data_1D17 # _entry.id 1D17 # _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 1D17 pdb_00001d17 10.2210/pdb1d17/pdb RCSB DDFA16 ? ? WWPDB D_1000172622 ? ? # 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 1991-07-15 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2011-08-24 5 'Structure model' 1 4 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' 'Atomic model' 4 4 'Structure model' 'Derived calculations' 5 5 'Structure model' 'Data collection' 6 5 'Structure model' 'Database references' 7 5 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 5 'Structure model' chem_comp_atom 2 5 'Structure model' chem_comp_bond 3 5 'Structure model' database_2 4 5 'Structure model' struct_conn 5 5 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 4 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 5 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 6 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1D17 _pdbx_database_status.recvd_initial_deposition_date 1990-08-08 _pdbx_database_status.deposit_site BNL _pdbx_database_status.process_site BNL _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Egli, M.' 1 'Williams, L.D.' 2 'Frederick, C.A.' 3 'Rich, A.' 4 # 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 'DNA-nogalamycin interactions.' Biochemistry 30 1364 1372 1991 BICHAW US 0006-2960 0033 ? 1991116 10.1021/bi00219a029 1 'Structure of Nogalamycin Bound to a DNA Hexamer' Proc.Natl.Acad.Sci.USA 87 2225 2229 1990 PNASA6 US 0027-8424 0040 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Egli, M.' 1 ? primary 'Williams, L.D.' 2 ? primary 'Frederick, C.A.' 3 ? primary 'Rich, A.' 4 ? 1 'Williams, L.D.' 5 ? 1 'Egli, M.' 6 ? 1 'Gao, Q.' 7 ? 1 'Bash, P.' 8 ? 1 'Van Der Marel, G.A.' 9 ? 1 'Van Boom, J.H.' 10 ? 1 'Rich, A.' 11 ? 1 'Frederick, C.A.' 12 ? # 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(*(5CM)P*GP*TP*AP*(5CM)P*G)-3') ; 1837.271 1 ? ? ? ? 2 non-polymer syn NOGALAMYCIN 787.803 1 ? ? ? ? 3 water nat water 18.015 39 ? ? ? ? # _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 '(5CM)(DG)(DT)(DA)(5CM)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGTACG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 NOGALAMYCIN NGM 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 5CM n 1 2 DG n 1 3 DT n 1 4 DA n 1 5 5CM n 1 6 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 5CM 'DNA linking' n "5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O7 P' 321.224 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 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 NGM non-polymer . NOGALAMYCIN ? 