data_2DQP # _entry.id 2DQP # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.380 _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 2DQP pdb_00002dqp 10.2210/pdb2dqp/pdb NDB AH0023 ? ? RCSB RCSB025730 ? ? WWPDB D_1000025730 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 479D ;Same hybrid duplex sequence but without the 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine ; unspecified PDB 2DQO . unspecified PDB 2DQQ . unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2DQP _pdbx_database_status.recvd_initial_deposition_date 2006-05-29 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Juan, E.C.M.' 1 'Kondo, J.' 2 'Ito, T.' 3 'Ueno, Y.' 4 'Matsuda, A.' 5 'Takenaka, A.' 6 # _citation.id primary _citation.title ;Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 35 _citation.page_first 1969 _citation.page_last 1977 _citation.year 2007 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 17341465 _citation.pdbx_database_id_DOI 10.1093/nar/gkl821 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Juan, E.C.M.' 1 ? primary 'Kondo, J.' 2 ? primary 'Kurihara, T.' 3 ? primary 'Ito, T.' 4 ? primary 'Ueno, Y.' 5 ? primary 'Matsuda, A.' 6 ? primary 'Takenaka, A.' 7 ? # _cell.entry_id 2DQP _cell.length_a 52.240 _cell.length_b 52.240 _cell.length_c 42.620 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _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 2DQP _symmetry.space_group_name_H-M 'P 61' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _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 ;DNA (5'-D(*DCP*(OMU)P*DCP*DTP*(OMU)P*DCP*DTP*DTP*DC)-3') ; 2664.734 1 ? ? ? ? 2 polymer syn ;RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*G)-3') ; 2981.895 1 ? ? ? ? 3 non-polymer syn '(6-AMINOHEXYL)CARBAMIC ACID' 160.214 2 ? ? ? ? 4 water nat water 18.015 46 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no yes '(DC)(OMU)(DC)(DT)(OMU)(DC)(DT)(DT)(DC)' CUCTUCTTC A ? 2 polyribonucleotide no no GAAGAAGAG GAAGAAGAG B ? # 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 OMU n 1 3 DC n 1 4 DT n 1 5 OMU n 1 6 DC n 1 7 DT n 1 8 DT n 1 9 DC n 2 1 G n 2 2 A n 2 3 A n 2 4 G n 2 5 A n 2 6 A n 2 7 G n 2 8 A n 2 9 G n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _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 1 1 sample ? ? ? ? ? 'synthetic constructs' 2 1 sample ? ? ? ? ? 'synthetic constructs' # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 PDB 2DQP 1 'C(OMU)CT(OMU)CTTC' 1 2DQP ? 2 PDB 2DQP 2 GAAGAAGAG 10 2DQP ? # 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 2DQP A 1 ? 9 ? 2DQP 1 ? 9 ? 1 9 2 2 2DQP B 1 ? 9 ? 2DQP 10 ? 18 ? 10 18 # 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 CMY non-polymer . '(6-AMINOHEXYL)CARBAMIC ACID' ? 'C7 H16 N2 O2' 160.214 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 OMU 'RNA linking' n ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; ? 'C10 H15 N2 O9 P' 338.208 # _exptl.entry_id 2DQP _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.94 _exptl_crystal.density_percent_sol 58.16 _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.