data_4GPX # _entry.id 4GPX # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.388 _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 4GPX pdb_00004gpx 10.2210/pdb4gpx/pdb NDB NA2006 ? ? RCSB RCSB074490 ? ? WWPDB D_1000074490 ? ? # 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 2013-04-03 2 'Structure model' 1 1 2013-07-17 3 'Structure model' 1 2 2024-03-20 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 4GPX _pdbx_database_status.recvd_initial_deposition_date 2012-08-22 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 4F8U . unspecified PDB 4F8V . unspecified PDB 4GPW . unspecified PDB 4GPY . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kondo, J.' 1 'Koganei, M.' 2 'Maianti, J.P.' 3 'Ly, V.L.' 4 'Hanessian, S.' 5 # _citation.id primary _citation.title ;Crystal structures of a bioactive 6'-hydroxy variant of sisomicin bound to the bacterial and protozoal ribosomal decoding sites ; _citation.journal_abbrev Chemmedchem _citation.journal_volume 8 _citation.page_first 733 _citation.page_last 739 _citation.year 2013 _citation.journal_id_ASTM ? _citation.country DE _citation.journal_id_ISSN 1860-7179 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 23436717 _citation.pdbx_database_id_DOI 10.1002/cmdc.201200579 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kondo, J.' 1 ? primary 'Koganei, M.' 2 ? primary 'Maianti, J.P.' 3 ? primary 'Ly, V.L.' 4 ? primary 'Hanessian, S.' 5 ? # 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 (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3') ; 7386.424 2 ? ? ? ? 2 non-polymer syn ;(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(hydroxymethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside ; 448.511 2 ? ? ? ? 3 water nat water 18.015 11 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code UUGCGUCGCGCCGGCGAAGUCGC _entity_poly.pdbx_seq_one_letter_code_can UUGCGUCGCGCCGGCGAAGUCGC _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 ;(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(hydroxymethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside ; 6HS 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 U n 1 2 U n 1 3 G n 1 4 C n 1 5 G n 1 6 U n 1 7 C n 1 8 G n 1 9 C n 1 10 G n 1 11 C n 1 12 C n 1 13 G n 1 14 G n 1 15 C n 1 16 G n 1 17 A n 1 18 A n 1 19 G n 1 20 U n 1 21 C n 1 22 G n 1 23 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 6HS non-polymer . ;(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(hydroxymethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside ; "6'-hydroxysisomicin" 'C19 H36 N4 O8' 448.511 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 HOH non-polymer . WATER ? 'H2 O' 18.015 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 U 1 1 ? ? ? A . n A 1 2 U 2 2 ? ? ? A . n A 1 3 G 3 3 3 G G A . n A 1 4 C 4 4 4 C C A . n A 1 5 G 5 5 5 G G A . n A 1 6 U 6 6 6 U U A . n A 1 7 C 7 7 7 C C A . n A 1 8 G 8 8 8 G G A . n A 1 9 C 9 9 9 C C A . n A 1 10 G 10 10 10 G G A . n A 1 11 C 11 11 11 C C A . n A 1 12 C 12 12 12 C C A . n A 1 13 G 13 13 13 G G A . n A 1 14 G 14 14 14 G G A . n A 1 15 C 15 15 15 C C A . n A 1 16 G 16 16 16 G G A . n A 1 17 A 17 17 17 A A A . n A 1 18 A 18 18 18 A A A . n A 1 19 G 19 19 19 G G A . n A 1 20 U 20 20 20 U U A . n A 1 21 C 21 21 21 C C A . n A 1 22 G 22 22 22 G G A . n A 1 23 C 23 23 23 C C A . n B 1 1 U 1 24 ? ? ? B . n B 1 2 U 2 25 ? ? ? B . n B 1 3 G 3 26 26 G G B . n B 1 4 C 4 27 27 C C B . n B 1 5 G 5 28 28 G G B . n B 1 6 U 6 29 29 U U B . n B 1 7 C 7 30 30 C C B . n B 1 8 G 8 31 31 G G B . n B 1 9 C 9 32 32 C C B . n B 1 10 G 10 33 33 G G B . n B 1 11 C 11 34 34 C C B . n B 1 12 C 12 35 35 C C B . n B 1 13 G 13 36 