data_1UB8 # _entry.id 1UB8 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1UB8 pdb_00001ub8 10.2210/pdb1ub8/pdb NDB UD0027 ? ? RCSB RCSB005643 ? ? WWPDB D_1000005643 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2004-03-09 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2023-12-27 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1UB8 _pdbx_database_status.recvd_initial_deposition_date 2003-03-31 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Sunami, T.' 1 'Kondo, J.' 2 'Hirao, I.' 3 'Watanabe, K.' 4 'Miura, K.' 5 'Takenaka, A.' 6 # _citation.id primary _citation.title ;Structures of d(GCGAAGC) and d(GCGAAAGC) (tetragonal form): a switching of partners of the sheared G.A pairs to form a functional G.AxA.G crossing. ; _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 60 _citation.page_first 422 _citation.page_last 431 _citation.year 2004 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 14993665 _citation.pdbx_database_id_DOI 10.1107/S0907444903028415 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Sunami, T.' 1 ? primary 'Kondo, J.' 2 ? primary 'Hirao, I.' 3 ? primary 'Watanabe, K.' 4 ? primary 'Miura, K.' 5 ? primary 'Takenaka, A.' 6 ? # 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 "5'-D(*GP*CP*GP*AP*AP*GP*C)-3'" 2147.437 6 ? ? ? ? 2 non-polymer syn 'COBALT HEXAMMINE(III)' 161.116 9 ? ? ? ? 3 water nat water 18.015 304 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DG)(DC)(DG)(DA)(DA)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCGAAGC _entity_poly.pdbx_strand_id A,B,C,D,E,F _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'COBALT HEXAMMINE(III)' NCO 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DC n 1 3 DG n 1 4 DA n 1 5 DA n 1 6 DG n 1 7 DC n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'chemically synthesized' # 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 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 HOH non-polymer . WATER ? 'H2 O' 18.015 NCO non-polymer . 'COBALT HEXAMMINE(III)' ? 'Co H18 N6 3' 161.116 # 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 DG 1 1 1 DG GUA A . n A 1 2 DC 2 2 2 DC CYT A . n A 1 3 DG 3 3 3 DG GUA A . n A 1 4 DA 4 4 4 DA ADE A . n A 1 5 DA 5 5 5 DA ADE A . n A 1 6 DG 6 6 6 DG GUA A . n A 1 7 DC 7 7 7 DC CYT A . n B 1 1 DG 1 1 1 DG GUA B . n B 1 2 DC 2 2 2 DC CYT B . n B 1 3 DG 3 3 3 DG GUA B . n B 1 4 DA 4 4 4 DA ADE B . n B 1 5 DA 5 5 5 DA ADE B . n B 1 6 DG 6 6 6 DG GUA B . n B 1 7 DC 7 7 7 DC CYT B . n C 1 1 DG 1 1 1 DG GUA C . n C 1 2 DC 2 2 2 DC CYT C . n C 1 3 DG 3 3 3 DG GUA C . n C 1 4 DA 4 4 4 DA ADE C . n C 1 5 DA 5 5 5 DA ADE C . n C 1 6 DG 6 6 6 DG GUA C . n C 1 7 DC 7 7 7 DC CYT C . n D 1 1 DG 1 1 1 DG GUA D . n D 1 2 DC 2 2 2 DC CYT D . n D 1 3 DG 3 3 3 DG GUA D . n D 1 4 DA 4 4 4 DA ADE D . n D 1 5 DA 5 5 5 DA ADE D . n D 1 6 DG 6 6 6 DG GUA D . n D 1 7 DC 7 7 7 DC CYT D . n E 1 1 DG 1 1 1 DG GUA E . n E 1 2 DC 2 2 2 DC CYT E . n E 1 3 DG 3 3 3 DG GUA E . n E 1 4 DA 4 4 4 DA ADE E . n E 1 5 DA 5 5 5 DA ADE E . n E 1 6 DG 6 6 6 DG GUA E . n E 1 7 DC 7 7 7 DC CYT E . n F 1 1 DG 1 1 1 DG GUA F . n F 1 2 DC 2 2 2 DC CYT F . n F 1 3 DG 3 3 3 DG GUA F . n F 1 4 DA 4 4 4 DA ADE F . n F 1 5 DA 5 5 5 DA ADE F . n F 1 6 DG 6 6 6 DG GUA F . n F 1 7 DC 7 7 7 DC CYT F . 