data_1KH6 # _entry.id 1KH6 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.386 _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 1KH6 pdb_00001kh6 10.2210/pdb1kh6/pdb NDB UR0018 ? ? RCSB RCSB014955 ? ? WWPDB D_1000014955 ? ? # 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 2002-04-26 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-02-08 5 'Structure model' 1 4 2024-02-14 # _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' 'Database references' 4 4 'Structure model' 'Structure summary' 5 5 'Structure model' 'Data collection' 6 5 'Structure model' 'Database references' 7 5 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 5 'Structure model' chem_comp_atom 2 5 'Structure model' chem_comp_bond 3 5 'Structure model' database_2 4 5 'Structure model' struct_conn # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1KH6 _pdbx_database_status.recvd_initial_deposition_date 2001-11-29 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_mr ? _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 'Kieft, J.S.' 1 'Zhou, K.' 2 'Grech, A.' 3 'Jubin, R.' 4 'Doudna, J.A.' 5 # _citation.id primary _citation.title 'Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation.' _citation.journal_abbrev Nat.Struct.Biol. _citation.journal_volume 9 _citation.page_first 370 _citation.page_last 374 _citation.year 2002 _citation.journal_id_ASTM NSBIEW _citation.country US _citation.journal_id_ISSN 1072-8368 _citation.journal_id_CSD 2024 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 11927953 _citation.pdbx_database_id_DOI 10.1038/nsb781 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kieft, J.S.' 1 ? primary 'Zhou, K.' 2 ? primary 'Grech, A.' 3 ? primary 'Jubin, R.' 4 ? primary 'Doudna, J.A.' 5 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description JIIIabc _entity.formula_weight 17634.660 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ;JIIIabc is the structure of an RNA four-way junction from the Hepatitis C virus internal ribosome entry site. The junction joins domains IIIa, IIIb, and IIIc to the rest of domain III, and is critical for IRES function. ; # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'GGCGGAACCGGUGAG(5BU)ACACCGGAA(5BU)CCGAAAGGA(5BU)(5BU)(5BU)GGGCG(5BU)GCCCCCGCC' _entity_poly.pdbx_seq_one_letter_code_can GGCGGAACCGGUGAGUACACCGGAAUCCGAAAGGAUUUGGGCGUGCCCCCGCC _entity_poly.pdbx_strand_id A _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 G n 1 2 G n 1 3 C n 1 4 G n 1 5 G n 1 6 A n 1 7 A n 1 8 C n 1 9 C n 1 10 G n 1 11 G n 1 12 U n 1 13 G n 1 14 A n 1 15 G n 1 16 5BU n 1 17 A n 1 18 C n 1 19 A n 1 20 C n 1 21 C n 1 22 G n 1 23 G n 1 24 A n 1 25 A n 1 26 5BU n 1 27 C n 1 28 C n 1 29 G n 1 30 A n 1 31 A n 1 32 A n 1 33 G n 1 34 G n 1 35 A n 1 36 5BU n 1 37 5BU n 1 38 5BU n 1 39 G n 1 40 G n 1 41 G n 1 42 C n 1 43 G n 1 44 5BU n 1 45 G n 1 46 C n 1 47 C n 1 48 C n 1 49 C n 1 50 C n 1 51 G n 1 52 C n 1 53 C 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 'The sequence is from Hepatitis C virus genotype 1B. In Vitro Transcription.' # 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 5BU 'RNA linking' n "5-BROMO-URIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O9 P' 403.077 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # 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 G 1 1 1 G GUA A . n A 1 2 G 2 2 2 G GUA A . n A 1 3 C 3 3 3 C CYT A . n A 1 4 G 4 4 4 G GUA A . n A 1 5 G 5 5 5 G GUA A . n A 1 6 A 6 6 6 A ADE A . n A 1 7 A 7 7 7 A ADE A . n A 1 8 C 8 8 8 C CYT A . n A 1 9 C 9 9 9 C CYT A . n A 1 10 G 10 10 10 G GUA A . n A 1 11 G 11 11 ? ? ? A . n A 1 12 U 12 12 ? ? ? A . n A 1 13 G 13 13 ? ? ? A . n A 1 14 A 14 14 ? ? ? A . n A 1 15 G 15 15 ? ? ? A . n A 1 16 5BU 16 16 16 5BU URI A . n A 1 17 A 17 17 17 A ADE A . n A 1 18 C 18 18 18 C CYT A . n A 1 19 A 19 19 19 A ADE A . n A 1 20 C 20 20 20 C CYT A . n A 1 21 C 21 21 21 C CYT A . n A 1 22 G 22 22 22 G GUA A . n A 1 23 G 23 23 23 G GUA A . n A 1 24 A 24 24 24 A ADE A . n A 1 25 A 25 25 25 A ADE A . n A 1 26 5BU 26 26 26 5BU URI A . n A 1 27 C 27 27 27 C CYT A . n A 1 28 C 28 28 28 C CYT A . n A 1 29 G 29 29 29 G GUA A . n A 1 30 A 30 30 30 A ADE A . n A 1 31 A 31 31 31 A ADE A . n A 1 32 A 32 32 32 A ADE A . n A 1 33 G 33 33 33 G GUA A . n A 1 34 G 34 34 34 G GUA A . n A 1 35 A 35 35 35 A ADE A . n A 1 36 5BU 36 36 36 5BU URI A . n A 1 37 5BU 37 37 37 5BU URI A . n A 1 38 5BU 38 38 38 5BU URI A . n A 1 39 G 39 39 39 G GUA A . n A 1 40 G 40 40 40 G GUA A . n A 1 41 G 41 41 41 G GUA A . n A 1 42 C 42 42 42 C CYT A . n A 1 43 G 43 43 43 G GUA A . n A 1 44 5BU 44 44 44 5BU URI A . n A 1 45 G 45 45 45 G GUA A . n A 1 46 C 46 46 46 C CYT A . n A 1 47 C 47 47 47 C CYT A . n A 1 48 C 48 48 48 C CYT A . n A 1 49 C 49 49 49 C CYT A . n A 1 50 C 50 50 50 C CYT A . n A 1 51 G 51 51 51 G GUA A . n A 1 52 C 52 52 52 C CYT A . n A 1 53 C 53 53 53 C CYT A . n # 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 Y 1 A G 1 ? "O5'" ? A G 1 "O5'" 2 1 Y 1 A 5BU 16 ? P ? A 5BU 16 P 3 1 Y 1 A 5BU 16 ? OP1 ? A 5BU 16 OP1 4 1 Y 1 A 5BU 16 ? OP2 ? A 5BU 16 OP2 5 1 Y 1 A 5BU 44 ? P ? A 5BU 44 P 6 1 Y 1 A 5BU 44 ? OP1 ? A 5BU 44 OP1 7 1 Y 1 A 5BU 44 ? OP2 ? A 5BU 44 OP2 # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement . ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 CNS phasing . ? 4 # _cell.entry_id 1KH6 _cell.length_a 66.532 _cell.length_b 66.532 _cell.length_c 95.850 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _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 1KH6 _symmetry.space_group_name_H-M 'P 42 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1KH6 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.01 _exptl_crystal.density_percent_sol 59.10 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 303 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 4.6 _exptl_crystal_grow.pdbx_details ;30% MPD, 0.1 M sodium citrate pH 5.6, 0.2 M ammonium acetate, 2.5 mM magnesium chloride, and 1 mM spermidine, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 303K ; _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 MPD ? ? ? 1 2 1 'sodium citrate' ? ? ? 1 3 1 'ammonium acetate' ? ? ? 1 4 1 MgCl ? ? ? 1 5 1 spermidine ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _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 MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.9204 1.0 2 0.9197 1.0 3 0.9273 1.0 4 0.9020 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X25' _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X25 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '0.9204, 0.9197, 0.9273, 0.9020' # _reflns.entry_id 1KH6 _reflns.observed_criterion_sigma_I 0.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 50 _reflns.d_resolution_high 2.8 _reflns.number_obs 9652 _reflns.number_all ? _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _refine.entry_id 1KH6 _refine.ls_number_reflns_obs 8744 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 10000 _refine.pdbx_data_cutoff_low_absF ? _refine.ls_d_res_low 50 _refine.ls_d_res_high 2.9 _refine.ls_percent_reflns_obs 95.9 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.283 _refine.ls_R_factor_R_free 0.2792 _refine.ls_R_factor_R_free_error 0.004 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.8 _refine.ls_number_reflns_R_free 893 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details random _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.correlation_coeff_Fo_to_Fc ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_phase_error ? _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_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 1025 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1025 _refine_hist.d_res_high 2.9 _refine_hist.d_res_low 50 # _database_PDB_matrix.entry_id 1KH6 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 1KH6 _struct.title 'Crystal Structure of an RNA Tertiary Domain Essential to HCV IRES-mediated Translation Initiation.' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1KH6 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'translation, RNA structure, IRES, HCV, bromine, four-way junction, RNA' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1KH6 _struct_ref.pdbx_db_accession 1KH6 _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 1KH6 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 53 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1KH6 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 53 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 53 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _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 5BU 16 "O3'" ? ? ? 1_555 A A 17 P ? ? A 5BU 16 A A 17 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale2 covale both ? A A 25 "O3'" ? ? ? 1_555 A 5BU 26 P ? ? A A 25 A 5BU 26 1_555 ? ? ? ? ? ? ? 1.620 ? ? covale3 covale both ? A 5BU 26 "O3'" ? ? ? 1_555 A C 27 P ? ? A 5BU 26 A C 27 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale4 covale both ? A A 35 "O3'" ? ? ? 1_555 A 5BU 36 P ? ? A A 35 A 5BU 36 1_555 ? ? ? ? ? ? ? 1.615 ? ? covale5 covale both ? A 5BU 36 "O3'" ? ? ? 1_555 A 5BU 37 P ? ? A 5BU 36 A 5BU 37 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale6 covale both ? A 5BU 37 "O3'" ? ? ? 1_555 A 5BU 38 P ? ? A 5BU 37 A 5BU 38 1_555 ? ? ? ? ? ? ? 1.617 ? ? covale7 covale both ? A 5BU 38 "O3'" ? ? ? 1_555 A G 39 P ? ? A 5BU 38 A G 39 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale8 covale both ? A 5BU 44 "O3'" ? ? ? 1_555 A G 45 P ? ? A 5BU 44 A G 45 1_555 ? ? ? ? ? ? ? 1.623 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 A C 53 N3 ? ? A G 1 A C 53 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 A C 53 O2 ? ? A G 1 A C 53 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 A C 53 N4 ? ? A G 1 A C 53 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 A C 52 N3 ? ? A G 2 A C 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 A C 52 O2 ? ? A G 2 A C 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 A C 52 N4 ? ? A G 2 A C 52 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 A G 51 N1 ? ? A C 3 A G 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 A G 51 O6 ? ? A C 3 A G 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 A G 51 N2 ? ? A C 3 A G 51 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N1 ? ? ? 1_555 A C 50 N3 ? ? A G 4 A C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 N2 ? ? ? 1_555 A C 50 O2 ? ? A G 4 A C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 4 O6 ? ? ? 1_555 A C 50 N4 ? ? A G 4 A C 50 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 5 N1 ? ? ? 1_555 A C 49 N3 ? ? A G 5 A C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 5 N2 ? ? ? 1_555 A C 49 O2 ? ? A G 5 A C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 5 O6 ? ? ? 1_555 A C 49 N4 ? ? A G 5 A C 49 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A A 6 N6 ? ? ? 