data_1RRU # _entry.id 1RRU # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.381 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1RRU pdb_00001rru 10.2210/pdb1rru/pdb NDB UP0004 ? ? RCSB RCSB020994 ? ? WWPDB D_1000020994 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1PUP 'Peptide nucleic acid duplex hexamer at 1.7 A resolution' unspecified PDB 1QPY 'Crystal Structure Of a Backbone Modified Pna Hexamer' unspecified PDB 1HZS 'Crystal structure of Peptide nucleic acid containing a bicyclic analogue of Thymine' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1RRU _pdbx_database_status.recvd_initial_deposition_date 2003-12-09 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Rasmussen, H.' 1 'Liljefors, T.' 2 'Petersson, B.' 3 'Nielsen, P.E.' 4 'Kastrup, J.S.' 5 # 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 'The Influence of a Chiral Amino Acid on the Helical Handedness of PNA in Solution and in Crystals' J.Biomol.Struct.Dyn. 21 495 502 2004 JBSDD6 US 0739-1102 0646 ? 14692794 ? 1 'Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 A resolution' Nat.Struct.Biol. 4 98 101 1997 NSBIEW US 1072-8368 2024 ? ? ? 2 'Peptide nucleic acids (PNA) derived from N-(N-methylaminoethyl) glycine. Synthesis, hybridization and structural properties' 'New J.Chem.' 23 833 840 1999 ? FR 1144-0546 ? ? ? 10.1039/a902091h 3 '1,8-Naphthyridin-2(1H)-ones. Novel bi- and tricyclic analogues of Thymine in Peptide nucleic acids (PNA)' Eur.J.Org.Chem. ? 1781 1790 2001 ? GE 1434-193X ? ? ? '10.1002/1099-0690(200105)2001:9<1781::AID-EJOC1781>3.0.CO;2-K' # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Rasmussen, H.' 1 ? primary 'Liljefors, T.' 2 ? primary 'Petersson, B.' 3 ? primary 'Nielsen, P.E.' 4 ? primary 'Kastrup, J.S.' 5 ? 1 'Rasmussen, H.' 6 ? 1 'Kastrup, J.S.' 7 ? 1 'Nielsen, J.N.' 8 ? 1 'Nielsen, J.M.' 9 ? 1 'Nielsen, P.E.' 10 ? 2 'Haiima, G.' 11 ? 2 'Rasmussen, H.' 12 ? 2 'Schmidt, G.' 13 ? 2 'Jensen, D.K.' 14 ? 2 'Kastrup, J.S.' 15 ? 2 'Stafshede, P.W.' 16 ? 2 'Norden, B.' 17 ? 2 'Buckhardt, O.' 18 ? 2 'Nielsen, P.E.' 19 ? 3 'Eldrup, A.B.' 20 ? 3 'Nielsen, B.B.' 21 ? 3 'Haiima, G.' 22 ? 3 'Rasmussen, H.' 23 ? 3 'Kastrup, J.S.' 24 ? 3 'Christensen, C.' 25 ? 3 'Nielsen, P.E.' 26 ? # _cell.entry_id 1RRU _cell.length_a 36.75 _cell.length_b 44.07 _cell.length_c 31.22 _cell.angle_alpha 90.00 _cell.angle_beta 91.51 _cell.angle_gamma 90.00 _cell.pdbx_unique_axis ? _cell.Z_PDB 8 # _symmetry.entry_id 1RRU _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.Int_Tables_number 5 _symmetry.cell_setting ? # 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 'Peptide Nucleic Acid, (H-P(*CPN*GPN*TPN*APN*CPN*GPN)-LYS-NH2)' 1714.813 2 ? ? ? ? 2 water nat water 18.015 28 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name PNA # _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 '(CPN)(GPN)(TPN)(APN)(CPN)(GPN)K(NH2)' _entity_poly.pdbx_seq_one_letter_code_can XXXXXXKX _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 CPN n 1 2 GPN n 1 3 TPN n 1 4 APN n 1 5 CPN n 1 6 GPN n 1 7 LYS n 1 8 NH2 n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1RRU _struct_ref.pdbx_db_accession 1RRU _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 1RRU A 1 ? 8 ? 1RRU 1 ? 8 ? 1 8 2 1 1RRU B 1 ? 8 ? 1RRU 9 ? 16 ? 9 16 # 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 APN peptide-like . 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE ? 'C11 H16 N7 O3 1' 294.290 CPN peptide-like . 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE ? 'C10 H16 N5 O4 1' 270.265 GPN peptide-like . 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE ? 'C11 H16 N7 O4 1' 310.289 HOH non-polymer . WATER ? 'H2 O' 18.015 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 NH2 non-polymer . 'AMINO GROUP' ? 