'C39 H49 N O16' 787.803 # 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 5CM 1 1 1 5CM 5CM A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DT 3 3 3 DT DT A . n A 1 4 DA 4 4 4 DA DA A . n A 1 5 5CM 5 5 5 5CM 5CM A . n A 1 6 DG 6 6 6 DG DG A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 NGM 1 7 7 NGM NGM A . C 3 HOH 1 8 8 HOH HOH A . C 3 HOH 2 9 9 HOH HOH A . C 3 HOH 3 10 10 HOH HOH A . C 3 HOH 4 11 11 HOH HOH A . C 3 HOH 5 12 12 HOH HOH A . C 3 HOH 6 13 13 HOH HOH A . C 3 HOH 7 14 14 HOH HOH A . C 3 HOH 8 15 15 HOH HOH A . C 3 HOH 9 16 16 HOH HOH A . C 3 HOH 10 17 17 HOH HOH A . C 3 HOH 11 18 18 HOH HOH A . C 3 HOH 12 19 19 HOH HOH A . C 3 HOH 13 20 20 HOH HOH A . C 3 HOH 14 21 21 HOH HOH A . C 3 HOH 15 22 22 HOH HOH A . C 3 HOH 16 23 23 HOH HOH A . C 3 HOH 17 24 24 HOH HOH A . C 3 HOH 18 25 25 HOH HOH A . C 3 HOH 19 26 26 HOH HOH A . C 3 HOH 20 27 27 HOH HOH A . C 3 HOH 21 28 28 HOH HOH A . C 3 HOH 22 29 29 HOH HOH A . C 3 HOH 23 30 30 HOH HOH A . C 3 HOH 24 31 31 HOH HOH A . C 3 HOH 25 32 32 HOH HOH A . C 3 HOH 26 33 33 HOH HOH A . C 3 HOH 27 34 34 HOH HOH A . C 3 HOH 28 35 35 HOH HOH A . C 3 HOH 29 36 36 HOH HOH A . C 3 HOH 30 37 37 HOH HOH A . C 3 HOH 31 38 38 HOH HOH A . C 3 HOH 32 39 39 HOH HOH A . C 3 HOH 33 40 40 HOH HOH A . C 3 HOH 34 41 41 HOH HOH A . C 3 HOH 35 42 42 HOH HOH A . C 3 HOH 36 43 43 HOH HOH A . C 3 HOH 37 44 44 HOH HOH A . C 3 HOH 38 45 45 HOH HOH A . C 3 HOH 39 46 46 HOH HOH A . # _software.name X-PLOR _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # _cell.entry_id 1D17 _cell.length_a 26.300 _cell.length_b 26.300 _cell.length_c 100.010 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 1D17 _symmetry.space_group_name_H-M 'P 61 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1D17 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 54.73 _exptl_crystal.density_Matthews 2.72 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details 'ROOM TEMPERATURE' _exptl_crystal_grow.pH 6.00 _exptl_crystal_grow.pdbx_details 'pH 6.00, VAPOR DIFFUSION, SITTING 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 METHANOL ? ? ? 1 4 1 'NA CACODYLATE' ? ? ? 1 5 1 MGCL2 ? ? ? 1 6 1 SPERMINE ? ? ? 1 7 2 WATER ? ? ? 1 8 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 300.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector DIFFRACTOMETER _diffrn_detector.type 'RIGAKU AFC-5' _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 ? # _refine.entry_id 1D17 _refine.ls_number_reflns_obs 809 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low ? _refine.ls_d_res_high 2.000 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.206 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.206 _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_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_overall_phase_error ? _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.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_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 122 _refine_hist.pdbx_number_atoms_ligand 56 _refine_hist.number_atoms_solvent 39 _refine_hist.number_atoms_total 217 _refine_hist.d_res_high 2.000 _refine_hist.d_res_low . # _database_PDB_matrix.entry_id 1D17 _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 1D17 _struct.title 'DNA-NOGALAMYCIN INTERACTIONS' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1D17 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'RIGHT HANDED DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, MODIFIED, 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 2 ? C N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1D17 _struct_ref.pdbx_db_accession 1D17 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1D17 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 6 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1D17 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 6 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 6 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 11_655 -x+y+1,y,-z+1/2 -1.0000000000 0.0000000000 0.0000000000 26.3000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 50.0050000000 # _struct_biol.id 1 _struct_biol.details ? # 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 5CM 1 "O3'" ? ? ? 1_555 A DG 2 P ? ? A 5CM 1 A DG 2 1_555 ? ? ? ? ? ? ? 1.656 ? ? covale2 covale both ? A DA 4 "O3'" ? ? ? 1_555 A 5CM 5 P ? ? A DA 4 A 5CM 5 1_555 ? ? ? ? ? ? ? 1.620 ? ? covale3 covale both ? A 5CM 5 "O3'" ? ? ? 1_555 A DG 6 P ? ? A 5CM 5 A DG 6 1_555 ? ? ? ? ? ? ? 1.643 ? ? hydrog1 hydrog ? ? A 5CM 1 N3 ? ? ? 1_555 A DG 6 N1 ? ? A 5CM 1 A DG 6 11_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A 5CM 1 N4 ? ? ? 1_555 A DG 6 O6 ? ? A 5CM 1 A DG 6 11_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A 5CM 1 O2 ? ? ? 1_555 A DG 6 N2 ? ? A 5CM 1 A DG 6 11_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 A 5CM 5 N3 ? ? A DG 2 A 5CM 5 11_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 A 5CM 5 O2 ? ? A DG 2 A 5CM 5 11_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 A 5CM 5 N4 ? ? A DG 2 A 5CM 5 11_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 A DA 4 N1 ? ? A DT 3 A DA 4 11_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 A DA 4 N6 ? ? A DT 3 A DA 4 11_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 A DT 3 N3 ? ? A DA 4 A DT 3 11_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 A DT 3 O4 ? ? A DA 4 A DT 3 11_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A 5CM 5 N3 ? ? ? 1_555 A DG 2 N1 ? ? A 5CM 5 A DG 2 11_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A 5CM 5 N4 ? ? ? 1_555 A DG 2 O6 ? ? A 5CM 5 A DG 2 11_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A 5CM 5 O2 ? ? ? 1_555 A DG 2 N2 ? ? A 5CM 5 A DG 2 11_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 N1 ? ? ? 1_555 A 5CM 1 N3 ? ? A DG 6 A 5CM 1 11_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 N2 ? ? ? 1_555 A 5CM 1 O2 ? ? A DG 6 A 5CM 1 11_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 O6 ? ? ? 1_555 A 5CM 1 N4 ? ? A DG 6 A 5CM 1 11_655 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A NGM 7 ? 14 'BINDING SITE FOR RESIDUE NGM A 7' 1 ? ? ? ? ? ? ? # 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 14 5CM A 1 ? 5CM A 1 . ? 1_555 ? 2 AC1 14 DG A 2 ? DG A 2 . ? 1_555 ? 3 AC1 14 DG A 2 ? DG A 2 . ? 9_655 ? 4 AC1 14 DT A 3 ? DT A 3 . ? 1_555 ? 5 AC1 14 DT A 3 ? DT A 3 . ? 5_564 ? 6 AC1 14 DA A 4 ? DA A 4 . ? 1_555 ? 7 AC1 14 5CM A 5 ? 5CM A 5 . ? 11_655 ? 