1_555 A A 25 N3 ? ? A A 6 A A 25 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog17 hydrog ? ? A A 6 N6 ? ? ? 1_555 A 5BU 37 O2 ? ? A A 6 A 5BU 37 1_555 ? ? ? ? ? ? 'A-5BU PAIR' ? ? ? hydrog18 hydrog ? ? A A 7 N6 ? ? ? 1_555 A A 24 N3 ? ? A A 7 A A 24 1_555 ? ? ? ? ? ? 'A-A MISPAIR' ? ? ? hydrog19 hydrog ? ? A A 7 N6 ? ? ? 1_555 A 5BU 38 O4 ? ? A A 7 A 5BU 38 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog20 hydrog ? ? A A 7 N7 ? ? ? 1_555 A 5BU 38 N3 ? ? A A 7 A 5BU 38 1_555 ? ? ? ? ? ? HOOGSTEEN ? ? ? hydrog21 hydrog ? ? A C 8 N3 ? ? ? 1_555 A G 23 N1 ? ? A C 8 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 8 N4 ? ? ? 1_555 A G 23 O6 ? ? A C 8 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 8 O2 ? ? ? 1_555 A G 23 N2 ? ? A C 8 A G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 9 O2 ? ? ? 1_555 A G 22 N2 ? ? A C 9 A G 22 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog25 hydrog ? ? A G 10 N1 ? ? ? 1_555 A C 21 N3 ? ? A G 10 A C 21 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog26 hydrog ? ? A A 24 N1 ? ? ? 1_555 A 5BU 37 N3 ? ? A A 24 A 5BU 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A A 24 N6 ? ? ? 1_555 A 5BU 37 O4 ? ? A A 24 A 5BU 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A A 25 N1 ? ? ? 1_555 A 5BU 36 N3 ? ? A A 25 A 5BU 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A A 25 N6 ? ? ? 1_555 A 5BU 36 O4 ? ? A A 25 A 5BU 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A 5BU 26 N3 ? ? ? 1_555 A A 35 N1 ? ? A 5BU 26 A A 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A 5BU 26 O4 ? ? ? 1_555 A A 35 N6 ? ? A 5BU 26 A A 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 27 O2 ? ? ? 1_555 A G 34 N1 ? ? A C 27 A G 34 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog33 hydrog ? ? A C 28 N3 ? ? ? 1_555 A G 33 N1 ? ? A C 28 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 28 N4 ? ? ? 1_555 A G 33 O6 ? ? A C 28 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 28 O2 ? ? ? 1_555 A G 33 N2 ? ? A C 28 A G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 39 N1 ? ? ? 1_555 A C 48 N3 ? ? A G 39 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 39 N2 ? ? ? 1_555 A C 48 O2 ? ? A G 39 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 39 O6 ? ? ? 1_555 A C 48 N4 ? ? A G 39 A C 48 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A G 40 N1 ? ? ? 1_555 A C 47 N3 ? ? A G 40 A C 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A G 40 N2 ? ? ? 1_555 A C 47 O2 ? ? A G 40 A C 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A G 40 O6 ? ? ? 1_555 A C 47 N4 ? ? A G 40 A C 47 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 41 N1 ? ? ? 1_555 A C 46 N3 ? ? A G 41 A C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A G 41 N2 ? ? ? 1_555 A C 46 O2 ? ? A G 41 A C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A G 41 O6 ? ? ? 1_555 A C 46 N4 ? ? A G 41 A C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 42 N3 ? ? ? 1_555 A G 45 N1 ? ? A C 42 A G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A C 42 N4 ? ? ? 1_555 A G 45 O6 ? ? A C 42 A G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A C 42 O2 ? ? ? 1_555 A G 45 N2 ? ? A C 42 A G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A G 43 N1 ? ? ? 1_555 A 5BU 44 O2 ? ? A G 43 A 5BU 44 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? hydrog49 hydrog ? ? A G 43 O6 ? ? ? 