36 G G B . n B 1 14 G 14 37 37 G G B . n B 1 15 C 15 38 38 C C B . n B 1 16 G 16 39 39 G G B . n B 1 17 A 17 40 40 A A B . n B 1 18 A 18 41 41 A A B . n B 1 19 G 19 42 42 G G B . n B 1 20 U 20 43 43 U U B . n B 1 21 C 21 44 44 C C B . n B 1 22 G 22 45 45 G G B . n B 1 23 C 23 46 46 C C B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 6HS 1 101 51 6HS 6HS A . D 2 6HS 1 101 50 6HS 6HS B . E 3 HOH 1 201 102 HOH HOH A . E 3 HOH 2 202 103 HOH HOH A . E 3 HOH 3 203 104 HOH HOH A . E 3 HOH 4 204 106 HOH HOH A . F 3 HOH 1 201 108 HOH HOH B . F 3 HOH 2 202 101 HOH HOH B . F 3 HOH 3 203 105 HOH HOH B . F 3 HOH 4 204 107 HOH HOH B . F 3 HOH 5 205 109 HOH HOH B . F 3 HOH 6 206 110 HOH HOH B . F 3 HOH 7 207 111 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal ADSC 'data collection' Quantum ? 1 PHENIX 'model building' . ? 2 CNS refinement 1.3 ? 3 CrystalClear 'data reduction' . ? 4 CrystalClear 'data scaling' . ? 5 PHENIX phasing . ? 6 # _cell.entry_id 4GPX _cell.length_a 47.200 _cell.length_b 51.623 _cell.length_c 58.903 _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 4GPX _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # _exptl.entry_id 4GPX _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.43 _exptl_crystal.density_percent_sol 49.36 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.pdbx_details 'Na Cacodylate, Spermine, NaCl, MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 210' _diffrn_detector.pdbx_collection_date 2012-06-16 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'PHOTON FACTORY BEAMLINE AR-NW12A' _diffrn_source.pdbx_synchrotron_site 'Photon Factory' _diffrn_source.pdbx_synchrotron_beamline AR-NW12A _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0 # _reflns.entry_id 4GPX _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 36.8 _reflns.d_resolution_high 2.6 _reflns.number_obs 4696 _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.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _refine.entry_id 4GPX _refine.ls_number_reflns_obs 4695 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 36.8 _refine.ls_d_res_high 2.6 _refine.ls_percent_reflns_obs 99.1000 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.223 _refine.ls_R_factor_R_free 0.252 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 10.4000 _refine.ls_number_reflns_R_free 492 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 67.4001 _refine.solvent_model_param_bsol 37.9883 _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 27.4180 _refine.aniso_B[2][2] 3.8960 _refine.aniso_B[3][3] -31.3140 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.B_iso_max 104.200 _refine.B_iso_min 34.750 _refine.pdbx_overall_phase_error ? _refine.occupancy_max 1.000 _refine.occupancy_min 1.000 _refine.ls_redundancy_reflns_obs ? _refine.solvent_model_details ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _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_refine_id 'X-RAY DIFFRACTION' _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 902 _refine_hist.pdbx_number_atoms_ligand 62 _refine_hist.number_atoms_solvent 11 _refine_hist.number_atoms_total 975 _refine_hist.d_res_high 2.6 _refine_hist.d_res_low 36.8 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' c_bond_d ? 0.005 ? ? ? 'X-RAY DIFFRACTION' c_angle_d ? 0.894 ? ? ? 'X-RAY DIFFRACTION' c_mcbond_it ? 0.000 1.500 ? ? 'X-RAY DIFFRACTION' c_scbond_it ? 1.495 2.000 ? ? 'X-RAY DIFFRACTION' c_mcangle_it ? 0.000 2.000 ? ? 'X-RAY DIFFRACTION' c_scangle_it ? 2.239 2.500 ? ? # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.pdbx_refine_id _refine_ls_shell.redundancy_reflns_obs 2.6000 2.6900 10 100.0000 409 . 0.4543 0.4270 . 