8 AC1 14 DG A 6 ? DG A 6 . ? 11_655 ? 9 AC1 14 HOH C . ? HOH A 35 . ? 1_555 ? 10 AC1 14 HOH C . ? HOH A 38 . ? 5_564 ? 11 AC1 14 HOH C . ? HOH A 41 . ? 1_555 ? 12 AC1 14 HOH C . ? HOH A 42 . ? 1_555 ? 13 AC1 14 HOH C . ? HOH A 44 . ? 1_555 ? 14 AC1 14 HOH C . ? HOH A 46 . ? 1_555 ? # 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 C5 A DT 3 ? ? C7 A DT 3 ? ? 1.550 1.496 0.054 0.006 N 2 1 N9 A DA 4 ? ? C4 A DA 4 ? ? 1.337 1.374 -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 "C3'" A 5CM 1 ? ? "O3'" A 5CM 1 ? ? P A DG 2 ? ? 128.67 119.70 8.97 1.20 Y 2 1 "C5'" A DG 2 ? ? "C4'" A DG 2 ? ? "O4'" A DG 2 ? ? 116.43 109.80 6.63 1.10 N 3 1 "C1'" A DG 2 ? ? "O4'" A DG 2 ? ? "C4'" A DG 2 ? ? 100.87 110.10 -9.23 1.00 N 4 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? "C2'" A DG 2 ? ? 100.39 105.90 -5.51 0.80 N 5 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 115.38 108.30 7.08 0.30 N 6 1 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 115.94 108.30 7.64 0.30 N 7 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 103.74 108.00 -4.26 0.70 N 8 1 C5 A DA 4 ? ? N7 A DA 4 ? ? C8 A DA 4 ? ? 100.65 103.90 -3.25 0.50 N 9 1 N7 A DA 4 ? ? C8 A DA 4 ? ? N9 A DA 4 ? ? 117.60 113.80 3.80 0.50 N 10 1 C8 A DA 4 ? ? N9 A DA 4 ? ? C4 A DA 4 ? ? 103.31 105.80 -2.49 0.40 N 11 1 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 112.31 108.30 4.01 0.30 N 12 1 C8 A DG 6 ? ? N9 A DG 6 ? ? C4 A DG 6 ? ? 103.92 106.40 -2.48 0.40 N 13 1 N9 A DG 6 ? ? C4 A DG 6 ? ? C5 A DG 6 ? ? 108.00 105.40 2.60 0.40 N 14 1 N1 A DG 6 ? ? C6 A DG 6 ? ? O6 A DG 6 ? ? 115.56 119.90 -4.34 0.60 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 DT A 3 ? ? 0.133 'SIDE CHAIN' 2 1 DA A 4 ? ? 0.055 'SIDE CHAIN' # 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 5CM 1 A 5CM 1 ? DC ? 2 A 5CM 5 A 5CM 5 ? DC ? # _struct_site_keywords.site_id 1 _struct_site_keywords.text INTERCALATION # 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 5CM N1 N N N 1 5CM C2 C N N 2 5CM N3 N N N 3 5CM C4 C N N 4 5CM C5 C N N 5 5CM C5A C N N 6 5CM C6 C N N 7 5CM O2 O N N 8 5CM N4 N N N 9 5CM "C1'" C N R 10 5CM "C2'" C N N 11 5CM "C3'" C N S 12 5CM "C4'" C N R 13 5CM "O4'" O N N 14 5CM "O3'" O N N 15 5CM "C5'" C N N 16 5CM "O5'" O N N 17 5CM P P N N 18 5CM OP1 O N N 19 5CM OP2 O N N 20 5CM OP3 O N N 21 5CM H5A1 H N N 22 5CM H5A2 H N N 23 5CM H5A3 H N N 24 5CM H6 H N N 25 5CM HN41 H N N 26 5CM HN42 H N N 27 5CM "H1'" H N N 28 5CM "H2'" H N N 29 5CM "H2''" H N N 30 5CM "H3'" H N N 31 5CM "H4'" H N N 32 5CM "HO3'" H N N 33 5CM "H5'" H N N 34 5CM "H5''" H N N 35 5CM HOP2 H N N 36 5CM HOP3 H N N 37 DA OP3 O N N 38 DA P P N N 39 DA OP1 O N N 40 DA OP2 O N N 41 DA "O5'" O N N 42 DA "C5'" C N N 43 DA "C4'" C N R 44 DA "O4'" O N N 45 DA "C3'" C N S 46 DA "O3'" O N N 47 DA "C2'" C N N 48 DA "C1'" C N R 49 DA N9 N Y N 50 DA C8 C Y N 51 DA N7 N Y N 52 DA C5 C Y N 53 DA C6 C Y N 54 DA N6 N N N 55 DA N1 N Y N 56 DA C2 C Y N 57 DA N3 N Y N 58 DA C4 C Y N 59 DA HOP3 H N N 60 DA HOP2 H N N 61 DA "H5'" H N N 62 DA "H5''" H N N 63 DA "H4'" H N N 64 DA "H3'" H N N 65 DA "HO3'" H N N 66 DA "H2'" H N N 67 DA "H2''" H N N 68 DA "H1'" H N N 69 DA H8 H N N 70 DA H61 H N N 71 DA H62 H N N 72 DA H2 H N N 73 DG OP3 O N N 74 DG P P N N 75 DG OP1 O N N 76 DG OP2 O N N 77 DG "O5'" O N N 78 DG "C5'" C N N 79 DG "C4'" C N R 80 DG "O4'" O N N 81 DG "C3'" C N S 82 DG "O3'" O N N 83 DG "C2'" C N N 84 DG "C1'" C N R 85 DG N9 N Y N 86 DG C8 C Y N 87 DG N7 N Y N 88 DG C5 C Y N 89 DG C6 C N N 90 DG O6 O N N 91 DG N1 N N N 92 DG C2 C N N 93 DG N2 N N N 94 DG N3 N N N 95 DG C4 C Y N 96 DG HOP3 H N N 97 DG HOP2 H N N 98 DG "H5'" H N N 99 DG "H5''" H N N 100 DG "H4'" H N N 101 DG "H3'" H N N 102 DG "HO3'" H N N 103 DG "H2'" H N N 104 DG "H2''" H N N 105 DG "H1'" H N N 106 DG H8 H N N 107 DG H1 H N N 108 DG H21 H N N 109 DG H22 H N N 110 DT OP3 O N N 111 DT P P N N 112 DT OP1 O N N 113 DT OP2 O N N 114 DT "O5'" O N N 115 DT "C5'" C N N 116 DT "C4'" C N R 117 DT "O4'" O N N 118 DT "C3'" C N S 119 DT "O3'" O N N 120 DT "C2'" C N N 121 DT "C1'" C N R 122 DT N1 N N N 123 DT C2 C N N 124 DT O2 O N N 125 DT N3 N N N 126 DT C4 C N N 127 DT O4 O N N 128 DT C5 C N N 129 DT C7 C N N 130 DT C6 C N N 131 DT HOP3 H N N 132 DT HOP2 H N N 133 DT "H5'" H N N 134 DT "H5''" H N N 135 DT "H4'" H N N 136 DT "H3'" H N N 137 DT "HO3'" H N N 138 DT "H2'" H N N 139 DT "H2''" H N N 140 DT "H1'" H N N 141 DT H3 H N N 142 DT H71 H N N 143 DT H72 H N N 144 DT H73 H N N 145 DT H6 H N N 146 HOH O O N N 147 HOH H1 H N N 148 HOH H2 H N N 149 NGM C1 C Y N 150 NGM C2 C Y N 151 NGM C3 C Y N 152 NGM C4 C Y N 153 NGM C5 C N N 154 NGM C6 C Y N 155 NGM C7 C N S 156 NGM C8 C N N 157 NGM C9 C N S 158 NGM C10 C N R 159 NGM C11 C Y N 160 NGM C12 C N N 161 NGM C13 C N N 162 NGM C14 C N N 163 NGM C15 C N N 164 NGM C16 C Y N 165 NGM C17 C Y N 166 NGM C18 C Y N 167 NGM C19 C Y N 168 NGM C20 C Y N 169 NGM C21 C Y N 170 NGM C22 C N N 171 NGM C23 C N N 172 NGM C24 C N N 173 NGM C25 C N N 174 NGM C26 C N N 175 NGM C27 C N N 176 NGM C28 C N N 177 NGM C29 C N N 178 NGM C30 C N S 179 NGM C31 C N S 180 NGM C32 C N R 181 NGM C33 C N R 182 NGM C34 C N R 183 NGM "C1'" C N R 184 NGM "C2'" C N R 185 NGM "C3'" C N R 186 NGM "C4'" C N S 187 NGM "C5'" C N S 188 NGM N1 N N N 189 NGM O1 O N N 190 NGM O2 O N N 191 NGM O4 O N N 192 NGM O5 O N N 193 NGM O6 O N N 194 NGM O7 O N N 195 NGM O9 O N N 196 NGM O10 O N N 197 NGM O14 O N N 198 NGM O12 O N N 199 NGM O15 O N N 200 NGM O16 O N N 201 NGM "O1'" O N N 202 NGM "O2'" O N N 203 NGM "O3'" O N N 204 NGM "O4'" O N N 205 NGM H3 H N N 206 NGM H7 H N N 207 NGM H81 H N N 208 NGM H82 H N N 209 NGM H10 H N N 210 NGM H11 H N N 211 NGM H131 H N N 212 NGM H132 H N N 213 NGM H133 H N N 214 NGM H151 H N N 215 NGM H152 H N N 216 NGM H153 H N N 217 NGM H221 H N N 218 NGM H222 H N N 219 NGM H223 H N N 220 NGM H231 H N N 221 NGM H232 H N N 222 NGM H233 H N N 223 NGM H241 H N N 224 NGM H242 H N N 225 NGM H243 H N N 226 NGM H251 H N N 227 NGM H252 H N N 228 NGM H253 H N N 229 NGM H261 H N N 230 NGM H262 H N N 231 NGM H263 H N N 232 NGM H271 