'H2 N' 16.023 TPN peptide-like . 2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE ? 'C11 H17 N4 O5 1' 285.276 # _exptl.entry_id 1RRU _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 66.62 _exptl_crystal.description ? _exptl_crystal.density_Matthews 3.68 # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details 'glycerol, magnesium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _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 glycerol ? ? ? 1 2 1 'magnesium formate' ? ? ? 1 3 1 H2O ? ? ? 1 4 2 'magnesium formate' ? ? ? 1 5 2 H2O ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 293 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS II' _diffrn_detector.pdbx_collection_date 1997-04-16 _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 ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _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 RU200' _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 # _reflns.entry_id 1RRU _reflns.observed_criterion_sigma_F 0.00 _reflns.observed_criterion_sigma_I 0.00 _reflns.d_resolution_high 2.35 _reflns.d_resolution_low 25.0 _reflns.number_all 2069 _reflns.number_obs 2069 _reflns.percent_possible_obs 98.8 _reflns.pdbx_Rmerge_I_obs 0.06 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 15.9 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.4 _reflns.R_free_details ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 2.35 _reflns_shell.d_res_low 2.39 _reflns_shell.percent_possible_all 95.8 _reflns_shell.Rmerge_I_obs 0.316 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 3.2 _reflns_shell.pdbx_redundancy 3.0 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 92 _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 1RRU _refine.ls_d_res_high 2.35 _refine.ls_d_res_low 6.00 _refine.pdbx_ls_sigma_F 3.0 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 1955 _refine.ls_number_reflns_obs 1453 _refine.ls_number_reflns_R_free 129 _refine.ls_percent_reflns_obs 74 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.219 _refine.ls_R_factor_R_free 0.292 _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 1PUP' _refine.pdbx_ls_cross_valid_method troughout _refine.pdbx_R_Free_selection_details random _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _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 isotropic _refine.B_iso_mean 38.4 _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.details 'Own parameter and topology file created' _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_B ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _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 254 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 28 _refine_hist.number_atoms_total 282 _refine_hist.d_res_high 2.35 _refine_hist.d_res_low 6.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function x_bond_d 0.021 ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg 3.5 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 2.35 _refine_ls_shell.d_res_low 2.45 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.321 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.366 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 15 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 1RRU _struct.title 'The influence of a chiral amino acid on the helical handedness of PNA in solution and in crystals' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1RRU _struct_keywords.pdbx_keywords 'PEPTIDE NUCLEIC ACID' _struct_keywords.text 'PNA, peptide nucleic acid, L-Lysine, helical handedness, P-form, molecular mechanics' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? # 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 CPN 1 C ? ? ? 1_555 A GPN 2 N ? ? A CPN 1 A GPN 2 1_555 ? ? ? ? ? ? ? 