data_488D # _entry.id 488D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _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 488D pdb_0000488d 10.2210/pdb488d/pdb NDB UR0010 ? ? RCSB RCSB001434 ? ? WWPDB D_1000001434 ? ? # 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 2000-03-06 2 'Structure model' 1 1 2008-04-26 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-12-27 # _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' # 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_struct_conn_angle 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_conn_type 7 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' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_asym_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 17 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 18 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 19 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 20 4 'Structure model' '_pdbx_struct_conn_angle.value' 21 4 'Structure model' '_struct_conn.conn_type_id' 22 4 'Structure model' '_struct_conn.id' 23 4 'Structure model' '_struct_conn.pdbx_dist_value' 24 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 25 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 26 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 27 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 28 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 29 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 30 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 31 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 32 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 33 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 34 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 35 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 36 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 37 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 38 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 39 4 'Structure model' '_struct_conn_type.id' 40 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 41 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 42 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 488D _pdbx_database_status.recvd_initial_deposition_date 2000-02-25 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _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.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Murray, J.B.' 1 'Szoke, H.' 2 'Szoke, A.' 3 'Scott, W.G.' 4 # _citation.id primary _citation.title ;Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction. ; _citation.journal_abbrev Mol.Cell _citation.journal_volume 5 _citation.page_first 279 _citation.page_last 287 _citation.year 2000 _citation.journal_id_ASTM MOCEFL _citation.country US _citation.journal_id_ISSN 1097-2765 _citation.journal_id_CSD 2168 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 10882069 _citation.pdbx_database_id_DOI '10.1016/S1097-2765(00)80423-2' # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Murray, J.B.' 1 ? primary 'Szoke, H.' 2 ? primary 'Szoke, A.' 3 ? primary 'Scott, W.G.' 4 ? # 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 'RNA RIBOZYME STRAND' 5170.103 1 ? ? ? 16-MER 2 polymer syn 'FIRST RNA FRAGMENT OF CLEAVED SUBSTRATE' 6507.884 1 ? ? ? ;20-MER, 3'-END CYCLIC PHOSPHATE ; 3 polymer syn 'SECOND RNA FRAGMENT OF CLEAVED SUBSTRATE' 1529.000 1 ? ? ? 5-MER 4 polymer syn 'UNCLEAVED RNA SUBSTRATE' 8019.876 1 ? ? ? 25-MER 5 non-polymer syn 'CADMIUM ION' 112.411 8 ? ? ? ? # 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 polyribonucleotide no no GUGGUCUGAUGAGGCC GUGGUCUGAUGAGGCC A ? 2 polyribonucleotide no yes 'GGCCGAAACUCGUAAGAGU(CCC)' GGCCGAAACUCGUAAGAGUC B ? 3 polyribonucleotide no no ACCAC ACCAC C ? 4 polyribonucleotide no no GGCCGAAACUCGUAAGAGUCACCAC GGCCGAAACUCGUAAGAGUCACCAC D ? # _pdbx_entity_nonpoly.entity_id 5 _pdbx_entity_nonpoly.name 'CADMIUM ION' _pdbx_entity_nonpoly.comp_id CD # 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 U n 1 3 G n 1 4 G n 1 5 U n 1 6 C n 1 7 U n 1 8 G n 1 9 A n 1 10 U n 1 11 G n 1 12 A n 1 13 G n 1 14 G n 1 15 C n 1 16 C n 2 1 G n 2 2 G n 2 3 C n 2 4 C n 2 5 G n 2 6 A n 2 7 A n 2 8 A n 2 9 C n 2 10 U n 2 11 C n 2 12 G n 2 13 U n 2 14 A n 2 15 A n 2 16 G n 2 17 A n 2 18 G n 2 19 U n 2 20 CCC n 3 1 A n 3 2 C n 3 3 C n 3 4 A n 3 5 C n 4 1 G n 4 2 G n 4 3 C n 4 4 C n 4 5 G n 4 6 A n 4 7 A n 4 8 A n 4 9 C n 4 10 U n 4 11 C n 4 12 G n 4 13 U n 4 14 A n 4 15 A n 4 16 G n 4 17 A n 4 18 G n 4 19 U n 4 20 C n 4 21 A n 4 22 C n 4 23 C n 4 24 A n 4 25 C n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight 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 CCC 'RNA linking' n ;CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE ; ? 