data_3QSF # _entry.id 3QSF # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.379 _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 3QSF pdb_00003qsf 10.2210/pdb3qsf/pdb NDB NA0988 ? ? RCSB RCSB064044 ? ? WWPDB D_1000064044 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3QSC 'The same human telomeric G-quadruplex bound to a similar metal-containing ligand (a copper complex).' unspecified PDB 3CE5 'The same human telomeric G-quadruplex bound to an acridine ligand (Braco19)' unspecified PDB 3CCO 'The same human telomeric G-quadruplex bound to a naphthalene diimide ligand.' unspecified PDB 3CDM 'The same human telomeric G-quadruplex bound to a naphthalene diimide ligand.' unspecified PDB 1KF1 'The same human telomeric G-quadruplex in its native (ligand-free) form.' unspecified PDB 1K8P 'The same human telomeric G-quadruplex in its native (ligand-free) form.' unspecified PDB 2HRI 'The same human telomeric G-quadruplex bound to a porphyrin ligand.' unspecified # _pdbx_database_status.entry_id 3QSF _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2011-02-21 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Campbell, N.H.' 1 'Abd Karim, N.H.' 2 'Parkinson, G.N.' 3 'Vilar, R.' 4 'Neidle, S.' 5 # _citation.id primary _citation.title 'Molecular basis of structure-activity relationships between salphen metal complexes and human telomeric DNA quadruplexes.' _citation.journal_abbrev J.Med.Chem. _citation.journal_volume 55 _citation.page_first 209 _citation.page_last 222 _citation.year 2012 _citation.journal_id_ASTM JMCMAR _citation.country US _citation.journal_id_ISSN 0022-2623 _citation.journal_id_CSD 0151 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22112241 _citation.pdbx_database_id_DOI 10.1021/jm201140v # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Campbell, N.H.' 1 ? primary 'Karim, N.H.' 2 ? primary 'Parkinson, G.N.' 3 ? primary 'Gunaratnam, M.' 4 ? primary 'Petrucci, V.' 5 ? primary 'Todd, A.K.' 6 ? primary 'Vilar, R.' 7 ? primary 'Neidle, S.' 8 ? # _cell.length_a 44.020 _cell.length_b 54.909 _cell.length_c 33.691 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 3QSF _cell.pdbx_unique_axis ? _cell.Z_PDB 8 _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.space_group_name_H-M 'C 2 2 2' _symmetry.entry_id 3QSF _symmetry.Int_Tables_number 21 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # 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 "5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*T)-3'" 3773.462 1 ? ? ? 'Human telomeric G-quadruplex DNA' 2 non-polymer syn 'POTASSIUM ION' 39.098 3 ? ? ? ? 3 non-polymer syn ;[2,2'-{(4,5-difluorobenzene-1,2-diyl)bis[(nitrilo-kappaN)methylylidene]}bis{5-[2-(piperidin-1-yl)ethoxy]phenolato-kappa O}(2-)]nickel (II) ; 663.380 1 ? ? ? ? 4 water nat water 18.015 20 ? ? ? ? # _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 '(DA)(DG)(DG)(DG)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT)' _entity_poly.pdbx_seq_one_letter_code_can AGGGTTAGGGTT _entity_poly.pdbx_strand_id X _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 DA n 1 2 DG n 1 3 DG n 1 4 DG n 1 5 DT n 1 6 DT n 1 7 DA n 1 8 DG n 1 9 DG n 1 10 DG n 1 11 DT n 1 12 DT n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'This sequence occurs naturally in humans' # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 3QSF _struct_ref.pdbx_db_accession 3QSF _struct_ref.entity_id 1 _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 3QSF _struct_ref_seq.pdbx_strand_id X _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 12 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3QSF _struct_ref_seq.db_align_beg 1001 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 1012 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1001 _struct_ref_seq.pdbx_auth_seq_align_end 1012 # 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 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 K non-polymer . 