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 G 2 NCO 1 1401 401 NCO NCO A . H 2 NCO 1 404 404 NCO NCO B . I 2 NCO 1 406 406 NCO NCO B . J 2 NCO 1 407 407 NCO NCO C . K 2 NCO 1 408 408 NCO NCO C . L 2 NCO 1 400 400 NCO NCO D . M 2 NCO 1 402 402 NCO NCO D . N 2 NCO 1 403 403 NCO NCO E . O 2 NCO 1 405 405 NCO NCO F . P 3 HOH 1 1402 1 HOH TIP A . P 3 HOH 2 1403 2 HOH TIP A . P 3 HOH 3 1404 3 HOH TIP A . P 3 HOH 4 1405 4 HOH TIP A . P 3 HOH 5 1406 6 HOH TIP A . P 3 HOH 6 1407 7 HOH TIP A . P 3 HOH 7 1408 8 HOH TIP A . P 3 HOH 8 1409 9 HOH TIP A . P 3 HOH 9 1410 12 HOH TIP A . P 3 HOH 10 1411 13 HOH TIP A . P 3 HOH 11 1412 16 HOH TIP A . P 3 HOH 12 1413 17 HOH TIP A . P 3 HOH 13 1414 19 HOH TIP A . P 3 HOH 14 1415 20 HOH TIP A . P 3 HOH 15 1416 21 HOH TIP A . P 3 HOH 16 1417 23 HOH TIP A . P 3 HOH 17 1418 67 HOH TIP A . P 3 HOH 18 1419 115 HOH TIP A . P 3 HOH 19 1420 119 HOH TIP A . P 3 HOH 20 1421 122 HOH TIP A . P 3 HOH 21 1422 123 HOH TIP A . P 3 HOH 22 1423 127 HOH TIP A . P 3 HOH 23 1424 133 HOH TIP A . P 3 HOH 24 1425 139 HOH TIP A . P 3 HOH 25 1426 144 HOH TIP A . P 3 HOH 26 1427 145 HOH TIP A . P 3 HOH 27 1428 151 HOH TIP A . P 3 HOH 28 1429 161 HOH TIP A . P 3 HOH 29 1430 164 HOH TIP A . P 3 HOH 30 1431 176 HOH TIP A . P 3 HOH 31 1432 38 HOH TIP A . P 3 HOH 32 1433 42 HOH TIP A . P 3 HOH 33 1434 63 HOH TIP A . P 3 HOH 34 1435 183 HOH TIP A . P 3 HOH 35 1436 190 HOH TIP A . P 3 HOH 36 1437 206 HOH TIP A . P 3 HOH 37 1438 238 HOH TIP A . P 3 HOH 38 1439 243 HOH TIP A . P 3 HOH 39 1440 262 HOH TIP A . P 3 HOH 40 1441 263 HOH TIP A . P 3 HOH 41 1442 270 HOH TIP A . P 3 HOH 42 1443 272 HOH TIP A . P 3 HOH 43 1444 277 HOH TIP A . P 3 HOH 44 1445 282 HOH TIP A . P 3 HOH 45 1446 306 HOH TIP A . P 3 HOH 46 1447 307 HOH TIP A . P 3 HOH 47 1448 314 HOH TIP A . P 3 HOH 48 1449 318 HOH TIP A . P 3 HOH 49 1450 319 HOH TIP A . P 3 HOH 50 1451 326 HOH TIP A . P 3 HOH 51 1452 335 HOH TIP A . P 3 HOH 52 1453 337 HOH TIP A . P 3 HOH 53 1454 349 HOH TIP A . P 3 HOH 54 1455 356 HOH TIP A . P 3 HOH 55 1456 367 HOH TIP A . P 3 HOH 56 1457 368 HOH TIP A . P 3 HOH 57 1458 370 HOH TIP A . P 3 HOH 58 1459 371 HOH TIP A . P 3 HOH 59 1460 372 HOH TIP A . P 3 HOH 60 1461 374 HOH TIP A . P 3 HOH 61 1462 378 HOH TIP A . P 3 HOH 62 1463 385 HOH TIP A . P 3 HOH 63 1464 392 HOH TIP A . P 3 HOH 64 1465 398 HOH TIP A . Q 3 HOH 1 11 11 HOH TIP B . Q 3 HOH 2 25 25 HOH TIP B . Q 3 HOH 3 26 26 HOH TIP B . Q 3 HOH 4 27 27 HOH TIP B . Q 3 HOH 5 28 28 HOH TIP B . Q 3 HOH 6 29 29 HOH TIP B . Q 3 HOH 7 30 30 HOH TIP B . Q 3 HOH 8 32 32 HOH TIP B . Q 3 HOH 9 33 33 HOH TIP B . Q 3 HOH 10 34 34 HOH TIP B . Q 3 HOH 11 35 35 HOH TIP B . Q 3 HOH 12 36 36 HOH TIP B . Q 3 HOH 13 37 37 HOH TIP B . Q 3 HOH 14 40 40 HOH TIP B . Q 3 HOH 15 41 41 HOH TIP B . Q 3 HOH 16 43 43 HOH TIP B . Q 3 HOH 17 44 44 HOH TIP B . Q 3 HOH 18 45 45 HOH TIP B . Q 3 HOH 19 47 47 HOH TIP B . Q 3 HOH 20 48 48 HOH TIP B . Q 3 HOH 21 66 66 HOH TIP B . Q 3 HOH 22 90 90 HOH TIP B . Q 3 HOH 23 118 118 HOH TIP B . Q 3 HOH 24 124 124 HOH TIP B . Q 3 HOH 25 125 125 HOH TIP B . Q 3 HOH 26 126 126 HOH TIP B . Q 3 HOH 27 130 130 HOH TIP B . Q 3 HOH 28 134 134 HOH TIP B . Q 3 HOH 29 143 143 HOH TIP B . Q 3 HOH 30 147 147 HOH TIP B . Q 3 HOH 31 155 155 HOH TIP B . Q 3 HOH 32 157 157 HOH TIP B . Q 3 HOH 33 186 186 HOH TIP B . Q 3 HOH 34 196 196 HOH TIP B . Q 3 HOH 35 202 202 HOH TIP B . Q 3 HOH 36 203 203 HOH TIP B . Q 3 HOH 37 207 207 HOH TIP B . Q 3 HOH 38 213 213 HOH TIP B . Q 3 HOH 39 214 214 HOH TIP B . Q 3 HOH 40 219 219 HOH TIP B . Q 3 HOH 41 220 220 HOH TIP B . Q 3 HOH 42 224 224 HOH TIP B . Q 3 HOH 43 231 231 HOH TIP B . Q 