data_3C3Z # _entry.id 3C3Z # _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 3C3Z pdb_00003c3z 10.2210/pdb3c3z/pdb NDB DR0041 ? ? RCSB RCSB046311 ? ? WWPDB D_1000046311 ? ? # 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 2008-05-06 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2024-03-13 # _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' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Structure summary' # 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 2 3 'Structure model' chem_comp_atom 3 3 'Structure model' chem_comp_bond 4 3 'Structure model' database_2 5 3 'Structure model' struct_conn 6 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' '_chem_comp.pdbx_synonyms' 2 3 'Structure model' '_database_2.pdbx_DOI' 3 3 'Structure model' '_database_2.pdbx_database_accession' 4 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3C3Z _pdbx_database_status.recvd_initial_deposition_date 2008-01-29 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2QEK 'Free subtype F HIV-1 DIS extended duplex RNA' unspecified PDB 3C44 . unspecified PDB 3C5D . unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Freisz, S.' 1 'Lang, K.' 2 'Micura, R.' 3 'Dumas, P.' 4 'Ennifar, E.' 5 # _citation.id primary _citation.title 'Binding of aminoglycoside antibiotics to the duplex form of the HIV-1 genomic RNA dimerization initiation site.' _citation.journal_abbrev Angew.Chem.Int.Ed.Engl. _citation.journal_volume 47 _citation.page_first 4110 _citation.page_last 4113 _citation.year 2008 _citation.journal_id_ASTM ACIEAY _citation.country GE _citation.journal_id_ISSN 0570-0833 _citation.journal_id_CSD 0179 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18435520 _citation.pdbx_database_id_DOI 10.1002/anie.200800726 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Freisz, S.' 1 ? primary 'Lang, K.' 2 ? primary 'Micura, R.' 3 ? primary 'Dumas, P.' 4 ? primary 'Ennifar, E.' 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 'HIV-1 subtype F genomic RNA' 7463.459 2 ? ? ? ? 2 non-polymer syn RIBOSTAMYCIN 454.473 2 ? ? ? ? 3 water nat water 18.015 164 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polydeoxyribonucleotide/polyribonucleotide hybrid' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code 'CU(UMS)GCUGAAGUGCACACAGCAAG' _entity_poly.pdbx_seq_one_letter_code_can CUUGCUGAAGUGCACACAGCAAG _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 RIBOSTAMYCIN RIO 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 U n 1 3 UMS n 1 4 G n 1 5 C n 1 6 U n 1 7 G n 1 8 A n 1 9 A n 1 10 G n 1 11 U n 1 12 G n 1 13 C n 1 14 A n 1 15 C n 1 16 A n 1 17 C n 1 18 A n 1 19 G n 1 20 C n 1 21 A n 1 22 A n 1 23 G 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 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 HOH non-polymer . WATER ? 'H2 O' 18.015 RIO non-polymer . RIBOSTAMYCIN ;5-AMINO-2-AMINOMETHYL-6-[4,6-DIAMINO-2-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-3-HYDROXY-CYCLOHEXYLOXY ]-TETRAHYDRO-PYRAN-3,4-DIOL; (1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside ; 'C17 H34 N4 O10' 454.473 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 UMS 'DNA linking' n "2'-METHYLSELENYL-2'-DEOXYURIDINE-5'-PHOSPHATE" ? 'C10 H15 N2 O8 P Se' 401.168 # 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 C 1 1 1 C CYT A . n A 1 2 U 2 2 2 U URI A . n A 1 3 UMS 3 3 3 UMS UMS A . n A 1 4 G 4 4 4 G GUA A . n A 1 5 C 5 5 5 C CYT A . n A 1 6 U 6 6 6 U URI A . n A 1 7 G 7 7 7 G GUA A . n A 1 8 A 8 8 8 A ADE A . n A 1 9 A 9 9 9 A ADE A . n A 1 10 G 10 10 10 G GUA A . n A 1 11 U 11 11 11 U URI A . n A 1 12 G 12 12 12 G GUA A . n A 1 13 C 13 13 13 C CYT A . n A 1 14 A 14 14 14 A ADE A . n A 1 15 C 15 15 15 C CYT A . n A 1 16 A 16 16 16 A ADE A . n A 1 17 C 17 17 17 C CYT A . n A 1 18 A 18 18 18 A ADE A . n A 1 19 G 19 19 19 G GUA A . n A 1 20 C 20 20 20 C CYT A . n A 1 21 A 21 21 21 A ADE A . n A 1 22 A 22 22 22 A ADE A . n A 1 23 G 23 23 23 G GUA A . n B 1 1 C 1 1 1 C CYT B . n B 1 2 U 2 2 2 U URI B . n B 1 3 UMS 3 3 3 UMS UMS B . n B 1 4 G 4 4 4 G GUA B . n B 1 5 C 5 5 5 C CYT B . n B 1 6 U 6 6 6 U URI B . n B 1 7 G 7 7 7 G GUA B . n B 1 8 A 8 8 8 A ADE B . n B 1 9 A 9 9 9 A ADE B . n B 1 10 G 10 10 10 G GUA B . n B 1 11 U 11 11 11 U URI B . n B 1 12 G 12 12 12 G GUA B . n B 1 13 C 13 13 13 C CYT B . n B 1 14 A 14 14 14 A ADE B . n B 1 15 C 15 15 15 C CYT B . n B 1 16 A 16 16 16 A ADE B . n B 1 17 C 17 17 17 C CYT B . n B 1 18 A 18 18 18 A ADE B . n B 1 19 G 19 19 19 G GUA B . n B 1 20 C 20 20 20 C CYT B . n B 1 21 A 21 21 21 A ADE B . n B 1 22 A 22 22 22 A ADE B . n B 1 23 G 23 23 23 G GUA B . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 RIO 1 24 24 RIO RIB A . D 2 RIO 1 24 24 RIO RIB B . E 3 HOH 1 25 3 HOH HOH A . E 3 HOH 2 26 5 HOH HOH A . E 3 HOH 3 27 6 HOH HOH A . E 3 HOH 4 28 9 HOH HOH A . E 3 HOH 5 29 10 HOH HOH A . E 3 HOH 6 30 12 HOH HOH A . E 3 HOH 7 31 17 HOH HOH A . E 3 HOH 8 32 18 HOH HOH A . E 3 HOH 9 33 22 HOH HOH A . E 3 HOH 10 34 26 HOH HOH A . E 3 HOH 11 35 29 HOH HOH A . E 3 HOH 12 36 31 HOH HOH A . E 3 HOH 13 37 32 HOH HOH A . E 3 HOH 14 38 33 HOH HOH A . E 3 HOH 15 39 34 HOH HOH A . E 3 HOH 16 40 35 HOH HOH A . E 3 HOH 17 41 36 HOH HOH A . E 3 HOH 18 42 39 HOH HOH A . E 3 HOH 19 43 45 HOH HOH A . E 3 HOH 20 44 47 HOH HOH A . E 3 HOH 21 45 49 HOH HOH A . E 3 HOH 22 46 50 HOH HOH A . E 3 HOH 23 47 52 HOH HOH A . E 3 HOH 24 48 56 HOH HOH A . E 3 HOH 25 49 58 HOH HOH A . E 3 HOH 26 50 59 HOH HOH A . E 3 HOH 27 51 63 HOH HOH A . E 3 HOH 28 52 64 HOH HOH A . E 3 HOH 29 53 66 HOH HOH A . E 3 HOH 30 54 69 HOH HOH A . E 3 HOH 31 55 70 HOH HOH A . E 3 HOH 32 56 71 HOH HOH A . E 3 HOH 33 57 72 HOH HOH A . E 3 HOH 34 58 74 HOH HOH A . E 3 HOH 35 59 76 HOH HOH A . E 3 HOH 36 60 78 HOH HOH A . E 3 HOH 37 61 80 HOH HOH A . E 3 HOH 38 62 81 HOH HOH A . E 3 HOH 39 63 82 HOH HOH A . E 3 HOH 40 64 87 HOH HOH A . E 3 HOH 41 65 88 HOH HOH A . E 3 HOH 42 66 90 HOH HOH A . E 3 HOH 43 67 91 HOH HOH A . E 3 HOH 44 68 93 HOH HOH A . E 3 HOH 45 69 94 HOH HOH A . E 3 HOH 46 70 96 HOH HOH A . E 3 HOH 47 71 97 HOH HOH A . E 3 HOH 48 72 100 HOH HOH A . E 3 HOH 49 73 101 HOH HOH A . E 3 HOH 50 74 102 HOH HOH A . E 3 HOH 51 75 105 HOH HOH A . E 3 HOH 52 76 108 HOH HOH A . E 3 HOH 53 77 109 HOH HOH A . E 3 HOH 54 78 110 HOH HOH A . E 3 HOH 55 79 111 HOH HOH A . E 3 HOH 56 80 112 HOH HOH A . E 3 HOH 57 81 114 HOH HOH A . E 3 HOH 58 82 115 HOH HOH A . E 3 HOH 59 83 116 HOH HOH A . E 3 HOH 60 84 117 HOH HOH A . E 3 HOH 61 85 119 HOH HOH A . E 3 HOH 62 86 120 HOH HOH A . E 3 HOH 63 87 123 HOH HOH A . E 3 HOH 64 88 127 HOH HOH A . E 3 HOH 65 89 128 HOH HOH A . E 3 HOH 66 90 132 HOH HOH A . E 3 HOH 67 91 133 HOH HOH A . E 3 HOH 68 92 135 HOH HOH A . E 3 HOH 69 93 136 HOH HOH A . E 3 HOH 70 94 138 HOH HOH A . E 3 HOH 71 95 141 HOH HOH A . E 3 HOH 72 96 142 HOH HOH A . E 3 HOH 73 97 143 HOH HOH A . E 3 HOH 74 98 144 HOH HOH A . E 3 HOH 75 99 145 HOH HOH A . E 3 HOH 76 100 146 HOH HOH A . E 3 HOH 77 101 147 HOH HOH A . E 3 HOH 78 102 150 HOH HOH A . E 3 HOH 79 103 151 HOH HOH A . E 3 HOH 80 104 152 HOH HOH A . E 3 HOH 81 105 153 HOH HOH A . E 3 HOH 82 106 155 HOH HOH A . E 3 HOH 83 107 156 HOH HOH A . E 3 HOH 84 108 161 HOH HOH A . E 3 HOH 85 109 162 HOH HOH A . E 3 HOH 86 110 25 HOH HOH A . F 3 HOH 1 25 1 HOH HOH B . F 3 HOH 2 26 2 HOH HOH B . F 3 HOH 3 27 4 HOH HOH B . F 3 HOH 4 28 7 HOH HOH B . F 3 HOH 5 29 8 HOH HOH B . F 3 HOH 6 30 11 HOH HOH B . F 3 HOH 7 31 13 HOH HOH B . F 3 HOH 8 32 14 HOH HOH B . F 3 HOH 9 33 15 HOH HOH B . F 3 HOH 10 34 16 HOH HOH B . F 3 HOH 11 35 19 HOH HOH B . F 3 HOH 12 36 20 HOH HOH B . F 3 HOH 13 37 21 HOH HOH B . F 3 HOH 14 38 23 HOH HOH B . F 3 HOH 15 39 24 HOH HOH B . F 3 HOH 16 41 27 HOH HOH B . F 3 HOH 17 42 28 HOH HOH B . F 3 HOH 18 43 30 HOH HOH B . F 3 HOH 19 44 37 HOH HOH B . F 3 HOH 20 45 38 HOH HOH B . F 3 HOH 21 46 40 HOH HOH B . F 3 HOH 22 47 41 HOH HOH B . F 3 HOH 23 48 42 HOH HOH B . F 3 HOH 24 49 43 HOH HOH B . F 3 HOH 25 50 44 HOH HOH B . F 3 HOH 26 51 46 HOH HOH B . F 3 HOH 27 52 48 HOH HOH B . F 3 HOH 28 53 51 HOH HOH B . F 3 HOH 29 54 53 HOH HOH B . F 3 HOH 30 55 54 HOH HOH B . F 3 HOH 31 56 55 HOH HOH B . F 3 HOH 32 57 57 HOH HOH B . F 3 HOH 33 58 60 HOH HOH B . F 3 HOH 34 59 61 HOH HOH B . F 3 HOH 35 60 62 HOH HOH B . F 3 HOH 36 61 65 HOH HOH B . F 3 HOH 37 62 67 HOH HOH B . F 3 HOH 38 63 68 HOH HOH B . F 3 HOH 39 64 73 HOH HOH B . F 3 HOH 40 65 75 HOH HOH B . F 3 HOH 41 66 77 HOH HOH B . F 3 HOH 42 67 79 HOH HOH B . F 3 HOH 43 68 83 HOH HOH B . F 3 HOH 44 69 84 HOH HOH B . F 3 HOH 45 70 85 HOH HOH B . F 3 HOH 46 71 86 HOH HOH B . F 3 HOH 47 72 89 HOH HOH B . F 3 HOH 48 73 92 HOH HOH B . F 3 HOH 49 74 95 HOH HOH B . F 3 HOH 50 75 98 HOH HOH B . F 3 HOH 51 76 99 HOH HOH B . F 3 HOH 52 77 103 HOH HOH B . F 3 HOH 53 78 104 HOH HOH B . F 3 HOH 54 79 106 HOH HOH B . F 3 HOH 55 80 107 HOH HOH B . F 3 HOH 56 81 113 HOH HOH B . F 3 HOH 57 82 118 HOH HOH B . F 3 HOH 58 83 121 HOH HOH B . F 3 HOH 59 84 122 HOH HOH B . F 3 HOH 60 85 124 HOH HOH B . F 3 HOH 61 86 125 HOH HOH B . F 3 HOH 62 87 126 HOH HOH B . F 3 HOH 63 88 129 HOH HOH B . F 3 HOH 64 89 130 HOH HOH B . F 3 HOH 65 90 131 HOH HOH B . F 3 HOH 66 91 134 HOH HOH B . F 3 HOH 67 92 137 HOH HOH B . F 3 HOH 68 93 139 HOH HOH B . F 3 HOH 69 94 140 HOH HOH B . F 3 HOH 70 95 148 HOH HOH B . F 3 HOH 71 96 149 HOH HOH B . F 3 HOH 72 97 154 HOH HOH B . F 3 HOH 73 98 157 HOH HOH B . F 3 HOH 74 99 158 HOH HOH B . F 3 HOH 75 100 159 HOH HOH B . F 3 HOH 76 101 160 HOH HOH B . F 3 HOH 77 102 163 HOH HOH B . F 3 HOH 78 103 164 HOH HOH B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CNS refinement 1.1 ? 