'POTASSIUM ION' ? 'K 1' 39.098 NUF non-polymer . ;[2,2'-{(4,5-difluorobenzene-1,2-diyl)bis[(nitrilo-kappaN)methylylidene]}bis{5-[2-(piperidin-1-yl)ethoxy]phenolato-kappa O}(2-)]nickel (II) ; 'N,N-Bis[4-[[1-(2-ethyl)piperidine]oxy]salicylidene]-4,5-difluoro-1,2-phenylenediamine-Nickel (II)' 'C34 H38 F2 N4 Ni O4' 663.380 # _exptl.crystals_number 1 _exptl.entry_id 3QSF _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.70 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 54.40 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.temp 293.15 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details ;Initial conditions in the 3 ul drop were: 1.25mM quadruplex DNA, 1.25mM ligand, 0.83% PEG (w/v) 10 000, 16.7mM potassium chloride, 16.7mM sodium chloride, 16.7mM lithium sulphate and 20 mM potassium cacodylate buffer at pH 7.0. This was equilibrated against a reservoir well solution of 50% (w/v) PEG 10000 , VAPOR DIFFUSION, HANGING DROP, temperature 293.15K ; _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 105 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315r' _diffrn_detector.pdbx_collection_date 2010-06-28 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.48660 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'DIAMOND BEAMLINE I03' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.48660 _diffrn_source.pdbx_synchrotron_site Diamond _diffrn_source.pdbx_synchrotron_beamline I03 # _reflns.entry_id 3QSF _reflns.d_resolution_high 2.308 _reflns.d_resolution_low 22.010 _reflns.number_all 1888 _reflns.number_obs 1888 _reflns.pdbx_netI_over_sigmaI 15.100 _reflns.pdbx_Rsym_value 0.053 _reflns.pdbx_redundancy 3.500 _reflns.percent_possible_obs 97.400 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.pdbx_Rmerge_I_obs ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 2.310 2.430 ? 658 ? 0.153 4.600 0.153 ? 2.700 ? 242 89.800 1 1 2.430 2.580 ? 981 ? 0.110 6.100 0.110 ? 3.700 ? 263 99.200 2 1 2.580 2.760 ? 919 ? 0.082 6.700 0.082 ? 3.800 ? 245 100.000 3 1 2.760 2.980 ? 863 ? 0.074 8.700 0.074 ? 3.800 ? 228 100.000 4 1 2.980 3.260 ? 829 ? 0.053 10.700 0.053 ? 3.800 ? 219 99.700 5 1 3.260 3.650 ? 675 ? 0.052 7.500 0.052 ? 3.600 ? 185 98.500 6 1 3.650 4.210 ? 634 ? 0.058 9.800 0.058 ? 3.500 ? 179 100.000 7 1 4.210 5.160 ? 531 ? 0.040 14.900 0.040 ? 3.500 ? 150 99.600 8 1 5.160 7.290 ? 389 ? 0.045 12.100 0.045 ? 3.300 ? 118 96.100 9 1 7.290 22.010 ? 183 ? 0.043 14.800 0.043 ? 3.100 ? 59 80.500 10 1 # _refine.entry_id 3QSF _refine.ls_d_res_high 2.4000 _refine.ls_d_res_low 15.0000 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 97.0000 _refine.ls_number_reflns_obs 1684 _refine.ls_number_reflns_all 1684 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2404 _refine.ls_R_factor_R_work 0.2369 _refine.ls_wR_factor_R_work 0.2714 _refine.ls_R_factor_R_free 0.3203 _refine.ls_wR_factor_R_free 0.3649 _refine.ls_percent_reflns_R_free 4.6000 _refine.ls_number_reflns_R_free 77 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 34.0311 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 0.7300 _refine.aniso_B[2][2] -0.0700 _refine.aniso_B[3][3] -0.6600 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9360 _refine.correlation_coeff_Fo_to_Fc_free 0.8720 _refine.overall_SU_R_Cruickshank_DPI 