3 HOH 44 241 241 HOH TIP B . Q 3 HOH 45 280 280 HOH TIP B . Q 3 HOH 46 287 287 HOH TIP B . Q 3 HOH 47 294 294 HOH TIP B . Q 3 HOH 48 298 298 HOH TIP B . Q 3 HOH 49 299 299 HOH TIP B . Q 3 HOH 50 303 303 HOH TIP B . Q 3 HOH 51 320 320 HOH TIP B . Q 3 HOH 52 323 323 HOH TIP B . Q 3 HOH 53 327 327 HOH TIP B . Q 3 HOH 54 334 334 HOH TIP B . Q 3 HOH 55 338 338 HOH TIP B . Q 3 HOH 56 348 348 HOH TIP B . Q 3 HOH 57 361 361 HOH TIP B . Q 3 HOH 58 376 376 HOH TIP B . Q 3 HOH 59 382 382 HOH TIP B . Q 3 HOH 60 383 383 HOH TIP B . Q 3 HOH 61 391 391 HOH TIP B . Q 3 HOH 62 401 401 HOH TIP B . Q 3 HOH 63 1184 184 HOH TIP B . R 3 HOH 1 51 51 HOH TIP C . R 3 HOH 2 52 52 HOH TIP C . R 3 HOH 3 53 53 HOH TIP C . R 3 HOH 4 54 54 HOH TIP C . R 3 HOH 5 55 55 HOH TIP C . R 3 HOH 6 148 148 HOH TIP C . R 3 HOH 7 168 168 HOH TIP C . R 3 HOH 8 171 171 HOH TIP C . R 3 HOH 9 174 174 HOH TIP C . R 3 HOH 10 175 175 HOH TIP C . R 3 HOH 11 194 194 HOH TIP C . R 3 HOH 12 242 242 HOH TIP C . R 3 HOH 13 244 244 HOH TIP C . R 3 HOH 14 253 253 HOH TIP C . R 3 HOH 15 254 254 HOH TIP C . R 3 HOH 16 264 264 HOH TIP C . R 3 HOH 17 274 274 HOH TIP C . R 3 HOH 18 281 281 HOH TIP C . R 3 HOH 19 291 291 HOH TIP C . R 3 HOH 20 300 300 HOH TIP C . R 3 HOH 21 315 315 HOH TIP C . R 3 HOH 22 344 344 HOH TIP C . R 3 HOH 23 366 366 HOH TIP C . S 3 HOH 1 10 10 HOH TIP D . S 3 HOH 2 57 57 HOH TIP D . S 3 HOH 3 58 58 HOH TIP D . S 3 HOH 4 59 59 HOH TIP D . S 3 HOH 5 60 60 HOH TIP D . S 3 HOH 6 61 61 HOH TIP D . S 3 HOH 7 64 64 HOH TIP D . S 3 HOH 8 65 65 HOH TIP D . S 3 HOH 9 68 68 HOH TIP D . S 3 HOH 10 69 69 HOH TIP D . S 3 HOH 11 73 73 HOH TIP D . S 3 HOH 12 75 75 HOH TIP D . S 3 HOH 13 121 121 HOH TIP D . S 3 HOH 14 136 136 HOH TIP D . S 3 HOH 15 137 137 HOH TIP D . S 3 HOH 16 153 153 HOH TIP D . S 3 HOH 17 154 154 HOH TIP D . S 3 HOH 18 156 156 HOH TIP D . S 3 HOH 19 159 159 HOH TIP D . S 3 HOH 20 160 160 HOH TIP D . S 3 HOH 21 165 165 HOH TIP D . S 3 HOH 22 166 166 HOH TIP D . S 3 HOH 23 167 167 HOH TIP D . S 3 HOH 24 184 184 HOH TIP D . S 3 HOH 25 189 189 HOH TIP D . S 3 HOH 26 199 199 HOH TIP D . S 3 HOH 27 201 201 HOH TIP D . S 3 HOH 28 209 209 HOH TIP D . S 3 HOH 29 210 210 HOH TIP D . S 3 HOH 30 215 215 HOH TIP D . S 3 HOH 31 229 229 HOH TIP D . S 3 HOH 32 261 261 HOH TIP D . S 3 HOH 33 289 289 HOH TIP D . S 3 HOH 34 295 295 HOH TIP D . S 3 HOH 35 316 316 HOH TIP D . S 3 HOH 36 341 341 HOH TIP D . S 3 HOH 37 377 377 HOH TIP D . S 3 HOH 38 393 393 HOH TIP D . T 3 HOH 1 31 31 HOH TIP E . T 3 HOH 2 39 39 HOH TIP E . T 3 HOH 3 81 81 HOH TIP E . T 3 HOH 4 82 82 HOH TIP E . T 3 HOH 5 83 83 HOH TIP E . T 3 HOH 6 85 85 HOH TIP E . T 3 HOH 7 86 86 HOH TIP E . T 3 HOH 8 87 87 HOH TIP E . T 3 HOH 9 88 88 HOH TIP E . T 3 HOH 10 89 89 HOH TIP E . T 3 HOH 11 92 92 HOH TIP E . T 3 HOH 12 93 93 HOH TIP E . T 3 HOH 13 94 94 HOH TIP E . T 3 HOH 14 95 95 HOH TIP E . T 3 HOH 15 96 96 HOH TIP E . T 3 HOH 16 97 97 HOH TIP E . T 3 HOH 17 98 98 HOH TIP E . T 3 HOH 18 100 100 HOH TIP E . T 3 HOH 19 101 101 HOH TIP E . T 3 HOH 20 128 128 HOH TIP E . T 3 HOH 21 129 129 HOH TIP E . T 3 HOH 22 131 131 HOH TIP E . T 3 HOH 23 138 138 HOH TIP E . T 3 HOH 24 141 141 HOH TIP E . T 3 HOH 25 142 142 HOH TIP E . T 3 HOH 26 146 146 HOH TIP E . T 3 HOH 27 152 152 HOH TIP E . T 3 HOH 28 158 158 HOH TIP E . T 3 HOH 29 169 169 HOH TIP E . T 3 HOH 30 170 170 HOH TIP E . T 3 HOH 31 173 173 HOH TIP E . T 3 HOH 32 177 177 HOH TIP E . T 3 HOH 33 185 185 HOH TIP E . T 3 