1 DNA 'data collection' . ? 2 DENZO 'data reduction' . ? 3 SCALEPACK 'data scaling' . ? 4 SHARP phasing . ? 5 # _cell.entry_id 3C3Z _cell.length_a 99.670 _cell.length_b 30.530 _cell.length_c 57.680 _cell.angle_alpha 90.00 _cell.angle_beta 121.31 _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 3C3Z _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? # _exptl.entry_id 3C3Z _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.51 _exptl_crystal.density_percent_sol 51.02 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 310 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.2 _exptl_crystal_grow.pdbx_details '300mM KCl, 2mM MgCl2, 50mM Na Cacodylate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 310K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.details 1 1 1 'Na cacodylate' ? ? ? 1 2 1 MgCl2 ? ? ? 1 3 1 KCl ? ? ? 1 4 2 'Na cacodylate' ? ? ? 1 5 2 MgCl2 ? ? ? 1 6 2 KCl ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 90 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2006-05-22 _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 crystal _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.9788 1.0 2 0.9793 1.0 3 0.9732 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID29' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID29 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list '0.9788, 0.9793, 0.9732' # _reflns.entry_id 3C3Z _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 30 _reflns.d_resolution_high 1.5 _reflns.number_obs 46246 _reflns.number_all ? _reflns.percent_possible_obs 98.6 _reflns.pdbx_Rmerge_I_obs 0.055 _reflns.pdbx_Rsym_value 0.055 _reflns.pdbx_netI_over_sigmaI 27.9 _reflns.B_iso_Wilson_estimate 20.1 _reflns.pdbx_redundancy 9.2 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.5 _reflns_shell.d_res_low 1.55 _reflns_shell.percent_possible_all 98.5 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.243 _reflns_shell.meanI_over_sigI_obs 5.9 _reflns_shell.pdbx_redundancy 8.6 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 4602 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 3C3Z _refine.ls_number_reflns_obs 45890 _refine.ls_number_reflns_all 46527 _refine.pdbx_ls_sigma_I 0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF 868917.80 _refine.pdbx_data_cutoff_low_absF 0.000000 _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 18.44 _refine.ls_d_res_high 1.50 _refine.ls_percent_reflns_obs 98.6 _refine.ls_R_factor_obs 0.221 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.221 _refine.ls_R_factor_R_free 0.227 _refine.ls_R_factor_R_free_error 0.004 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 7.8 _refine.ls_number_reflns_R_free 3583 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 31.6 _refine.aniso_B[1][1] -2.57 _refine.aniso_B[2][2] 13.44 _refine.aniso_B[3][3] -10.86 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] -0.47 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'FLAT MODEL' _refine.solvent_model_param_ksol 0.383433 _refine.solvent_model_param_bsol 52.1428 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_isotropic_thermal_model RESTRAINED _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.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_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 3C3Z _refine_analyze.Luzzati_coordinate_error_obs 0.23 _refine_analyze.Luzzati_sigma_a_obs 0.31 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.23 _refine_analyze.Luzzati_sigma_a_free 0.33 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _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 980 _refine_hist.pdbx_number_atoms_ligand 62 _refine_hist.number_atoms_solvent 164 _refine_hist.number_atoms_total 1206 _refine_hist.d_res_high 1.50 _refine_hist.d_res_low 18.44 # 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 c_bond_d 0.006 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.4 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 10.1 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 