H N N 233 NGM H272 H N N 234 NGM H273 H N N 235 NGM H281 H N N 236 NGM H282 H N N 237 NGM H283 H N N 238 NGM H291 H N N 239 NGM H292 H N N 240 NGM H293 H N N 241 NGM H30 H N N 242 NGM H31 H N N 243 NGM H32 H N N 244 NGM H33 H N N 245 NGM "H1'" H N N 246 NGM "H2'" H N N 247 NGM "H4'" H N N 248 NGM "H5'" H N N 249 NGM HO4 H N N 250 NGM HO6 H N N 251 NGM HO9 H N N 252 NGM H15 H N N 253 NGM H16 H N N 254 # 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 5CM N1 C2 sing N N 1 5CM N1 C6 sing N N 2 5CM N1 "C1'" sing N N 3 5CM C2 N3 sing N N 4 5CM C2 O2 doub N N 5 5CM N3 C4 doub N N 6 5CM C4 C5 sing N N 7 5CM C4 N4 sing N N 8 5CM C5 C5A sing N N 9 5CM C5 C6 doub N N 10 5CM C5A H5A1 sing N N 11 5CM C5A H5A2 sing N N 12 5CM C5A H5A3 sing N N 13 5CM C6 H6 sing N N 14 5CM N4 HN41 sing N N 15 5CM N4 HN42 sing N N 16 5CM "C1'" "C2'" sing N N 17 5CM "C1'" "O4'" sing N N 18 5CM "C1'" "H1'" sing N N 19 5CM "C2'" "C3'" sing N N 20 5CM "C2'" "H2'" sing N N 21 5CM "C2'" "H2''" sing N N 22 5CM "C3'" "C4'" sing N N 23 5CM "C3'" "O3'" sing N N 24 5CM "C3'" "H3'" sing N N 25 5CM "C4'" "O4'" sing N N 26 5CM "C4'" "C5'" sing N N 27 5CM "C4'" "H4'" sing N N 28 5CM "O3'" "HO3'" sing N N 29 5CM "C5'" "O5'" sing N N 30 5CM "C5'" "H5'" sing N N 31 5CM "C5'" "H5''" sing N N 32 5CM "O5'" P sing N N 33 5CM P OP1 doub N N 34 5CM P OP2 sing N N 35 5CM P OP3 sing N N 36 5CM OP2 HOP2 sing N N 37 5CM OP3 HOP3 sing N N 38 DA OP3 P sing N N 39 DA OP3 HOP3 sing N N 40 DA P OP1 doub N N 41 DA P OP2 sing N N 42 DA P "O5'" sing N N 43 DA OP2 HOP2 sing N N 44 DA "O5'" "C5'" sing N N 45 DA "C5'" "C4'" sing N N 46 DA "C5'" "H5'" sing N N 47 DA "C5'" "H5''" sing N N 48 DA "C4'" "O4'" sing N N 49 DA "C4'" "C3'" sing N N 50 DA "C4'" "H4'" sing N N 51 DA "O4'" "C1'" sing N N 52 DA "C3'" "O3'" sing N N 53 DA "C3'" "C2'" sing N N 54 DA "C3'" "H3'" sing N N 55 DA "O3'" "HO3'" sing N N 56 DA "C2'" "C1'" sing N N 57 DA "C2'" "H2'" sing N N 58 DA "C2'" "H2''" sing N N 59 DA "C1'" N9 sing N N 60 DA "C1'" "H1'" sing N N 61 DA N9 C8 sing Y N 62 DA N9 C4 sing Y N 63 DA C8 N7 doub Y N 64 DA C8 H8 sing N N 65 DA N7 C5 sing Y N 66 DA C5 C6 sing Y N 67 DA C5 C4 doub Y N 68 DA C6 N6 sing N N 69 DA C6 N1 doub Y N 70 DA N6 H61 sing N N 71 DA N6 H62 sing N N 72 DA N1 C2 sing Y N 73 DA C2 N3 doub Y N 74 DA C2 H2 sing N N 75 DA N3 C4 sing Y N 76 DG OP3 P sing N N 77 DG OP3 HOP3 sing N N 78 DG P OP1 doub N N 79 DG P OP2 sing N N 80 DG P "O5'" sing N N 81 DG OP2 HOP2 sing N N 82 DG "O5'" "C5'" sing N N 83 DG "C5'" "C4'" sing N N 84 DG "C5'" "H5'" sing N N 85 DG "C5'" "H5''" sing N N 86 DG "C4'" "O4'" sing N N 87 DG "C4'" "C3'" sing N N 88 DG "C4'" "H4'" sing N N 89 DG "O4'" "C1'" sing N N 90 DG "C3'" "O3'" sing N N 91 DG "C3'" "C2'" sing N N 92 DG "C3'" "H3'" sing N N 93 DG "O3'" "HO3'" sing N N 94 DG "C2'" "C1'" sing N N 95 DG "C2'" "H2'" sing N N 96 DG "C2'" "H2''" sing N N 97 DG "C1'" N9 sing N N 98 DG "C1'" "H1'" sing N N 99 DG N9 C8 sing Y N 100 DG N9 C4 sing Y N 101 DG C8 N7 doub Y N 102 DG C8 H8 sing N N 103 DG N7 C5 sing