1_555 A 5BU 44 N3 ? ? A G 43 A 5BU 44 1_555 ? ? ? ? ? ? TYPE_28_PAIR ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O4'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 G _pdbx_validate_rmsd_angle.auth_seq_id_1 43 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 "C1'" _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 G _pdbx_validate_rmsd_angle.auth_seq_id_2 43 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 N9 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 G _pdbx_validate_rmsd_angle.auth_seq_id_3 43 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 113.36 _pdbx_validate_rmsd_angle.angle_target_value 108.50 _pdbx_validate_rmsd_angle.angle_deviation 4.86 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.70 _pdbx_validate_rmsd_angle.linker_flag N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 G A 29 ? ? 0.079 'SIDE CHAIN' 2 1 A A 31 ? ? 0.056 'SIDE CHAIN' 3 1 G A 43 ? ? 0.051 'SIDE CHAIN' # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A 5BU 16 A 5BU 16 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 2 A 5BU 26 A 5BU 26 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 3 A 5BU 36 A 5BU 36 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 4 A 5BU 37 A 5BU 37 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 5 A 5BU 38 A 5BU 38 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" 6 A 5BU 44 A 5BU 44 ? U "5-BROMO-URIDINE-5'-MONOPHOSPHATE" # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A G 11 ? A G 11 2 1 Y 1 A U 12 ? A U 12 3 1 Y 1 A G 13 ? A G 13 4 1 Y 1 A A 14 ? A A 14 5 1 Y 1 A G 15 ? A G 15 # 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 5BU P P N N 1 5BU OP1 O N N 2 5BU OP2 O N N 3 5BU OP3 O N N 4 5BU "O5'" O N N 5 5BU "C5'" C N N 6 5BU "C4'" C N R 7 5BU "O4'" O N N 8 5BU "C3'" C N S 9 5BU "O3'" O N N 10 5BU "C2'" C N R 11 5BU "O2'" O N N 12 5BU "C1'" C N R 13 5BU N1 N N N 14 5BU C2 C N N 15 5BU O2 O N N 16 5BU N3 N N N 17 5BU C4 C N N 18 5BU O4 O N N 19 5BU C5 C N N 20 5BU C6 C N N 21 5BU BR BR N N 22 5BU HOP2 H N N 23 5BU HOP3 H N N 24 5BU "H5'" H N N 25 5BU "H5''" H N N 26 5BU "H4'" H N N 27 5BU "H3'" H N N 28 5BU "HO3'" H N N 29 5BU "H2'" H N N 30 5BU "HO2'" H N N 31 5BU "H1'" H N N 32 5BU H3 H N N 33 5BU H6 H N N 34 A OP3 O N N 35 A P P N N 36 A OP1 O N N 37 A OP2 O N N 38 A "O5'" O N N 39 A "C5'" C N N 40 A "C4'" C N R 41 A "O4'" O N N 42 A "C3'" C N S 43 A "O3'" O N N 44 A "C2'" C N R 45 A "O2'" O N N 46 A "C1'" C N R 47 A N9 N Y N 48 A C8 C Y N 49 A N7 N Y N 50 A C5 C Y N 51 A C6 C Y N 52 A N6 N N N 53 A N1 N Y N 54 A C2 C Y N 55 A N3 N Y N 56 A C4 C Y N 57 A HOP3 H N N 58 A HOP2 H N N 59 A "H5'" H N N 60 A "H5''" H N N 61 A "H4'" H N N 62 A "H3'" H N N 63 A "HO3'" H N N 64 A "H2'" H N N 65 A "HO2'" H N N 66 A "H1'" H N N 67 A H8 H N N 68 A H61 H N N 69 A H62 H N N 70 A H2 H N N 71 C OP3 O N N 72 C P P N N 73 C OP1 O N N 74 C OP2 O N N 75 C "O5'" O N N 76 C "C5'" C N N 77 C "C4'" C N R 78 C "O4'" O N N 79 C "C3'" C N S 80 C "O3'" O N N 81 C "C2'" C N R 82 C "O2'" O N N 83 C "C1'" C N R 84 C N1 N N N 85 C C2 C N N 86 C O2 O N N 87 C N3 N N N 88 C C4 C N N 89 C N4 N N N 90 C C5 C N N 91 C C6 C N N 92 C HOP3 H N N 93 C HOP2 H N N 94 C "H5'" H N N 95 C "H5''" H N N 96 C "H4'" H N N 97 C "H3'" H N N 98 C "HO3'" H N N 99 C "H2'" H N N 100 C "HO2'" H N N 101 C "H1'" H N N 102 C H41 H N N 103 C H42 H N N 104 C H5 H N N 105 C H6 H N N 106 G OP3 O N N 107 G P P N N 108 G OP1 O N N 109 G OP2 O N N 110 G "O5'" O N N 111 G "C5'" C N N 112 G "C4'" C N R 113 G "O4'" O N N 114 G "C3'" C N S 115 G "O3'" O N N 116 G "C2'" C N R 117 G "O2'" O N N 118 G "C1'" C N R 119 G N9 N Y N 120 G C8 C Y N 121 G N7 N Y N 122 G C5 C Y N 123 G C6 C N N 124 G O6 O N N 125 G N1 N N N 126 G C2 C N N 127 G N2 N N N 128 G N3 N N N 129 G C4 C Y N 130 G HOP3 H