4.90 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 1.50 _refine_ls_shell.d_res_low 1.59 _refine_ls_shell.number_reflns_R_work 7071 _refine_ls_shell.R_factor_R_work 0.413 _refine_ls_shell.percent_reflns_obs 99.0 _refine_ls_shell.R_factor_R_free 0.413 _refine_ls_shell.R_factor_R_free_error 0.016 _refine_ls_shell.percent_reflns_R_free 8.3 _refine_ls_shell.number_reflns_R_free 636 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 water_rep.param water.top 'X-RAY DIFFRACTION' 2 luc.param dna-rna.top 'X-RAY DIFFRACTION' 3 ion.param ion.top 'X-RAY DIFFRACTION' 4 ums_xplor.param ums_xplor.top 'X-RAY DIFFRACTION' 5 ribostamycine.param ribostamycine.top 'X-RAY DIFFRACTION' # _database_PDB_matrix.entry_id 3C3Z _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 3C3Z _struct.title 'Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3C3Z _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'HIV-1, RNA, antibiotic' # 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 3C3Z _struct_ref.pdbx_db_accession 3C3Z _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 3C3Z A 1 ? 23 ? 3C3Z 1 ? 23 ? 1 23 2 1 3C3Z B 1 ? 23 ? 3C3Z 1 ? 23 ? 1 23 # _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)' 5440 ? 1 MORE 1 ? 1 'SSA (A^2)' 7800 ? # _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 covale1 covale both ? A U 2 "O3'" ? ? ? 1_555 A UMS 3 P ? ? A U 2 A UMS 3 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale2 covale both ? A UMS 3 "O3'" ? ? ? 1_555 A G 4 P ? ? A UMS 3 A G 4 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale3 covale both ? B U 2 "O3'" ? ? ? 1_555 B UMS 3 P ? ? B U 2 B UMS 3 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale4 covale both ? B UMS 3 "O3'" ? ? ? 1_555 B G 4 P ? ? B UMS 3 B G 4 1_555 ? ? ? ? ? ? ? 1.604 ? ? hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 B G 23 N1 ? ? A C 1 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 B G 23 O6 ? ? A C 1 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 B G 23 N2 ? ? A C 1 B G 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A U 2 N3 ? ? ? 1_555 B A 22 N1 ? ? A U 2 B A 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A U 2 O4 ? ? ? 1_555 B A 22 N6 ? ? A U 2 B A 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A UMS 3 N3 ? ? ? 1_555 B A 21 N1 ? ? A UMS 3 B A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A UMS 3 O4 ? ? ? 1_555 B A 21 N6 ? ? A UMS 3 B A 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 4 N1 ? ? ? 1_555 B C 20 N3 ? ? A G 4 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N2 ? ? ? 1_555 B C 20 O2 ? ? A G 4 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 O6 ? ? ? 1_555 B C 20 N4 ? ? A G 4 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A C 5 N3 ? ? ? 1_555 B G 19 N1 ? ? A C 5 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A C 5 N4 ? ? ? 1_555 B G 19 O6 ? ? A C 5 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A C 5 O2 ? ? ? 1_555 B G 19 N2 ? ? A C 5 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 6 N3 ? ? ? 1_555 B A 18 N1 ? ? A U 6 B A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 6 O4 ? ? ? 1_555 B A 18 N6 ? ? A U 6 B A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A G 7 N1 ? ? ? 1_555 B C 17 N3 ? ? A G 7 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A G 7 N2 ? ? ? 1_555 B C 17 O2 ? ? A G 7 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A G 7 O6 ? ? ? 1_555 B C 17 N4 ? ? A G 7 B C 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A G 10 N1 ? ? ? 1_555 B C 15 N3 ? ? A G 10 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A G 10 N2 ? ? ? 1_555 B C 15 O2 ? ? A G 10 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A G 10 O6 ? ? ? 1_555 B C 15 N4 ? ? A G 10 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A U 11 N3 ? ? ? 1_555 B A 14 N1 ? ? A U 11 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A U 11 O4 ? ? ? 1_555 B A 14 N6 ? ? A U 11 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A G 12 N1 ? ? ? 1_555 B C 13 N3 ? ? A G 12 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A G 12 N2 ? ? ? 1_555 B C 13 O2 ? ? A G 12 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A G 12 O6 ? ? ? 1_555 B C 13 N4 ? ? A G 12 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A C 13 N3 ? ? ? 1_555 B G 12 N1 ? ? A C 13 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A C 13 N4 ? ? ? 1_555 B G 12 O6 ? ? A C 13 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A C 13 O2 ? ? ? 