59 . 468 . 'X-RAY DIFFRACTION' . 2.6900 2.8000 10 100.0000 410 . 0.4790 0.4502 . 48 . 458 . 'X-RAY DIFFRACTION' . 2.8000 2.9300 10 100.0000 417 . 0.4001 0.5160 . 45 . 462 . 'X-RAY DIFFRACTION' . 2.9300 3.0800 10 100.0000 406 . 0.3388 0.3820 . 44 . 450 . 'X-RAY DIFFRACTION' . 3.0800 3.2800 10 99.8000 433 . 0.2546 0.3231 . 42 . 475 . 'X-RAY DIFFRACTION' . 3.2800 3.5300 10 100.0000 412 . 0.2508 0.3485 . 50 . 462 . 'X-RAY DIFFRACTION' . 3.5300 3.8800 10 100.0000 425 . 0.2066 0.2366 . 49 . 474 . 'X-RAY DIFFRACTION' . 3.8800 4.4500 10 100.0000 426 . 0.1847 0.1661 . 51 . 477 . 'X-RAY DIFFRACTION' . 4.4500 5.6000 10 100.0000 429 . 0.1719 0.2257 . 56 . 485 . 'X-RAY DIFFRACTION' . 5.6000 100.0000 10 92.2000 436 . 0.1622 0.1842 . 48 . 484 . 'X-RAY DIFFRACTION' . # loop_ _pdbx_xplor_file.pdbx_refine_id _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file 'X-RAY DIFFRACTION' 1 dna-rna_rep.param ? 'X-RAY DIFFRACTION' 2 water_rep.param ? 'X-RAY DIFFRACTION' 3 ion.param ? 'X-RAY DIFFRACTION' 4 115_xplor.param ? # _database_PDB_matrix.entry_id 4GPX _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 4GPX _struct.title ;Crystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-hydroxysisomicin (P212121 form) ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4GPX _struct_keywords.pdbx_keywords RNA/ANTIBIOTIC _struct_keywords.text 'ribosome, aminoglycoside, RNA-ANTIBIOTIC complex, antiprotozoal activity, antibacterial activity' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? E N N 3 ? F N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4GPX _struct_ref.pdbx_db_accession 4GPX _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # 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 4GPX A 1 ? 23 ? 4GPX 1 ? 23 ? 1 23 2 1 4GPX B 1 ? 23 ? 4GPX 24 ? 46 ? 24 46 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2570 ? 1 MORE -15 ? 1 'SSA (A^2)' 7960 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A G 3 N1 ? ? ? 1_555 B C 23 N3 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 3 N2 ? ? ? 1_555 B C 23 O2 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 3 O6 ? ? ? 1_555 B C 23 N4 ? ? A G 3 B C 46 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 4 N3 ? ? ? 1_555 B G 22 N1 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 4 N4 ? ? ? 1_555 B G 22 O6 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 4 O2 ? ? ? 1_555 B G 22 N2 ? ? A C 4 B G 45 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 5 N1 ? ? ? 1_555 B C 21 N3 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 5 N2 ? ? ? 1_555 B C 21 O2 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 5 O6 ? ? ? 1_555 B C 21 N4 ? ? A G 5 B C 44 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A U 6 O4 ? ? ? 1_555 B U 20 N3 ? ? A U 6 B U 43 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog11 hydrog ? ? A C 7 N3 ? ? ? 1_555 B G 19 N1 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 7 N4 ? ? ? 1_555 B G 19 O6 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 7 O2 ? ? ? 1_555 B G 19 N2 ? ? A C 7 B G 42 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A C 9 N3 ? ? ? 1_555 B G 16 N1 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A C 9 N4 ? ? ? 1_555 B G 16 O6 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A C 9 O2 ? ? ? 1_555 B G 16 N2 ? ? A C 9 B G 39 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 10 N1 ? ? ? 1_555 B C 15 N3 ? ? A G 10 B C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 10 N2 ? ? ? 1_555 B C 15 O2 ? ? A G 10 B C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 10 O6 ? ? ? 1_555 B C 15 N4 ? ? A G 10 B C 38 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A C 11 N3 ? ? ? 