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details ;25mM sodium cacodylate, pH 7.0, 5mM spermine tetrahydrochloride, 25mM lithium chloride and 5% MPD, equilibrateda against 35% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K ; _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 'sodium cacodylate' ? ? ? 1 2 1 'spermine tetrahydrochloride' ? ? ? 1 3 1 'lithium chloride' ? ? ? 1 4 1 MPD ? ? ? 1 5 1 HOH ? ? ? 1 6 2 'sodium cacodylate' ? ? ? 1 7 2 'lithium chloride' ? ? ? 1 8 2 MPD ? ? ? 1 9 2 HOH ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2003-01-25 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'SI(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.000 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'PHOTON FACTORY BEAMLINE BL-18B' _diffrn_source.pdbx_synchrotron_site 'Photon Factory' _diffrn_source.pdbx_synchrotron_beamline BL-18B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.000 # _reflns.entry_id 2DQP _reflns.observed_criterion_sigma_F 0.0 _reflns.observed_criterion_sigma_I 0.0 _reflns.d_resolution_high 2.100 _reflns.d_resolution_low 42.622 _reflns.number_all ? _reflns.number_obs 3931 _reflns.percent_possible_obs 99.9 _reflns.pdbx_Rmerge_I_obs 0.069 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 5.1 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 2.10 _reflns_shell.d_res_low 2.21 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.247 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.0 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 2DQP _refine.ls_d_res_high 2.1 _refine.ls_d_res_low 10 _refine.pdbx_ls_sigma_F 3.0 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 3897 _refine.ls_number_reflns_obs 3864 _refine.ls_number_reflns_R_free 393 _refine.ls_percent_reflns_obs 99.2 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.2223 _refine.ls_R_factor_R_free 0.2509 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model 'PDB ENTRY 479D' _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values 'Maximum Likelihood' _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_mean ? _refine.aniso_B[1][1] 3.176 _refine.aniso_B[1][2] -6.284 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][2] 3.176 _refine.aniso_B[2][3] 0.000 _refine.aniso_B[3][3] -6.353 _refine.details ;The value of the item "Number reflections (observed) is the number of reflections used in refinement. This value excludes the reflections that have sigma(F) less than 3.0. ; _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.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_overall_ESU_R ? _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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_phase_error ? _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 374 _refine_hist.pdbx_number_atoms_ligand 20 _refine_hist.number_atoms_solvent 46 _refine_hist.number_atoms_total 440 _refine_hist.d_res_high 2.1 _refine_hist.d_res_low 10 # _struct.entry_id 2DQP _struct.title 'Structural analyses of DNA:DNA and RNA:DNA duplexes containing 5-(N-aminohexyl)carbamoyl modified uridines' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2DQP _struct_keywords.pdbx_keywords 'DNA-RNA HYBRID' _struct_keywords.text ;modified nucleotide, 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine, A-form RNA:DNA hybrid duplex, DNA-RNA HYBRID ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 3 ? E N N 4 ? 