N N 131 G HOP2 H N N 132 G "H5'" H N N 133 G "H5''" H N N 134 G "H4'" H N N 135 G "H3'" H N N 136 G "HO3'" H N N 137 G "H2'" H N N 138 G "HO2'" H N N 139 G "H1'" H N N 140 G H8 H N N 141 G H1 H N N 142 G H21 H N N 143 G H22 H N N 144 U OP3 O N N 145 U P P N N 146 U OP1 O N N 147 U OP2 O N N 148 U "O5'" O N N 149 U "C5'" C N N 150 U "C4'" C N R 151 U "O4'" O N N 152 U "C3'" C N S 153 U "O3'" O N N 154 U "C2'" C N R 155 U "O2'" O N N 156 U "C1'" C N R 157 U N1 N N N 158 U C2 C N N 159 U O2 O N N 160 U N3 N N N 161 U C4 C N N 162 U O4 O N N 163 U C5 C N N 164 U C6 C N N 165 U HOP3 H N N 166 U HOP2 H N N 167 U "H5'" H N N 168 U "H5''" H N N 169 U "H4'" H N N 170 U "H3'" H N N 171 U "HO3'" H N N 172 U "H2'" H N N 173 U "HO2'" H N N 174 U "H1'" H N N 175 U H3 H N N 176 U H5 H N N 177 U H6 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 5BU P OP1 doub N N 1 5BU P OP2 sing N N 2 5BU P OP3 sing N N 3 5BU P "O5'" sing N N 4 5BU OP2 HOP2 sing N N 5 5BU OP3 HOP3 sing N N 6 5BU "O5'" "C5'" sing N N 7 5BU "C5'" "C4'" sing N N 8 5BU "C5'" "H5'" sing N N 9 5BU "C5'" "H5''" sing N N 10 5BU "C4'" "O4'" sing N N 11 5BU "C4'" "C3'" sing N N 12 5BU "C4'" "H4'" sing N N 13 5BU "O4'" "C1'" sing N N 14 5BU "C3'" "O3'" sing N N 15 5BU "C3'" "C2'" sing N N 16 5BU "C3'" "H3'" sing N N 17 5BU "O3'" "HO3'" sing N N 18 5BU "C2'" "O2'" sing N N 19 5BU "C2'" "C1'" sing N N 20 5BU "C2'" "H2'" sing N N 21 5BU "O2'" "HO2'" sing N N 22 5BU "C1'" N1 sing N N 23 5BU "C1'" "H1'" sing N N 24 5BU N1 C2 sing N N 25 5BU N1 C6 sing N N 26 5BU C2 O2 doub N N 27 5BU C2 N3 sing N N 28 5BU N3 C4 sing N N 29 5BU N3 H3 sing N N 30 5BU C4 O4 doub N N 31 5BU C4 C5 sing N N 32 5BU C5 C6 doub N N 33 5BU C5 BR sing N N 34 5BU C6 H6 sing N N 35 A OP3 P sing N N 36 A OP3 HOP3 sing N N 37 A P OP1 doub N N 38 A P OP2 sing N N 39 A P "O5'" sing N N 40 A OP2 HOP2 sing N N 41 A "O5'" "C5'" sing N N 42 A "C5'" "C4'" sing N N 43 A "C5'" "H5'" sing N N 44 A "C5'" "H5''" sing N N 45 A "C4'" "O4'" sing N N 46 A "C4'" "C3'" sing N N 47 A "C4'" "H4'" sing N N 48 A "O4'" "C1'" sing N N 49 A "C3'" "O3'" sing N N 50 A "C3'" "C2'" sing N N 51 A "C3'" "H3'" sing N N 52 A "O3'" "HO3'" sing N N 53 A "C2'" "O2'" sing N N 54 A "C2'" "C1'" sing N N 55 A "C2'" "H2'" sing N N 56 A "O2'" "HO2'" sing N N 57 A "C1'" N9 sing N N 58 A "C1'" "H1'" sing N N 59 A N9 C8 sing Y N 60 A N9 C4 sing Y N 61 A C8 N7 doub Y N 62 A C8 H8 sing N N 63 A N7 C5 sing Y N 64 A C5 C6 sing Y N 65 A C5 C4 doub Y N 66 A C6 N6 sing N N 67 A C6 N1 doub Y N 68 A N6 H61 sing N N 69 A N6 H62 sing N N 70 A N1 C2 sing Y N 71 A C2 N3 doub Y N 72 A C2 H2 sing N N 73 A N3 C4 sing Y N 74 C OP3 P sing N N 75 C OP3 HOP3 sing N N 76 C P OP1 doub N N 77 C P OP2 sing N N 78 C P "O5'" sing N N 79 C OP2 HOP2 sing N N 80 C "O5'" "C5'" sing N N 81 C "C5'" "C4'" sing N N 82 C "C5'" "H5'" sing N N 83 C "C5'" "H5''" sing N N 84 C "C4'" "O4'" sing N N 85 C "C4'" "C3'" sing N N 86 C "C4'" "H4'" sing N N 87 C "O4'" "C1'" sing N N 88 C "C3'" "O3'" sing N N 89 C "C3'" "C2'" sing N N 90 C "C3'" "H3'" sing N N 91 C "O3'" "HO3'" sing N N 92 C "C2'" "O2'" sing N N 93 C "C2'" "C1'" sing N N 94 C "C2'" "H2'" sing N N 95 C "O2'" "HO2'" sing N N 96 C "C1'" N1 sing N N 97 C "C1'" "H1'" sing N N 98 C N1 C2 sing N N 99 C N1 C6 sing N N 100 C C2 O2 doub N N 101 C C2 N3 sing N N 102 C N3 C4 doub N N 103 C C4 N4 sing N N 104 C C4 C5 sing N N 105 C N4 H41 sing N N 106 C N4 H42 sing N N 107 C C5 C6 doub N N 108 C C5 H5 sing N N 109 C C6 H6 sing N N 110 G OP3 P sing N N 111 G OP3 HOP3 sing N N 112 G P OP1 doub N N 113 G P OP2 sing N N 114 G P "O5'" sing N N 115 G OP2 HOP2 sing N N 116 G "O5'" "C5'" sing