1_555 B G 12 N2 ? ? A C 13 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A A 14 N1 ? ? ? 1_555 B U 11 N3 ? ? A A 14 B U 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A A 14 N6 ? ? ? 1_555 B U 11 O4 ? ? A A 14 B U 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A C 15 N3 ? ? ? 1_555 B G 10 N1 ? ? A C 15 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A C 15 N4 ? ? ? 1_555 B G 10 O6 ? ? A C 15 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A C 15 O2 ? ? ? 1_555 B G 10 N2 ? ? A C 15 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A C 17 N3 ? ? ? 1_555 B G 7 N1 ? ? A C 17 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A C 17 N4 ? ? ? 1_555 B G 7 O6 ? ? A C 17 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? A C 17 O2 ? ? ? 1_555 B G 7 N2 ? ? A C 17 B G 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? A A 18 N1 ? ? ? 1_555 B U 6 N3 ? ? A A 18 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? A A 18 N6 ? ? ? 1_555 B U 6 O4 ? ? A A 18 B U 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog40 hydrog ? ? A G 19 N1 ? ? ? 1_555 B C 5 N3 ? ? A G 19 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog41 hydrog ? ? A G 19 N2 ? ? ? 1_555 B C 5 O2 ? ? A G 19 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog42 hydrog ? ? A G 19 O6 ? ? ? 1_555 B C 5 N4 ? ? A G 19 B C 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog43 hydrog ? ? A C 20 N3 ? ? ? 1_555 B G 4 N1 ? ? A C 20 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? A C 20 N4 ? ? ? 1_555 B G 4 O6 ? ? A C 20 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? A C 20 O2 ? ? ? 1_555 B G 4 N2 ? ? A C 20 B G 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? A A 21 N1 ? ? ? 1_555 B UMS 3 N3 ? ? A A 21 B UMS 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? A A 21 N6 ? ? ? 1_555 B UMS 3 O4 ? ? A A 21 B UMS 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? A A 22 N1 ? ? ? 1_555 B U 2 N3 ? ? A A 22 B U 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog49 hydrog ? ? A A 22 N6 ? ? ? 1_555 B U 2 O4 ? ? A A 22 B U 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog50 hydrog ? ? A G 23 N1 ? ? ? 1_555 B C 1 N3 ? ? A G 23 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog51 hydrog ? ? A G 23 N2 ? ? ? 1_555 B C 1 O2 ? ? A G 23 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog52 hydrog ? ? A G 23 O6 ? ? ? 1_555 B C 1 N4 ? ? A G 23 B C 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A RIO 24 ? 23 'BINDING SITE FOR RESIDUE RIO A 24' AC2 Software B RIO 24 ? 20 'BINDING SITE FOR RESIDUE RIO B 24' 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 23 G A 7 ? G A 7 . ? 1_555 ? 2 AC1 23 A A 8 ? A A 8 . ? 1_555 ? 3 AC1 23 A A 9 ? A A 9 . ? 1_555 ? 4 AC1 23 G A 10 ? G A 10 . ? 1_555 ? 5 AC1 23 U A 11 ? U A 11 . ? 1_555 ? 6 AC1 23 HOH E . ? HOH A 26 . ? 1_555 ? 7 AC1 23 HOH E . ? HOH A 32 . ? 1_555 ? 8 AC1 23 HOH E . ? HOH A 35 . ? 1_555 ? 9 AC1 23 HOH E . ? HOH A 40 . ? 1_555 ? 10 AC1 23 HOH E . ? HOH A 45 . ? 1_555 ? 11 AC1 23 HOH E . ? HOH A 48 . ? 1_555 ? 12 AC1 23 HOH E . ? HOH A 51 . ? 1_555 ? 13 AC1 23 HOH E . ? HOH A 52 . ? 1_555 ? 14 AC1 23 HOH E . ? HOH A 57 . ? 1_555 ? 15 AC1 23 HOH E . ? HOH A 62 . ? 1_555 ? 16 AC1 23 HOH E . ? HOH A 92 . ? 1_555 ? 17 AC1 23 A B 14 ? A B 14 . ? 1_555 ? 18 AC1 23 C B 15 ? C B 15 . ? 1_555 ? 19 AC1 23 A B 16 ? A B 16 . ? 1_555 ? 20 AC1 23 HOH F . ? HOH B 25 . ? 1_555 ? 21 AC1 23 HOH F . ? HOH B 29 . ? 1_555 ? 22 AC1 23 HOH F . ? HOH B 56 . ? 1_555 ? 23 AC1 23 HOH F . ? HOH B 73 . ? 1_555 ? 24 AC2 20 C A 13 ? C A 13 . ? 1_555 ? 25 AC2 20 A A 14 ? A A 14 . ? 1_555 ? 26 AC2 20 C A 15 ? C A 15 . ? 1_555 ? 27 AC2 20 A A 16 ? A A 16 . ? 1_555 ? 28 AC2 20 G B 7 ? G B 7 . ? 1_555 ? 29 AC2 20 A B 8 ? A B 8 . ? 1_555 ? 30 AC2 20 A B 9 ? A B 9 . ? 1_555 ? 31 AC2 20 G B 10 ? G B 10 . ? 1_555 ? 32 AC2 20 U B 11 ? U B 11 . ? 1_555 ? 33 AC2 20 G B 12 ? G B 12 . ? 1_555 ? 34 AC2 20 HOH F . ? HOH B 29 . ? 1_555 ? 35 AC2 20 HOH F . ? HOH B 36 . ? 1_555 ? 36 AC2 20 HOH F . ? HOH B 37 . ? 1_555 ? 37 AC2 20 HOH F . ? HOH B 38 . ? 1_555 ? 38 AC2 20 HOH F . ? HOH B 51 . ? 1_555 ? 39 AC2 20 HOH F . ? HOH B 57 . ? 1_555 ? 40 AC2 20 HOH F . ? HOH B 60 . ? 1_555 ? 41 AC2 20 HOH F . ? HOH B 63 . ? 1_555 ? 42 AC2 20 HOH F . ? HOH B 93 . ? 1_555 ? 43 AC2 20 HOH F . ? HOH B 96 . ? 1_555 ? # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id A _pdbx_validate_planes.auth_asym_id B _pdbx_validate_planes.auth_seq_id 8 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.055 _pdbx_validate_planes.type 'SIDE CHAIN' # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A UMS 3 A UMS 3 ? DU ? 