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 covale1 covale both ? A DC 1 "O3'" ? ? ? 1_555 A OMU 2 P ? ? A DC 1 A OMU 2 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale2 covale both ? A OMU 2 "O3'" ? ? ? 1_555 A DC 3 P ? ? A OMU 2 A DC 3 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale3 covale none ? A OMU 2 C5 ? ? ? 1_555 C CMY . C1Y ? ? A OMU 2 A CMY 102 1_555 ? ? ? ? ? ? ? 1.534 ? ? covale4 covale both ? A DT 4 "O3'" ? ? ? 1_555 A OMU 5 P ? ? A DT 4 A OMU 5 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale5 covale both ? A OMU 5 "O3'" ? ? ? 1_555 A DC 6 P ? ? A OMU 5 A DC 6 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale6 covale none ? A OMU 5 C5 ? ? ? 1_555 D CMY . C1Y ? ? A OMU 5 A CMY 105 1_555 ? ? ? ? ? ? ? 1.527 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B G 9 N1 ? ? A DC 1 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B G 9 O6 ? ? A DC 1 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B G 9 N2 ? ? A DC 1 B G 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A OMU 2 N3 ? ? ? 1_555 B A 8 N1 ? ? A OMU 2 B A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A OMU 2 O4 ? ? ? 1_555 B A 8 N6 ? ? A OMU 2 B A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B G 7 N1 ? ? A DC 3 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B G 7 O6 ? ? A DC 3 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B G 7 N2 ? ? A DC 3 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B A 6 N1 ? ? A DT 4 B A 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B A 6 N6 ? ? A DT 4 B A 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A OMU 5 N3 ? ? ? 1_555 B A 5 N1 ? ? A OMU 5 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A OMU 5 O4 ? ? ? 1_555 B A 5 N6 ? ? A OMU 5 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 6 N3 ? ? ? 1_555 B G 4 N1 ? ? A DC 6 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 6 N4 ? ? ? 1_555 B G 4 O6 ? ? A DC 6 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 6 O2 ? ? ? 1_555 B G 4 N2 ? ? A DC 6 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B A 3 N1 ? ? A DT 7 B A 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B A 3 N6 ? ? A DT 7 B A 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B A 2 N1 ? ? A DT 8 B A 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B A 2 N6 ? ? A DT 8 B A 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B G 1 N1 ? ? A DC 9 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B G 1 O6 ? ? A DC 9 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B G 1 N2 ? ? A DC 9 B G 10 1_555 ? ? ? ? ? ? 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 CMY 102 ? 2 'BINDING SITE FOR RESIDUE CMY A 102' AC2 Software A CMY 105 ? 3 'BINDING SITE FOR RESIDUE CMY A 105' # 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 2 DC A 1 ? DC A 1 . ? 1_555 ? 2 AC1 2 OMU A 2 ? OMU A 2 . ? 1_555 ? 3 AC2 3 DT A 4 ? DT A 4 . ? 1_555 ? 4 AC2 3 OMU A 5 ? OMU A 5 . ? 1_555 ? 5 AC2 3 HOH E . ? HOH A 124 . ? 