Y N 104 DG C5 C6 sing N N 105 DG C5 C4 doub Y N 106 DG C6 O6 doub N N 107 DG C6 N1 sing N N 108 DG N1 C2 sing N N 109 DG N1 H1 sing N N 110 DG C2 N2 sing N N 111 DG C2 N3 doub N N 112 DG N2 H21 sing N N 113 DG N2 H22 sing N N 114 DG N3 C4 sing N N 115 DT OP3 P sing N N 116 DT OP3 HOP3 sing N N 117 DT P OP1 doub N N 118 DT P OP2 sing N N 119 DT P "O5'" sing N N 120 DT OP2 HOP2 sing N N 121 DT "O5'" "C5'" sing N N 122 DT "C5'" "C4'" sing N N 123 DT "C5'" "H5'" sing N N 124 DT "C5'" "H5''" sing N N 125 DT "C4'" "O4'" sing N N 126 DT "C4'" "C3'" sing N N 127 DT "C4'" "H4'" sing N N 128 DT "O4'" "C1'" sing N N 129 DT "C3'" "O3'" sing N N 130 DT "C3'" "C2'" sing N N 131 DT "C3'" "H3'" sing N N 132 DT "O3'" "HO3'" sing N N 133 DT "C2'" "C1'" sing N N 134 DT "C2'" "H2'" sing N N 135 DT "C2'" "H2''" sing N N 136 DT "C1'" N1 sing N N 137 DT "C1'" "H1'" sing N N 138 DT N1 C2 sing N N 139 DT N1 C6 sing N N 140 DT C2 O2 doub N N 141 DT C2 N3 sing N N 142 DT N3 C4 sing N N 143 DT N3 H3 sing N N 144 DT C4 O4 doub N N 145 DT C4 C5 sing N N 146 DT C5 C7 sing N N 147 DT C5 C6 doub N N 148 DT C7 H71 sing N N 149 DT C7 H72 sing N N 150 DT C7 H73 sing N N 151 DT C6 H6 sing N N 152 HOH O H1 sing N N 153 HOH O H2 sing N N 154 NGM C1 C2 doub Y N 155 NGM C1 C16 sing Y N 156 NGM C1 O1 sing N N 157 NGM C2 C3 sing Y N 158 NGM C2 C34 sing N N 159 NGM C3 C4 doub Y N 160 NGM C3 H3 sing N N 161 NGM C4 C17 sing Y N 162 NGM C4 O4 sing N N 163 NGM C5 C17 sing N N 164 NGM C5 C18 sing N N 165 NGM C5 O5 doub N N 166 NGM C6 C18 doub Y N 167 NGM C6 C19 sing Y N 168 NGM C6 O6 sing N N 169 NGM C7 C8 sing N N 170 NGM C7 C19 sing N N 171 NGM C7 O7 sing N N 172 NGM C7 H7 sing N N 173 NGM C8 C9 sing N N 174 NGM C8 H81 sing N N 175 NGM C8 H82 sing N N 176 NGM C9 C10 sing N N 177 NGM C9 C13 sing N N 178 NGM C9 O9 sing N N 179 NGM C10 C14 sing N N 180 NGM C10 C20 sing N N 181 NGM C10 H10 sing N N 182 NGM C11 C20 sing Y N 183 NGM C11 C21 doub Y N 184 NGM C11 H11 sing N N 185 NGM C12 C16 sing N N 186 NGM C12 C21 sing N N 187 NGM C12 O12 doub N N 188 NGM C13 H131 sing N N 189 NGM C13 H132 sing N N 190 NGM C13 H133 sing N N 191 NGM C14 O10 sing N N 192 NGM C14 O14 doub N N 193 NGM C15 O10 sing N N 194 NGM C15 H151 sing N N 195 NGM C15 H152 sing N N 196 NGM C15 H153 sing N N 197 NGM C16 C17 doub Y N 198 NGM C18 C21 sing Y N 199 NGM C19 C20 doub Y N 200 NGM C22 C34 sing N N 201 NGM C22 H221 sing N N 202 NGM C22 H222 sing N N 203 NGM C22 H223 sing N N 204 NGM C23 N1 sing N N 205 NGM C23 H231 sing N N 206 NGM C23 H232 sing N N 207 NGM C23 H233 sing N N 208 NGM C24 N1 sing N N 209 NGM C24 H241 sing N N 210 NGM C24 H242 sing N N 211 NGM C24 H243 sing N N 212 NGM C25 "C5'" sing N N 213 NGM C25 H251 sing N N 214 NGM C25 H252 sing N N 215 NGM C25 H253 sing N N 216 NGM C26 "O4'" sing N N 217 NGM C26 H261 sing N N 218 NGM C26 H262 sing N N 219 NGM C26 H263 sing N N 220 NGM C27 "O3'" sing N N 221 NGM C27 H271 sing N N 222 NGM C27 H272 sing N N 223 NGM C27 H273 sing N N 224 NGM C28 "C3'" sing N N 225 NGM C28 H281 sing N N 226 NGM