1.322 ? ? covale2 covale both ? A GPN 2 C ? ? ? 1_555 A TPN 3 N ? ? A GPN 2 A TPN 3 1_555 ? ? ? ? ? ? ? 1.358 ? ? covale3 covale both ? A TPN 3 C A ? ? 1_555 A APN 4 N B ? A TPN 3 A APN 4 1_555 ? ? ? ? ? ? ? 0.811 ? ? covale4 covale both ? A TPN 3 C B ? ? 1_555 A APN 4 N A ? A TPN 3 A APN 4 1_555 ? ? ? ? ? ? ? 1.225 ? ? covale5 covale both ? A TPN 3 C A ? ? 1_555 A APN 4 N A ? A TPN 3 A APN 4 1_555 ? ? ? ? ? ? ? 1.372 ? ? covale6 covale both ? A TPN 3 C B ? ? 1_555 A APN 4 N B ? A TPN 3 A APN 4 1_555 ? ? ? ? ? ? ? 1.363 ? ? covale7 covale both ? A APN 4 C ? ? ? 1_555 A CPN 5 N ? ? A APN 4 A CPN 5 1_555 ? ? ? ? ? ? ? 1.298 ? ? covale8 covale both ? A CPN 5 C ? ? ? 1_555 A GPN 6 N ? ? A CPN 5 A GPN 6 1_555 ? ? ? ? ? ? ? 1.320 ? ? covale9 covale both ? A GPN 6 C ? ? ? 1_555 A LYS 7 N ? ? A GPN 6 A LYS 7 1_555 ? ? ? ? ? ? ? 1.351 ? ? covale10 covale both ? A LYS 7 C ? ? ? 1_555 A NH2 8 N ? ? A LYS 7 A NH2 8 1_555 ? ? ? ? ? ? ? 1.346 ? ? covale11 covale both ? B CPN 1 C ? ? ? 1_555 B GPN 2 N ? ? B CPN 9 B GPN 10 1_555 ? ? ? ? ? ? ? 1.337 ? ? covale12 covale both ? B GPN 2 C ? ? ? 1_555 B TPN 3 N ? ? B GPN 10 B TPN 11 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale13 covale both ? B TPN 3 C A ? ? 1_555 B APN 4 N B ? B TPN 11 B APN 12 1_555 ? ? ? ? ? ? ? 0.740 ? ? covale14 covale both ? B TPN 3 C B ? ? 1_555 B APN 4 N A ? B TPN 11 B APN 12 1_555 ? ? ? ? ? ? ? 1.314 ? ? covale15 covale both ? B TPN 3 C B ? ? 1_555 B APN 4 N B ? B TPN 11 B APN 12 1_555 ? ? ? ? ? ? ? 1.359 ? ? covale16 covale both ? B TPN 3 C A ? ? 1_555 B APN 4 N A ? B TPN 11 B APN 12 1_555 ? ? ? ? ? ? ? 1.365 ? ? covale17 covale both ? B APN 4 C ? ? ? 1_555 B CPN 5 N ? ? B APN 12 B CPN 13 1_555 ? ? ? ? ? ? ? 1.320 ? ? covale18 covale both ? B CPN 5 C ? ? ? 1_555 B GPN 6 N ? ? B CPN 13 B GPN 14 1_555 ? ? ? ? ? ? ? 1.317 ? ? covale19 covale both ? B GPN 6 C ? ? ? 1_555 B LYS 7 N ? ? B GPN 14 B LYS 15 1_555 ? ? ? ? ? ? ? 1.397 ? ? covale20 covale both ? B LYS 7 C ? ? ? 1_555 B NH2 8 N ? ? B LYS 15 B NH2 16 1_555 ? ? ? ? ? ? ? 1.312 ? ? hydrog1 hydrog ? ? A CPN 1 N3 ? ? ? 1_555 A GPN 6 N1 ? ? A CPN 1 A GPN 6 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A CPN 1 N4 ? ? ? 1_555 A GPN 6 O6 ? ? A CPN 1 A GPN 6 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A CPN 1 O2 ? ? ? 1_555 A GPN 6 N2 ? ? A CPN 1 A GPN 6 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A GPN 2 N1 ? ? ? 1_555 A CPN 5 N3 ? ? A GPN 2 A CPN 5 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A GPN 2 N2 ? ? ? 1_555 A CPN 5 O2 ? ? A GPN 2 A CPN 5 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A GPN 2 O6 ? ? ? 1_555 A CPN 5 N4 ? ? A GPN 2 A CPN 5 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A TPN 3 N3 ? ? ? 1_555 A APN 4 N1 ? ? A TPN 3 A APN 4 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A TPN 3 O4 ? ? ? 1_555 A APN 4 N6 ? ? A TPN 3 A APN 4 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A APN 4 N1 ? ? ? 1_555 A TPN 3 N3 ? ? A APN 4 A TPN 3 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A APN 4 N6 ? ? ? 1_555 A TPN 3 O4 ? ? A APN 4 A TPN 3 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A CPN 5 N3 ? ? ? 1_555 A GPN 2 N1 ? ? A CPN 5 A GPN 2 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A CPN 5 N4 ? ? ? 1_555 A GPN 2 O6 ? ? A CPN 5 A GPN 2 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A CPN 5 O2 ? ? ? 1_555 A GPN 2 N2 ? ? A CPN 5 A GPN 2 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A GPN 6 N1 ? ? ? 1_555 A CPN 1 N3 ? ? A GPN 6 A CPN 1 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A GPN 6 N2 ? ? ? 1_555 A CPN 1 O2 ? ? A GPN 6 A CPN 1 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A GPN 6 O6 ? ? ? 1_555 A CPN 1 N4 ? ? A GPN 6 A CPN 1 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? B CPN 1 N3 ? ? ? 