HOH 34 192 192 HOH TIP E . T 3 HOH 35 204 204 HOH TIP E . T 3 HOH 36 205 205 HOH TIP E . T 3 HOH 37 211 211 HOH TIP E . T 3 HOH 38 212 212 HOH TIP E . T 3 HOH 39 217 217 HOH TIP E . T 3 HOH 40 218 218 HOH TIP E . T 3 HOH 41 221 221 HOH TIP E . T 3 HOH 42 222 222 HOH TIP E . T 3 HOH 43 230 230 HOH TIP E . T 3 HOH 44 232 232 HOH TIP E . T 3 HOH 45 234 234 HOH TIP E . T 3 HOH 46 237 237 HOH TIP E . T 3 HOH 47 239 239 HOH TIP E . T 3 HOH 48 245 245 HOH TIP E . T 3 HOH 49 246 246 HOH TIP E . T 3 HOH 50 247 247 HOH TIP E . T 3 HOH 51 256 256 HOH TIP E . T 3 HOH 52 258 258 HOH TIP E . T 3 HOH 53 265 265 HOH TIP E . T 3 HOH 54 269 269 HOH TIP E . T 3 HOH 55 275 275 HOH TIP E . T 3 HOH 56 278 278 HOH TIP E . T 3 HOH 57 283 283 HOH TIP E . T 3 HOH 58 285 285 HOH TIP E . T 3 HOH 59 292 292 HOH TIP E . T 3 HOH 60 293 293 HOH TIP E . T 3 HOH 61 296 296 HOH TIP E . T 3 HOH 62 301 301 HOH TIP E . T 3 HOH 63 302 302 HOH TIP E . T 3 HOH 64 308 308 HOH TIP E . T 3 HOH 65 309 309 HOH TIP E . T 3 HOH 66 310 310 HOH TIP E . T 3 HOH 67 321 321 HOH TIP E . T 3 HOH 68 322 322 HOH TIP E . T 3 HOH 69 325 325 HOH TIP E . T 3 HOH 70 329 329 HOH TIP E . T 3 HOH 71 332 332 HOH TIP E . T 3 HOH 72 339 339 HOH TIP E . T 3 HOH 73 340 340 HOH TIP E . T 3 HOH 74 342 342 HOH TIP E . T 3 HOH 75 345 345 HOH TIP E . T 3 HOH 76 347 347 HOH TIP E . T 3 HOH 77 350 350 HOH TIP E . T 3 HOH 78 351 351 HOH TIP E . T 3 HOH 79 352 352 HOH TIP E . T 3 HOH 80 353 353 HOH TIP E . T 3 HOH 81 355 355 HOH TIP E . T 3 HOH 82 360 360 HOH TIP E . T 3 HOH 83 362 362 HOH TIP E . T 3 HOH 84 373 373 HOH TIP E . T 3 HOH 85 380 380 HOH TIP E . T 3 HOH 86 381 381 HOH TIP E . T 3 HOH 87 395 395 HOH TIP E . U 3 HOH 1 103 103 HOH TIP F . U 3 HOH 2 104 104 HOH TIP F . U 3 HOH 3 105 105 HOH TIP F . U 3 HOH 4 106 106 HOH TIP F . U 3 HOH 5 107 107 HOH TIP F . U 3 HOH 6 110 110 HOH TIP F . U 3 HOH 7 135 135 HOH TIP F . U 3 HOH 8 140 140 HOH TIP F . U 3 HOH 9 149 149 HOH TIP F . U 3 HOH 10 181 181 HOH TIP F . U 3 HOH 11 187 187 HOH TIP F . U 3 HOH 12 195 195 HOH TIP F . U 3 HOH 13 197 197 HOH TIP F . U 3 HOH 14 208 208 HOH TIP F . U 3 HOH 15 216 216 HOH TIP F . U 3 HOH 16 236 236 HOH TIP F . U 3 HOH 17 249 249 HOH TIP F . U 3 HOH 18 259 259 HOH TIP F . U 3 HOH 19 268 268 HOH TIP F . U 3 HOH 20 273 273 HOH TIP F . U 3 HOH 21 288 288 HOH TIP F . U 3 HOH 22 304 304 HOH TIP F . U 3 HOH 23 305 305 HOH TIP F . U 3 HOH 24 311 311 HOH TIP F . U 3 HOH 25 324 324 HOH TIP F . U 3 HOH 26 330 330 HOH TIP F . U 3 HOH 27 365 365 HOH TIP F . U 3 HOH 28 390 390 HOH TIP F . U 3 HOH 29 394 394 HOH TIP F . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal MOSFLM 'data reduction' . ? 1 SCALA 'data scaling' . ? 2 SOLVE phasing . ? 3 CNS refinement . ? 4 CCP4 'data scaling' '(SCALA)' ? 5 # _cell.entry_id 1UB8 _cell.length_a 48.675 _cell.length_b 48.856 _cell.length_c 63.761 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1UB8 _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 # _exptl.entry_id 1UB8 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.21 _exptl_crystal.density_percent_sol 43.92 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6 _exptl_crystal_grow.pdbx_details ;sodium cacodylate, sodium chloride, potassium chloride, hexaamminecobalt(III) chloride, MEGA-10, 2-methyl-2,4-pentanediol, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K ; _exptl_crystal_grow.pdbx_pH_range . # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 'sodium cacodylate' ? ? ? 