C28 H282 sing N N 227 NGM C28 H283 sing N N 228 NGM C29 "O2'" sing N N 229 NGM C29 H291 sing N N 230 NGM C29 H292 sing N N 231 NGM C29 H293 sing N N 232 NGM C30 C31 sing N N 233 NGM C30 O1 sing N N 234 NGM C30 O2 sing N N 235 NGM C30 H30 sing N N 236 NGM C31 C32 sing N N 237 NGM C31 O15 sing N N 238 NGM C31 H31 sing N N 239 NGM C32 C33 sing N N 240 NGM C32 N1 sing N N 241 NGM C32 H32 sing N N 242 NGM C33 C34 sing N N 243 NGM C33 O16 sing N N 244 NGM C33 H33 sing N N 245 NGM C34 O2 sing N N 246 NGM "C1'" "C2'" sing N N 247 NGM "C1'" O7 sing N N 248 NGM "C1'" "O1'" sing N N 249 NGM "C1'" "H1'" sing N N 250 NGM "C2'" "C3'" sing N N 251 NGM "C2'" "O2'" sing N N 252 NGM "C2'" "H2'" sing N N 253 NGM "C3'" "C4'" sing N N 254 NGM "C3'" "O3'" sing N N 255 NGM "C4'" "C5'" sing N N 256 NGM "C4'" "O4'" sing N N 257 NGM "C4'" "H4'" sing N N 258 NGM "C5'" "O1'" sing N N 259 NGM "C5'" "H5'" sing N N 260 NGM O4 HO4 sing N N 261 NGM O6 HO6 sing N N 262 NGM O9 HO9 sing N N 263 NGM O15 H15 sing N N 264 NGM O16 H16 sing N N 265 # _ndb_struct_conf_na.entry_id 1D17 _ndb_struct_conf_na.feature 'b-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 5CM 1 1_555 A DG 6 11_655 0.647 -0.449 0.046 12.620 -6.336 -0.820 1 A_5CM1:DG6_A A 1 ? A 6 ? 19 1 1 A DG 2 1_555 A 5CM 5 11_655 -0.803 -0.525 -0.580 -25.238 -0.324 -2.501 2 A_DG2:5CM5_A A 2 ? A 5 ? 19 1 1 A DT 3 1_555 A DA 4 11_655 -0.317 -0.219 0.279 -11.447 -6.537 1.196 3 A_DT3:DA4_A A 3 ? A 4 ? 20 1 1 A DA 4 1_555 A DT 3 11_655 0.317 -0.219 0.279 11.447 -6.537 1.196 4 A_DA4:DT3_A A 4 ? A 3 ? 20 1 1 A 5CM 5 1_555 A DG 2 11_655 0.803 -0.525 -0.580 25.238 -0.324 -2.501 5 A_5CM5:DG2_A A 5 ? A 2 ? 19 1 1 A DG 6 1_555 A 5CM 1 11_655 -0.647 -0.449 0.046 -12.620 -6.336 -0.820 6 A_DG6:5CM1_A A 6 ? A 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A 5CM 1 1_555 A DG 6 11_655 A DG 2 1_555 A 5CM 5 11_655 0.392 0.454 7.377 5.671 2.402 26.677 -0.395 2.370 7.313 5.119 -12.086 27.366 1 AA_5CM1DG2:5CM5DG6_AA A 1 ? A 6 ? A 2 ? A 5 ? 1 A DG 2 1_555 A 5CM 5 11_655 A DT 3 1_555 A DA 4 11_655 -0.816 -0.148 3.041 -7.055 -2.296 27.915 0.196 0.124 3.150 -4.657 14.306 28.865 2 AA_DG2DT3:DA45CM5_AA A 2 ? A 5 ? A 3 ? A 4 ? 1 A DT 3 1_555 A DA 4 11_655 A DA 4 1_555 A DT 3 11_655 0.000 -0.894 2.736 0.000 0.325 42.084 -1.273 0.000 2.729 0.453 0.000 42.085 3 AA_DT3DA4:DT3DA4_AA A 3 ? A 4 ? A 4 ? A 3 ? 1 A DA 4 1_555 A DT 3 11_655 A 5CM 5 1_555 A DG 2 11_655 0.816 -0.148 3.041 7.055 -2.296 27.915 0.196 -0.124 3.150 -4.657 -14.306 28.865 4 AA_DA45CM5:DG2DT3_AA A 4 ? A 3 ? A 5 ? A 2 ? 1 A 5CM 5 1_555 A DG 2 11_655 A DG 6 1_555 A 5CM 1 11_655 -0.392 0.454 7.377 -5.671 2.402 26.677 -0.395 -2.370 7.313 5.119 12.086 27.366 5 AA_5CM5DG6:5CM1DG2_AA A 5 ? A 2 ? A 6 ? A 1 ? # _atom_sites.entry_id 1D17 _atom_sites.fract_transf_matrix[1][1] 0.038023 _atom_sites.fract_transf_matrix[1][2] 0.021952 _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] 0.043905 _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] 0.009999 _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_