'C9 H13 N3 O10 P2' 385.161 CD non-polymer . 'CADMIUM ION' ? 'Cd 2' 112.411 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 25 25 G G A . n A 1 2 U 2 24 24 U U A . n A 1 3 G 3 23 23 G G A . n A 1 4 G 4 22 22 G G A . n A 1 5 U 5 21 21 U U A . n A 1 6 C 6 30 30 C C A . n A 1 7 U 7 40 40 U U A . n A 1 8 G 8 50 50 G G A . n A 1 9 A 9 60 60 A A A . n A 1 10 U 10 70 70 U U A . n A 1 11 G 11 80 80 G G A . n A 1 12 A 12 90 90 A A A . n A 1 13 G 13 101 101 G G A . n A 1 14 G 14 102 102 G G A . n A 1 15 C 15 103 103 C C A . n A 1 16 C 16 104 104 C C A . n B 2 1 G 1 114 114 G G B . n B 2 2 G 2 113 113 G G B . n B 2 3 C 3 112 112 C C B . n B 2 4 C 4 111 111 C C B . n B 2 5 G 5 120 120 G G B . n B 2 6 A 6 130 130 A A B . n B 2 7 A 7 140 140 A A B . n B 2 8 A 8 151 151 A A B . n B 2 9 C 9 152 152 C C B . n B 2 10 U 10 153 153 U U B . n B 2 11 C 11 154 154 C C B . n B 2 12 G 12 31 31 G G B L n B 2 13 U 13 32 32 U U B L n B 2 14 A 14 33 33 A A B L n B 2 15 A 15 34 34 A A B L n B 2 16 G 16 164 164 G G B . n B 2 17 A 17 163 163 A A B . n B 2 18 G 18 162 162 G G B . n B 2 19 U 19 161 161 U U B . n B 2 20 CCC 20 170 170 CCC CCC B . n C 3 1 A 1 11 11 A A C . n C 3 2 C 2 12 12 C C C . n C 3 3 C 3 13 13 C C C . n C 3 4 A 4 14 14 A A C . n C 3 5 C 5 15 15 C C C . n D 4 1 G 1 114 114 G G D . n D 4 2 G 2 113 113 G G D . n D 4 3 C 3 112 112 C C D . n D 4 4 C 4 111 111 C C D . n D 4 5 G 5 120 120 G G D . n D 4 6 A 6 130 130 A A D . n D 4 7 A 7 140 140 A A D . n D 4 8 A 8 151 151 A A D . n D 4 9 C 9 152 152 C C D . n D 4 10 U 10 153 153 U U D . n D 4 11 C 11 154 154 C C D . n D 4 12 G 12 31 31 G G D L n D 4 13 U 13 32 32 U U D L n D 4 14 A 14 33 33 A A D L n D 4 15 A 15 34 34 A A D L n D 4 16 G 16 164 164 G G D . n D 4 17 A 17 163 163 A A D . n D 4 18 G 18 162 162 G G D . n D 4 19 U 19 161 161 U U D . n D 4 20 C 20 170 170 C C D . n D 4 21 A 21 11 11 A A D . n D 4 22 C 22 12 12 C C D . n D 4 23 C 23 13 13 C C D . n D 4 24 A 24 14 14 A A D . n D 4 25 C 25 15 15 C C D . 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 E 5 CD 1 1 1 CD CD A . F 5 CD 1 2 2 CD CD A . G 5 CD 1 6 6 CD CD A . H 5 CD 1 8 8 CD CD A . I 5 CD 1 3 3 CD CD B . J 5 CD 1 4 4 CD CD B . K 5 CD 1 5 5 CD CD B . L 5 CD 1 7 7 CD CD B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' . ? 1 X-PLOR refinement 3.851 ? 2 MOSFLM 'data reduction' . ? 3 CCP4 'data scaling' '(SCALA)' ? 4 X-PLOR phasing . ? 5 # _cell.entry_id 488D _cell.length_a 65.503 _cell.length_b 65.503 _cell.length_c 136.484 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 488D _symmetry.space_group_name_H-M 'P 31 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting trigonal _symmetry.Int_Tables_number 152 # _exptl.entry_id 488D _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 3.98 _exptl_crystal.density_percent_sol 78.0 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 5.00 _exptl_crystal_grow.pdbx_details 'pH 5.00, VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'BRANDEIS - B4' _diffrn_detector.pdbx_collection_date 1999-10-15 _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 1.200 _diffrn_radiation_wavelength.wt 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 1.200 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 488D _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 24.600 _reflns.d_resolution_high 3.100 _reflns.number_obs 6553 _reflns.number_all 6553 _reflns.percent_possible_obs 95.5 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.1040000 _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 1.700 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 3.10 _reflns_shell.d_res_low 3.40 _reflns_shell.percent_possible_all 91.3 _reflns_shell.Rmerge_I_obs 0.2750000 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy 1.70 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 488D _refine.ls_number_reflns_obs 6553 _refine.ls_number_reflns_all 6553 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 24.60 _refine.ls_d_res_high 3.10 _refine.ls_percent_reflns_obs 95.5 _refine.ls_R_factor_obs 0.2580000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.2580000 _refine.ls_R_factor_R_free 0.3010000 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 9.4 _refine.ls_number_reflns_R_free 618 _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 ;THE CRYSTAL IS A MIXTURE OF 40% CLEAVED HAMMERHEAD RNA AND 60% UNCLEAVED HAMMERHEAD RNA. THE OCCUPANCY OF THE