0.4976 _refine.overall_SU_R_free 0.3403 _refine.pdbx_overall_ESU_R_Free 0.3400 _refine.overall_SU_ML 0.2110 _refine.overall_SU_B 9.9490 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.4000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model 3QSC _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.7240 _refine.B_iso_max 68.950 _refine.B_iso_min 4.510 _refine.occupancy_max 1.000 _refine.occupancy_min 0.250 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _refine.pdbx_diffrn_id 1 _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 231 _refine_hist.pdbx_number_atoms_ligand 48 _refine_hist.number_atoms_solvent 20 _refine_hist.number_atoms_total 299 _refine_hist.d_res_high 2.4000 _refine_hist.d_res_low 15.0000 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 312 0.014 0.021 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 478 1.608 3.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 45 0.059 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 169 0.021 0.020 ? 'X-RAY DIFFRACTION' ? r_scbond_it 312 2.864 3.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 478 4.428 4.500 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 2.4000 _refine_ls_shell.d_res_low 2.4610 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 92.9700 _refine_ls_shell.number_reflns_R_work 114 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.3810 _refine_ls_shell.R_factor_R_free 0.3470 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 5 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 119 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3QSF _struct.title 'The first crystal structure of a human telomeric G-quadruplex DNA bound to a metal-containing ligand (a nickel complex)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3QSF _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Parallel, telomere, nickel, drug, DNA, metal complex' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 4 ? # _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 metalc1 metalc ? ? A DG 2 O6 ? ? ? 1_555 C K . K ? ? X DG 1002 X K 2014 1_555 ? ? ? ? ? ? ? 2.721 ? ? metalc2 metalc ? ? A DG 2 O6 ? ? ? 1_555 D K . K ? ? X DG 1002 X K 2015 1_555 ? ? ? ? ? ? ? 2.353 ? ? metalc3 metalc ? ? A DG 3 O6 ? ? ? 1_555 B K . K ? ? X DG 1003 X K 2013 1_555 ? ? ? ? ? ? ? 2.882 ? ? metalc4 metalc ? ? A DG 3 O6 ? ? ? 1_555 C K . K ? ? X DG 1003 X K 2014 1_555 ? ? ? ? ? ? ? 2.951 ? ? metalc5 metalc ? ? A DG 4 O6 ? ? ? 1_555 B K . K ? ? X DG 1004 X K 2013 1_555 ? ? ? ? ? ? ? 2.876 ? ? metalc6 metalc ? ? A DG 8 O6 ? ? ? 1_555 C K . K ? ? X DG 1008 X K 2014 1_555 ? ? ? ? ? ? ? 2.750 ? ? metalc7 metalc ? ? A DG 8 O6 ? ? ? 1_555 D K . K ? ? X DG 1008 X K 2015 1_555 ? ? ? ? ? ? ? 2.411 ? ? metalc8 metalc ? ? A DG 9 O6 ? ? ? 1_555 B K . K ? ? X DG 1009 X K 2013 1_555 ? ? ? ? ? ? ? 2.739 ? ? metalc9 metalc ? ? A DG 9 O6 ? ? ? 1_555 C K . K ? ? X DG 1009 X K 2014 1_555 ? ? ? ? ? ? ? 2.842 ? ? metalc10 metalc ? ? A DG 10 O6 ? ? ? 1_555 B K . K ? ? X DG 1010 X K 2013 1_555 ? ? ? ? ? ? ? 2.582 ? ? hydrog1 hydrog ? ? A DG 2 N1 ? ? ? 1_555 A DG 8 O6 ? ? X DG 1002 X DG 1008 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog2 hydrog ? ? A DG 2 N2 ? ? ? 1_555 A DG 8 N7 ? ? X DG 1002 X DG 1008 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog3 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DG 9 O6 ? ? X DG 1003 X DG 1009 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog4 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DG 9 N7 ? ? X DG 1003 X DG 1009 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog5 hydrog ? ? A DG 4 N1 ? ? ? 