1_555 B GPN 6 N1 ? ? B CPN 9 B GPN 14 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? B CPN 1 N4 ? ? ? 1_555 B GPN 6 O6 ? ? B CPN 9 B GPN 14 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? B CPN 1 O2 ? ? ? 1_555 B GPN 6 N2 ? ? B CPN 9 B GPN 14 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? B GPN 2 N1 ? ? ? 1_555 B CPN 5 N3 ? ? B GPN 10 B CPN 13 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? B GPN 2 N2 ? ? ? 1_555 B CPN 5 O2 ? ? B GPN 10 B CPN 13 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? B GPN 2 O6 ? ? ? 1_555 B CPN 5 N4 ? ? B GPN 10 B CPN 13 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? B TPN 3 N3 ? ? ? 1_555 B APN 4 N1 ? ? B TPN 11 B APN 12 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? B TPN 3 O4 ? ? ? 1_555 B APN 4 N6 ? ? B TPN 11 B APN 12 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? B APN 4 N1 ? ? ? 1_555 B TPN 3 N3 ? ? B APN 12 B TPN 11 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? B APN 4 N6 ? ? ? 1_555 B TPN 3 O4 ? ? B APN 12 B TPN 11 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? B CPN 5 N3 ? ? ? 1_555 B GPN 2 N1 ? ? B CPN 13 B GPN 10 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? B CPN 5 N4 ? ? ? 1_555 B GPN 2 O6 ? ? B CPN 13 B GPN 10 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? B CPN 5 O2 ? ? ? 1_555 B GPN 2 N2 ? ? B CPN 13 B GPN 10 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? B GPN 6 N1 ? ? ? 1_555 B CPN 1 N3 ? ? B GPN 14 B CPN 9 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? B GPN 6 N2 ? ? ? 1_555 B CPN 1 O2 ? ? B GPN 14 B CPN 9 2_656 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? B GPN 6 O6 ? ? ? 1_555 B CPN 1 N4 ? ? B GPN 14 B CPN 9 2_656 ? ? ? ? ? ? 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 NH2 8 ? 1 'BINDING SITE FOR RESIDUE NH2 A 8' AC2 Software B NH2 16 ? 2 'BINDING SITE FOR RESIDUE NH2 B 16' # 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 1 LYS A 7 ? LYS A 7 . ? 1_555 ? 2 AC2 2 GPN B 6 ? GPN B 14 . ? 2_656 ? 3 AC2 2 LYS B 7 ? LYS B 15 . ? 2_656 ? # _database_PDB_matrix.entry_id 1RRU _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 1RRU _atom_sites.fract_transf_matrix[1][1] 0.027211 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000717 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.022691 _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] 0.032042 _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 # 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 CPN 1 1 1 CPN CPN A . n A 1 2 GPN 2 2 2 GPN GPN A . n A 1 3 TPN 3 3 3 TPN TPN A . n A 1 4 APN 4 4 4 APN APN A . n A 1 5 CPN 5 5 5 CPN CPN A . n A 1 6 GPN 6 6 6 GPN GPN A . n A 1 7 LYS 7 7 7 LYS LYS A . n A 1 8 NH2 8 8 8 NH2 NH2 A . n B 1 1 CPN 1 9 9 CPN CPN B . n B 1 2 GPN 2 10 10 GPN GPN B . n B 1 3 TPN 3 11 11 TPN TPN B . n B 1 4 APN 4 12 12 APN APN B . n B 1 5 CPN 5 13 13 CPN CPN B . n B 1 6 GPN 6 14 14 GPN GPN B . n B 1 7 LYS 7 15 15 LYS LYS B . n B 1 8 NH2 8 16 16 NH2 NH2 B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 HOH 1 17 17 HOH HOH A . C 2 HOH 2 20 20 HOH HOH A . C 2 HOH 3 21 21 HOH HOH A . C 2 HOH 4 22 22 HOH HOH A . C 2 HOH 5 23 23 HOH HOH A . C 2 HOH 6 25 25 HOH HOH A . C 2 HOH 7 27 27 HOH HOH A . C 2 HOH 8 28 28 HOH HOH A . C 2 HOH 9 29 29 HOH HOH A . C 2 HOH 10 30 30 HOH HOH A . C 2 HOH 11 33 33 HOH HOH A . C 2 HOH 12 36 36 HOH HOH A . C 2 HOH 13 38 38 HOH HOH A . C 2 HOH 14 39 39 HOH HOH A . C 2 HOH 15 43 43 HOH HOH A . D 2 HOH 1 18 18 HOH HOH B . D 2 HOH 2 19 19 HOH HOH B . D 2 HOH 3 24 24 HOH HOH B . D 2 HOH 4 26 26 HOH HOH B . D 2 HOH 5 31 31 HOH HOH B . D 2 HOH 6 32 32 HOH HOH B . D 2 HOH 7 34 34 HOH HOH B . D 2 HOH 8 35 35 HOH HOH B . D 2 HOH 9 37 37 HOH HOH B . D 2 HOH 10 40 40 HOH HOH B . D 2 HOH 11 41 41 HOH HOH B . D 2 HOH 12 42 42 HOH HOH B . D 2 HOH 13 44 44 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 CPN 1 A CPN 1 ? DC ? 