1_555 ? # _database_PDB_matrix.entry_id 2DQP _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 2DQP _atom_sites.fract_transf_matrix[1][1] 0.019142 _atom_sites.fract_transf_matrix[1][2] 0.011052 _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] 0.022104 _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] 0.023463 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC CYT A . n A 1 2 OMU 2 2 2 OMU THY A . n A 1 3 DC 3 3 3 DC CYT A . n A 1 4 DT 4 4 4 DT THY A . n A 1 5 OMU 5 5 5 OMU THY A . n A 1 6 DC 6 6 6 DC CYT A . n A 1 7 DT 7 7 7 DT THY A . n A 1 8 DT 8 8 8 DT THY A . n A 1 9 DC 9 9 9 DC CYT A . n B 2 1 G 1 10 10 G GUA B . n B 2 2 A 2 11 11 A ADE B . n B 2 3 A 3 12 12 A ADE B . n B 2 4 G 4 13 13 G GUA B . n B 2 5 A 5 14 14 A ADE B . n B 2 6 A 6 15 15 A ADE B . n B 2 7 G 7 16 16 G GUA B . n B 2 8 A 8 17 17 A ADE B . n B 2 9 G 9 18 18 G GUA 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 3 CMY 1 102 2 CMY THY A . D 3 CMY 1 105 5 CMY THY A . E 4 HOH 1 106 1 HOH HOH A . E 4 HOH 2 107 4 HOH HOH A . E 4 HOH 3 108 5 HOH HOH A . E 4 HOH 4 109 6 HOH HOH A . E 4 HOH 5 110 8 HOH HOH A . E 4 HOH 6 111 9 HOH HOH A . E 4 HOH 7 112 12 HOH HOH A . E 4 HOH 8 113 13 HOH HOH A . E 4 HOH 9 114 15 HOH HOH A . E 4 HOH 10 115 16 HOH HOH A . E 4 HOH 11 116 17 HOH HOH A . E 4 HOH 12 117 19 HOH HOH A . E 4 HOH 13 118 20 HOH HOH A . E 4 HOH 14 119 25 HOH HOH A . E 4 HOH 15 120 27 HOH HOH A . E 4 HOH 16 121 29 HOH HOH A . E 4 HOH 17 122 32 HOH HOH A . E 4 HOH 18 123 33 HOH HOH A . E 4 HOH 19 124 35 HOH HOH A . E 4 HOH 20 125 37 HOH HOH A . E 4 HOH 21 126 38 HOH HOH A . E 4 HOH 22 127 39 HOH HOH A . E 4 HOH 23 128 40 HOH HOH A . E 4 HOH 24 129 41 HOH HOH A . E 4 HOH 25 130 42 HOH HOH A . E 4 HOH 26 131 44 HOH HOH A . F 4 HOH 1 19 2 HOH HOH B . F 4 HOH 2 20 3 HOH HOH B . F 4 HOH 3 21 7 HOH HOH B . F 4 HOH 4 22 10 HOH HOH B . F 4 HOH 5 23 11 HOH HOH B . F 4 HOH 6 24 14 HOH HOH B . F 4 HOH 7 25 18 HOH HOH B . F 4 HOH 8 26 21 HOH HOH B . F 4 HOH 9 27 22 HOH HOH B . F 4 HOH 10 28 23 HOH HOH B . F 4 HOH 11 29 24 HOH HOH B . F 4 HOH 12 30 26 HOH HOH B . F 4 HOH 13 31 28 HOH HOH B . F 4 HOH 14 32 30 HOH HOH B . F 4 HOH 15 33 31 HOH HOH B . F 4 HOH 16 34 34 HOH HOH B . F 4 HOH 17 35 36 HOH HOH B . F 4 HOH 18 36 43 HOH HOH B . F 4 HOH 19 37 45 HOH HOH B . F 4 HOH 20 38 46 HOH HOH B . # 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 OMU 2 A OMU 2 ? U ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; 2 A OMU 5 A OMU 5 ? U ;O2'-METHYLURIDINE 5'-MONOPHOSPHATE ; # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2007-04-17 2 'Structure model' 1 1 2007-12-26 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-10-25 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_initial_refinement_model 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_conn.pdbx_dist_value' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 6 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 7 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 8 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 9 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 10 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 11 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 12 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 13 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 14 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 15 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 16 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 17 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 18 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 SCALEPACK 'data scaling' . ? 