1 2 1 'sodium chloride' ? ? ? 1 3 1 'potassium chloride' ? ? ? 1 4 1 'hexaamminecobalt(III) chloride' ? ? ? 1 5 1 MEGA-10 ? ? ? 1 6 1 2-methyl-2,4-pentanediol ? ? ? 1 7 2 'sodium cacodylate' ? ? ? 1 8 2 'sodium chloride' ? ? ? 1 9 2 'potassium chloride' ? ? ? # _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 4' _diffrn_detector.pdbx_collection_date 2000-12-12 _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 MAD _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 BL-18B' _diffrn_source.pdbx_synchrotron_site 'Photon Factory' _diffrn_source.pdbx_synchrotron_beamline BL-18B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.0 # _reflns.entry_id 1UB8 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.d_resolution_high 1.6 _reflns.d_resolution_low 24 _reflns.number_all 20712 _reflns.number_obs 20709 _reflns.percent_possible_obs 100 _reflns.pdbx_Rmerge_I_obs 0.067 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 6.4 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.6 _reflns_shell.d_res_low 1.69 _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.299 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.2 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1UB8 _refine.ls_d_res_high 1.6 _refine.ls_d_res_low 24 _refine.pdbx_ls_sigma_F 3 _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all 20662 _refine.ls_number_reflns_obs 20173 _refine.ls_number_reflns_R_free 1999 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_work 0.1942 _refine.ls_R_factor_R_free 0.2315 _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_starting_model ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_stereochemistry_target_values ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.details ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 858 _refine_hist.pdbx_number_atoms_ligand 63 _refine_hist.number_atoms_solvent 304 _refine_hist.number_atoms_total 1225 _refine_hist.d_res_high 1.6 _refine_hist.d_res_low 24 # 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_angle_deg 0.7 ? ? ? 'X-RAY DIFFRACTION' ? c_bond_d 0.003 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 1.6 _refine_ls_shell.d_res_low 1.66 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.2413 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.2721 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 195 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _database_PDB_matrix.entry_id 1UB8 _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 1UB8 _struct.title 'Crystal structure of d(GCGAAGC), bending duplex with a bulge-in residue' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1UB8 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA, sheared G:A pair, bulge-in duplex, G:AxA:G crossing' # 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 1 ? D N N 1 ? E N N 1 ? F N N 1 ? G N N 2 ? H N N 2 ? I N N 2 ? J N N 2 ? K N N 2 ? L N N 2 ? M N N 2 ? N N N 2 ? O N N 2 ? P N N 3 ? Q N N 3 ? R N N 3 ? S N N 3 ? T N N 3 ? U N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1UB8 _struct_ref.pdbx_db_accession 1UB8 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 1UB8 A 1 ? 7 ? 1UB8 1 ? 7 ? 1 7 2 1 1UB8 B 1 ? 7 ? 1UB8 1 ? 7 ? 1 7 3 1 1UB8 C 1 ? 7 ? 1UB8 1 ? 7 ? 1 7 4 1 1UB8 D 1 ? 7 ? 1UB8 1 ? 7 ? 1 7 5 1 1UB8 E 1 ? 7 ? 1UB8 1 ? 7 ? 1 7 6 1 1UB8 F 1 ? 7 ? 1UB8 1 ? 7 ? 