2 A GPN 2 A GPN 2 ? DG ? 3 A TPN 3 A TPN 3 ? DT ? 4 A APN 4 A APN 4 ? DA ? 5 A CPN 5 A CPN 5 ? DC ? 6 A GPN 6 A GPN 6 ? DG ? 7 B CPN 1 B CPN 9 ? DC ? 8 B GPN 2 B GPN 10 ? DG ? 9 B TPN 3 B TPN 11 ? DT ? 10 B APN 4 B APN 12 ? DA ? 11 B CPN 5 B CPN 13 ? DC ? 12 B GPN 6 B GPN 14 ? DG ? # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? dimeric 2 2 author_defined_assembly ? dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1,2 A,C 2 1,3 B,D # 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_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 3 'crystal symmetry operation' 2_656 -x+1,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 35.9273086356 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 31.2091585743 # 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 2004-01-13 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2019-08-28 5 'Structure model' 1 4 2023-08-23 6 'Structure model' 2 0 2023-11-15 # _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' 'Non-polymer description' 3 3 'Structure model' 'Version format compliance' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Derived calculations' 6 5 'Structure model' 'Data collection' 7 5 'Structure model' 'Database references' 8 5 'Structure model' 'Derived calculations' 9 5 'Structure model' 'Refinement description' 10 6 'Structure model' 'Atomic model' 11 6 'Structure model' 'Data collection' 12 6 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' ndb_struct_conf_na 2 4 'Structure model' ndb_struct_na_base_pair 3 4 'Structure model' ndb_struct_na_base_pair_step 4 4 'Structure model' struct_biol 5 4 'Structure model' struct_conn 6 5 'Structure model' chem_comp_atom 7 5 'Structure model' chem_comp_bond 8 5 'Structure model' database_2 9 5 'Structure model' pdbx_initial_refinement_model 10 5 'Structure model' struct_conn 11 5 'Structure model' struct_site 12 6 'Structure model' atom_site 13 6 'Structure model' chem_comp_atom 14 6 'Structure model' chem_comp_bond 15 6 'Structure model' struct_conn # 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_dist_value' 4 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 5 'Structure model' '_struct_conn.pdbx_ptnr1_label_alt_id' 6 5 'Structure model' '_struct_conn.pdbx_ptnr2_label_alt_id' 7 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 8 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 9 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 10 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 11 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 12 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 13 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 14 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 15 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 16 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 17 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 18 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 19 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 20 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 21 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 22 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 23 5 'Structure model' '_struct_site.pdbx_auth_seq_id' 24 6 'Structure model' '_atom_site.auth_atom_id' 25 6 'Structure model' '_atom_site.label_atom_id' 26 6 'Structure model' '_chem_comp_atom.atom_id' 27 6 'Structure model' '_chem_comp_bond.atom_id_1' 28 6 'Structure model' '_chem_comp_bond.atom_id_2' 29 6 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 30 6 'Structure model' '_struct_conn.ptnr1_label_atom_id' 31 6 'Structure model' '_struct_conn.ptnr2_label_atom_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data reduction' . ? 