2 AMoRE phasing . ? 3 CNS refinement 1.1 ? 4 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 N 0 A CMY 102 ? C4Y ? C CMY ? C4Y 2 1 N 0 A CMY 102 ? C5Y ? C CMY ? C5Y 3 1 N 0 A CMY 102 ? C6Y ? C CMY ? C6Y 4 1 N 0 A CMY 102 ? C7Y ? C CMY ? C7Y 5 1 N 0 A CMY 102 ? N2Y ? C CMY ? N2Y 6 1 N 0 A CMY 105 ? C4Y ? D CMY ? C4Y 7 1 N 0 A CMY 105 ? C5Y ? D CMY ? C5Y 8 1 N 0 A CMY 105 ? C6Y ? D CMY ? C6Y 9 1 N 0 A CMY 105 ? C7Y ? D CMY ? C7Y 10 1 N 0 A CMY 105 ? N2Y ? D CMY ? N2Y # 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 A OP3 O N N 1 A P P N N 2 A OP1 O N N 3 A OP2 O N N 4 A "O5'" O N N 5 A "C5'" C N N 6 A "C4'" C N R 7 A "O4'" O N N 8 A "C3'" C N S 9 A "O3'" O N N 10 A "C2'" C N R 11 A "O2'" O N N 12 A "C1'" C N R 13 A N9 N Y N 14 A C8 C Y N 15 A N7 N Y N 16 A C5 C Y N 17 A C6 C Y N 18 A N6 N N N 19 A N1 N Y N 20 A C2 C Y N 21 A N3 N Y N 22 A C4 C Y N 23 A HOP3 H N N 24 A HOP2 H N N 25 A "H5'" H N N 26 A "H5''" H N N 27 A "H4'" H N N 28 A "H3'" H N N 29 A "HO3'" H N N 30 A "H2'" H N N 31 A "HO2'" H N N 32 A "H1'" H N N 33 A H8 H N N 34 A H61 H N N 35 A H62 H N N 36 A H2 H N N 37 CMY O1Y O N N 38 CMY C1Y C N N 39 CMY N1Y N N N 40 CMY C2Y C N N 41 CMY C3Y C N N 42 CMY C4Y C N N 43 CMY C5Y C N N 44 CMY C6Y C N N 45 CMY C7Y C N N 46 CMY N2Y N N N 47 CMY O1 O N N 48 CMY H1Y H N N 49 CMY H1 H N N 50 CMY H2Y1 H N N 51 CMY H2Y2 H N N 52 CMY H3Y1 H N N 53 CMY H3Y2 H N N 54 CMY H4Y1 H N N 55 CMY H4Y2 H N N 56 CMY H5Y1 H N N 57 CMY H5Y2 H N N 58 CMY H6Y1 H N N 59 CMY H6Y2 H N N 60 CMY H7Y1 H N N 61 CMY H7Y2 H N N 62 CMY H11 H N N 63 CMY H12 H N N 64 DC OP3 O N N 65 DC P P N N 66 DC OP1 O N N 67 DC OP2 O N N 68 DC "O5'" O N N 69 DC "C5'" C N N 70 DC "C4'" C N R 71 DC "O4'" O N N 72 DC "C3'" C N S 73 DC "O3'" O N N 74 DC "C2'" C N N 75 DC "C1'" C N R 76 DC N1 N N N 77 DC C2 C N N 78 DC O2 O N N 79 DC N3 N N N 80 DC C4 C N N 81 DC N4 N N N 82 DC C5 C N N 83 DC C6 C N N 84 DC HOP3 H N N 85 DC HOP2 H N N 86 DC "H5'" H N N 87 DC "H5''" H N N 88 DC "H4'" H N N 89 DC "H3'" H N N 90 DC "HO3'" H N N 91 DC "H2'" H N N 92 DC "H2''" H N N 93 DC "H1'" H N N 94 DC H41 H N N 95 DC H42 H N N 96 DC H5 H N N 97 DC H6 H N N 98 DT OP3 O N N 99 DT P P N N 100 DT OP1 O N N 101 DT OP2 O N N 102 DT "O5'" O N N 103 DT "C5'" C N N 104 DT "C4'" C N R 105 DT "O4'" O N N 106 DT "C3'" C N S 107 DT "O3'" O N N 108 DT "C2'" C N N 109 DT "C1'" C N R 110 DT N1 N N N 111 DT C2 C N N 112 DT O2 O N N 113 DT N3 N N N 114 DT C4 C N N 115 DT O4 O N N 116 DT C5 C N N 117 DT C7 C N N 118 DT C6 C N N 119 DT HOP3 H N N 120 DT HOP2 H N N 121 DT "H5'" H N N 122 DT "H5''" H N N 123 DT "H4'" H N N 124 DT "H3'" H N N 125 DT "HO3'" H N N 126 DT "H2'" H N N 127 DT "H2''" H N N 128 DT "H1'" H N N 129 DT