1_555 B G 14 N1 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A C 11 N4 ? ? ? 1_555 B G 14 O6 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A C 11 O2 ? ? ? 1_555 B G 14 N2 ? ? A C 11 B G 37 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A C 12 N3 ? ? ? 1_555 B G 13 N1 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A C 12 N4 ? ? ? 1_555 B G 13 O6 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A C 12 O2 ? ? ? 1_555 B G 13 N2 ? ? A C 12 B G 36 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 13 N1 ? ? ? 1_555 B C 12 N3 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A G 13 N2 ? ? ? 1_555 B C 12 O2 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A G 13 O6 ? ? ? 1_555 B C 12 N4 ? ? A G 13 B C 35 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A G 14 N1 ? ? ? 1_555 B C 11 N3 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A G 14 N2 ? ? ? 1_555 B C 11 O2 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A G 14 O6 ? ? ? 1_555 B C 11 N4 ? ? A G 14 B C 34 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 15 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 15 B G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 15 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 15 B G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 15 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 15 B G 33 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A G 16 N1 ? ? ? 1_555 B C 9 N3 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A G 16 N2 ? ? ? 1_555 B C 9 O2 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A G 16 O6 ? ? ? 1_555 B C 9 N4 ? ? A G 16 B C 32 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A G 19 N1 ? ? ? 1_555 B C 7 N3 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A G 19 N2 ? ? ? 1_555 B C 7 O2 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A G 19 O6 ? ? ? 1_555 B C 7 N4 ? ? A G 19 B C 30 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A U 20 N3 ? ? ? 1_555 B U 6 O4 ? ? A U 20 B U 29 1_555 ? ? ? ? ? ? 'U-U MISPAIR' ? ? ? hydrog42 hydrog ? ? A C 21 N3 ? ? ? 1_555 B G 5 N1 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A C 21 N4 ? ? ? 1_555 B G 5 O6 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 21 O2 ? ? ? 1_555 B G 5 N2 ? ? A C 21 B G 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A G 22 N1 ? ? ? 1_555 B C 4 N3 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A G 22 N2 ? ? ? 1_555 B C 4 O2 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A G 22 O6 ? ? ? 1_555 B C 4 N4 ? ? A G 22 B C 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A C 23 N3 ? ? ? 1_555 B G 3 N1 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A C 23 N4 ? ? ? 1_555 B G 3 O6 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A C 23 O2 ? ? ? 1_555 B G 3 N2 ? ? A C 23 B G 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # 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 6HS 101 ? 10 'BINDING SITE FOR RESIDUE 6HS A 101' AC2 Software B 6HS 101 ? 12 'BINDING SITE FOR RESIDUE 6HS B 101' 1 ? ? ? ? ? ? ? # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 10 C A 4 ? C A 4 . ? 1_555 ? 2 AC1 10 G A 5 ? G A 5 . ? 1_555 ? 3 AC1 10 U A 6 ? U A 6 . ? 1_555 ? 4 AC1 10 C A 7 ? C A 7 . ? 1_555 ? 5 AC1 10 G A 8 ? G A 8 . ? 1_555 ? 6 AC1 10 G B 16 ? G B 39 . ? 1_555 ? 7 AC1 10 A B 17 ? A B 40 . ? 1_555 ? 8 AC1 10 A B 18 ? A B 41 . ? 1_555 ? 9 AC1 10 G B 19 ? G B 42 . ? 1_555 ? 10 AC1 10 U B 20 ? U B 43 . ? 1_555 ? 11 AC2 12 G A 16 ? G A 16 . ? 1_555 ? 12 AC2 12 A A 17 ? A A 17 . ? 1_555 ? 13 AC2 12 A A 18 ? A A 18 . ? 1_555 ? 14 AC2 12 G A 19 ? G A 19 . ? 1_555 ? 15 AC2 12 U A 20 ? U A 20 . ? 