ENZYME STRAND AND METALS PRESENT ARE SET TO 1.0 AND THE CHAIN IS LABELLED 'A'. THE OCCUPANCY OF THE SUBSTRATE STRAND IS SET TO 0.6 AND LABELLED AS CHAIN 'D'. THE OCCUPANCY OF THE PRODUCT STRAND (OR CLEAVED STRAND) IS 0.4 AND IS LABELLED 'B' AND 'C'. THE RELATIVE OCCUPANCIES WERE DETERMINED BY HPLC. A SECOND CRYSTAL WHOSE STRUCTURE IS ESSENTIALLY IDENTICAL WAS ALSO ANALYZED, IN WHICH 60% OF THE RNA HAD CLEAVED. HOWEVER, THE QUALITY OF THE DATA FOR THE SUBMITTED CRYSTAL STRUCTURE IS SOMEWHAT HIGHER. ; _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 ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _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.pdbx_overall_phase_error ? _refine.overall_SU_R_Cruickshank_DPI ? _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 1404 _refine_hist.pdbx_number_atoms_ligand 8 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 1412 _refine_hist.d_res_high 3.10 _refine_hist.d_res_low 24.60 # 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 0.010 ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_bond_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg 1.89 ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_angle_deg_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_dihedral_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_na ? ? ? ? 'X-RAY DIFFRACTION' ? x_improper_angle_d_prot ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_mcangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scbond_it ? ? ? ? 'X-RAY DIFFRACTION' ? x_scangle_it ? ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 488D _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 488D _struct.title 'CATALYTIC RNA ENZYME-PRODUCT COMPLEX' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 488D _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'CATALYTIC RNA, RIBOZYME, ENZYME-PRODUCT COMPLEX, CRYSTAL LATTICE TRAPPING, RNA' # 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 4 ? E N N 5 ? F N N 5 ? G N N 5 ? H N N 5 ? I N N 5 ? J N N 5 ? K N N 5 ? L N N 5 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 488D 488D ? ? ? 2 2 PDB 488D 488D ? ? ? 3 3 PDB 488D 488D ? ? ? 4 4 PDB 488D 488D ? ? ? # 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 488D A 1 ? 16 ? 488D 25 ? 104 ? 25 104 2 2 488D B 1 ? 20 ? 488D 114 ? 170 ? 114 170 3 3 488D C 1 ? 5 ? 488D 11 ? 15 ? 11 15 4 4 488D D 1 ? 25 ? 488D 114 ? 15 ? 114 15 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _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,G,H,I,J,K,L # _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 # 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 ? B U 19 "O3'" ? ? ? 1_555 B CCC 20 P ? ? B U 161 B CCC 170 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale2 covale none ? B CCC 20 OP1 ? ? ? 1_555 D C 20 OP1 ? ? B CCC 170 D C 170 1_555 ? ? ? ? ? ? ? 1.838 ? ? covale3 covale one ? B CCC 20 P ? ? ? 1_555 D C 20 OP1 ? ? B CCC 170 D C 170 1_555 ? ? ? ? ? ? ? 1.635 ? ? metalc1 metalc ? ? E CD . CD ? ? ? 1_555 A G 3 N7 ? ? A CD 1 A G 23 1_555 ? ? ? ? ? ? ? 2.096 ? ? metalc2 metalc ? ? E CD . CD ? ? ? 1_555 A G 3 O6 ? ? A CD 1 A G 23 1_555 ? ? ? ? ? ? ? 3.065 ? ? metalc3 metalc ? ? F CD . CD ? ? ? 1_555 A G 8 N7 ? ? A CD 2 A G 50 1_555 ? ? ? ? ? ? ? 1.987 ? ? metalc4 metalc ? ? F CD . CD ? ? ? 1_555 A G 8 O6 ? ? A CD 2 A G 50 1_555 ? ? ? ? ? ? ? 2.999 ? ? metalc5 metalc ? ? G CD . CD ? ? ? 1_555 A G 1 N7 ? ? A CD 6 A G 25 1_555 ? ? ? ? ? ? ? 1.965 ? ? metalc6 metalc ? ? G CD . CD ? ? ? 1_555 A G 1 O6 ? ? A CD 6 A G 25 1_555 ? ? ? ? ? ? ? 2.968 ? ? metalc7 metalc ? ? H CD . CD ? ? ? 1_555 A A 12 OP2 ? ? A CD 8 A A 90 1_555 ? ? ? ? ? ? ? 2.198 ? ? metalc8 metalc ? ? H CD . CD ? ? ? 1_555 A G 13 N7 ? ? A CD 8 A G 101 1_555 ? ? ? ? ? ? ? 1.911 ? ? metalc9 metalc ? ? H CD . CD ? ? ? 1_555 A G 13 O6 ? ? A CD 8 A G 101 1_555 ? ? ? ? ? ? ? 2.962 ? ? metalc10 metalc ? ? I CD . CD ? ? ? 1_555 B G 16 N7 ? ? B CD 3 B G 164 1_555 ? ? ? ? ? ? ? 1.967 ? ? metalc11 metalc ? ? I CD . CD ? ? ? 1_555 B G 16 O6 ? ? B CD 3 B G 164 1_555 ? ? ? ? ? ? ? 2.974 ? ? metalc12 metalc ? ? I CD . CD ? ? ? 1_555 D G 16 N7 ? ? B CD 3 D G 164 1_555 ? ? ? ? ? ? ? 1.967 ? ? metalc13 metalc ? ? I CD . CD ? ? ? 1_555 D G 16 O6 ? ? B CD 3 D G 164 1_555 ? ? ? ? ? ? ? 2.974 ? ? metalc14 metalc ? ? J CD . CD ? ? ? 1_555 B G 1 N7 ? ? B CD 4 B G 114 1_555 ? ? ? ? ? ? ? 1.973 ? ? metalc15 metalc ? ? J CD . CD ? ? ? 1_555 B G 1 O6 ? ? B CD 4 B G 114 1_555 ? ? ? ? ? ? ? 2.947 ? ? metalc16 metalc ? ? J CD . CD ? ? ? 1_555 D G 1 N7 ? ? B CD 4 D G 114 1_555 ? ? ? ? ? ? ? 1.973 ? ? metalc17 metalc ? ? J CD . CD ? ? ? 