1 TRUNCATE 'data reduction' . ? 2 AMoRE phasing . ? 3 X-PLOR refinement 3.851 ? 4 CCP4 'data scaling' '(TRUNCATE)' ? 5 # 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 APN "C8'" C N N 1 APN "C7'" C N N 2 APN "O7'" O N N 3 APN "C5'" C N N 4 APN C C N N 5 APN O O N N 6 APN OXT O N N 7 APN "N4'" N N N 8 APN "C3'" C N N 9 APN "C2'" C N N 10 APN N N N N 11 APN N9 N Y N 12 APN C8 C Y N 13 APN N7 N Y N 14 APN C5 C Y N 15 APN C6 C Y N 16 APN N6 N N N 17 APN N1 N Y N 18 APN C2 C Y N 19 APN N3 N Y N 20 APN C4 C Y N 21 APN "H8'1" H N N 22 APN "H8'2" H N N 23 APN "H5'1" H N N 24 APN "H5'2" H N N 25 APN HXT H N N 26 APN "H3'1" H N N 27 APN "H3'2" H N N 28 APN "H2'1" H N N 29 APN "H2'2" H N N 30 APN H H N N 31 APN H2 H N N 32 APN H3 H N N 33 APN H8 H N N 34 APN HN61 H N N 35 APN HN62 H N N 36 APN H21 H N N 37 CPN "C8'" C N N 38 CPN "C7'" C N N 39 CPN "O7'" O N N 40 CPN "C5'" C N N 41 CPN C C N N 42 CPN O O N N 43 CPN OXT O N N 44 CPN "N4'" N N N 45 CPN "C3'" C N N 46 CPN "C2'" C N N 47 CPN N N N N 48 CPN N1 N N N 49 CPN C2 C N N 50 CPN N3 N N N 51 CPN C4 C N N 52 CPN C5 C N N 53 CPN C6 C N N 54 CPN O2 O N N 55 CPN N4 N N N 56 CPN "H8'1" H N N 57 CPN "H8'2" H N N 58 CPN "H5'1" H N N 59 CPN "H5'2" H N N 60 CPN HXT H N N 61 CPN "H3'1" H N N 62 CPN "H3'2" H N N 63 CPN "H2'1" H N N 64 CPN "H2'2" H N N 65 CPN H H N N 66 CPN H2 H N N 67 CPN H3 H N N 68 CPN H5 H N N 69 CPN H6 H N N 70 CPN HN41 H N N 71 CPN HN42 H N N 72 GPN "C8'" C N N 73 GPN "C7'" C N N 74 GPN "O7'" O N N 75 GPN "C5'" C N N 76 GPN C C N N 77 GPN O O N N 78 GPN OXT O N N 79 GPN "N4'" N N N 80 GPN "C3'" C N N 81 GPN "C2'" C N N 82 GPN N N N N 83 GPN N9 N Y N 84 GPN C8 C Y N 85 GPN N7 N Y N 86 GPN C5 C Y N 87 GPN C6 C N N 88 GPN O6 O N N 89 GPN N1 N N N 90 GPN C2 C N N 91 GPN N2 N N N 92 GPN N3 N N N 93 GPN C4 C Y N 94 GPN "H8'1" H N N 95 GPN "H8'2" H N N 96 GPN "H5'1" H N N 97 GPN "H5'2" H N N 98 GPN HXT H N N 99 GPN "H3'1" H N N 100 GPN "H3'2" H N N 101 GPN "H2'1" H N N 102 GPN "H2'2" H N N 103 GPN H H N N 104 GPN H2 H N N 105 GPN H3 H N N 106 GPN H8 H N N 107 GPN HN1 H N N 108 GPN HN21 H N N 109 GPN HN22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 LYS N N N N 114 LYS CA C N S 115 LYS C C N N 116 LYS O O N N 117 LYS CB C N N 118 LYS CG C N N 119 LYS CD C N N 120 LYS CE C N N 121 LYS NZ N N N 122 LYS OXT O N N 123 LYS H H N N 124 LYS H2 H N N 125 LYS HA H N N 126 LYS HB2 H N N 127 LYS HB3 H N N 128 LYS HG2 H N N 129 LYS HG3 H N N 130 LYS HD2 H N N 131 LYS HD3 H N N 132 LYS HE2 H N N 133 LYS HE3 H N N 134 LYS HZ1 H N N 135 LYS HZ2 H N N 136 LYS HZ3 H N N 137 LYS HXT H N N 138 NH2 N N N N 139 NH2 HN1 H N N 140 NH2 HN2 H N N 141 TPN "C8'" C N N 142 TPN "C7'" C N N 143 TPN "O7'" O N N 144 TPN "C5'" C N N 145 TPN C C N N 146 TPN O O N N 147 TPN OXT O N N 148 TPN "N4'" N N N 149 TPN "C3'" C N N 150 TPN "C2'" C N N 151 TPN N N N N 152 TPN N1 N N N 153 TPN C6 C N N 154 TPN C2 C N N 155 TPN O2 O N N 156 TPN N3 N N N 157 TPN C4 C N N 158 TPN O4 O N N 159 TPN C5 C N N 160 TPN C5M C N N 161 TPN "H8'1" H N N 162 TPN "H8'2" H N N 163 TPN "H5'1" H N N 164 TPN "H5'2" H N N 165 TPN HXT H N N 166 TPN "H3'1" H N N 167 TPN "H3'2" H N N 168 TPN "H2'1" H N N 169 TPN "H2'2" H N N 170 TPN H H N N 171 TPN H2 H N N 172 TPN H3 H N N 173 TPN H6 H N N 174 TPN HN3 H N N 175 TPN HM51 H N N 176 TPN HM52 H N N 177 TPN HM53 H N N 178 # 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 APN "C8'" "C7'" sing N N 1 APN "C8'" N9 sing N N 2 APN "C8'" "H8'1" sing N N 3 APN "C8'" "H8'2" sing N N 4 APN "C7'" "O7'" doub N N 5 APN "C7'" "N4'" sing N N 6 APN "C5'" C sing N N 7 APN "C5'" "N4'" sing N N 8 APN "C5'" "H5'1" sing N N 9 APN "C5'" "H5'2" sing N N 10 APN C O doub N N 11 APN C OXT sing N N 12 APN OXT HXT sing N N 13 APN "N4'" "C3'" sing N N 14 