1_555 ? 16 AC2 12 HOH E . ? HOH A 202 . ? 1_555 ? 17 AC2 12 C B 4 ? C B 27 . ? 1_555 ? 18 AC2 12 G B 5 ? G B 28 . ? 1_555 ? 19 AC2 12 U B 6 ? U B 29 . ? 1_555 ? 20 AC2 12 C B 7 ? C B 30 . ? 1_555 ? 21 AC2 12 G B 8 ? G B 31 . ? 1_555 ? 22 AC2 12 C B 9 ? C B 32 . ? 1_555 ? # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id G _pdbx_validate_planes.auth_asym_id A _pdbx_validate_planes.auth_seq_id 16 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.058 _pdbx_validate_planes.type 'SIDE CHAIN' # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'MAJOR GROOVE BINDER' # 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 U 1 ? A U 1 2 1 Y 1 A U 2 ? A U 2 3 1 Y 1 B U 24 ? B U 1 4 1 Y 1 B U 25 ? B U 2 # 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 6HS C11 C N S 1 6HS C12 C N R 2 6HS C13 C N R 3 6HS C21 C N R 4 6HS C22 C N N 5 6HS C23 C N R 6 6HS C31 C N N 7 6HS C32 C N S 8 6HS C33 C N R 9 6HS C41 C N N 10 6HS C42 C N R 11 6HS C43 C N R 12 6HS C51 C N N 13 6HS C52 C N S 14 6HS C53 C N N 15 6HS C61 C N N 16 6HS C62 C N S 17 6HS C83 C N N 18 6HS C93 C N N 19 6HS N12 N N N 20 6HS N21 N N N 21 6HS N32 N N N 22 6HS N33 N N N 23 6HS O61 O N N 24 6HS O11 O N N 25 6HS O23 O N N 26 6HS O43 O N N 27 6HS O51 O N N 28 6HS O52 O N N 29 6HS O53 O N N 30 6HS O62 O N N 31 6HS H1 H N N 32 6HS H2 H N N 33 6HS H3 H N N 34 6HS H4 H N N 35 6HS H5 H N N 36 6HS H6 H N N 37 6HS H7 H N N 38 6HS H8 H N N 39 6HS H9 H N N 40 6HS H10 H N N 41 6HS H11 H N N 42 6HS H12 H N N 43 6HS H13 H N N 44 6HS H14 H N N 45 6HS H15 H N N 46 6HS H16 H N N 47 6HS H17 H N N 48 6HS H18 H N N 49 6HS H19 H N N 50 6HS H20 H N N 51 6HS H21 H N N 52 6HS H22 H N N 53 6HS H23 H N N 54 6HS H24 H N N 55 6HS H25 H N N 56 6HS H26 H N N 57 6HS H27 H N N 58 6HS H29 H N N 59 6HS H30 H N N 60 6HS H32 H N N 61 6HS H33 H N N 62 6HS H35 H N N 63 6HS H37 H N N 64 6HS H38 H N N 65 6HS H39 H N N 66 6HS H40 H N N 67 A OP3 O N N 68 A P P N N 69 A OP1 O N N 70 A OP2 O N N 71 A "O5'" O N N 72 A "C5'" C N N 73 A "C4'" C N R 74 A "O4'" O N N 75 A "C3'" C N S 76 A "O3'" O N N 77 A "C2'" C N R 78 A "O2'" O N N 79 A "C1'" C N R 80 A N9 N Y N 81 A C8 C Y N 82 A N7 N Y N 83 A C5 C Y N 84 A C6 C Y N 85 A N6 N N N 86 A N1 N Y N 87 A C2 C Y N 88 A N3 N Y N 89 A C4 C Y N 90 A HOP3 H N N 91 A HOP2 H N N 92 A "H5'" H N N 93 A "H5''" H N N 94 A "H4'" H N N 95 A "H3'" H N N 96 A "HO3'" H N N 97 A "H2'" H N N 98 A "HO2'" H N N 99 A "H1'" H N N 100 A H8 H N N 101 A H61 H N N 102 A H62 H N N 103 A H2 H N N 104 C OP3 O N N 105 C P P N N 106 C OP1 O N N 107 C OP2 O N N 108 C "O5'" O N N 109 C "C5'" C N N 110 C "C4'" C N R 111 C "O4'" O N N 112 C "C3'" C N S 113 C "O3'" O N N 114 C "C2'" C N R 115 C "O2'" O N N 116 C "C1'" C N R 117 C N1 N N N 118 C C2 C N N 119 C O2 O N N 120 C N3 N N N 121 C C4 C N N 122 C N4 N N N 123 C C5 C N N 124 C C6 C N N 125 C HOP3 H N N 126 C HOP2 H N N 127 C "H5'" H N N 128 C "H5''" H N N 129 C "H4'" H N N 130 C "H3'" H N N 131 C "HO3'" H N N 132 C "H2'" H N N 133 C "HO2'" H N N 134 C "H1'" H N N 135 C H41 H N N 136 C H42 H N N 137 C H5 H N N 138 C H6 H N N 139 G OP3 O N N 140 G P P N N 141 G OP1 O N N 142 G OP2 O N N 143 G "O5'" O N N 144 G "C5'" C N N 145 G "C4'" C N R 146 G "O4'" O N N 147 G "C3'" C N S 148 G "O3'" O N N 149 G "C2'" C N R 150 G "O2'" O N N 151 G "C1'" C N R 152 G N9 N Y N 153 G C8 C Y N 154 G N7 N Y N 155 G C5 C Y N 156 G C6 C N N 157 G O6 O N N 158 G N1 N N N 159 G C2 C N N 160 G N2 N N N 161 G N3 N N N 162 G C4 C Y N 163 G HOP3 H N N 164 G HOP2 H N N 165 G "H5'" H N N 166 G "H5''" H N N 167 G "H4'" H N N 168 G "H3'" H N N 169 G "HO3'" H N N 170 G "H2'" H N N 171 G "HO2'" H N N 172 G "H1'" H N N 173 G H8 H N N 174 G H1 H N