1_555 D G 1 O6 ? ? B CD 4 D G 114 1_555 ? ? ? ? ? ? ? 2.947 ? ? metalc18 metalc ? ? K CD . CD ? ? ? 1_555 B G 5 O6 ? ? B CD 5 B G 120 1_555 ? ? ? ? ? ? ? 3.055 ? ? metalc19 metalc ? ? K CD . CD ? ? ? 1_555 B G 5 N7 ? ? B CD 5 B G 120 1_555 ? ? ? ? ? ? ? 2.207 ? ? metalc20 metalc ? ? K CD . CD ? ? ? 1_555 D G 5 O6 ? ? B CD 5 D G 120 1_555 ? ? ? ? ? ? ? 3.055 ? ? metalc21 metalc ? ? K CD . CD ? ? ? 1_555 D G 5 N7 ? ? B CD 5 D G 120 1_555 ? ? ? ? ? ? ? 2.207 ? ? metalc22 metalc ? ? L CD . CD ? ? ? 1_555 B G 18 N7 ? ? B CD 7 B G 162 1_555 ? ? ? ? ? ? ? 2.032 ? ? metalc23 metalc ? ? L CD . CD ? ? ? 1_555 B G 18 O6 ? ? B CD 7 B G 162 1_555 ? ? ? ? ? ? ? 2.966 ? ? metalc24 metalc ? ? L CD . CD ? ? ? 1_555 D G 18 N7 ? ? B CD 7 D G 162 1_555 ? ? ? ? ? ? ? 2.032 ? ? metalc25 metalc ? ? L CD . CD ? ? ? 1_555 D G 18 O6 ? ? B CD 7 D G 162 1_555 ? ? ? ? ? ? ? 2.966 ? ? hydrog1 hydrog ? ? A G 1 O6 ? ? ? 1_555 C A 4 N6 ? ? A G 25 C A 14 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog2 hydrog ? ? A G 1 O6 ? ? ? 1_555 D A 24 N6 ? ? A G 25 D A 14 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog3 hydrog ? ? A U 2 N3 ? ? ? 1_555 C A 4 N1 ? ? A U 24 C A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 2 O4 ? ? ? 1_555 C A 4 N6 ? ? A U 24 C A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A U 2 N3 ? ? ? 1_555 D A 24 N1 ? ? A U 24 D A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A U 2 O4 ? ? ? 1_555 D A 24 N6 ? ? A U 24 D A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 C C 3 N3 ? ? A G 23 C C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 C C 3 O2 ? ? A G 23 C C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 C C 3 N4 ? ? A G 23 C C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 3 N1 ? ? ? 1_555 D C 23 N3 ? ? A G 23 D C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 3 N2 ? ? ? 1_555 D C 23 O2 ? ? A G 23 D C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 3 O6 ? ? ? 1_555 D C 23 N4 ? ? A G 23 D C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A G 4 N1 ? ? ? 1_555 C C 2 N3 ? ? A G 22 C C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A G 4 N2 ? ? ? 1_555 C C 2 O2 ? ? A G 22 C C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A G 4 O6 ? ? ? 1_555 C C 2 N4 ? ? A G 22 C C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 4 N1 ? ? ? 1_555 D C 22 N3 ? ? A G 22 D C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 4 N2 ? ? ? 1_555 D C 22 O2 ? ? A G 22 D C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 4 O6 ? ? ? 1_555 D C 22 N4 ? ? A G 22 D C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A U 5 N3 ? ? ? 1_555 C A 1 N1 ? ? A U 21 C A 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A U 5 O4 ? ? ? 1_555 C A 1 N6 ? ? A U 21 C A 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A U 5 N3 ? ? ? 1_555 D A 21 N1 ? ? A U 21 D A 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A U 5 O4 ? ? ? 1_555 D A 21 N6 ? ? A U 21 D A 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 6 N3 ? ? ? 1_555 D C 20 N4 ? ? A C 30 D C 170 1_555 ? ? ? ? ? ? 'C-C MISPAIR' ? ? ? hydrog24 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 101 B C 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 13 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 101 B C 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 13 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 101 B C 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 13 N1 ? ? ? 1_555 D C 4 N3 ? ? A G 101 D C 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 13 N2 ? ? ? 1_555 D C 4 O2 ? ? A G 101 D C 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 13 O6 ? ? ? 1_555 D C 4 N4 ? ? A G 101 D C 111 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 14 N1 ? ? ? 1_555 B C 3 N3 ? ? A G 102 B C 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 14 N2 ? ? ? 1_555 B C 3 O2 ? ? A G 102 B C 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A G 14 O6 ? ? ? 1_555 B C 3 N4 ? ? A G 102 B C 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A G 14 N1 ? ? ? 1_555 D C 3 N3 ? ? A G 102 D C 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A G 14 N2 ? ? ? 1_555 D C 3 O2 ? ? A G 102 D C 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 14 O6 ? ? ? 1_555 D C 3 N4 ? ? A G 102 D C 112 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A C 15 N3 ? ? ? 1_555 B G 2 N1 ? ? A C 103 B G 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A C 15 N4 ? ? ? 1_555 B G 2 O6 ? ? A C 103 B G 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A C 15 O2 ? ? ? 