1 7 # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? dimeric 2 2 author_defined_assembly ? dimeric 2 3 author_defined_assembly ? dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,G,H,I,P,Q 2 1 C,D,J,K,L,M,R,S 3 1 E,F,N,O,T,U # _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 # loop_ _struct_biol.id _struct_biol.pdbx_parent_biol_id _struct_biol.details 1 ? ? 2 ? ? 3 ? ? # 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 DG 1 N1 ? ? ? 1_555 B DC 7 N3 ? ? A DG 1 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 7 O2 ? ? A DG 1 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 7 N4 ? ? A DG 1 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 2 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 2 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 2 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DA 4 N7 ? ? A DG 3 B DA 4 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog8 hydrog ? ? A DG 3 N3 ? ? ? 1_555 B DA 4 N6 ? ? A DG 3 B DA 4 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog9 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DG 3 N3 ? ? A DA 4 B DG 3 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog10 hydrog ? ? A DA 4 N7 ? ? ? 1_555 B DG 3 N2 ? ? A DA 4 B DG 3 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog11 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 6 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 6 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 6 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 7 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 7 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 7 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 7 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 7 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 7 B DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? C DG 1 N1 ? ? ? 1_555 D DC 7 N3 ? ? C DG 1 D DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? C DG 1 N2 ? ? ? 1_555 D DC 7 O2 ? ? C DG 1 D DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? C DG 1 O6 ? ? ? 1_555 D DC 7 N4 ? ? C DG 1 D DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? C DC 2 N3 ? ? ? 1_555 D DG 6 N1 ? ? C DC 2 D DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? C DC 2 N4 ? ? ? 1_555 D DG 6 O6 ? ? C DC 2 D DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? C DC 2 O2 ? ? ? 1_555 D DG 6 N2 ? ? C DC 2 D DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? C DG 3 N2 ? ? ? 1_555 D DA 4 N7 ? ? C DG 3 D DA 4 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog24 hydrog ? ? C DG 3 N3 ? ? ? 1_555 D DA 4 N6 ? ? C DG 3 D DA 4 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog25 hydrog ? ? C DA 4 N6 ? ? ? 1_555 D DG 3 N3 ? ? C DA 4 D DG 3 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog26 hydrog ? ? C DA 4 N7 ? ? ? 1_555 D DG 3 N2 ? ? C DA 4 D DG 3 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog27 hydrog ? ? C DG 6 N1 ? ? ? 1_555 D DC 2 N3 ? ? C DG 6 D DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? C DG 6 N2 ? ? ? 1_555 D DC 2 O2 ? ? C DG 6 D DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? C DG 6 O6 ? ? ? 1_555 D DC 2 N4 ? ? C DG 6 D DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? C DC 7 N3 ? ? ? 1_555 D DG 1 N1 ? ? C DC 7 D DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? C DC 7 N4 ? ? ? 1_555 D DG 1 O6 ? ? C DC 7 D DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? C DC 7 O2 ? ? ? 1_555 D DG 1 N2 ? ? C DC 7 D DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? E DG 1 N1 ? ? ? 