N 175 G H21 H N N 176 G H22 H N N 177 HOH O O N N 178 HOH H1 H N N 179 HOH H2 H N N 180 U OP3 O N N 181 U P P N N 182 U OP1 O N N 183 U OP2 O N N 184 U "O5'" O N N 185 U "C5'" C N N 186 U "C4'" C N R 187 U "O4'" O N N 188 U "C3'" C N S 189 U "O3'" O N N 190 U "C2'" C N R 191 U "O2'" O N N 192 U "C1'" C N R 193 U N1 N N N 194 U C2 C N N 195 U O2 O N N 196 U N3 N N N 197 U C4 C N N 198 U O4 O N N 199 U C5 C N N 200 U C6 C N N 201 U HOP3 H N N 202 U HOP2 H N N 203 U "H5'" H N N 204 U "H5''" H N N 205 U "H4'" H N N 206 U "H3'" H N N 207 U "HO3'" H N N 208 U "H2'" H N N 209 U "HO2'" H N N 210 U "H1'" H N N 211 U H3 H N N 212 U H5 H N N 213 U H6 H N N 214 # 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 6HS N21 C21 sing N N 1 6HS C21 C31 sing N N 2 6HS C21 C11 sing N N 3 6HS C31 C41 sing N N 4 6HS C83 C43 sing N N 5 6HS C11 O51 sing N N 6 6HS C11 O11 sing N N 7 6HS C41 C51 doub N N 8 6HS O51 C51 sing N N 9 6HS C53 C43 sing N N 10 6HS C53 O53 sing N N 11 6HS C51 C61 sing N N 12 6HS O52 C52 sing N N 13 6HS O43 C43 sing N N 14 6HS C43 C33 sing N N 15 6HS C61 O61 sing N N 16 6HS O11 C42 sing N N 17 6HS O53 C13 sing N N 18 6HS C52 C42 sing N N 19 6HS C52 C62 sing N N 20 6HS C42 C32 sing N N 21 6HS C33 N33 sing N N 22 6HS C33 C23 sing N N 23 6HS C13 O62 sing N N 24 6HS C13 C23 sing N N 25 6HS N33 C93 sing N N 26 6HS O62 C62 sing N N 27 6HS C62 C12 sing N N 28 6HS C23 O23 sing N N 29 6HS C32 N32 sing N N 30 6HS C32 C22 sing N N 31 6HS C12 C22 sing N N 32 6HS C12 N12 sing N N 33 6HS C11 H1 sing N N 34 6HS C12 H2 sing N N 35 6HS C13 H3 sing N N 36 6HS C21 H4 sing N N 37 6HS C22 H5 sing N N 38 6HS C22 H6 sing N N 39 6HS C23 H7 sing N N 40 6HS C31 H8 sing N N 41 6HS C31 H9 sing N N 42 6HS C32 H10 sing N N 43 6HS C33 H11 sing N N 44 6HS C41 H12 sing N N 45 6HS C42 H13 sing N N 46 6HS C52 H14 sing N N 47 6HS C53 H15 sing N N 48 6HS C53 H16 sing N N 49 6HS C61 H17 sing N N 50 6HS C61 H18 sing N N 51 6HS C62 H19 sing N N 52 6HS C83 H20 sing N N 53 6HS C83 H21 sing N N 54 6HS C83 H22 sing N N 55 6HS C93 H23 sing N N 56 6HS C93 H24 sing N N 57 6HS C93 H25 sing N N 58 6HS N12 H26 sing N N 59 6HS N12 H27 sing N N 60 6HS N21 H29 sing N N 61 6HS N21 H30 sing N N 62 6HS N32 H32 sing N N 63 6HS N32 H33 sing N N 64 6HS N33 H35 sing N N 65 6HS O61 H37 sing N N 66 6HS O23 H38 sing N N 67 6HS O43 H39 sing N N 68 6HS O52 H40 sing N N 69 A OP3 P sing N N 70 A OP3 HOP3 sing N N 71 A P OP1 doub N N 72 A P OP2 sing N N 73 A P "O5'" sing N N 74 A OP2 HOP2 sing N N 75 A "O5'" "C5'" sing N N 76 A "C5'" "C4'" sing N N 77 A "C5'" "H5'" sing N N 78 A "C5'" "H5''" sing N N 79 A "C4'" "O4'" sing N N 80 A "C4'" "C3'" sing N N 81 A "C4'" "H4'" sing N N 82 A "O4'" "C1'" sing N N 83 A "C3'" "O3'" sing N N 84 A "C3'" "C2'" sing N N 85 A "C3'" "H3'" sing N N 86 A "O3'" "HO3'" sing N N 87 A "C2'" "O2'" sing N N 88 A "C2'" "C1'" sing N N 89 A "C2'" "H2'" sing N N 90 A "O2'" "HO2'" sing N N 91 A "C1'" N9 sing N N 92 A "C1'" "H1'" sing N N 93 A N9 C8 sing Y N 94 A N9 C4 sing Y N 95 A C8 N7 doub Y N 96 A C8 H8 sing N N 97 A N7 C5 sing Y N 98 A C5 C6 sing Y N 99 A C5 C4 doub Y N 100 A C6 N6 sing N N 101 A C6 N1 doub Y N 102 A N6 H61 sing N N 103 A N6 H62 sing N N 104 A N1 C2 sing Y N 105 A C2 N3 doub Y N 106 A C2 H2 sing N N 107 A N3 C4 sing Y N 108 C OP3 P sing N N 109 C OP3 HOP3 sing N N 110 C P OP1 doub N N 111 C P OP2 sing N N 112 C P "O5'" sing N N 113 C OP2 HOP2 sing N N 114 C "O5'" "C5'" sing N N 115 C "C5'" "C4'" sing N N 116 C "C5'" "H5'" sing N N 117 C "C5'" "H5''" sing N N 118 C "C4'" "O4'" sing N N 119 C "C4'" "C3'" sing N N 120 C "C4'" "H4'" sing N N 121 C "O4'" "C1'" sing N N 122 C "C3'" "O3'" sing N N 123 C "C3'" "C2'" sing N N 124 