1_555 A DG 10 O6 ? ? X DG 1004 X DG 1010 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog6 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A DG 10 N7 ? ? X DG 1004 X DG 1010 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? 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 X K 2013 ? 10 'BINDING SITE FOR RESIDUE K X 2013' AC2 Software X K 2014 ? 12 'BINDING SITE FOR RESIDUE K X 2014' AC3 Software X K 2015 ? 10 'BINDING SITE FOR RESIDUE K X 2015' AC4 Software X NUF 3016 ? 8 'BINDING SITE FOR RESIDUE NUF X 3016' # 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 10 DG A 3 ? DG X 1003 . ? 1_555 ? 2 AC1 10 DG A 3 ? DG X 1003 . ? 2_665 ? 3 AC1 10 DG A 4 ? DG X 1004 . ? 1_555 ? 4 AC1 10 DG A 4 ? DG X 1004 . ? 2_665 ? 5 AC1 10 DG A 9 ? DG X 1009 . ? 2_665 ? 6 AC1 10 DG A 9 ? DG X 1009 . ? 1_555 ? 7 AC1 10 DG A 10 ? DG X 1010 . ? 2_665 ? 8 AC1 10 DG A 10 ? DG X 1010 . ? 1_555 ? 9 AC1 10 K C . ? K X 2014 . ? 2_665 ? 10 AC1 10 K C . ? K X 2014 . ? 1_555 ? 11 AC2 12 DG A 2 ? DG X 1002 . ? 1_555 ? 12 AC2 12 DG A 2 ? DG X 1002 . ? 2_665 ? 13 AC2 12 DG A 3 ? DG X 1003 . ? 2_665 ? 14 AC2 12 DG A 3 ? DG X 1003 . ? 1_555 ? 15 AC2 12 DG A 8 ? DG X 1008 . ? 2_665 ? 16 AC2 12 DG A 8 ? DG X 1008 . ? 1_555 ? 17 AC2 12 DG A 9 ? DG X 1009 . ? 1_555 ? 18 AC2 12 DG A 9 ? DG X 1009 . ? 2_665 ? 19 AC2 12 K B . ? K X 2013 . ? 2_665 ? 20 AC2 12 K B . ? K X 2013 . ? 1_555 ? 21 AC2 12 K D . ? K X 2015 . ? 2_665 ? 22 AC2 12 K D . ? K X 2015 . ? 1_555 ? 23 AC3 10 DG A 2 ? DG X 1002 . ? 1_555 ? 24 AC3 10 DG A 2 ? DG X 1002 . ? 2_665 ? 25 AC3 10 DG A 2 ? DG X 1002 . ? 3_656 ? 26 AC3 10 DG A 2 ? DG X 1002 . ? 4_566 ? 27 AC3 10 DG A 8 ? DG X 1008 . ? 1_555 ? 28 AC3 10 DG A 8 ? DG X 1008 . ? 2_665 ? 29 AC3 10 DG A 8 ? DG X 1008 . ? 3_656 ? 30 AC3 10 DG A 8 ? DG X 1008 . ? 4_566 ? 31 AC3 10 K C . ? K X 2014 . ? 2_665 ? 32 AC3 10 K C . ? K X 2014 . ? 1_555 ? 33 AC4 8 DG A 4 ? DG X 1004 . ? 1_555 ? 34 AC4 8 DG A 4 ? DG X 1004 . ? 2_665 ? 35 AC4 8 DT A 5 ? DT X 1005 . ? 1_555 ? 36 AC4 8 DG A 10 ? DG X 1010 . ? 1_555 ? 37 AC4 8 DG A 10 ? DG X 1010 . ? 2_665 ? 38 AC4 8 DT A 11 ? DT X 1011 . ? 4_565 ? 39 AC4 8 DT A 11 ? DT X 1011 . ? 1_555 ? 40 AC4 8 DT A 11 ? DT X 1011 . ? 2_665 ? # _atom_sites.entry_id 3QSF _atom_sites.fract_transf_matrix[1][1] 0.022717 _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] 0.018212 _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] 0.029682 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C F K N NI 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 DA 1 1001 1001 DA A X . n A 1 2 DG 2 1002 1002 DG G X . n A 1 3 DG 3 1003 1003 DG G X . n A 1 4 DG 4 1004 1004 DG G X . n A 1 5 DT 5 1005 1005 DT T X . n A 1 6 DT 6 1006 1006 DT T X . n A 1 7 DA 7 1007 1007 DA A X . n A 1 8 DG 8 1008 1008 DG G X . n A 1 9 DG 9 1009 1009 DG G X . n A 1 10 DG 10 1010 1010 DG G X . n A 1 11 DT 11 1011 1011 DT T X . n A 1 12 DT 12 1012 ? ? ? X . 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 K 1 2013 2013 K K X . C 2 K 1 2014 2014 K K X . D 2 K 1 2015 2015 K K X . E 3 NUF 1 3016 3016 NUF NUF X . F 4 HOH 1 1 1 HOH HOH X . F 4 HOH 2 2 2 HOH HOH X . F 4 HOH 3 3 3 HOH HOH X . F 4 HOH 4 4 4 HOH HOH X . F 4 HOH 5 5 5 HOH HOH X . F 4 HOH 6 6 6 HOH HOH X . F 4 HOH 7 7 7 HOH HOH X . F 4 HOH 8 8 8 HOH HOH X . F 4 HOH 9 9 9 HOH HOH X . F 4 HOH 10 10 10 HOH HOH X . F 4 HOH 11 11 11 HOH HOH X . F 4 HOH 12 12 12 HOH HOH X . F 4 HOH 13 13 13 HOH HOH X . F 4 HOH 14 14 14 HOH HOH X . F 4 HOH 15 15 15 HOH HOH X . F 4 HOH 16 16 16 HOH HOH X . F 4 HOH 17 17 17 HOH HOH X . F 4 HOH 18 18 18 HOH HOH X . F 4 HOH 19 19 19 HOH HOH X . F 4 HOH 20 20 20 HOH HOH X . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1730 ? 1 MORE -1 ? 1 'SSA (A^2)' 4770 ? # 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' 2_665 -x+1,-y+1,z -1.0000000000 0.0000000000 0.0000000000 44.0200000000 0.0000000000 -1.0000000000 0.0000000000 54.9090000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 X K 2013 ? B K . 2 1 X K 2014 ? C K . 3 1 X K 2015 ? D K . 4 1 X HOH 20 ? F HOH . # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O6 ? A DG 2 ? X DG 1002 ? 1_555 K ? C K . ? X K 2014 ? 1_555 O6 ? A DG 3 ? X DG 1003 ? 1_555 78.9 ? 2 O6 ? A DG 2 ? X DG 1002 ? 1_555 K ? C K . ? X K 2014 ? 1_555 O6 ? A DG 8 ? X DG 1008 ? 1_555 66.1 ? 3 O6 ? A DG 3 ? X DG 1003 ? 1_555 K ? C K . ? X K 2014 ? 1_555 O6 ? A DG 8 ? X DG 1008 ? 1_555 91.1 ? 4 O6 ? A DG 2 ? X DG 1002 ? 1_555 K ? C K . ? X K 2014 ? 1_555 O6 ? A DG 9 ? X DG 1009 ? 1_555 135.5 ? 5 O6 ? A DG 3 ? X DG 1003 ? 1_555 K ? C K . ? X K 2014 ? 1_555 O6 ? A DG 9 ? X DG 1009 ? 1_555 68.4 ? 6 O6 ? A DG 8 ? X DG 1008 ? 1_555 K ? C K . ? X K 2014 ? 1_555 O6 ? A DG 9 ? X DG 1009 ? 1_555 84.6 ? 7 O6 ? A DG 2 ? X DG 1002 ? 1_555 K ? D K . ? X K 2015 ? 1_555 O6 ? A DG 8 ? X DG 1008 ? 1_555 77.6 ? 8 O6 ? A DG 3 ? X DG 1003 ? 1_555 K ? B K . ? X K 2013 ? 1_555 O6 ? A DG 4 ? X DG 1004 ? 1_555 68.2 ? 9 O6 ? A DG 3 ? X DG 1003 ? 1_555 K ? B K . ? X K 2013 ? 1_555 O6 ? A DG 9 ? X DG 1009 ? 1_555 70.8 ? 10 O6 ? A DG 4 ? X DG 1004 ? 1_555 K ? B K . ? X K 2013 ? 1_555 O6 ? A DG 9 ? X DG 1009 ? 1_555 93.8 ? 11 O6 ? A DG 3 ? X DG 1003 ? 1_555 K ? B K . ? X K 2013 ? 1_555 O6 ? A DG 10 ? X DG 1010 ? 1_555 133.7 ? 12 O6 ? A DG 4 ? X DG 1004 ? 1_555 K ? B K . ? X K 2013 ? 1_555 O6 ? A DG 10 ? X DG 1010 ? 1_555 83.6 ? 13 O6 ? A DG 9 ? X DG 1009 ? 1_555 K ? B K . ? X K 2013 ? 1_555 O6 ? A DG 10 ? X DG 1010 ? 1_555 75.4 ? # 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 2011-12-07 2 'Structure model' 1 1 2012-04-18 3 'Structure model' 1 2 2023-09-13 # _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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Refinement description' 6 3 'Structure model' 'Structure summary' # 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 3 'Structure model' chem_comp 2 3 'Structure model' chem_comp_atom 3 3 'Structure model' chem_comp_bond 4 3 'Structure model' database_2 5 3 'Structure model' entity 6 3 'Structure model' pdbx_entity_nonpoly 7 3 'Structure model' pdbx_initial_refinement_model 8 3 'Structure model' pdbx_struct_conn_angle 9 3 'Structure model' struct_conn 10 3 '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 3 'Structure model' '_chem_comp.name' 2 3 'Structure model' '_database_2.pdbx_DOI' 3 3 'Structure model' '_database_2.pdbx_database_accession' 4 3 'Structure model' '_entity.pdbx_description' 5 3 'Structure model' '_pdbx_entity_nonpoly.name' 6 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 7 3 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 8 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 9 3 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 10 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 11 3 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 12 3 'Structure model' '_pdbx_struct_conn_angle.value' 13 3 'Structure model' '_struct_conn.pdbx_dist_value' 14 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 15 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 16 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 17 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 18 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 19 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 20 