APN "C3'" "C2'" sing N N 15 APN "C3'" "H3'1" sing N N 16 APN "C3'" "H3'2" sing N N 17 APN "C2'" N sing N N 18 APN "C2'" "H2'1" sing N N 19 APN "C2'" "H2'2" sing N N 20 APN N H sing N N 21 APN N H2 sing N N 22 APN N H3 sing N N 23 APN N9 C8 sing Y N 24 APN N9 C4 sing Y N 25 APN C8 N7 doub Y N 26 APN C8 H8 sing N N 27 APN N7 C5 sing Y N 28 APN C5 C6 sing Y N 29 APN C5 C4 doub Y N 30 APN C6 N6 sing N N 31 APN C6 N1 doub Y N 32 APN N6 HN61 sing N N 33 APN N6 HN62 sing N N 34 APN N1 C2 sing Y N 35 APN C2 N3 doub Y N 36 APN C2 H21 sing N N 37 APN N3 C4 sing Y N 38 CPN "C8'" "C7'" sing N N 39 CPN "C8'" N1 sing N N 40 CPN "C8'" "H8'1" sing N N 41 CPN "C8'" "H8'2" sing N N 42 CPN "C7'" "O7'" doub N N 43 CPN "C7'" "N4'" sing N N 44 CPN "C5'" C sing N N 45 CPN "C5'" "N4'" sing N N 46 CPN "C5'" "H5'1" sing N N 47 CPN "C5'" "H5'2" sing N N 48 CPN C O doub N N 49 CPN C OXT sing N N 50 CPN OXT HXT sing N N 51 CPN "N4'" "C3'" sing N N 52 CPN "C3'" "C2'" sing N N 53 CPN "C3'" "H3'1" sing N N 54 CPN "C3'" "H3'2" sing N N 55 CPN "C2'" N sing N N 56 CPN "C2'" "H2'1" sing N N 57 CPN "C2'" "H2'2" sing N N 58 CPN N H sing N N 59 CPN N H2 sing N N 60 CPN N H3 sing N N 61 CPN N1 C2 sing N N 62 CPN N1 C6 sing N N 63 CPN C2 N3 sing N N 64 CPN C2 O2 doub N N 65 CPN N3 C4 doub N N 66 CPN C4 C5 sing N N 67 CPN C4 N4 sing N N 68 CPN C5 C6 doub N N 69 CPN C5 H5 sing N N 70 CPN C6 H6 sing N N 71 CPN N4 HN41 sing N N 72 CPN N4 HN42 sing N N 73 GPN "C8'" "C7'" sing N N 74 GPN "C8'" N9 sing N N 75 GPN "C8'" "H8'1" sing N N 76 GPN "C8'" "H8'2" sing N N 77 GPN "C7'" "O7'" doub N N 78 GPN "C7'" "N4'" sing N N 79 GPN "C5'" C sing N N 80 GPN "C5'" "N4'" sing N N 81 GPN "C5'" "H5'1" sing N N 82 GPN "C5'" "H5'2" sing N N 83 GPN C O doub N N 84 GPN C OXT sing N N 85 GPN OXT HXT sing N N 86 GPN "N4'" "C3'" sing N N 87 GPN "C3'" "C2'" sing N N 88 GPN "C3'" "H3'1" sing N N 89 GPN "C3'" "H3'2" sing N N 90 GPN "C2'" N sing N N 91 GPN "C2'" "H2'1" sing N N 92 GPN "C2'" "H2'2" sing N N 93 GPN N H sing N N 94 GPN N H2 sing N N 95 GPN N H3 sing N N 96 GPN N9 C8 sing Y N 97 GPN N9 C4 sing Y N 98 GPN C8 N7 doub Y N 99 GPN C8 H8 sing N N 100 GPN N7 C5 sing Y N 101 GPN C5 C6 sing N N 102 GPN C5 C4 doub Y N 103 GPN C6 O6 doub N N 104 GPN C6 N1 sing N N 105 GPN N1 C2 sing N N 106 GPN N1 HN1 sing N N 107 GPN C2 N2 sing N N 108 GPN C2 N3 doub N N 109 GPN N2 HN21 sing N N 110 GPN N2 HN22 sing N N 111 GPN N3 C4 sing N N 112 HOH O H1 sing N N 113 HOH O H2 sing N N 114 LYS N CA sing N N 115 LYS N H sing N N 116 LYS N H2 sing N N 117 LYS CA C sing N N 118 LYS CA CB sing N N 119 LYS CA HA sing N N 120 LYS C O doub N N 121 LYS C OXT sing N N 122 LYS CB CG sing N N 123 LYS CB HB2 sing N N 124 LYS CB HB3 sing N N 125 LYS CG CD sing N N 126 LYS CG HG2 sing N N 127 LYS CG HG3 sing N N 128 LYS CD CE sing N N 129 LYS CD HD2 sing N N 130 LYS CD HD3 sing N N 131 LYS CE NZ sing N N 132 LYS CE HE2 sing N N 133 LYS CE HE3 sing N N 134 LYS NZ HZ1 sing N N 135 LYS NZ HZ2 sing N N 136 LYS NZ HZ3 sing N N 137 LYS OXT HXT sing N N 138 NH2 N HN1 sing N N 139 NH2 N HN2 sing N N 140 TPN "C8'" "C7'" sing N N 141 TPN "C8'" N1 sing N N 142 TPN "C8'" "H8'1" sing N N 143 TPN "C8'" "H8'2" sing N N 144 TPN "C7'" "O7'" doub N N 145 TPN "C7'" "N4'" sing N N 146 TPN "C5'" C sing N N 147 TPN "C5'" "N4'" sing N N 148 TPN "C5'" "H5'1" sing N N 149 TPN "C5'" "H5'2" sing N N 150 TPN C O doub N N 151 TPN C OXT sing N N 152 TPN OXT HXT sing N N 153 TPN "N4'" "C3'" sing N N 154 TPN "C3'" "C2'" sing N N 155 TPN "C3'" "H3'1" sing N N 156 TPN "C3'" "H3'2" sing N N 157 TPN "C2'" N sing N N 158 TPN "C2'" "H2'1" sing N N 159 TPN "C2'" "H2'2" sing N N 160 TPN N H sing N N 161 TPN N H2 sing N N 162 TPN N H3 sing N N 163 TPN N1 C6 sing N N 164 TPN N1 C2 sing N N 165 TPN C6 C5 doub N N 166 TPN C6 H6 sing N N 167 TPN C2 O2 doub N N 168 TPN C2 N3 sing N N 169 TPN N3 C4 sing N N 170 TPN N3 HN3 sing N N 171 TPN C4 O4 doub N N 172 TPN C4 C5 sing N N 173 TPN C5 C5M sing N N 174 TPN C5M HM51 sing N N 175 TPN C5M HM52 sing N N 176 TPN C5M HM53 sing N N 177 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1RRU 'double helix' 1RRU 'z-form double helix' 1RRU '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 CPN 1 1_555 A GPN 6 2_555 -0.972 -0.412 -0.093 4.721 0.092 -3.324 1 A_CPN1:GPN6_A A 1 ? A 6 ? 