1_555 B G 2 N2 ? ? A C 103 B G 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A C 15 N3 ? ? ? 1_555 D G 2 N1 ? ? A C 103 D G 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A C 15 N4 ? ? ? 1_555 D G 2 O6 ? ? A C 103 D G 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A C 15 O2 ? ? ? 1_555 D G 2 N2 ? ? A C 103 D G 113 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? B A 8 N6 ? ? ? 1_555 D U 19 O4 ? ? B A 151 D U 161 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog43 hydrog ? ? B C 9 N4 ? ? ? 1_555 B G 18 O6 ? ? B C 152 B G 162 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog44 hydrog ? ? B C 9 N4 ? ? ? 1_555 D G 18 O6 ? ? B C 152 D G 162 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog45 hydrog ? ? B U 10 N3 ? ? ? 1_555 B A 17 N1 ? ? B U 153 B A 163 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? B U 10 O4 ? ? ? 1_555 B A 17 N6 ? ? B U 153 B A 163 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? B U 10 N3 ? ? ? 1_555 D A 17 N1 ? ? B U 153 D A 163 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? B U 10 O4 ? ? ? 1_555 D A 17 N6 ? ? B U 153 D A 163 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? B C 11 N3 ? ? ? 1_555 B G 16 N1 ? ? B C 154 B G 164 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? B C 11 N4 ? ? ? 1_555 B G 16 O6 ? ? B C 154 B G 164 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? B C 11 O2 ? ? ? 1_555 B G 16 N2 ? ? B C 154 B G 164 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? B C 11 N3 ? ? ? 1_555 D G 16 N1 ? ? B C 154 D G 164 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog53 hydrog ? ? B C 11 N4 ? ? ? 1_555 D G 16 O6 ? ? B C 154 D G 164 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog54 hydrog ? ? B C 11 O2 ? ? ? 1_555 D G 16 N2 ? ? B C 154 D G 164 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog55 hydrog ? ? B G 12 N2 ? L ? 1_555 B A 15 N7 ? L B G 31 B A 34 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog56 hydrog ? ? B G 12 N2 ? L ? 1_555 D A 15 N7 ? L B G 31 D A 34 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? hydrog57 hydrog ? ? B A 15 N7 ? L ? 1_555 D G 12 N2 ? L B A 34 D G 31 1_555 ? ? ? ? ? ? 'A-G MISPAIR' ? ? ? hydrog58 hydrog ? ? B G 16 N1 ? ? ? 1_555 D C 11 N3 ? ? B G 164 D C 154 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog59 hydrog ? ? B G 16 N2 ? ? ? 1_555 D C 11 O2 ? ? B G 164 D C 154 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog60 hydrog ? ? B G 16 O6 ? ? ? 1_555 D C 11 N4 ? ? B G 164 D C 154 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog61 hydrog ? ? B A 17 N1 ? ? ? 1_555 D U 10 N3 ? ? B A 163 D U 153 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog62 hydrog ? ? B A 17 N6 ? ? ? 1_555 D U 10 O4 ? ? B A 163 D U 153 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog63 hydrog ? ? B G 18 N2 ? ? ? 1_555 D C 9 N3 ? ? B G 162 D C 152 1_555 ? ? ? ? ? ? 'G-C PAIR' ? ? ? hydrog64 hydrog ? ? D A 8 N6 ? ? ? 1_555 D U 19 O4 ? ? D A 151 D U 161 1_555 ? ? ? ? ? ? 'A-U PAIR' ? ? ? hydrog65 hydrog ? ? D C 9 N4 ? ? ? 1_555 D G 18 O6 ? ? D C 152 D G 162 1_555 ? ? ? ? ? ? 'C-G PAIR' ? ? ? hydrog66 hydrog ? ? D U 10 N3 ? ? ? 1_555 D A 17 N1 ? ? D U 153 D A 163 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog67 hydrog ? ? D U 10 O4 ? ? ? 1_555 D A 17 N6 ? ? D U 153 D A 163 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog68 hydrog ? ? D C 11 N3 ? ? ? 1_555 D G 16 N1 ? ? D C 154 D G 164 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog69 hydrog ? ? D C 11 N4 ? ? ? 1_555 D G 16 O6 ? ? D C 154 D G 164 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog70 hydrog ? ? D C 11 O2 ? ? ? 1_555 D G 16 N2 ? ? D C 154 D G 164 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog71 hydrog ? ? D G 12 N2 ? L ? 1_555 D A 15 N7 ? L D G 31 D A 34 1_555 ? ? ? ? ? ? 'G-A MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 N7 ? A G 3 ? A G 23 ? 1_555 CD ? E CD . ? A CD 1 ? 1_555 O6 ? A G 3 ? A G 23 ? 1_555 70.0 ? 2 N7 ? A G 8 ? A G 50 ? 1_555 CD ? F CD . ? A CD 2 ? 1_555 O6 ? A G 8 ? A G 50 ? 1_555 73.8 ? 3 N7 ? A G 1 ? A G 25 ? 1_555 CD ? G CD . ? A CD 6 ? 1_555 O6 ? A G 1 ? A G 25 ? 1_555 73.7 ? 4 OP2 ? A A 12 ? A A 90 ? 1_555 CD ? H CD . ? A CD 8 ? 1_555 N7 ? A G 13 ? A G 101 ? 1_555 84.6 ? 5 OP2 ? A A 12 ? A A 90 ? 1_555 CD ? H CD . ? A CD 8 ? 1_555 O6 ? A G 13 ? A G 101 ? 1_555 123.5 ? 6 N7 ? A G 13 ? A G 101 ? 1_555 CD ? H CD . ? A CD 8 ? 1_555 O6 ? A G 13 ? A G 101 ? 1_555 75.7 ? 7 N7 ? B G 16 ? B G 164 ? 1_555 CD ? I CD . ? B CD 3 ? 1_555 O6 ? B G 16 ? B G 164 ? 1_555 70.5 ? 8 N7 ? B G 16 ? B G 164 ? 