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_phasing_MR.entry_id 3QSF _pdbx_phasing_MR.method_rotation ? _pdbx_phasing_MR.method_translation ? _pdbx_phasing_MR.model_details 'Phaser MODE: MR_AUTO' _pdbx_phasing_MR.R_factor 36.360 _pdbx_phasing_MR.R_rigid_body ? _pdbx_phasing_MR.correlation_coeff_Fo_to_Fc ? _pdbx_phasing_MR.correlation_coeff_Io_to_Ic ? _pdbx_phasing_MR.d_res_high_rotation 2.500 _pdbx_phasing_MR.d_res_low_rotation 22.010 _pdbx_phasing_MR.d_res_high_translation 2.500 _pdbx_phasing_MR.d_res_low_translation 22.010 _pdbx_phasing_MR.packing ? _pdbx_phasing_MR.reflns_percent_rotation ? _pdbx_phasing_MR.reflns_percent_translation ? _pdbx_phasing_MR.sigma_F_rotation ? _pdbx_phasing_MR.sigma_F_translation ? _pdbx_phasing_MR.sigma_I_rotation ? _pdbx_phasing_MR.sigma_I_translation ? # _phasing.method MR # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 SCALA 3.3.16 2010/01/06 other 'Phil R. Evans' pre@mrc-lmb.cam.ac.uk 'data scaling' http://www.ccp4.ac.uk/dist/html/scala.html Fortran_77 ? 2 PHASER 2.1.4 'Wed Jun 24 14:00:05 2009' program 'Randy J. Read' cimr-phaser@lists.cam.ac.uk phasing http://www-structmed.cimr.cam.ac.uk/phaser/ ? ? 3 REFMAC . ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 4 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 5 ADSC Quantum ? ? ? ? 'data collection' ? ? ? 6 XDS . ? ? ? ? 'data reduction' ? ? ? # 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 "O3'" X DT 1005 ? ? "C3'" X DT 1005 ? ? 1.361 1.419 -0.058 0.006 N 2 1 "O3'" X DA 1007 ? ? "C3'" X DA 1007 ? ? 1.373 1.419 -0.046 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 "O4'" X DG 1004 ? ? "C1'" X DG 1004 ? ? N9 X DG 1004 ? ? 111.46 108.30 3.16 0.30 N 2 1 "O4'" X DG 1008 ? ? "C1'" X DG 1008 ? ? N9 X DG 1008 ? ? 112.00 108.30 3.70 0.30 N 3 1 "O4'" X DG 1010 ? ? "C1'" X DG 1010 ? ? N9 X DG 1010 ? ? 110.78 108.30 2.48 0.30 N 4 1 "O4'" X DT 1011 ? ? "C1'" X DT 1011 ? ? N1 X DT 1011 ? ? 111.40 108.30 3.10 0.30 N 5 1 N3 X DT 1011 ? ? C4 X DT 1011 ? ? O4 X DT 1011 ? ? 123.50 119.90 3.60 0.60 N # _pdbx_unobs_or_zero_occ_residues.id 1 _pdbx_unobs_or_zero_occ_residues.PDB_model_num 1 _pdbx_unobs_or_zero_occ_residues.polymer_flag Y _pdbx_unobs_or_zero_occ_residues.occupancy_flag 1 _pdbx_unobs_or_zero_occ_residues.auth_asym_id X _pdbx_unobs_or_zero_occ_residues.auth_comp_id DT _pdbx_unobs_or_zero_occ_residues.auth_seq_id 1012 _pdbx_unobs_or_zero_occ_residues.PDB_ins_code ? _pdbx_unobs_or_zero_occ_residues.label_asym_id A _pdbx_unobs_or_zero_occ_residues.label_comp_id DT _pdbx_unobs_or_zero_occ_residues.label_seq_id 12 # 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 DG OP3 O N N 37 DG P P N N 38 DG OP1 O N N 39 DG OP2 O N N 40 DG "O5'" O N N 41 DG "C5'" C N N 42 DG "C4'" C N R 43 DG "O4'" O N N 44 DG "C3'" C N S 45 DG "O3'" O N N 46 DG "C2'" C N N 47 DG "C1'" C N R 48 DG N9 N Y N 49 DG C8 C Y N 50 DG N7 N Y N 51 DG C5 C Y N 52 DG C6 C N N 53 DG O6 O N N 54 DG N1 N N N 55 DG C2 C N N 56 DG N2 N N N 57 DG N3 N N N 58 DG C4 C Y N 59 DG HOP3 H N N 60 DG HOP2 H N N 61 DG "H5'" H N N 62 DG "H5''" H N N 63 DG "H4'" H N N 64 DG "H3'" H N N 65 DG "HO3'" H N N 66 DG "H2'" H N N 67 DG "H2''" H N N 68 DG "H1'" H N N 69 DG H8 H N N 70 DG H1 H N N 71 DG H21 H N N 72 DG H22 H N N 73 DT OP3 O N N 74 DT P P N N 75 DT OP1 O N N 76 DT OP2 O N N 77 DT "O5'" O N N 78 DT "C5'" C N N 79 DT "C4'" C N R 80 DT "O4'" O N N 81 DT "C3'" C N S 82 DT "O3'" O N N 83 DT "C2'" C N N 84 DT "C1'" C N R 85 DT N1 N N N 86 DT C2 C N N 87 DT O2 O N N 88 DT N3 N N N 89 DT C4 C N N 90 DT O4 O N N 91 DT C5 C N N 92 DT C7 C N N 93 DT C6 C N N 94 DT HOP3 H N N 95 DT