19 1 1 A GPN 2 1_555 A CPN 5 2_555 0.770 -0.473 -0.278 -3.942 -9.056 -3.170 2 A_GPN2:CPN5_A A 2 ? A 5 ? 19 1 1 A TPN 3 1_555 A APN 4 2_555 -0.148 -0.519 -0.498 0.640 -7.447 -1.452 3 A_TPN3:APN4_A A 3 ? A 4 ? 20 1 1 A APN 4 1_555 A TPN 3 2_555 0.148 -0.519 -0.498 -0.640 -7.447 -1.452 4 A_APN4:TPN3_A A 4 ? A 3 ? 20 1 1 A CPN 5 1_555 A GPN 2 2_555 -0.770 -0.473 -0.278 3.942 -9.056 -3.170 5 A_CPN5:GPN2_A A 5 ? A 2 ? 19 1 1 A GPN 6 1_555 A CPN 1 2_555 0.972 -0.412 -0.093 -4.721 0.092 -3.324 6 A_GPN6:CPN1_A A 6 ? A 1 ? 19 1 1 B CPN 1 1_555 B GPN 6 2_656 -0.642 -0.126 -0.374 12.009 8.225 0.203 7 B_CPN9:GPN14_B B 9 ? B 14 ? 19 1 1 B GPN 2 1_555 B CPN 5 2_656 0.917 -0.669 0.033 -0.460 5.800 3.948 8 B_GPN10:CPN13_B B 10 ? B 13 ? 19 1 1 B TPN 3 1_555 B APN 4 2_656 -0.256 -0.438 -0.425 1.880 7.536 0.270 9 B_TPN11:APN12_B B 11 ? B 12 ? 20 1 1 B APN 4 1_555 B TPN 3 2_656 0.256 -0.438 -0.425 -1.880 7.536 0.270 10 B_APN12:TPN11_B B 12 ? B 11 ? 20 1 1 B CPN 5 1_555 B GPN 2 2_656 -0.917 -0.669 0.033 0.460 5.800 3.948 11 B_CPN13:GPN10_B B 13 ? B 10 ? 19 1 1 B GPN 6 1_555 B CPN 1 2_656 0.642 -0.126 -0.374 -12.009 8.225 0.203 12 B_GPN14:CPN9_B B 14 ? B 9 ? 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 CPN 1 1_555 A GPN 6 2_555 A GPN 2 1_555 A CPN 5 2_555 -0.026 -2.279 3.698 1.750 3.132 28.762 -5.310 0.475 3.428 6.273 -3.506 28.981 1 AA_CPN1GPN2:CPN5GPN6_AA A 1 ? A 6 ? A 2 ? A 5 ? 1 A GPN 2 1_555 A CPN 5 2_555 A TPN 3 1_555 A APN 4 2_555 -0.572 -2.843 3.244 2.423 1.575 13.095 -13.689 4.778 2.733 6.798 -10.458 13.408 2 AA_GPN2TPN3:APN4CPN5_AA A 2 ? A 5 ? A 3 ? A 4 ? 1 A TPN 3 1_555 A APN 4 2_555 A APN 4 1_555 A TPN 3 2_555 0.000 -1.064 3.621 0.000 6.477 17.169 -7.108 0.000 3.018 20.760 0.000 18.342 3 AA_TPN3APN4:TPN3APN4_AA A 3 ? A 4 ? A 4 ? A 3 ? 1 A APN 4 1_555 A TPN 3 2_555 A CPN 5 1_555 A GPN 2 2_555 0.572 -2.843 3.244 -2.423 1.575 13.095 -13.689 -4.778 2.733 6.798 10.458 13.408 4 AA_APN4CPN5:GPN2TPN3_AA A 4 ? A 3 ? A 5 ? A 2 ? 1 A CPN 5 1_555 A GPN 2 2_555 A GPN 6 1_555 A CPN 1 2_555 0.026 -2.279 3.698 -1.750 3.132 28.762 -5.310 -0.475 3.428 6.273 3.506 28.981 5 AA_CPN5GPN6:CPN1GPN2_AA A 5 ? A 2 ? A 6 ? A 1 ? 1 B CPN 1 1_555 B GPN 6 2_656 B GPN 2 1_555 B CPN 5 2_656 0.243 -2.459 3.749 -5.908 -5.987 -8.741 18.905 -6.020 1.611 31.302 -30.889 -12.125 6 BB_CPN9GPN10:CPN13GPN14_BB B 9 ? B 14 ? B 10 ? B 13 ? 1 B GPN 2 1_555 B CPN 5 2_656 B TPN 3 1_555 B APN 4 2_656 0.023 -2.447 3.252 4.192 5.299 -30.954 3.451 0.860 3.577 -9.784 7.740 -31.665 7 BB_GPN10TPN11:APN12CPN13_BB B 10 ? B 13 ? B 11 ? B 12 ? 1 B TPN 3 1_555 B APN 4 2_656 B APN 4 1_555 B TPN 3 2_656 0.000 -1.729 3.590 0.000 -12.108 -13.916 11.415 0.000 1.585 41.200 0.000 -18.426 8 BB_TPN11APN12:TPN11APN12_BB B 11 ? B 12 ? B 12 ? B 11 ? 1 B APN 4 1_555 B TPN 3 2_656 B CPN 5 1_555 B GPN 2 2_656 -0.023 -2.447 3.252 -4.192 5.299 -30.954 3.451 -0.860 3.577 -9.784 -7.740 -31.665 9 BB_APN12CPN13:GPN10TPN11_BB B 12 ? B 11 ? B 13 ? B 10 ? 1 B CPN 5 1_555 B GPN 2 2_656 B GPN 6 1_555 B CPN 1 2_656 -0.243 -2.459 3.749 5.908 -5.987 -8.741 18.905 6.020 1.611 31.302 30.889 -12.125 10 BB_CPN13GPN14:CPN9GPN10_BB B 13 ? B 10 ? B 14 ? B 9 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id 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 1PUP _pdbx_initial_refinement_model.details 'PDB entry 1PUP' #