2 B UMS 3 B UMS 3 ? DU ? # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'MAJOR GROOVE BINDER' # 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 G OP3 O N N 73 G P P N N 74 G OP1 O N N 75 G OP2 O N N 76 G "O5'" O N N 77 G "C5'" C N N 78 G "C4'" C N R 79 G "O4'" O N N 80 G "C3'" C N S 81 G "O3'" O N N 82 G "C2'" C N R 83 G "O2'" O N N 84 G "C1'" C N R 85 G N9 N Y N 86 G C8 C Y N 87 G N7 N Y N 88 G C5 C Y N 89 G C6 C N N 90 G O6 O N N 91 G N1 N N N 92 G C2 C N N 93 G N2 N N N 94 G N3 N N N 95 G C4 C Y N 96 G HOP3 H N N 97 G HOP2 H N N 98 G "H5'" H N N 99 G "H5''" H N N 100 G "H4'" H N N 101 G "H3'" H N N 102 G "HO3'" H N N 103 G "H2'" H N N 104 G "HO2'" H N N 105 G "H1'" H N N 106 G H8 H N N 107 G H1 H N N 108 G H21 H N N 109 G H22 H N N 110 HOH O O N N 111 HOH H1 H N N 112 HOH H2 H N N 113 RIO O1 O N N 114 RIO C1 C N N 115 RIO C2 C N R 116 RIO O2 O N N 117 RIO C3 C N S 118 RIO O3 O N N 119 RIO C4 C N R 120 RIO C5 C N S 121 RIO O4 O N N 122 RIO C6 C N R 123 RIO N1 N N N 124 RIO C7 C N N 125 RIO C8 C N S 126 RIO N2 N N N 127 RIO C9 C N R 128 RIO O5 O N N 129 RIO C10 C N R 130 RIO O6 O N N 131 RIO C11 C N R 132 RIO C12 C N N 133 RIO N3 N N N 134 RIO C13 C N S 135 RIO O7 O N N 136 RIO C14 C N R 137 RIO O8 O N N 138 RIO C15 C N R 139 RIO N4 N N N 140 RIO C16 C N R 141 RIO O9 O N N 142 RIO C17 C N S 143 RIO O10 O N N 144 RIO HO1 H N N 145 RIO H1 H N N 146 RIO H1A H N N 147 RIO H2 H N N 148 RIO H3 H N N 149 RIO H4 H N N 150 RIO H5 H N N 151 RIO HO4 H N N 152 RIO H6 H N N 153 RIO HN1 H N N 154 RIO HN1A H N N 155 RIO H7 H N N 156 RIO H7A H N N 157 RIO H8 H N N 158 RIO HN2 H N N 159 RIO HN2A H N N 160 RIO H9 H N N 161 RIO H10 H N N 162 RIO H11 H N N 163 RIO H12 H N N 164 RIO H12A H N N 165 RIO HN3 H N N 166 RIO HN3A H N N 167 RIO H13 H N N 168 RIO HO7 H N N 169 RIO H14 H N N 170 RIO HO8 H N N 171 RIO H15 H N N 172 RIO HN4 H N N 173 RIO HN4A H N N 174 RIO H16 H N N 175 RIO HO9 H N N 176 RIO H17 H N N 177 RIO HO10 H N N 178 U OP3 O N N 179 U P P N N 180 U OP1 O N N 181 U OP2 O N N 182 U "O5'" O N N 183 U "C5'" C N N 184 U "C4'" C N R 185 U "O4'" O N N 186 U "C3'" C N S 187 U "O3'" O N N 188 U "C2'" C N R 189 U "O2'" O N N 190 U "C1'" C N R 191 U N1 N N N 192 U C2 C N N 193 U O2 O N N 194 U N3 N N N 195 U C4 C N N 196 U O4 O N N 197 U C5 C N N 198 U C6 C N N 199 U HOP3 H N N 200 U HOP2 H N N 201 U "H5'" H N N 202 U "H5''" H N N 203 U "H4'" H N N 204 U "H3'" H N N 205 U "HO3'" H N N 206 U "H2'" H N N 207 U "HO2'" H N N 208 U "H1'" H N N 209 U H3 H N N 210 U H5 H N N 211 U H6 H N N 212 UMS OP3 O N N 213 UMS P P N N 214 UMS OP1 O N N 215 UMS OP2 O N N 216 UMS "O5'" O N N 217 UMS "C5'" C N N 218 UMS "C4'" C N R 219 UMS "O4'" O N N 220 UMS "C3'" C N R 221 UMS "O3'" O N N 222 UMS "C2'" C N R 223 UMS "SE2'" SE N N 224 UMS "C1'" C N R 225 UMS "CA'" C N N 226 UMS N1 N N N 227 UMS C2 C N N 228 UMS O2 O N N 229 UMS N3 N N N 230 UMS C4 C N N 231 UMS O4 O N N 232 UMS C5 C N N 233 UMS C6 C N N 234 UMS HOP3 H N N 235 UMS HOP2 H N N 236 UMS "H5'" H N N 237 UMS "H5'2" H N N 238 UMS "H4'" H N N 239 UMS "H3'" H N N 240 UMS "HO3'" H N N 241 UMS "H2'" H N N 242 UMS "H1'" H N N 243 UMS "HA'" H N N 244 UMS "HA'2" H N N 245 UMS "HA'3" H N N 246 UMS H3 H N N 247 UMS H5 H N N 248 UMS H6 H N N 249 # 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 G OP3 P sing N N 76 G OP3 HOP3 sing N N 77 G P OP1 doub N N 78 G P OP2 sing N N 79 G P "O5'" sing N N 80 G OP2 HOP2 sing N N 81 G "O5'" "C5'" sing N N 82 G "C5'" "C4'" sing N N 83 G "C5'" "H5'" sing N N 84 G "C5'" "H5''" sing N N 85 G "C4'" "O4'" sing N N 86 G "C4'" "C3'" sing N N 87 G "C4'" "H4'" sing N N 88 G "O4'" "C1'" sing N N 89 G "C3'" "O3'" sing N N 90 G "C3'" "C2'" sing N N 91 G "C3'" "H3'" sing N N 92 G "O3'" "HO3'" sing N N 93 G "C2'" "O2'" sing N N 94 G "C2'" "C1'" sing N N 95 G "C2'" "H2'" sing N N 96 G "O2'" "HO2'" sing N N 97 G "C1'" N9 sing N N 98 G "C1'" "H1'" sing N N 99 G N9 C8 sing Y N 100 G N9 C4 sing Y N 101 G C8 N7 doub Y N 102 G C8 H8 sing N N 103 G N7 C5 sing Y N 104 G C5 C6 sing N N 105 G C5 C4 doub Y N 106 G C6 O6 doub N N 107 G C6 N1 sing N N 108 G N1 C2 sing N N 109 G N1 H1 sing N N 110 G C2 N2 sing N N 111 G C2 N3 doub N N 112 G N2 H21 sing N N 113 G N2 H22 sing N N 114 G N3 C4 sing N N 115 HOH O H1 sing N N 116 HOH O H2 sing N N 117 RIO O1 C1 sing N N 118 RIO C1 C2 sing N N 119 RIO C2 O2 sing N N 120 RIO C2 C17 sing N N 121 RIO O2 C3 sing N N 122 RIO C3 O3 sing N N 123 RIO C3 C16 sing N N 124 RIO O3 C4 sing N N 125 RIO C4 C5 sing N N 126 RIO C4 