C "C3'" "H3'" sing N N 125 C "O3'" "HO3'" sing N N 126 C "C2'" "O2'" sing N N 127 C "C2'" "C1'" sing N N 128 C "C2'" "H2'" sing N N 129 C "O2'" "HO2'" sing N N 130 C "C1'" N1 sing N N 131 C "C1'" "H1'" sing N N 132 C N1 C2 sing N N 133 C N1 C6 sing N N 134 C C2 O2 doub N N 135 C C2 N3 sing N N 136 C N3 C4 doub N N 137 C C4 N4 sing N N 138 C C4 C5 sing N N 139 C N4 H41 sing N N 140 C N4 H42 sing N N 141 C C5 C6 doub N N 142 C C5 H5 sing N N 143 C C6 H6 sing N N 144 G OP3 P sing N N 145 G OP3 HOP3 sing N N 146 G P OP1 doub N N 147 G P OP2 sing N N 148 G P "O5'" sing N N 149 G OP2 HOP2 sing N N 150 G "O5'" "C5'" sing N N 151 G "C5'" "C4'" sing N N 152 G "C5'" "H5'" sing N N 153 G "C5'" "H5''" sing N N 154 G "C4'" "O4'" sing N N 155 G "C4'" "C3'" sing N N 156 G "C4'" "H4'" sing N N 157 G "O4'" "C1'" sing N N 158 G "C3'" "O3'" sing N N 159 G "C3'" "C2'" sing N N 160 G "C3'" "H3'" sing N N 161 G "O3'" "HO3'" sing N N 162 G "C2'" "O2'" sing N N 163 G "C2'" "C1'" sing N N 164 G "C2'" "H2'" sing N N 165 G "O2'" "HO2'" sing N N 166 G "C1'" N9 sing N N 167 G "C1'" "H1'" sing N N 168 G N9 C8 sing Y N 169 G N9 C4 sing Y N 170 G C8 N7 doub Y N 171 G C8 H8 sing N N 172 G N7 C5 sing Y N 173 G C5 C6 sing N N 174 G C5 C4 doub Y N 175 G C6 O6 doub N N 176 G C6 N1 sing N N 177 G N1 C2 sing N N 178 G N1 H1 sing N N 179 G C2 N2 sing N N 180 G C2 N3 doub N N 181 G N2 H21 sing N N 182 G N2 H22 sing N N 183 G N3 C4 sing N N 184 HOH O H1 sing N N 185 HOH O H2 sing N N 186 U OP3 P sing N N 187 U OP3 HOP3 sing N N 188 U P OP1 doub N N 189 U P OP2 sing N N 190 U P "O5'" sing N N 191 U OP2 HOP2 sing N N 192 U "O5'" "C5'" sing N N 193 U "C5'" "C4'" sing N N 194 U "C5'" "H5'" sing N N 195 U "C5'" "H5''" sing N N 196 U "C4'" "O4'" sing N N 197 U "C4'" "C3'" sing N N 198 U "C4'" "H4'" sing N N 199 U "O4'" "C1'" sing N N 200 U "C3'" "O3'" sing N N 201 U "C3'" "C2'" sing N N 202 U "C3'" "H3'" sing N N 203 U "O3'" "HO3'" sing N N 204 U "C2'" "O2'" sing N N 205 U "C2'" "C1'" sing N N 206 U "C2'" "H2'" sing N N 207 U "O2'" "HO2'" sing N N 208 U "C1'" N1 sing N N 209 U "C1'" "H1'" sing N N 210 U N1 C2 sing N N 211 U N1 C6 sing N N 212 U C2 O2 doub N N 213 U C2 N3 sing N N 214 U N3 C4 sing N N 215 U N3 H3 sing N N 216 U C4 O4 doub N N 217 U C4 C5 sing N N 218 U C5 C6 doub N N 219 U C5 H5 sing N N 220 U C6 H6 sing N N 221 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 4GPX 'a-form double helix' 4GPX 'mismatched base pair' 4GPX 'internal loop' # 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 3 1_555 B C 23 1_555 0.201 -0.041 0.268 -0.265 -2.539 0.278 1 A_G3:C46_B A 3 ? B 46 ? 19 1 1 A C 4 1_555 B G 22 1_555 -0.277 0.020 -0.059 3.975 -7.850 3.547 2 A_C4:G45_B A 4 ? B 45 ? 19 1 1 A G 5 1_555 B C 21 1_555 -0.294 0.031 0.091 1.391 -1.124 7.078 3 A_G5:C44_B A 5 ? B 44 ? 19 1 1 A U 6 1_555 B U 20 1_555 -2.092 -1.107 -0.294 13.312 -8.623 -10.670 4 A_U6:U43_B A 6 ? B 43 ? ? ? 1 A C 7 1_555 B G 19 1_555 0.337 0.055 -0.338 8.055 -2.167 4.325 5 A_C7:G42_B A 7 ? B 42 ? 19 1 1 A C 9 1_555 B G 16 1_555 0.237 0.091 -0.283 6.995 -12.452 3.716 6 A_C9:G39_B A 9 ? B 39 ? 19 1 1 A G 10 1_555 B C 15 1_555 -0.339 -0.044 -0.098 -6.429 -23.290 4.200 7 A_G10:C38_B A 10 ? B 38 ? 19 1 1 A C 11 1_555 B G 14 1_555 0.356 -0.159 -0.229 1.463 -16.916 0.643 8 A_C11:G37_B A 11 ? B 37 ? 19 1 1 A C 12 1_555 B G 13 1_555 0.472 -0.174 0.577 -1.305 -8.788 5.094 9 A_C12:G36_B A 12 ? B 36 ? 19 1 1 A G 13 1_555 B C 12 1_555 -0.344 0.020 0.161 -0.763 -10.785 1.281 10 A_G13:C35_B A 13 ? B 35 ? 19 1 1 A G 14 1_555 B C 11 1_555 -0.168 -0.108 0.038 -1.901 -13.157 3.729 11 A_G14:C34_B A 14 ? B 34 ? 19 1 1 A C 15 1_555 B G 10 1_555 0.443 -0.117 -0.047 2.786 -14.283 1.689 12 A_C15:G33_B A 15 ? B 33 ? 