HOP2 H N N 96 DT "H5'" H N N 97 DT "H5''" H N N 98 DT "H4'" H N N 99 DT "H3'" H N N 100 DT "HO3'" H N N 101 DT "H2'" H N N 102 DT "H2''" H N N 103 DT "H1'" H N N 104 DT H3 H N N 105 DT H71 H N N 106 DT H72 H N N 107 DT H73 H N N 108 DT H6 H N N 109 HOH O O N N 110 HOH H1 H N N 111 HOH H2 H N N 112 K K K N N 113 NUF C1 C Y N 114 NUF F1 F N N 115 NUF N1 N N N 116 NUF O1 O N N 117 NUF NI1 NI N N 118 NUF C2 C Y N 119 NUF F2 F N N 120 NUF N2 N N N 121 NUF O2 O N N 122 NUF C3 C Y N 123 NUF N3 N N N 124 NUF O3 O N N 125 NUF C4 C Y N 126 NUF N4 N N N 127 NUF O4 O N N 128 NUF C5 C Y N 129 NUF C6 C Y N 130 NUF C7 C N N 131 NUF C8 C Y N 132 NUF C9 C Y N 133 NUF C10 C Y N 134 NUF C11 C Y N 135 NUF C12 C Y N 136 NUF C13 C Y N 137 NUF C14 C N N 138 NUF C15 C Y N 139 NUF C16 C Y N 140 NUF C17 C Y N 141 NUF C18 C Y N 142 NUF C19 C Y N 143 NUF C20 C Y N 144 NUF C21 C N N 145 NUF C22 C N N 146 NUF C23 C N N 147 NUF C24 C N N 148 NUF C25 C N N 149 NUF C26 C N N 150 NUF C27 C N N 151 NUF C28 C N N 152 NUF C29 C N N 153 NUF C30 C N N 154 NUF C31 C N N 155 NUF C32 C N N 156 NUF C33 C N N 157 NUF C34 C N N 158 NUF H2 H N N 159 NUF H4 H N N 160 NUF H5 H N N 161 NUF H7 H N N 162 NUF H9 H N N 163 NUF H12 H N N 164 NUF H14 H N N 165 NUF H16 H N N 166 NUF H17 H N N 167 NUF H19 H N N 168 NUF H21 H N N 169 NUF H21A H N N 170 NUF H22 H N N 171 NUF H22A H N N 172 NUF H23 H N N 173 NUF H23A H N N 174 NUF H24 H N N 175 NUF H24A H N N 176 NUF H25 H N N 177 NUF H25A H N N 178 NUF H26 H N N 179 NUF H26A H N N 180 NUF H27 H N N 181 NUF H27A H N N 182 NUF H28 H N N 183 NUF H28A H N N 184 NUF H29 H N N 185 NUF H29A H N N 186 NUF H30 H N N 187 NUF H30A H N N 188 NUF H31 H N N 189 NUF H31A H N N 190 NUF H32 H N N 191 NUF H32A H N N 192 NUF H33 H N N 193 NUF H33A H N N 194 NUF H34 H N N 195 NUF H34A H N N 196 # 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 DG OP3 P sing N N 39 DG OP3 HOP3 sing N N 40 DG P OP1 doub N N 41 DG P OP2 sing N N 42 DG P "O5'" sing N N 43 DG OP2 HOP2 sing N N 44 DG "O5'" "C5'" sing N N 45 DG "C5'" "C4'" sing N N 46 DG "C5'" "H5'" sing N N 47 DG "C5'" "H5''" sing N N 48 DG "C4'" "O4'" sing N N 49 DG "C4'" "C3'" sing N N 50 DG "C4'" "H4'" sing N N 51 DG "O4'" "C1'" sing N N 52 DG "C3'" "O3'" sing N N 53 DG "C3'" "C2'" sing N N 54 DG "C3'" "H3'" sing N N 55 DG "O3'" "HO3'" sing N N 56 DG "C2'" "C1'" sing N N 57 DG "C2'" "H2'" sing N N 58 DG "C2'" "H2''" sing N N 59 DG "C1'" N9 sing N N 60 DG "C1'" "H1'" sing N N 61 DG N9 C8 sing Y N 62 DG N9 C4 sing Y N 63 DG C8 N7 doub Y N 64 DG C8 H8 sing N N 65 DG N7 C5 sing Y N 66 DG C5 C6 sing N N 67 DG C5 C4 doub Y N 68 DG C6 O6 doub N N 69 DG C6 N1 sing N N 70 DG N1 C2 sing N N 71 DG N1 H1 sing N N 72 DG C2 N2 sing N N 73 DG C2 N3 doub N N 74 DG N2 H21 sing N N 75 DG N2 H22 sing N N 76 DG N3 C4 sing N N 77 DT OP3 P sing N N 78 DT OP3 HOP3 sing N N 79 DT P OP1 doub N N 80 DT P OP2 sing N N 81 DT P "O5'" sing N N 82 DT OP2 HOP2 sing N N 83 DT "O5'" "C5'" sing N N 84 DT "C5'" "C4'" sing N N 85 DT "C5'" "H5'" sing N N 86 DT "C5'" "H5''" sing N N 87 DT "C4'" "O4'" sing N N 88 DT "C4'" "C3'" sing N N 89 DT "C4'" "H4'" sing N N 90 DT "O4'" "C1'" sing N N 91 DT "C3'" "O3'" sing N N 92 DT "C3'" "C2'" sing N N 93 DT "C3'" "H3'" sing N N 94 DT "O3'" "HO3'" sing N N 95 DT "C2'" "C1'" sing N N 96 DT "C2'" "H2'" sing N N 97 DT "C2'" "H2''" sing N N 98 DT "C1'" N1 sing N N 99 DT "C1'" "H1'" sing N N 100 DT N1 C2 sing N N 101 DT N1 C6 sing N N 102 DT C2 O2 doub N N 103 DT C2 N3 sing N N 104 DT N3 C4 sing N N 105 DT N3 H3 sing N N 106 DT C4 O4 doub N N 107 DT C4 C5 sing N N 108 DT C5 C7 sing N N 109 DT C5 C6 doub N N 110 DT