C9 sing N N 127 RIO C5 O4 sing N N 128 RIO C5 C6 sing N N 129 RIO C6 N1 sing N N 130 RIO C6 C7 sing N N 131 RIO C7 C8 sing N N 132 RIO C8 N2 sing N N 133 RIO C8 C9 sing N N 134 RIO C9 O5 sing N N 135 RIO O5 C10 sing N N 136 RIO C10 O6 sing N N 137 RIO C10 C15 sing N N 138 RIO O6 C11 sing N N 139 RIO C11 C12 sing N N 140 RIO C11 C13 sing N N 141 RIO C12 N3 sing N N 142 RIO C13 O7 sing N N 143 RIO C13 C14 sing N N 144 RIO C14 O8 sing N N 145 RIO C14 C15 sing N N 146 RIO C15 N4 sing N N 147 RIO C16 O9 sing N N 148 RIO C16 C17 sing N N 149 RIO C17 O10 sing N N 150 RIO O1 HO1 sing N N 151 RIO C1 H1 sing N N 152 RIO C1 H1A sing N N 153 RIO C2 H2 sing N N 154 RIO C3 H3 sing N N 155 RIO C4 H4 sing N N 156 RIO C5 H5 sing N N 157 RIO O4 HO4 sing N N 158 RIO C6 H6 sing N N 159 RIO N1 HN1 sing N N 160 RIO N1 HN1A sing N N 161 RIO C7 H7 sing N N 162 RIO C7 H7A sing N N 163 RIO C8 H8 sing N N 164 RIO N2 HN2 sing N N 165 RIO N2 HN2A sing N N 166 RIO C9 H9 sing N N 167 RIO C10 H10 sing N N 168 RIO C11 H11 sing N N 169 RIO C12 H12 sing N N 170 RIO C12 H12A sing N N 171 RIO N3 HN3 sing N N 172 RIO N3 HN3A sing N N 173 RIO C13 H13 sing N N 174 RIO O7 HO7 sing N N 175 RIO C14 H14 sing N N 176 RIO O8 HO8 sing N N 177 RIO C15 H15 sing N N 178 RIO N4 HN4 sing N N 179 RIO N4 HN4A sing N N 180 RIO C16 H16 sing N N 181 RIO O9 HO9 sing N N 182 RIO C17 H17 sing N N 183 RIO O10 HO10 sing N N 184 U OP3 P sing N N 185 U OP3 HOP3 sing N N 186 U P OP1 doub N N 187 U P OP2 sing N N 188 U P "O5'" sing N N 189 U OP2 HOP2 sing N N 190 U "O5'" "C5'" sing N N 191 U "C5'" "C4'" sing N N 192 U "C5'" "H5'" sing N N 193 U "C5'" "H5''" sing N N 194 U "C4'" "O4'" sing N N 195 U "C4'" "C3'" sing N N 196 U "C4'" "H4'" sing N N 197 U "O4'" "C1'" sing N N 198 U "C3'" "O3'" sing N N 199 U "C3'" "C2'" sing N N 200 U "C3'" "H3'" sing N N 201 U "O3'" "HO3'" sing N N 202 U "C2'" "O2'" sing N N 203 U "C2'" "C1'" sing N N 204 U "C2'" "H2'" sing N N 205 U "O2'" "HO2'" sing N N 206 U "C1'" N1 sing N N 207 U "C1'" "H1'" sing N N 208 U N1 C2 sing N N 209 U N1 C6 sing N N 210 U C2 O2 doub N N 211 U C2 N3 sing N N 212 U N3 C4 sing N N 213 U N3 H3 sing N N 214 U C4 O4 doub N N 215 U C4 C5 sing N N 216 U C5 C6 doub N N 217 U C5 H5 sing N N 218 U C6 H6 sing N N 219 UMS OP3 P sing N N 220 UMS OP3 HOP3 sing N N 221 UMS P OP1 doub N N 222 UMS P OP2 sing N N 223 UMS P "O5'" sing N N 224 UMS OP2 HOP2 sing N N 225 UMS "O5'" "C5'" sing N N 226 UMS "C5'" "C4'" sing N N 227 UMS "C5'" "H5'" sing N N 228 UMS "C5'" "H5'2" sing N N 229 UMS "C4'" "O4'" sing N N 230 UMS "C4'" "C3'" sing N N 231 UMS "C4'" "H4'" sing N N 232 UMS "O4'" "C1'" sing N N 233 UMS "C3'" "O3'" sing N N 234 UMS "C3'" "C2'" sing N N 235 UMS "C3'" "H3'" sing N N 236 UMS "O3'" "HO3'" sing N N 237 UMS "C2'" "SE2'" sing N N 238 UMS "C2'" "C1'" sing N N 239 UMS "C2'" "H2'" sing N N 240 UMS "SE2'" "CA'" sing N N 241 UMS "C1'" N1 sing N N 242 UMS "C1'" "H1'" sing N N 243 UMS "CA'" "HA'" sing N N 244 UMS "CA'" "HA'2" sing N N 245 UMS "CA'" "HA'3" sing N N 246 UMS N1 C2 sing N N 247 UMS N1 C6 sing N N 248 UMS C2 O2 doub N N 249 UMS C2 N3 sing N N 250 UMS N3 C4 sing N N 251 UMS N3 H3 sing N N 252 UMS C4 O4 doub N N 253 UMS C4 C5 sing N N 254 UMS C5 C6 doub N N 255 UMS C5 H5 sing N N 256 UMS C6 H6 sing N N 257 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3C3Z 'double helix' 3C3Z 'a-form double helix' 3C3Z '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 C 1 1_555 B G 23 1_555 0.008 -0.241 0.105 11.095 -23.151 -2.353 1 A_C1:G23_B A 1 ? B 23 ? 19 1 1 A U 2 1_555 B A 22 1_555 -0.360 -0.125 0.209 -1.214 -17.101 -0.119 2 A_U2:A22_B A 2 ? B 22 ? 20 1 1 A UMS 3 1_555 B A 21 1_555 0.291 -0.340 -0.100 4.845 -13.664 0.932 3 A_UMS3:A21_B A 3 ? B 21 ? 20 1 1 A G 4 1_555 B C 20 1_555 -0.235 -0.316 0.074 -2.400 -14.612 -0.559 4 A_G4:C20_B A 4 ? B 20 ? 19 1 1 A C 5 1_555 B G 19 1_555 0.193 -0.044 0.172 -1.408 -13.546 3.107 5 A_C5:G19_B A 5 ? B 19 ? 19 1 1 A U 6 1_555 B A 18 1_555 0.002 -0.089 0.229 3.240 -13.674 7.452 6 A_U6:A18_B A 6 ? B 18 ? 20 1 1 A G 7 1_555 B C 17 1_555 -0.330 -0.107 -0.031 -8.152 -24.669 3.730 7 A_G7:C17_B A 7 ? B 17 ? 19 1 1 A G 10 1_555 B C 15 1_555 -0.233 -0.151 -0.246 -6.347 -3.491 -0.795 8 A_G10:C15_B A 10 ? B 15 ? 19 1 1 A U 11 1_555 B A 14 1_555 -0.165 -0.152 0.033 -4.513 -5.450 4.044 9 A_U11:A14_B A 11 ? B 14 ? 20 1 1 A G 12 1_555 B C 13 1_555 -0.056 -0.142 0.134 3.781 -4.639 -0.427 10 A_G12:C13_B A 12 ? B 13 ? 19 1 1 A C 13 1_555 B G 12 1_555 0.161 -0.080 -0.052 4.326 -17.392 4.775 11 A_C13:G12_B A 13 ? B 12 ? 