N N 117 G "C5'" "C4'" sing N N 118 G "C5'" "H5'" sing N N 119 G "C5'" "H5''" sing N N 120 G "C4'" "O4'" sing N N 121 G "C4'" "C3'" sing N N 122 G "C4'" "H4'" sing N N 123 G "O4'" "C1'" sing N N 124 G "C3'" "O3'" sing N N 125 G "C3'" "C2'" sing N N 126 G "C3'" "H3'" sing N N 127 G "O3'" "HO3'" sing N N 128 G "C2'" "O2'" sing N N 129 G "C2'" "C1'" sing N N 130 G "C2'" "H2'" sing N N 131 G "O2'" "HO2'" sing N N 132 G "C1'" N9 sing N N 133 G "C1'" "H1'" sing N N 134 G N9 C8 sing Y N 135 G N9 C4 sing Y N 136 G C8 N7 doub Y N 137 G C8 H8 sing N N 138 G N7 C5 sing Y N 139 G C5 C6 sing N N 140 G C5 C4 doub Y N 141 G C6 O6 doub N N 142 G C6 N1 sing N N 143 G N1 C2 sing N N 144 G N1 H1 sing N N 145 G C2 N2 sing N N 146 G C2 N3 doub N N 147 G N2 H21 sing N N 148 G N2 H22 sing N N 149 G N3 C4 sing N N 150 U OP3 P sing N N 151 U OP3 HOP3 sing N N 152 U P OP1 doub N N 153 U P OP2 sing N N 154 U P "O5'" sing N N 155 U OP2 HOP2 sing N N 156 U "O5'" "C5'" sing N N 157 U "C5'" "C4'" sing N N 158 U "C5'" "H5'" sing N N 159 U "C5'" "H5''" sing N N 160 U "C4'" "O4'" sing N N 161 U "C4'" "C3'" sing N N 162 U "C4'" "H4'" sing N N 163 U "O4'" "C1'" sing N N 164 U "C3'" "O3'" sing N N 165 U "C3'" "C2'" sing N N 166 U "C3'" "H3'" sing N N 167 U "O3'" "HO3'" sing N N 168 U "C2'" "O2'" sing N N 169 U "C2'" "C1'" sing N N 170 U "C2'" "H2'" sing N N 171 U "O2'" "HO2'" sing N N 172 U "C1'" N1 sing N N 173 U "C1'" "H1'" sing N N 174 U N1 C2 sing N N 175 U N1 C6 sing N N 176 U C2 O2 doub N N 177 U C2 N3 sing N N 178 U N3 C4 sing N N 179 U N3 H3 sing N N 180 U C4 O4 doub N N 181 U C4 C5 sing N N 182 U C5 C6 doub N N 183 U C5 H5 sing N N 184 U C6 H6 sing N N 185 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1KH6 'double helix' 1KH6 'a-form double helix' 1KH6 'hairpin loop' 1KH6 'quadruple 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 G 1 1_555 A C 53 1_555 0.026 -0.137 -0.481 -17.637 -7.010 -5.299 1 A_G1:C53_A A 1 ? A 53 ? 19 1 1 A G 2 1_555 A C 52 1_555 0.157 -0.566 -0.031 -3.225 -9.093 -2.713 2 A_G2:C52_A A 2 ? A 52 ? 19 1 1 A C 3 1_555 A G 51 1_555 0.115 -0.411 -0.040 4.419 -5.535 1.561 3 A_C3:G51_A A 3 ? A 51 ? 19 1 1 A G 4 1_555 A C 50 1_555 -0.255 -0.307 -0.268 -4.081 -12.379 -1.585 4 A_G4:C50_A A 4 ? A 50 ? 19 1 1 A G 5 1_555 A C 49 1_555 0.375 -0.201 -0.118 -7.414 -10.145 -7.232 5 A_G5:C49_A A 5 ? A 49 ? 19 1 1 A G 39 1_555 A C 48 1_555 -0.054 -0.444 -0.473 -6.391 -2.065 -2.370 6 A_G39:C48_A A 39 ? A 48 ? 19 1 1 A G 40 1_555 A C 47 1_555 -0.068 -0.350 -0.070 -7.295 -1.305 0.483 7 A_G40:C47_A A 40 ? A 47 ? 19 1 1 A G 41 1_555 A C 46 1_555 -0.305 -0.218 -0.210 -12.926 -11.846 1.626 8 A_G41:C46_A A 41 ? A 46 ? 19 1 1 A C 42 1_555 A G 45 1_555 0.733 -0.484 -0.040 -6.216 -2.079 -1.282 9 A_C42:G45_A A 42 ? A 45 ? 19 1 1 A G 43 1_555 A 5BU 44 1_555 -1.584 -0.354 -0.313 -5.973 -13.098 -4.976 10 A_G43:5BU44_A A 43 ? A 44 ? 28 1 1 A C 21 1_555 A G 10 1_555 -0.702 -0.743 1.470 15.389 37.782 0.957 11 A_C21:G10_A A 21 ? A 10 ? ? ? 1 A G 22 1_555 A C 9 1_555 0.216 0.461 -0.272 6.092 11.052 21.328 12 A_G22:C9_A A 22 ? A 9 ? ? 1 1 A G 23 1_555 A C 8 1_555 0.694 -0.217 -0.505 -5.742 -18.131 5.468 13 A_G23:C8_A A 23 ? A 8 ? 19 1 1 A 5BU 38 1_555 A A 7 1_555 0.177 2.578 0.344 7.680 -10.249 -67.396 14 A_5BU38:A7_A A 38 ? A 7 ? 23 3 1 A A 24 1_555 A 5BU 37 1_555 -0.140 -0.010 0.347 0.333 -8.169 1.522 15 A_A24:5BU37_A A 24 ? A 37 ? 20 1 1 A A 25 1_555 A 5BU 36 1_555 -0.707 -0.486 0.392 9.843 -12.399 2.195 16 A_A25:5BU36_A A 25 ? A 36 ? 20 1 1 A 5BU 26 1_555 A A 35 1_555 0.925 -0.354 0.297 3.899 -16.750 12.340 17 A_5BU26:A35_A A 26 ? A 35 ? 