H3 H N N 130 DT H71 H N N 131 DT H72 H N N 132 DT H73 H N N 133 DT H6 H N N 134 G OP3 O N N 135 G P P N N 136 G OP1 O N N 137 G OP2 O N N 138 G "O5'" O N N 139 G "C5'" C N N 140 G "C4'" C N R 141 G "O4'" O N N 142 G "C3'" C N S 143 G "O3'" O N N 144 G "C2'" C N R 145 G "O2'" O N N 146 G "C1'" C N R 147 G N9 N Y N 148 G C8 C Y N 149 G N7 N Y N 150 G C5 C Y N 151 G C6 C N N 152 G O6 O N N 153 G N1 N N N 154 G C2 C N N 155 G N2 N N N 156 G N3 N N N 157 G C4 C Y N 158 G HOP3 H N N 159 G HOP2 H N N 160 G "H5'" H N N 161 G "H5''" H N N 162 G "H4'" H N N 163 G "H3'" H N N 164 G "HO3'" H N N 165 G "H2'" H N N 166 G "HO2'" H N N 167 G "H1'" H N N 168 G H8 H N N 169 G H1 H N N 170 G H21 H N N 171 G H22 H N N 172 HOH O O N N 173 HOH H1 H N N 174 HOH H2 H N N 175 OMU N1 N N N 176 OMU C2 C N N 177 OMU N3 N N N 178 OMU C4 C N N 179 OMU C5 C N N 180 OMU C6 C N N 181 OMU O2 O N N 182 OMU O4 O N N 183 OMU "C1'" C N R 184 OMU "C2'" C N R 185 OMU "O2'" O N N 186 OMU CM2 C N N 187 OMU "C3'" C N R 188 OMU "C4'" C N R 189 OMU "O3'" O N N 190 OMU "O4'" O N N 191 OMU "C5'" C N N 192 OMU "O5'" O N N 193 OMU P P N N 194 OMU OP1 O N N 195 OMU OP2 O N N 196 OMU OP3 O N N 197 OMU HN3 H N N 198 OMU H5 H N N 199 OMU H6 H N N 200 OMU "H1'" H N N 201 OMU "H2'" H N N 202 OMU HM21 H N N 203 OMU HM22 H N N 204 OMU HM23 H N N 205 OMU "H3'" H N N 206 OMU "H4'" H N N 207 OMU "HO3'" H N N 208 OMU "H5'" H N N 209 OMU "H5''" H N N 210 OMU HOP2 H N N 211 OMU HOP3 H N N 212 # 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 A OP3 P sing N N 1 A OP3 HOP3 sing N N 2 A P OP1 doub N N 3 A P OP2 sing N N 4 A P "O5'" sing N N 5 A OP2 HOP2 sing N N 6 A "O5'" "C5'" sing N N 7 A "C5'" "C4'" sing N N 8 A "C5'" "H5'" sing N N 9 A "C5'" "H5''" sing N N 10 A "C4'" "O4'" sing N N 11 A "C4'" "C3'" sing N N 12 A "C4'" "H4'" sing N N 13 A "O4'" "C1'" sing N N 14 A "C3'" "O3'" sing N N 15 A "C3'" "C2'" sing N N 16 A "C3'" "H3'" sing N N 17 A "O3'" "HO3'" sing N N 18 A "C2'" "O2'" sing N N 19 A "C2'" "C1'" sing N N 20 A "C2'" "H2'" sing N N 21 A "O2'" "HO2'" sing N N 22 A "C1'" N9 sing N N 23 A "C1'" "H1'" sing N N 24 A N9 C8 sing Y N 25 A N9 C4 sing Y N 26 A C8 N7 doub Y N 27 A C8 H8 sing N N 28 A N7 C5 sing Y N 29 A C5 C6 sing Y N 30 A C5 C4 doub Y N 31 A C6 N6 sing N N 32 A C6 N1 doub Y N 33 A N6 H61 sing N N 34 A N6 H62 sing N N 35 A N1 C2 sing Y N 36 A C2 N3 doub Y N 37 A C2 H2 sing N N 38 A N3 C4 sing Y N 39 CMY O1Y C1Y sing N N 40 CMY O1Y H1Y sing N N 41 CMY C1Y N1Y sing N N 42 CMY C1Y O1 doub N N 43 CMY N1Y C2Y sing N N 44 CMY N1Y H1 sing N N 45 CMY C2Y C3Y sing N N 46 CMY C2Y H2Y1 sing N N 47 CMY C2Y H2Y2 sing N N 48 CMY C3Y C4Y sing N N 49 CMY C3Y H3Y1 sing N N 50 CMY C3Y H3Y2 sing N N 51 CMY C4Y C5Y sing N N 52 CMY C4Y H4Y1 sing N N 53 CMY C4Y H4Y2 sing N N 54 CMY C5Y C6Y sing N N 55 CMY C5Y H5Y1 sing N N 56 CMY C5Y H5Y2 sing N N 57 CMY C6Y C7Y sing N N 58 CMY C6Y H6Y1 sing N N 59 CMY C6Y H6Y2 sing N N 60 CMY C7Y N2Y sing N N 61 CMY C7Y H7Y1 sing N N 62 CMY C7Y H7Y2 sing N N 63 CMY N2Y H11 sing N N 64 CMY N2Y H12 sing N N 65 DC OP3 P sing N N 66 DC OP3 HOP3 sing N N 67 DC P OP1 doub N N 68 DC P OP2 sing N N 69 DC P "O5'" sing N N 70 DC OP2 HOP2 sing N