C7 H71 sing N N 111 DT C7 H72 sing N N 112 DT C7 H73 sing N N 113 DT C6 H6 sing N N 114 HOH O H1 sing N N 115 HOH O H2 sing N N 116 NUF C1 O1 sing N N 117 NUF C1 C2 doub Y N 118 NUF C1 C6 sing Y N 119 NUF F1 C11 sing N N 120 NUF N1 NI1 sing N N 121 NUF N1 C7 doub N N 122 NUF N1 C8 sing N N 123 NUF O1 NI1 sing N N 124 NUF NI1 N2 sing N N 125 NUF NI1 O2 sing N N 126 NUF C2 C3 sing Y N 127 NUF C2 H2 sing N N 128 NUF F2 C10 sing N N 129 NUF N2 C13 sing N N 130 NUF N2 C14 doub N N 131 NUF O2 C20 sing N N 132 NUF C3 O3 sing N N 133 NUF C3 C4 doub Y N 134 NUF N3 C22 sing N N 135 NUF N3 C23 sing N N 136 NUF N3 C27 sing N N 137 NUF O3 C21 sing N N 138 NUF C4 C5 sing Y N 139 NUF C4 H4 sing N N 140 NUF N4 C29 sing N N 141 NUF N4 C30 sing N N 142 NUF N4 C34 sing N N 143 NUF O4 C18 sing N N 144 NUF O4 C28 sing N N 145 NUF C5 C6 doub Y N 146 NUF C5 H5 sing N N 147 NUF C6 C7 sing N N 148 NUF C7 H7 sing N N 149 NUF C8 C9 doub Y N 150 NUF C8 C13 sing Y N 151 NUF C9 C10 sing Y N 152 NUF C9 H9 sing N N 153 NUF C10 C11 doub Y N 154 NUF C11 C12 sing Y N 155 NUF C12 C13 doub Y N 156 NUF C12 H12 sing N N 157 NUF C14 C15 sing N N 158 NUF C14 H14 sing N N 159 NUF C15 C16 doub Y N 160 NUF C15 C20 sing Y N 161 NUF C16 C17 sing Y N 162 NUF C16 H16 sing N N 163 NUF C17 C18 doub Y N 164 NUF C17 H17 sing N N 165 NUF C18 C19 sing Y N 166 NUF C19 C20 doub Y N 167 NUF C19 H19 sing N N 168 NUF C21 C22 sing N N 169 NUF C21 H21 sing N N 170 NUF C21 H21A sing N N 171 NUF C22 H22 sing N N 172 NUF C22 H22A sing N N 173 NUF C23 C24 sing N N 174 NUF C23 H23 sing N N 175 NUF C23 H23A sing N N 176 NUF C24 C25 sing N N 177 NUF C24 H24 sing N N 178 NUF C24 H24A sing N N 179 NUF C25 C26 sing N N 180 NUF C25 H25 sing N N 181 NUF C25 H25A sing N N 182 NUF C26 C27 sing N N 183 NUF C26 H26 sing N N 184 NUF C26 H26A sing N N 185 NUF C27 H27 sing N N 186 NUF C27 H27A sing N N 187 NUF C28 C29 sing N N 188 NUF C28 H28 sing N N 189 NUF C28 H28A sing N N 190 NUF C29 H29 sing N N 191 NUF C29 H29A sing N N 192 NUF C30 C31 sing N N 193 NUF C30 H30 sing N N 194 NUF C30 H30A sing N N 195 NUF C31 C32 sing N N 196 NUF C31 H31 sing N N 197 NUF C31 H31A sing N N 198 NUF C32 C33 sing N N 199 NUF C32 H32 sing N N 200 NUF C32 H32A sing N N 201 NUF C33 C34 sing N N 202 NUF C33 H33 sing N N 203 NUF C33 H33A sing N N 204 NUF C34 H34 sing N N 205 NUF C34 H34A sing N N 206 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3QSF 'double helix' 3QSF 'parallel strands' 3QSF 'mismatched base pair' # 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 A DG 8 1_555 1.348 3.418 0.122 -8.706 -7.726 -93.042 1 X_DG1002:DG1008_X X 1002 ? X 1008 ? 6 3 1 A DG 3 1_555 A DG 9 1_555 1.570 3.537 0.444 -14.223 3.740 -87.185 2 X_DG1003:DG1009_X X 1003 ? X 1009 ? 6 3 1 A DG 4 1_555 A DG 10 1_555 1.839 3.721 -0.205 2.844 -3.448 -83.727 3 X_DG1004:DG1010_X X 1004 ? X 1010 ? 6 3 # 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 A DG 8 1_555 A DG 3 1_555 A DG 9 1_555 -0.559 -1.113 3.492 -1.083 0.419 33.224 -2.020 0.784 3.494 0.732 1.893 33.244 1 XX_DG1002DG1003:DG1009DG1008_XX X 1002 ? X 1008 ? X 1003 ? X 1009 ? 1 A DG 3 1_555 A DG 9 1_555 A DG 4 1_555 A DG 10 1_555 -0.551 -0.423 3.159 3.891 2.512 25.573 -1.596 2.241 2.988 5.615 -8.700 25.982 2 XX_DG1003DG1004:DG1010DG1009_XX X 1003 ? X 1009 ? X 1004 ? X 1010 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'POTASSIUM ION' K 3 ;[2,2'-{(4,5-difluorobenzene-1,2-diyl)bis[(nitrilo-kappaN)methylylidene]}bis{5-[2-(piperidin-1-yl)ethoxy]phenolato-kappa O}(2-)]nickel (II) ; NUF 4 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 3QSC _pdbx_initial_refinement_model.details ? #