1_555 CD ? I CD . ? B CD 3 ? 1_555 N7 ? D G 16 ? D G 164 ? 1_555 0.0 ? 9 O6 ? B G 16 ? B G 164 ? 1_555 CD ? I CD . ? B CD 3 ? 1_555 N7 ? D G 16 ? D G 164 ? 1_555 70.5 ? 10 N7 ? B G 16 ? B G 164 ? 1_555 CD ? I CD . ? B CD 3 ? 1_555 O6 ? D G 16 ? D G 164 ? 1_555 70.5 ? 11 O6 ? B G 16 ? B G 164 ? 1_555 CD ? I CD . ? B CD 3 ? 1_555 O6 ? D G 16 ? D G 164 ? 1_555 0.0 ? 12 N7 ? D G 16 ? D G 164 ? 1_555 CD ? I CD . ? B CD 3 ? 1_555 O6 ? D G 16 ? D G 164 ? 1_555 70.5 ? 13 N7 ? B G 1 ? B G 114 ? 1_555 CD ? J CD . ? B CD 4 ? 1_555 O6 ? B G 1 ? B G 114 ? 1_555 76.2 ? 14 N7 ? B G 1 ? B G 114 ? 1_555 CD ? J CD . ? B CD 4 ? 1_555 N7 ? D G 1 ? D G 114 ? 1_555 0.0 ? 15 O6 ? B G 1 ? B G 114 ? 1_555 CD ? J CD . ? B CD 4 ? 1_555 N7 ? D G 1 ? D G 114 ? 1_555 76.2 ? 16 N7 ? B G 1 ? B G 114 ? 1_555 CD ? J CD . ? B CD 4 ? 1_555 O6 ? D G 1 ? D G 114 ? 1_555 76.2 ? 17 O6 ? B G 1 ? B G 114 ? 1_555 CD ? J CD . ? B CD 4 ? 1_555 O6 ? D G 1 ? D G 114 ? 1_555 0.0 ? 18 N7 ? D G 1 ? D G 114 ? 1_555 CD ? J CD . ? B CD 4 ? 1_555 O6 ? D G 1 ? D G 114 ? 1_555 76.2 ? 19 O6 ? B G 5 ? B G 120 ? 1_555 CD ? K CD . ? B CD 5 ? 1_555 N7 ? B G 5 ? B G 120 ? 1_555 68.8 ? 20 O6 ? B G 5 ? B G 120 ? 1_555 CD ? K CD . ? B CD 5 ? 1_555 O6 ? D G 5 ? D G 120 ? 1_555 0.0 ? 21 N7 ? B G 5 ? B G 120 ? 1_555 CD ? K CD . ? B CD 5 ? 1_555 O6 ? D G 5 ? D G 120 ? 1_555 68.8 ? 22 O6 ? B G 5 ? B G 120 ? 1_555 CD ? K CD . ? B CD 5 ? 1_555 N7 ? D G 5 ? D G 120 ? 1_555 68.8 ? 23 N7 ? B G 5 ? B G 120 ? 1_555 CD ? K CD . ? B CD 5 ? 1_555 N7 ? D G 5 ? D G 120 ? 1_555 0.0 ? 24 O6 ? D G 5 ? D G 120 ? 1_555 CD ? K CD . ? B CD 5 ? 1_555 N7 ? D G 5 ? D G 120 ? 1_555 68.8 ? 25 N7 ? B G 18 ? B G 162 ? 1_555 CD ? L CD . ? B CD 7 ? 1_555 O6 ? B G 18 ? B G 162 ? 1_555 73.1 ? 26 N7 ? B G 18 ? B G 162 ? 1_555 CD ? L CD . ? B CD 7 ? 1_555 N7 ? D G 18 ? D G 162 ? 1_555 0.0 ? 27 O6 ? B G 18 ? B G 162 ? 1_555 CD ? L CD . ? B CD 7 ? 1_555 N7 ? D G 18 ? D G 162 ? 1_555 73.1 ? 28 N7 ? B G 18 ? B G 162 ? 1_555 CD ? L CD . ? B CD 7 ? 1_555 O6 ? D G 18 ? D G 162 ? 1_555 73.1 ? 29 O6 ? B G 18 ? B G 162 ? 1_555 CD ? L CD . ? B CD 7 ? 1_555 O6 ? D G 18 ? D G 162 ? 1_555 0.0 ? 30 N7 ? D G 18 ? D G 162 ? 1_555 CD ? L CD . ? B CD 7 ? 1_555 O6 ? D G 18 ? D G 162 ? 1_555 73.1 ? # 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 CD 1 ? 1 'BINDING SITE FOR RESIDUE CD A 1' AC2 Software A CD 2 ? 1 'BINDING SITE FOR RESIDUE CD A 2' AC3 Software B CD 3 ? 2 'BINDING SITE FOR RESIDUE CD B 3' AC4 Software B CD 4 ? 2 'BINDING SITE FOR RESIDUE CD B 4' AC5 Software B CD 5 ? 2 'BINDING SITE FOR RESIDUE CD B 5' AC6 Software A CD 6 ? 1 'BINDING SITE FOR RESIDUE CD A 6' AC7 Software B CD 7 ? 2 'BINDING SITE FOR RESIDUE CD B 7' AC8 Software A CD 8 ? 2 'BINDING SITE FOR RESIDUE CD A 8' # 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 G A 3 ? G A 23 . ? 1_555 ? 2 AC2 1 G A 8 ? G A 50 . ? 1_555 ? 3 AC3 2 G B 16 ? G B 164 . ? 1_555 ? 4 AC3 2 G D 16 ? G D 164 . ? 1_555 ? 5 AC4 2 G B 1 ? G B 114 . ? 1_555 ? 6 AC4 2 G D 1 ? G D 114 . ? 1_555 ? 7 AC5 2 G B 5 ? G B 120 . ? 1_555 ? 8 AC5 2 G D 5 ? G D 120 . ? 1_555 ? 9 AC6 1 G A 1 ? G A 25 . ? 1_555 ? 10 AC7 2 G B 18 ? G B 162 . ? 1_555 ? 11 AC7 2 G D 18 ? G D 162 . ? 1_555 ? 12 AC8 2 A A 12 ? A A 90 . ? 1_555 ? 13 AC8 2 G A 13 ? G A 101 . ? 1_555 ? # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 C5 B G 164 ? ? C6 B G 164 ? ? 1.351 1.419 -0.068 0.010 N 2 1 C5 D G 164 ? ? C6 D G 164 ? ? 1.351 1.419 -0.068 0.010 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 N9 A A 90 ? ? "C1'" A A 90 ? ? "C2'" A A 90 ? ? 104.33 112.00 -7.67 1.10 N 2 1 N1 B C 112 ? ? "C1'" B C 112 ? ? "C2'" B C 112 ? ? 103.66 112.00 -8.34 1.10 N 3 1 N9 B A 140 ? ? "C1'" B A 140 ? ? "C2'" B A 140 ? ? 104.18 112.00 -7.82 1.10 N 4 1 "C2'" C C 15 ? ? "C3'" C C 15 ? ? "O3'" C C 15 ? ? 125.44 113.70 11.74 1.60 N 5 1 N1 D C 112 ? ? "C1'" D C 112 ? ? "C2'" D C 112 ? ? 103.66 112.00 -8.34 1.10 N 6 1 N9 D A 140 ? ? "C1'" D A 140 ? ? "C2'" D A 140 ? ? 104.18 112.00 -7.82 1.10 N 7 1 "C2'" D C 15 ? ? "C3'" D C 15 ? ? "O3'" D C 15 ? ? 125.44 113.70 11.74 1.60 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 A B 140 ? ? 0.061 'SIDE CHAIN' 2 1 A B 33 L ? 0.068 'SIDE CHAIN' 3 1 U B 161 ? ? 0.071 'SIDE CHAIN' 4 1 A C 14 ? ? 0.069 'SIDE CHAIN' 5 1 A D 140 ? ? 0.061 'SIDE CHAIN' 6 1 A D 33 L ? 0.068 'SIDE CHAIN' 7 1 U D 161 ? ? 0.093 'SIDE CHAIN' 8 1 A D 14 ? ? 