N 71 DC "O5'" "C5'" sing N N 72 DC "C5'" "C4'" sing N N 73 DC "C5'" "H5'" sing N N 74 DC "C5'" "H5''" sing N N 75 DC "C4'" "O4'" sing N N 76 DC "C4'" "C3'" sing N N 77 DC "C4'" "H4'" sing N N 78 DC "O4'" "C1'" sing N N 79 DC "C3'" "O3'" sing N N 80 DC "C3'" "C2'" sing N N 81 DC "C3'" "H3'" sing N N 82 DC "O3'" "HO3'" sing N N 83 DC "C2'" "C1'" sing N N 84 DC "C2'" "H2'" sing N N 85 DC "C2'" "H2''" sing N N 86 DC "C1'" N1 sing N N 87 DC "C1'" "H1'" sing N N 88 DC N1 C2 sing N N 89 DC N1 C6 sing N N 90 DC C2 O2 doub N N 91 DC C2 N3 sing N N 92 DC N3 C4 doub N N 93 DC C4 N4 sing N N 94 DC C4 C5 sing N N 95 DC N4 H41 sing N N 96 DC N4 H42 sing N N 97 DC C5 C6 doub N N 98 DC C5 H5 sing N N 99 DC C6 H6 sing N N 100 DT OP3 P sing N N 101 DT OP3 HOP3 sing N N 102 DT P OP1 doub N N 103 DT P OP2 sing N N 104 DT P "O5'" sing N N 105 DT OP2 HOP2 sing N N 106 DT "O5'" "C5'" sing N N 107 DT "C5'" "C4'" sing N N 108 DT "C5'" "H5'" sing N N 109 DT "C5'" "H5''" sing N N 110 DT "C4'" "O4'" sing N N 111 DT "C4'" "C3'" sing N N 112 DT "C4'" "H4'" sing N N 113 DT "O4'" "C1'" sing N N 114 DT "C3'" "O3'" sing N N 115 DT "C3'" "C2'" sing N N 116 DT "C3'" "H3'" sing N N 117 DT "O3'" "HO3'" sing N N 118 DT "C2'" "C1'" sing N N 119 DT "C2'" "H2'" sing N N 120 DT "C2'" "H2''" sing N N 121 DT "C1'" N1 sing N N 122 DT "C1'" "H1'" sing N N 123 DT N1 C2 sing N N 124 DT N1 C6 sing N N 125 DT C2 O2 doub N N 126 DT C2 N3 sing N N 127 DT N3 C4 sing N N 128 DT N3 H3 sing N N 129 DT C4 O4 doub N N 130 DT C4 C5 sing N N 131 DT C5 C7 sing N N 132 DT C5 C6 doub N N 133 DT C7 H71 sing N N 134 DT C7 H72 sing N N 135 DT C7 H73 sing N N 136 DT C6 H6 sing N N 137 G OP3 P sing N N 138 G OP3 HOP3 sing N N 139 G P OP1 doub N N 140 G P OP2 sing N N 141 G P "O5'" sing N N 142 G OP2 HOP2 sing N N 143 G "O5'" "C5'" sing N N 144 G "C5'" "C4'" sing N N 145 G "C5'" "H5'" sing N N 146 G "C5'" "H5''" sing N N 147 G "C4'" "O4'" sing N N 148 G "C4'" "C3'" sing N N 149 G "C4'" "H4'" sing N N 150 G "O4'" "C1'" sing N N 151 G "C3'" "O3'" sing N N 152 G "C3'" "C2'" sing N N 153 G "C3'" "H3'" sing N N 154 G "O3'" "HO3'" sing N N 155 G "C2'" "O2'" sing N N 156 G "C2'" "C1'" sing N N 157 G "C2'" "H2'" sing N N 158 G "O2'" "HO2'" sing N N 159 G "C1'" N9 sing N N 160 G "C1'" "H1'" sing N N 161 G N9 C8 sing Y N 162 G N9 C4 sing Y N 163 G C8 N7 doub Y N 164 G C8 H8 sing N N 165 G N7 C5 sing Y N 166 G C5 C6 sing N N 167 G C5 C4 doub Y N 168 G C6 O6 doub N N 169 G C6 N1 sing N N 170 G N1 C2 sing N N 171 G N1 H1 sing N N 172 G C2 N2 sing N N 173 G C2 N3 doub N N 174 G N2 H21 sing N N 175 G N2 H22 sing N N 176 G N3 C4 sing N N 177 HOH O H1 sing N N 178 HOH O H2 sing N N 179 OMU N1 C2 sing N N 180 OMU N1 C6 sing N N 181 OMU N1 "C1'" sing N N 182 OMU C2 N3 sing N N 183 OMU C2 O2 doub N N 184 OMU N3 C4 sing N N 185 OMU N3 HN3 sing N N 186 OMU C4 C5 sing N N 187 OMU C4 O4 doub N N 188 OMU C5 C6 doub N N 189 OMU C5 H5 sing N N 190 OMU C6 H6 sing N N 191 OMU "C1'" "C2'" sing N N 192 OMU "C1'" "O4'" sing N N 193 OMU "C1'" "H1'" sing N N 194 OMU "C2'" "O2'" sing N N 195 OMU "C2'" "C3'" sing N N 196 OMU "C2'" "H2'" sing N N 197 OMU "O2'" CM2 sing N N 198 OMU CM2 HM21 sing N N 199 OMU CM2 