19 1 1 A A 14 1_555 B U 11 1_555 0.239 -0.012 -0.073 -2.134 -8.414 -1.966 12 A_A14:U11_B A 14 ? B 11 ? 20 1 1 A C 15 1_555 B G 10 1_555 0.314 -0.080 0.010 1.999 -2.218 -2.248 13 A_C15:G10_B A 15 ? B 10 ? 19 1 1 A C 17 1_555 B G 7 1_555 0.303 -0.199 -0.064 9.224 -23.315 2.667 14 A_C17:G7_B A 17 ? B 7 ? 19 1 1 A A 18 1_555 B U 6 1_555 -0.116 -0.141 0.195 -1.186 -16.527 7.962 15 A_A18:U6_B A 18 ? B 6 ? 20 1 1 A G 19 1_555 B C 5 1_555 -0.134 -0.146 0.120 1.027 -14.222 1.335 16 A_G19:C5_B A 19 ? B 5 ? 19 1 1 A C 20 1_555 B G 4 1_555 0.259 -0.141 -0.034 0.968 -14.899 1.188 17 A_C20:G4_B A 20 ? B 4 ? 19 1 1 A A 21 1_555 B UMS 3 1_555 0.100 -0.068 0.045 -3.464 -13.549 -1.207 18 A_A21:UMS3_B A 21 ? B 3 ? 20 1 1 A A 22 1_555 B U 2 1_555 0.104 -0.189 0.446 1.285 -13.408 2.689 19 A_A22:U2_B A 22 ? B 2 ? 20 1 1 A G 23 1_555 B C 1 1_555 -0.109 -0.194 -0.025 -7.163 -21.795 0.213 20 A_G23:C1_B A 23 ? B 1 ? 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 C 1 1_555 B G 23 1_555 A U 2 1_555 B A 22 1_555 -0.488 -1.569 3.474 -5.602 13.322 34.154 -4.248 0.021 2.739 21.526 9.053 37.002 1 AA_C1U2:A22G23_BB A 1 ? B 23 ? A 2 ? B 22 ? 1 A U 2 1_555 B A 22 1_555 A UMS 3 1_555 B A 21 1_555 -0.118 -1.036 3.062 0.667 7.472 34.807 -2.679 0.280 2.785 12.314 -1.099 35.582 2 AA_U2UMS3:A21A22_BB A 2 ? B 22 ? A 3 ? B 21 ? 1 A UMS 3 1_555 B A 21 1_555 A G 4 1_555 B C 20 1_555 0.032 -1.393 3.247 -0.821 17.553 30.930 -4.575 -0.159 2.169 30.065 1.407 35.467 3 AA_UMS3G4:C20A21_BB A 3 ? B 21 ? A 4 ? B 20 ? 1 A G 4 1_555 B C 20 1_555 A C 5 1_555 B G 19 1_555 0.701 -1.507 3.207 1.441 5.808 34.527 -3.331 -0.960 2.948 9.694 -2.406 35.026 4 AA_G4C5:G19C20_BB A 4 ? B 20 ? A 5 ? B 19 ? 1 A C 5 1_555 B G 19 1_555 A U 6 1_555 B A 18 1_555 0.303 -1.885 3.087 1.301 6.281 25.768 -5.561 -0.358 2.574 13.813 -2.860 26.541 5 AA_C5U6:A18G19_BB A 5 ? B 19 ? A 6 ? B 18 ? 1 A U 6 1_555 B A 18 1_555 A G 7 1_555 B C 17 1_555 -0.362 -1.556 3.376 0.994 12.977 31.951 -4.534 0.757 2.557 22.446 -1.719 34.436 6 AA_U6G7:C17A18_BB A 6 ? B 18 ? A 7 ? B 17 ? 1 A G 10 1_555 B C 15 1_555 A U 11 1_555 B A 14 1_555 -0.385 -2.297 3.354 -2.259 0.212 32.788 -4.097 0.284 3.358 0.375 3.995 32.864 7 AA_G10U11:A14C15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A U 11 1_555 B A 14 1_555 A G 12 1_555 B C 13 1_555 -0.792 -1.704 2.992 -0.237 7.831 27.375 -4.983 1.566 2.427 16.132 0.488 28.453 8 AA_U11G12:C13A14_BB A 11 ? B 14 ? A 12 ? B 13 ? 1 A G 12 1_555 B C 13 1_555 A C 13 1_555 B G 12 1_555 0.858 -1.405 3.244 2.713 13.711 33.281 -4.071 -1.032 2.548 22.733 -4.498 36.020 9 AA_G12C13:G12C13_BB A 12 ? B 13 ? A 13 ? B 12 ? 1 A C 13 1_555 B G 12 1_555 A A 14 1_555 B U 11 1_555 -0.061 -1.666 3.316 0.798 13.607 32.607 -4.602 0.210 2.446 23.021 -1.350 35.269 10 AA_C13A14:U11G12_BB A 13 ? B 12 ? A 14 ? B 11 ? 1 A A 14 1_555 B U 11 1_555 A C 15 1_555 B G 10 1_555 0.691 -2.697 3.136 1.005 1.494 28.964 -5.692 -1.171 3.018 2.984 -2.007 29.019 11 AA_A14C15:G10U11_BB A 14 ? B 11 ? A 15 ? B 10 ? 1 A C 15 1_555 B G 10 1_555 A C 17 1_555 B G 7 1_555 1.613 -3.980 6.042 -3.803 19.992 78.932 -3.948 -1.409 5.024 15.491 2.947 81.097 12 AA_C15C17:G7G10_BB A 15 ? B 10 ? A 17 ? B 7 ? 1 A C 17 1_555 B G 7 1_555 A A 18 1_555 B U 6 1_555 0.496 -1.579 3.391 -1.500 13.300 31.123 -4.737 -1.081 2.501 23.475 2.647 33.813 13 AA_C17A18:U6G7_BB A 17 ? B 7 ? A 18 ? B 6 ? 1 A A 18 1_555 B U 6 1_555 A G 19 1_555 B C 5 1_555 -0.849 -1.684 3.104 -3.246 7.094 29.198 -4.534 1.033 2.706 13.765 6.299 30.200 14 AA_A18G19:C5U6_BB A 18 ? B 6 ? A 19 ? B 5 ? 1 A G 19 1_555 B C 5 1_555 A C 20 1_555 B G 4 1_555 -0.129 -1.403 3.224 0.066 6.024 34.005 -3.251 0.228 2.939 10.201 -0.112 34.519 15 AA_G19C20:G4C5_BB A 19 ? B 5 ? A 20 ? B 4 ? 1 A C 20 1_555 B G 4 1_555 A A 21 1_555 B UMS 3 1_555 0.043 -1.581 3.224 -0.320 15.199 31.486 -4.672 -0.114 2.246 26.185 0.551 34.880 16 AA_C20A21:UMS3G4_BB A 20 ? B 4 ? A 21 ? B 3 ? 1 A A 21 1_555 B UMS 3 1_555 A A 22 1_555 B U 2 1_555 0.109 -1.165 3.024 -1.288 6.157 30.762 -3.184 -0.417 2.738 11.456 2.397 31.384 17 AA_A21A22:U2UMS3_BB A 21 ? B 3 ? A 22 ? B 2 ? 1 A A 22 1_555 B U 2 1_555 A G 23 1_555 B C 1 1_555 0.632 -1.528 3.418 7.896 12.984 32.856 -4.275 0.081 2.719 21.576 -13.121 36.112 18 AA_A22G23:C1U2_BB A 22 ? B 2 ? A 23 ? B 1 ? # _atom_sites.entry_id 3C3Z _atom_sites.fract_transf_matrix[1][1] 0.010033 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.006103 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.032755 _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] 0.020292 _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 SE # loop_