1_555 F DC 7 N3 ? ? E DG 1 F DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? E DG 1 N2 ? ? ? 1_555 F DC 7 O2 ? ? E DG 1 F DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? E DG 1 O6 ? ? ? 1_555 F DC 7 N4 ? ? E DG 1 F DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? E DC 2 N3 ? ? ? 1_555 F DG 6 N1 ? ? E DC 2 F DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog37 hydrog ? ? E DC 2 N4 ? ? ? 1_555 F DG 6 O6 ? ? E DC 2 F DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog38 hydrog ? ? E DC 2 O2 ? ? ? 1_555 F DG 6 N2 ? ? E DC 2 F DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog39 hydrog ? ? E DG 3 N2 ? ? ? 1_555 F DA 4 N7 ? ? E DG 3 F DA 4 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog40 hydrog ? ? E DG 3 N3 ? ? ? 1_555 F DA 4 N6 ? ? E DG 3 F DA 4 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog41 hydrog ? ? E DA 4 N6 ? ? ? 1_555 F DG 3 N3 ? ? E DA 4 F DG 3 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog42 hydrog ? ? E DA 4 N7 ? ? ? 1_555 F DG 3 N2 ? ? E DA 4 F DG 3 1_555 ? ? ? ? ? ? TYPE_11_PAIR ? ? ? hydrog43 hydrog ? ? E DG 6 N1 ? ? ? 1_555 F DC 2 N3 ? ? E DG 6 F DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog44 hydrog ? ? E DG 6 N2 ? ? ? 1_555 F DC 2 O2 ? ? E DG 6 F DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog45 hydrog ? ? E DG 6 O6 ? ? ? 1_555 F DC 2 N4 ? ? E DG 6 F DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog46 hydrog ? ? E DC 7 N3 ? ? ? 1_555 F DG 1 N1 ? ? E DC 7 F DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog47 hydrog ? ? E DC 7 N4 ? ? ? 1_555 F DG 1 O6 ? ? E DC 7 F DG 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog48 hydrog ? ? E DC 7 O2 ? ? ? 1_555 F DG 1 N2 ? ? E DC 7 F DG 1 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 D NCO 400 ? 8 'BINDING SITE FOR RESIDUE NCO D 400' AC2 Software A NCO 1401 ? 8 'BINDING SITE FOR RESIDUE NCO A 1401' AC3 Software D NCO 402 ? 12 'BINDING SITE FOR RESIDUE NCO D 402' AC4 Software E NCO 403 ? 11 'BINDING SITE FOR RESIDUE NCO E 403' AC5 Software B NCO 404 ? 11 'BINDING SITE FOR RESIDUE NCO B 404' AC6 Software F NCO 405 ? 7 'BINDING SITE FOR RESIDUE NCO F 405' AC7 Software B NCO 406 ? 7 'BINDING SITE FOR RESIDUE NCO B 406' AC8 Software C NCO 407 ? 5 'BINDING SITE FOR RESIDUE NCO C 407' AC9 Software C NCO 408 ? 5 'BINDING SITE FOR RESIDUE NCO C 408' # 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 8 DA A 5 ? DA A 5 . ? 4_555 ? 2 AC1 8 DG A 6 ? DG A 6 . ? 4_555 ? 3 AC1 8 HOH P . ? HOH A 1430 . ? 4_555 ? 4 AC1 8 HOH Q . ? HOH B 11 . ? 4_555 ? 5 AC1 8 HOH Q . ? HOH B 37 . ? 4_555 ? 6 AC1 8 DC D 7 ? DC D 7 . ? 4_555 ? 7 AC1 8 HOH S . ? HOH D 10 . ? 4_555 ? 8 AC1 8 HOH S . ? HOH D 393 . ? 4_555 ? 9 AC2 8 DC A 2 ? DC A 2 . ? 1_555 ? 10 AC2 8 DG A 3 ? DG A 3 . ? 1_555 ? 11 AC2 8 HOH P . ? HOH A 1405 . ? 1_555 ? 12 AC2 8 HOH P . ? HOH A 1433 . ? 1_555 ? 13 AC2 8 HOH P . ? HOH A 1443 . ? 1_555 ? 14 AC2 8 HOH P . ? HOH A 1456 . ? 1_555 ? 15 AC2 8 DG B 3 ? DG B 3 . ? 1_555 ? 16 AC2 8 DA D 5 ? DA D 5 . ? 1_555 ? 17 AC3 12 DG A 3 ? DG A 3 . ? 1_555 ? 18 AC3 12 DG C 1 ? DG C 1 . ? 1_555 ? 19 AC3 12 DC C 2 ? DC C 2 . ? 1_555 ? 20 AC3 12 DA D 5 ? DA D 5 . ? 1_555 ? 21 AC3 12 DG D 6 ? DG D 6 . ? 1_555 ? 22 AC3 12 DC D 7 ? DC D 7 . ? 1_555 ? 23 AC3 12 HOH S . ? HOH D 59 . ? 1_555 ? 24 AC3 12 HOH S . ? HOH D 65 . ? 1_555 ? 25 AC3 12 HOH S . ? HOH D 68 . ? 1_555 ? 26 AC3 12 HOH S . ? HOH D 159 . ? 4_455 ? 