HM22 sing N N 200 OMU CM2 HM23 sing N N 201 OMU "C3'" "C4'" sing N N 202 OMU "C3'" "O3'" sing N N 203 OMU "C3'" "H3'" sing N N 204 OMU "C4'" "O4'" sing N N 205 OMU "C4'" "C5'" sing N N 206 OMU "C4'" "H4'" sing N N 207 OMU "O3'" "HO3'" sing N N 208 OMU "C5'" "O5'" sing N N 209 OMU "C5'" "H5'" sing N N 210 OMU "C5'" "H5''" sing N N 211 OMU "O5'" P sing N N 212 OMU P OP1 doub N N 213 OMU P OP2 sing N N 214 OMU P OP3 sing N N 215 OMU OP2 HOP2 sing N N 216 OMU OP3 HOP3 sing N N 217 # _ndb_struct_conf_na.entry_id 2DQP _ndb_struct_conf_na.feature 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B G 9 1_555 0.089 -0.076 -0.097 4.341 -3.034 -0.019 1 A_DC1:G18_B A 1 ? B 18 ? 19 1 1 A OMU 2 1_555 B A 8 1_555 -0.312 -0.192 -0.217 1.489 -10.560 6.239 2 A_OMU2:A17_B A 2 ? B 17 ? 20 1 1 A DC 3 1_555 B G 7 1_555 0.247 -0.232 0.075 4.972 -5.497 1.594 3 A_DC3:G16_B A 3 ? B 16 ? 19 1 1 A DT 4 1_555 B A 6 1_555 0.027 -0.156 -0.157 7.158 -11.030 1.754 4 A_DT4:A15_B A 4 ? B 15 ? 20 1 1 A OMU 5 1_555 B A 5 1_555 -0.094 -0.083 -0.194 5.556 -17.496 8.673 5 A_OMU5:A14_B A 5 ? B 14 ? 20 1 1 A DC 6 1_555 B G 4 1_555 0.280 -0.248 -0.003 -4.010 0.706 1.179 6 A_DC6:G13_B A 6 ? B 13 ? 19 1 1 A DT 7 1_555 B A 3 1_555 -0.220 -0.131 -0.133 5.596 -5.135 -2.360 7 A_DT7:A12_B A 7 ? B 12 ? 20 1 1 A DT 8 1_555 B A 2 1_555 0.178 -0.023 -0.393 17.013 -7.194 -0.659 8 A_DT8:A11_B A 8 ? B 11 ? 20 1 1 A DC 9 1_555 B G 1 1_555 0.498 -0.158 -0.562 17.177 -5.671 -2.139 9 A_DC9:G10_B A 9 ? B 10 ? 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 DC 1 1_555 B G 9 1_555 A OMU 2 1_555 B A 8 1_555 -0.151 -2.416 3.384 0.132 2.634 27.941 -5.604 0.342 3.146 5.441 -0.274 28.063 1 AA_DC1OMU2:A17G18_BB A 1 ? B 18 ? A 2 ? B 17 ? 1 A OMU 2 1_555 B A 8 1_555 A DC 3 1_555 B G 7 1_555 -0.792 -1.484 3.201 -5.016 4.737 30.747 -3.587 0.556 3.032 8.795 9.313 31.493 2 AA_OMU2DC3:G16A17_BB A 2 ? B 17 ? A 3 ? B 16 ? 1 A DC 3 1_555 B G 7 1_555 A DT 4 1_555 B A 6 1_555 0.003 -1.535 3.240 2.068 4.329 32.540 -3.422 0.333 3.011 7.674 -3.665 32.882 3 AA_DC3DT4:A15G16_BB A 3 ? B 16 ? A 4 ? B 15 ? 1 A DT 4 1_555 B A 6 1_555 A OMU 5 1_555 B A 5 1_555 0.507 -1.321 3.280 0.655 5.434 29.969 -3.567 -0.838 3.009 10.399 -1.254 30.453 4 AA_DT4OMU5:A14A15_BB A 4 ? B 15 ? A 5 ? B 14 ? 1 A OMU 5 1_555 B A 5 1_555 A DC 6 1_555 B G 4 1_555 -0.505 -1.792 3.452 -2.439 15.980 33.133 -4.898 0.487 2.396 26.173 3.994 36.766 5 AA_OMU5DC6:G13A14_BB A 5 ? B 14 ? A 6 ? B 13 ? 1 A DC 6 1_555 B G 4 1_555 A DT 7 1_555 B A 3 1_555 0.003 -1.431 3.096 3.015 5.608 27.125 -4.185 0.647 2.735 11.752 -6.317 27.849 6 AA_DC6DT7:A12G13_BB A 6 ? B 13 ? A 7 ? B 12 ? 1 A DT 7 1_555 B A 3 1_555 A DT 8 1_555 B A 2 1_555 -0.303 -1.753 3.075 0.828 5.237 27.510 -4.725 0.800 2.691 10.884 -1.721 28.007 7 AA_DT7DT8:A11A12_BB A 7 ? B 12 ? A 8 ? B 11 ? 1 A DT 8 1_555 B A 2 1_555 A DC 9 1_555 B G 1 1_555 0.502 -1.699 3.421 0.912 7.954 33.567 -4.089 -0.706 2.965 13.534 -1.552 34.482 8 AA_DT8DC9:G10A11_BB A 8 ? B 11 ? A 9 ? B 10 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 '(6-AMINOHEXYL)CARBAMIC ACID' CMY 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 479D _pdbx_initial_refinement_model.details 'PDB ENTRY 479D' #