0.069 'SIDE CHAIN' # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id B _pdbx_struct_mod_residue.label_comp_id CCC _pdbx_struct_mod_residue.label_seq_id 20 _pdbx_struct_mod_residue.auth_asym_id B _pdbx_struct_mod_residue.auth_comp_id CCC _pdbx_struct_mod_residue.auth_seq_id 170 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id C _pdbx_struct_mod_residue.details ? # 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 C OP3 O N N 38 C P P N N 39 C OP1 O N N 40 C OP2 O N N 41 C "O5'" O N N 42 C "C5'" C N N 43 C "C4'" C N R 44 C "O4'" O N N 45 C "C3'" C N S 46 C "O3'" O N N 47 C "C2'" C N R 48 C "O2'" O N N 49 C "C1'" C N R 50 C N1 N N N 51 C C2 C N N 52 C O2 O N N 53 C N3 N N N 54 C C4 C N N 55 C N4 N N N 56 C C5 C N N 57 C C6 C N N 58 C HOP3 H N N 59 C HOP2 H N N 60 C "H5'" H N N 61 C "H5''" H N N 62 C "H4'" H N N 63 C "H3'" H N N 64 C "HO3'" H N N 65 C "H2'" H N N 66 C "HO2'" H N N 67 C "H1'" H N N 68 C H41 H N N 69 C H42 H N N 70 C H5 H N N 71 C H6 H N N 72 CCC PC P N S 73 CCC O1C O N N 74 CCC O2C O N N 75 CCC P P N N 76 CCC OP1 O N N 77 CCC OP2 O N N 78 CCC OP3 O N N 79 CCC "O5'" O N N 80 CCC "C5'" C N N 81 CCC "C4'" C N R 82 CCC "O4'" O N N 83 CCC "C3'" C N R 84 CCC "O3'" O N N 85 CCC "C2'" C N R 86 CCC "O2'" O N N 87 CCC "C1'" C N R 88 CCC N1 N N N 89 CCC C2 C N N 90 CCC O2 O N N 91 CCC N3 N N N 92 CCC C4 C N N 93 CCC N4 N N N 94 CCC C5 C N N 95 CCC C6 C N N 96 CCC HOC2 H N N 97 CCC HOP2 H N N 98 CCC HOP3 H N N 99 CCC "H5'" H N N 100 CCC "H5''" H N N 101 CCC "H4'" H N N 102 CCC "H3'" H N N 103 CCC "H2'" H N N 104 CCC "H1'" H N N 105 CCC H41 H N N 106 CCC H42 H N N 107 CCC H5 H N N 108 CCC H6 H N N 109 CD CD CD N N 110 G OP3 O N N 111 G P P N N 112 G OP1 O N N 113 G OP2 O N N 114 G "O5'" O N N 115 G "C5'" C N N 116 G "C4'" C N R 117 G "O4'" O N N 118 G "C3'" C N S 119 G "O3'" O N N 120 G "C2'" C N R 121 G "O2'" O N N 122 G "C1'" C N R 123 G N9 N Y N 124 G C8 C Y N 125 G N7 N Y N 126 G C5 C Y N 127 G C6 C N N 128 G O6 O N N 129 G N1 N N N 130 G C2 C N N 131 G N2 N N N 132 G N3 N N N 133 G C4 C Y N 134 G HOP3 H N N 135 G HOP2 H N N 136 G "H5'" H N N 137 G "H5''" H N N 138 G "H4'" H N N 139 G "H3'" H N N 140 G "HO3'" H N N 141 G "H2'" H N N 142 G "HO2'" H N N 143 G "H1'" H N N 144 G H8 H N N 145 G H1 H N N 146 G H21 H N N 147 G H22 H N N 148 U OP3 O N N 149 U P P N N 150 U OP1 O N N 151 U OP2 O N N 152 U "O5'" O N N 153 U "C5'" C N N 154 U "C4'" C N R 155 U "O4'" O N N 156 U "C3'" C N S 157 U "O3'" O N N 158 U "C2'" C N R 159 U "O2'" O N N 160 U "C1'" C N R 161 U N1 N N N 162 U C2 C N N 163 U O2 O N N 164 U N3 N N N 165 U C4 C N N 166 U O4 O N N 167 U C5 C N N 168 U C6 C N N 169 U HOP3 H N N 170 U HOP2 H N N 171 U "H5'" H N N 172 U "H5''" H N N 173 U "H4'" H N N 174 U "H3'" H N N 175 U "HO3'" H N N 176 U "H2'" H N N 177 U "HO2'" H N N 178 U "H1'" H N N 179 U H3 H N N 180 U H5 H N N 181 U H6 H N N 182 # 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 C OP3 P sing N N 40 C OP3 HOP3 sing N N 41 C P OP1 doub N N 42 C P OP2 sing N N 43 C P "O5'" sing N N 44 C OP2 HOP2 sing N N 45 C "O5'" "C5'" sing N N 46 C "C5'" "C4'" sing N N 47 C "C5'" "H5'" sing N N 48 C "C5'" "H5''" sing N N 49 C "C4'" "O4'" sing N N 50 C "C4'" "C3'" sing N N 51 C "C4'" "H4'" sing N N 52 C "O4'" "C1'" sing N N 53 C "C3'" "O3'" sing N N 54 C "C3'" "C2'" sing N N 55 C "C3'" "H3'" sing N N 56 C "O3'" "HO3'" sing N N 57 C "C2'" "O2'" sing N N 58 C "C2'" "C1'" sing N N 59 C "C2'" "H2'" sing N N 60 C "O2'" "HO2'" sing N N 61 C "C1'" N1 sing N N 62 C "C1'" "H1'" sing N N 63 C N1 C2 sing N N 64 C N1 C6 sing N N 65 C C2 O2 doub N N 66 C C2 N3 sing N N 67 C N3 C4 doub N N 68 C C4 N4 sing N N 69 C C4 C5 sing N N 70 C N4 H41 sing N N 71 C N4 H42 sing N N 72 C C5 C6 doub N N 73 C C5 H5 sing N N 74 C C6 H6 sing N N 75 CCC PC O1C doub N N 76 CCC PC O2C sing N N 77 CCC PC "O3'" sing N N 78 CCC PC "O2'" sing N N 79 CCC O2C HOC2 sing N N 80 CCC P OP1 doub N N 81 CCC P OP2 sing N N 82 CCC P OP3 sing N N 83 CCC P "O5'" sing N N 84 CCC OP2 HOP2 sing N N 85 CCC OP3 HOP3 sing N N 86 CCC "O5'" "C5'" sing N N 87 CCC "C5'" "C4'" sing N N 88 CCC "C5'" "H5'" sing N N 89 CCC "C5'" "H5''" sing N N 90 CCC "C4'" "O4'" sing N N 91 CCC "C4'" "C3'" sing N N 92 CCC "C4'" "H4'" sing N N 93 CCC "O4'" "C1'" sing N N 94 CCC "C3'" "O3'" sing N N 95 CCC "C3'" "C2'" sing N N 96 CCC "C3'" "H3'" sing N N 97 CCC "C2'" "O2'" sing N N 98 CCC "C2'" "C1'" sing N N 99 CCC "C2'" "H2'" sing N N 100 CCC "C1'" N1 sing N N 101 CCC "C1'" "H1'" sing N N 102 CCC N1 C2 sing N N 103 CCC N1 C6 sing N N 104 CCC C2 O2 doub N N 105 CCC C2 N3 sing N N 106 CCC N3 C4 doub N N 107 CCC C4 N4 sing N N 108 CCC C4 C5 sing N N 109 CCC N4 H41 sing N N 110 CCC N4 H42 sing N N 111 CCC C5 C6 doub N N 112 CCC C5 H5 sing N N 113 CCC C6 H6 sing N N 114 G OP3 P sing N N 115 G OP3 HOP3 sing N N 116 G P OP1 doub N N 