11 A_DG13:DC14_B A 13 ? B 14 ? 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 2 1_555 B DC 12 1_555 A DC 3 1_555 B DG 11 1_555 0.679 0.405 3.804 7.212 -11.330 32.490 2.656 0.138 3.539 -19.256 -12.256 35.088 1 AA_DG2DC3:DG24DC25_BB A 2 ? B 25 ? A 3 ? B 24 ? 1 A DC 3 1_555 B DG 11 1_555 A DG 5 1_555 B DC 10 1_555 -1.981 1.136 6.726 2.876 -9.848 41.965 3.482 3.259 6.177 -13.510 -3.945 43.146 2 AA_DC3DG5:DC23DG24_BB A 3 ? B 24 ? A 5 ? B 23 ? 1 A DG 5 1_555 B DC 10 1_555 A DA 6 1_555 B DT 9 1_555 -0.916 -0.014 3.576 2.685 3.113 45.080 -0.319 1.450 3.510 4.050 -3.493 45.257 3 AA_DG5DA6:DT22DC23_BB A 5 ? B 23 ? A 6 ? B 22 ? 1 A DA 6 1_555 B DT 9 1_555 A DA 7 1_555 B DT 8 1_555 0.301 0.039 2.980 3.882 -5.527 34.832 0.807 0.027 2.955 -9.126 -6.411 35.461 4 AA_DA6DA7:DT21DT22_BB A 6 ? B 22 ? A 7 ? B 21 ? 1 A DA 7 1_555 B DT 8 1_555 A DT 8 1_555 B DA 7 1_555 -0.958 -0.830 3.392 -2.572 3.866 31.456 -2.246 1.262 3.335 7.083 4.711 31.788 5 AA_DA7DT8:DA20DT21_BB A 7 ? B 21 ? A 8 ? B 20 ? 1 A DT 8 1_555 B DA 7 1_555 A DT 9 1_555 B DA 6 1_555 0.091 0.046 2.954 -0.333 1.496 39.482 -0.090 -0.170 2.952 2.213 0.493 39.510 6 AA_DT8DT9:DA19DA20_BB A 8 ? B 20 ? A 9 ? B 19 ? 1 A DT 9 1_555 B DA 6 1_555 A DC 10 1_555 B DG 5 1_555 0.176 -0.516 3.859 -7.657 -2.534 39.760 -0.411 -1.263 3.787 -3.679 11.120 40.537 7 AA_DT9DC10:DG18DA19_BB A 9 ? B 19 ? A 10 ? B 18 ? 1 A DC 10 1_555 B DG 5 1_555 A DG 11 1_555 B DC 3 1_555 0.149 -0.136 3.418 7.612 0.257 38.188 -0.236 0.746 3.384 0.388 -11.495 38.912 8 AA_DC10DG11:DC16DG18_BB A 10 ? B 18 ? A 11 ? B 16 ? 1 A DG 11 1_555 B DC 3 1_555 A DC 12 1_555 B DG 2 1_555 1.686 -0.132 3.424 -1.107 6.683 30.765 -1.534 -3.320 3.262 12.408 2.055 31.485 9 AA_DG11DC12:DG15DC16_BB A 11 ? B 16 ? A 12 ? B 15 ? 1 A DC 12 1_555 B DG 2 1_555 A DG 13 1_555 B DC 1 1_555 0.854 1.817 3.326 -4.857 4.980 40.987 2.015 -1.737 3.396 7.051 6.876 41.548 10 AA_DC12DG13:DC14DG15_BB A 12 ? B 15 ? A 13 ? B 14 ? # _atom_sites.entry_id 1D31 _atom_sites.fract_transf_matrix[1][1] 0.012742 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.002100 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.023343 _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] 0.040282 _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_