20 1 1 A C 27 1_555 A G 34 1_555 1.666 0.205 -0.162 4.352 -9.439 17.436 18 A_C27:G34_A A 27 ? A 34 ? ? 1 1 A C 28 1_555 A G 33 1_555 0.200 0.003 -0.609 5.976 4.036 5.433 19 A_C28:G33_A A 28 ? A 33 ? 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 G 1 1_555 A C 53 1_555 A G 2 1_555 A C 52 1_555 0.111 -1.635 2.911 -8.225 11.572 29.565 -4.497 -1.331 2.043 21.205 15.071 32.728 1 AA_G1G2:C52C53_AA A 1 ? A 53 ? A 2 ? A 52 ? 1 A G 2 1_555 A C 52 1_555 A C 3 1_555 A G 51 1_555 -0.158 -1.825 3.091 -0.481 1.201 32.774 -3.425 0.202 3.026 2.127 0.851 32.799 2 AA_G2C3:G51C52_AA A 2 ? A 52 ? A 3 ? A 51 ? 1 A C 3 1_555 A G 51 1_555 A G 4 1_555 A C 50 1_555 -0.170 -2.231 3.455 2.588 10.433 24.391 -7.358 0.993 2.293 23.301 -5.779 26.622 3 AA_C3G4:C50G51_AA A 3 ? A 51 ? A 4 ? A 50 ? 1 A G 4 1_555 A C 50 1_555 A G 5 1_555 A C 49 1_555 0.286 -2.014 3.345 0.053 8.056 35.125 -4.353 -0.455 2.829 13.136 -0.087 36.008 4 AA_G4G5:C49C50_AA A 4 ? A 50 ? A 5 ? A 49 ? 1 A G 5 1_555 A C 49 1_555 A G 39 1_555 A C 48 1_555 -0.975 -1.834 3.308 6.819 13.268 39.337 -3.808 2.003 2.400 18.904 -9.716 41.965 5 AA_G5G39:C48C49_AA A 5 ? A 49 ? A 39 ? A 48 ? 1 A G 39 1_555 A C 48 1_555 A G 40 1_555 A C 47 1_555 0.000 -2.367 3.295 -1.163 2.439 32.001 -4.709 -0.205 3.109 4.415 2.104 32.112 6 AA_G39G40:C47C48_AA A 39 ? A 48 ? A 40 ? A 47 ? 1 A G 40 1_555 A C 47 1_555 A G 41 1_555 A C 46 1_555 0.686 -2.501 3.333 7.260 7.489 27.476 -6.463 0.129 2.664 15.095 -14.634 29.354 7 AA_G40G41:C46C47_AA A 40 ? A 47 ? A 41 ? A 46 ? 1 A G 41 1_555 A C 46 1_555 A C 42 1_555 A G 45 1_555 -0.465 -1.153 3.035 0.988 1.617 36.741 -2.030 0.860 2.971 2.563 -1.567 36.788 8 AA_G41C42:G45C46_AA A 41 ? A 46 ? A 42 ? A 45 ? 1 A C 42 1_555 A G 45 1_555 A G 43 1_555 A 5BU 44 1_555 1.208 -2.611 3.201 4.920 11.506 22.424 -8.585 -1.568 1.877 27.049 -11.567 25.640 9 AA_C42G43:5BU44G45_AA A 42 ? A 45 ? A 43 ? A 44 ? 1 A C 21 1_555 A G 10 1_555 A G 22 1_555 A C 9 1_555 2.022 -2.477 2.982 16.354 17.777 37.827 -4.702 -1.336 2.309 24.603 -22.634 44.642 10 AA_C21G22:C9G10_AA A 21 ? A 10 ? A 22 ? A 9 ? 1 A G 22 1_555 A C 9 1_555 A G 23 1_555 A C 8 1_555 -0.106 -1.811 3.546 3.631 12.372 33.990 -4.625 0.675 2.719 20.281 -5.953 36.286 11 AA_G22G23:C8C9_AA A 22 ? A 9 ? A 23 ? A 8 ? 1 A G 23 1_555 A C 8 1_555 A 5BU 38 1_555 A A 7 1_555 -0.809 -3.792 0.211 -149.582 -81.258 176.071 -1.894 0.401 0.297 -40.630 74.794 179.665 12 AA_G235BU38:A7C8_AA A 23 ? A 8 ? A 38 ? A 7 ? 1 A 5BU 38 1_555 A A 7 1_555 A A 24 1_555 A 5BU 37 1_555 5.370 -2.210 -3.068 159.266 -21.567 -35.453 0.657 -0.695 -6.290 11.680 86.252 -161.643 13 AA_5BU38A24:5BU37A7_AA A 38 ? A 7 ? A 24 ? A 37 ? 1 A A 24 1_555 A 5BU 37 1_555 A A 25 1_555 A 5BU 36 1_555 -0.242 -1.352 2.930 -4.059 2.096 30.749 -2.880 -0.239 2.841 3.925 7.601 31.078 14 AA_A24A25:5BU365BU37_AA A 24 ? A 37 ? A 25 ? A 36 ? 1 A A 25 1_555 A 5BU 36 1_555 A 5BU 26 1_555 A A 35 1_555 0.473 -0.903 3.392 -1.407 -0.458 40.991 -1.236 -0.834 3.384 -0.654 2.008 41.017 15 AA_A255BU26:A355BU36_AA A 25 ? A 36 ? A 26 ? A 35 ? 1 A 5BU 26 1_555 A A 35 1_555 A C 27 1_555 A G 34 1_555 0.011 -1.455 3.191 3.870 4.021 32.858 -3.173 0.592 2.979 7.045 -6.780 33.316 16 AA_5BU26C27:G34A35_AA A 26 ? A 35 ? A 27 ? A 34 ? 1 A C 27 1_555 A G 34 1_555 A C 28 1_555 A G 33 1_555 -1.224 -1.945 3.281 1.319 5.504 21.537 -6.939 3.625 2.629 14.412 -3.453 22.260 17 AA_C27C28:G33G34_AA A 27 ? A 34 ? A 28 ? A 33 ? # _atom_sites.entry_id 1KH6 _atom_sites.fract_transf_matrix[1][1] 0.015030 _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] 0.015030 _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] 0.010433 _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 BR C N O P # loop_