19 1 1 A G 16 1_555 B C 9 1_555 0.121 -0.155 -0.106 -5.137 -16.784 -0.134 13 A_G16:C32_B A 16 ? B 32 ? 19 1 1 A G 19 1_555 B C 7 1_555 -0.053 -0.295 -0.554 -10.398 -8.024 0.229 14 A_G19:C30_B A 19 ? B 30 ? 19 1 1 A U 20 1_555 B U 6 1_555 2.023 -1.133 -0.262 -11.396 -6.770 -5.707 15 A_U20:U29_B A 20 ? B 29 ? ? ? 1 A C 21 1_555 B G 5 1_555 0.350 -0.074 -0.468 7.786 -4.022 4.133 16 A_C21:G28_B A 21 ? B 28 ? 19 1 1 A G 22 1_555 B C 4 1_555 0.148 -0.080 -0.121 -6.250 -7.084 -3.846 17 A_G22:C27_B A 22 ? B 27 ? 19 1 1 A C 23 1_555 B G 3 1_555 0.543 0.039 0.029 4.764 1.170 6.104 18 A_C23:G26_B A 23 ? B 26 ? 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 3 1_555 B C 23 1_555 A C 4 1_555 B G 22 1_555 -0.413 -2.111 3.124 0.002 1.925 30.953 -4.294 0.772 2.991 3.603 -0.003 31.011 1 AA_G3C4:G45C46_BB A 3 ? B 46 ? A 4 ? B 45 ? 1 A C 4 1_555 B G 22 1_555 A G 5 1_555 B C 21 1_555 0.077 -1.855 3.218 -2.790 6.588 30.020 -4.673 -0.647 2.741 12.495 5.292 30.842 2 AA_C4G5:C44G45_BB A 4 ? B 45 ? A 5 ? B 44 ? 1 A G 5 1_555 B C 21 1_555 A U 6 1_555 B U 20 1_555 -1.045 -1.997 2.919 -1.468 -1.045 26.195 -4.140 1.940 3.048 -2.301 3.234 26.255 3 AA_G5U6:U43C44_BB A 5 ? B 44 ? A 6 ? B 43 ? 1 A U 6 1_555 B U 20 1_555 A C 7 1_555 B G 19 1_555 1.242 -2.038 3.591 -0.096 1.050 41.320 -3.010 -1.771 3.538 1.488 0.135 41.333 4 AA_U6C7:G42U43_BB A 6 ? B 43 ? A 7 ? B 42 ? 1 A C 9 1_555 B G 16 1_555 A G 10 1_555 B C 15 1_555 0.082 -1.499 3.445 -0.932 16.628 31.438 -4.770 -0.264 2.377 28.336 1.588 35.479 5 AA_C9G10:C38G39_BB A 9 ? B 39 ? A 10 ? B 38 ? 1 A G 10 1_555 B C 15 1_555 A C 11 1_555 B G 14 1_555 -0.491 -0.896 3.012 0.456 4.356 35.368 -2.036 0.862 2.879 7.136 -0.747 35.629 6 AA_G10C11:G37C38_BB A 10 ? B 38 ? A 11 ? B 37 ? 1 A C 11 1_555 B G 14 1_555 A C 12 1_555 B G 13 1_555 0.536 -1.391 3.332 -4.096 6.445 33.508 -3.335 -1.530 2.938 11.002 6.992 34.343 7 AA_C11C12:G36G37_BB A 11 ? B 37 ? A 12 ? B 36 ? 1 A C 12 1_555 B G 13 1_555 A G 13 1_555 B C 12 1_555 -0.400 -1.930 2.999 2.340 7.195 26.654 -5.490 1.309 2.364 15.222 -4.949 27.688 8 AA_C12G13:C35G36_BB A 12 ? B 36 ? A 13 ? B 35 ? 1 A G 13 1_555 B C 12 1_555 A G 14 1_555 B C 11 1_555 0.090 -1.259 3.148 -0.785 8.917 33.972 -3.310 -0.256 2.737 14.942 1.316 35.097 9 AA_G13G14:C34C35_BB A 13 ? B 35 ? A 14 ? B 34 ? 1 A G 14 1_555 B C 11 1_555 A C 15 1_555 B G 10 1_555 -0.320 -1.115 3.140 0.958 1.767 36.734 -1.995 0.631 3.076 2.802 -1.518 36.787 10 AA_G14C15:G33C34_BB A 14 ? B 34 ? A 15 ? B 33 ? 1 A C 15 1_555 B G 10 1_555 A G 16 1_555 B C 9 1_555 0.543 -1.716 3.216 2.228 15.406 30.704 -5.012 -0.615 2.167 27.026 -3.909 34.340 11 AA_C15G16:C32G33_BB A 15 ? B 33 ? A 16 ? B 32 ? 1 A G 19 1_555 B C 7 1_555 A U 20 1_555 B U 6 1_555 -0.774 -1.811 3.421 -0.730 2.459 38.495 -3.054 1.079 3.317 3.725 1.106 38.578 12 AA_G19U20:U29C30_BB A 19 ? B 30 ? A 20 ? B 29 ? 1 A U 20 1_555 B U 6 1_555 A C 21 1_555 B G 5 1_555 0.565 -1.785 2.777 4.820 0.646 25.878 -4.068 -0.132 2.789 1.427 -10.642 26.323 13 AA_U20C21:G28U29_BB A 20 ? B 29 ? A 21 ? B 28 ? 1 A C 21 1_555 B G 5 1_555 A G 22 1_555 B C 4 1_555 0.073 -2.061 3.699 -1.019 6.752 27.504 -5.861 -0.397 3.110 13.930 2.101 28.323 14 AA_C21G22:C27G28_BB A 21 ? B 28 ? A 22 ? B 27 ? 1 A G 22 1_555 B C 4 1_555 A C 23 1_555 B G 3 1_555 0.417 -1.847 3.043 -0.580 1.186 34.817 -3.250 -0.778 2.973 1.980 0.969 34.842 15 AA_G22C23:G26C27_BB A 22 ? B 27 ? A 23 ? B 26 ? # _atom_sites.entry_id 4GPX _atom_sites.fract_transf_matrix[1][1] 0.021186 _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] 0.019371 _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] 0.016977 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O P # loop_