117 G P OP2 sing N N 118 G P "O5'" sing N N 119 G OP2 HOP2 sing N N 120 G "O5'" "C5'" sing N N 121 G "C5'" "C4'" sing N N 122 G "C5'" "H5'" sing N N 123 G "C5'" "H5''" sing N N 124 G "C4'" "O4'" sing N N 125 G "C4'" "C3'" sing N N 126 G "C4'" "H4'" sing N N 127 G "O4'" "C1'" sing N N 128 G "C3'" "O3'" sing N N 129 G "C3'" "C2'" sing N N 130 G "C3'" "H3'" sing N N 131 G "O3'" "HO3'" sing N N 132 G "C2'" "O2'" sing N N 133 G "C2'" "C1'" sing N N 134 G "C2'" "H2'" sing N N 135 G "O2'" "HO2'" sing N N 136 G "C1'" N9 sing N N 137 G "C1'" "H1'" sing N N 138 G N9 C8 sing Y N 139 G N9 C4 sing Y N 140 G C8 N7 doub Y N 141 G C8 H8 sing N N 142 G N7 C5 sing Y N 143 G C5 C6 sing N N 144 G C5 C4 doub Y N 145 G C6 O6 doub N N 146 G C6 N1 sing N N 147 G N1 C2 sing N N 148 G N1 H1 sing N N 149 G C2 N2 sing N N 150 G C2 N3 doub N N 151 G N2 H21 sing N N 152 G N2 H22 sing N N 153 G N3 C4 sing N N 154 U OP3 P sing N N 155 U OP3 HOP3 sing N N 156 U P OP1 doub N N 157 U P OP2 sing N N 158 U P "O5'" sing N N 159 U OP2 HOP2 sing N N 160 U "O5'" "C5'" sing N N 161 U "C5'" "C4'" sing N N 162 U "C5'" "H5'" sing N N 163 U "C5'" "H5''" sing N N 164 U "C4'" "O4'" sing N N 165 U "C4'" "C3'" sing N N 166 U "C4'" "H4'" sing N N 167 U "O4'" "C1'" sing N N 168 U "C3'" "O3'" sing N N 169 U "C3'" "C2'" sing N N 170 U "C3'" "H3'" sing N N 171 U "O3'" "HO3'" sing N N 172 U "C2'" "O2'" sing N N 173 U "C2'" "C1'" sing N N 174 U "C2'" "H2'" sing N N 175 U "O2'" "HO2'" sing N N 176 U "C1'" N1 sing N N 177 U "C1'" "H1'" sing N N 178 U N1 C2 sing N N 179 U N1 C6 sing N N 180 U C2 O2 doub N N 181 U C2 N3 sing N N 182 U N3 C4 sing N N 183 U N3 H3 sing N N 184 U C4 O4 doub N N 185 U C4 C5 sing N N 186 U C5 C6 doub N N 187 U C5 H5 sing N N 188 U C6 H6 sing N N 189 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 488D 'double helix' 488D 'a-form double helix' 488D 'triple helix' 488D '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 D A 24 1_555 1.393 1.934 -2.439 0.503 -30.179 -46.093 1 A_G25:A14_D A 25 ? D 14 ? ? ? 1 A U 2 1_555 C A 4 1_555 0.652 0.011 0.302 -1.742 -16.912 0.390 2 A_U24:A14_C A 24 ? C 14 ? 20 1 1 A G 3 1_555 C C 3 1_555 1.079 -0.182 0.063 1.395 -3.863 -9.476 3 A_G23:C13_C A 23 ? C 13 ? 19 1 1 A G 4 1_555 C C 2 1_555 0.185 -0.510 0.221 0.402 -21.893 1.027 4 A_G22:C12_C A 22 ? C 12 ? 19 1 1 A U 5 1_555 C A 1 1_555 -0.912 -0.437 -0.766 10.537 -1.715 7.673 5 A_U21:A11_C A 21 ? C 11 ? 20 1 1 A C 6 1_555 D C 20 1_555 2.770 -1.689 0.593 18.829 -8.756 -5.431 6 A_C30:C170_D A 30 ? D 170 ? ? ? 1 A G 13 1_555 B C 4 1_555 0.916 0.350 0.227 -1.586 -19.485 0.288 7 A_G101:C111_B A 101 ? B 111 ? 19 1 1 A G 14 1_555 B C 3 1_555 -0.172 -0.770 0.301 1.269 -23.833 -2.095 8 A_G102:C112_B A 102 ? B 112 ? 19 1 1 A C 15 1_555 B G 2 1_555 -0.602 -0.093 0.498 -1.136 -18.456 -14.483 9 A_C103:G113_B A 103 ? B 113 ? 19 1 1 B A 8 1_555 D U 19 1_555 0.599 1.463 0.939 16.600 -16.618 35.800 10 B_A151:U161_D B 151 ? D 161 ? ? ? # 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 D A 24 1_555 A U 2 1_555 C A 4 1_555 -0.616 -0.705 1.329 3.622 6.374 22.926 -2.438 1.901 0.992 15.535 -8.827 24.054 1 AA_G25U24:A14A14_CD A 25 ? D 14 ? A 24 ? C 14 ? 1 A U 2 1_555 C A 4 1_555 A G 3 1_555 C C 3 1_555 -0.214 -1.012 3.183 0.926 2.450 33.821 -2.113 0.510 3.098 4.203 -1.589 33.919 2 AA_U24G23:C13A14_CC A 24 ? C 14 ? A 23 ? C 13 ? 1 A G 3 1_555 C C 3 1_555 A G 4 1_555 C C 2 1_555 0.874 -2.530 3.004 3.692 6.359 22.591 -7.904 -1.106 2.326 15.708 -9.118 23.743 3 AA_G23G22:C12C13_CC A 23 ? C 13 ? A 22 ? C 12 ? 1 A G 4 1_555 C C 2 1_555 A U 5 1_555 C A 1 1_555 0.218 -2.115 3.233 6.034 -5.748 22.405 -3.090 1.594 3.592 -14.177 -14.883 23.886 4 AA_G22U21:A11C12_CC A 22 ? C 12 ? A 21 ? C 11 ? 1 A U 5 1_555 C A 1 1_555 A C 6 1_555 D C 20 1_555 0.433 -1.209 2.857 -11.128 7.321 47.433 -1.912 -1.219 2.500 8.897 13.525 49.163 5 AA_U21C30:C170A11_DC A 21 ? C 11 ? A 30 ? D 170 ? 1 A G 13 1_555 B C 4 1_555 A G 14 1_555 B C 3 1_555 0.132 -2.569 2.774 0.740 8.902 26.641 -6.814 -0.145 1.838 18.664 -1.552 28.074 6 AA_G101G102:C112C111_BB A 101 ? B 111 ? A 102 ? B 112 ? 1 A G 14 1_555 B C 3 1_555 A C 15 1_555 B G 2 1_555 -0.445 -1.435 3.249 -1.944 4.521 22.333 -5.161 0.460 2.932 11.494 4.941 22.862 7 AA_G102C103:G113C112_BB A 102 ? B 112 ? A 103 ? B 113 ? # _atom_sites.entry_id 488D _atom_sites.fract_transf_matrix[1][1] 0.015266 _atom_sites.fract_transf_matrix[1][2] 0.008814 _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] 0.017628 _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] 0.007327 _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 CD N O P # loop_