27 AC3 12 HOH S . ? HOH D 209 . ? 1_555 ? 28 AC3 12 HOH S . ? HOH D 377 . ? 1_555 ? 29 AC4 11 DG B 3 ? DG B 3 . ? 1_555 ? 30 AC4 11 HOH Q . ? HOH B 224 . ? 1_555 ? 31 AC4 11 DA E 5 ? DA E 5 . ? 1_555 ? 32 AC4 11 DG E 6 ? DG E 6 . ? 1_555 ? 33 AC4 11 DC E 7 ? DC E 7 . ? 1_555 ? 34 AC4 11 HOH T . ? HOH E 39 . ? 1_555 ? 35 AC4 11 HOH T . ? HOH E 87 . ? 1_555 ? 36 AC4 11 HOH T . ? HOH E 93 . ? 1_555 ? 37 AC4 11 HOH T . ? HOH E 94 . ? 1_555 ? 38 AC4 11 DG F 1 ? DG F 1 . ? 1_555 ? 39 AC4 11 HOH U . ? HOH F 110 . ? 1_555 ? 40 AC5 11 HOH P . ? HOH A 1406 . ? 1_555 ? 41 AC5 11 DA B 5 ? DA B 5 . ? 1_555 ? 42 AC5 11 DG B 6 ? DG B 6 . ? 1_555 ? 43 AC5 11 DC B 7 ? DC B 7 . ? 1_555 ? 44 AC5 11 HOH Q . ? HOH B 27 . ? 1_555 ? 45 AC5 11 HOH Q . ? HOH B 30 . ? 3_445 ? 46 AC5 11 HOH Q . ? HOH B 36 . ? 1_555 ? 47 AC5 11 HOH Q . ? HOH B 157 . ? 1_555 ? 48 AC5 11 DC E 7 ? DC E 7 . ? 1_555 ? 49 AC5 11 HOH T . ? HOH E 89 . ? 4_456 ? 50 AC5 11 HOH T . ? HOH E 129 . ? 4_456 ? 51 AC6 7 DG E 1 ? DG E 1 . ? 4_456 ? 52 AC6 7 HOH T . ? HOH E 395 . ? 4_456 ? 53 AC6 7 DA F 5 ? DA F 5 . ? 4_456 ? 54 AC6 7 DG F 6 ? DG F 6 . ? 4_456 ? 55 AC6 7 DC F 7 ? DC F 7 . ? 4_456 ? 56 AC6 7 HOH U . ? HOH F 187 . ? 1_555 ? 57 AC6 7 HOH U . ? HOH F 268 . ? 4_456 ? 58 AC7 7 DA B 5 ? DA B 5 . ? 1_555 ? 59 AC7 7 HOH Q . ? HOH B 303 . ? 1_555 ? 60 AC7 7 DC E 2 ? DC E 2 . ? 4_456 ? 61 AC7 7 DG E 3 ? DG E 3 . ? 4_456 ? 62 AC7 7 HOH T . ? HOH E 234 . ? 4_456 ? 63 AC7 7 DG F 3 ? DG F 3 . ? 4_456 ? 64 AC7 7 HOH U . ? HOH F 394 . ? 4_456 ? 65 AC8 5 HOH P . ? HOH A 1465 . ? 4_555 ? 66 AC8 5 DA C 5 ? DA C 5 . ? 1_555 ? 67 AC8 5 DG C 6 ? DG C 6 . ? 1_555 ? 68 AC8 5 HOH R . ? HOH C 174 . ? 1_555 ? 69 AC8 5 DG D 1 ? DG D 1 . ? 1_555 ? 70 AC9 5 DA A 5 ? DA A 5 . ? 4_555 ? 71 AC9 5 DC C 2 ? DC C 2 . ? 1_555 ? 72 AC9 5 DG C 3 ? DG C 3 . ? 1_555 ? 73 AC9 5 HOH R . ? HOH C 291 . ? 1_555 ? 74 AC9 5 DG D 3 ? DG D 3 . ? 1_555 ? # 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 DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 HOH O O N N 108 HOH H1 H N N 109 HOH H2 H N N 110 NCO CO CO N N 111 NCO N1 N N N 112 NCO N2 N N N 113 NCO N3 N N N 114 NCO N4 N N N 115 NCO N5 N N N 116 NCO N6 N N N 117 NCO HN11 H N N 118 NCO HN12 H N N 119 NCO HN13 H N N 120 NCO HN21 H N N 121 NCO HN22 H N N 122 NCO HN23 H N N 123 NCO HN31 H N N 124 NCO HN32 H N N 125 NCO HN33 H N N 126 NCO HN41 H N N 127 NCO HN42 H N N 128 NCO HN43 H N N 129 NCO HN51 H N N 130 NCO HN52 H N N 131 NCO HN53 H N N 132 NCO HN61 H N N 133 NCO HN62 H N N 134 NCO HN63 H N N 135 # 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 DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 HOH O H1 sing N N 113 HOH O H2 sing N N 114 NCO CO N1 sing N N 115 NCO CO N2 sing N N 116 NCO CO N3 sing N N 117 NCO CO N4 sing N N 118 NCO CO N5 sing N N 119 NCO CO N6 sing N N 120 NCO N1 HN11 sing N N 121 NCO N1 HN12 sing N N 122 NCO N1 HN13 sing N N 123 NCO N2 HN21 sing N N 124 NCO N2 HN22 sing N N 125 NCO N2 HN23 sing N N 126 NCO N3 HN31 sing N N 127 NCO N3 HN32 sing N N 128 NCO N3 HN33 sing N N 129 NCO N4 HN41 sing N N 130 NCO N4 HN42 sing N N 131 NCO N4 HN43 sing N N 132 NCO N5 HN51 sing N N 133 NCO N5 HN52 sing N N 134 NCO N5 HN53 sing N N 135 NCO N6 HN61 sing N N 136 NCO N6 HN62 sing N N 137 NCO N6 HN63 sing N N 138 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1UB8 'double helix' 1UB8 'bulge 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 DG 1 1_555 B DC 7 1_555 -0.187 -0.073 0.201 6.944 -1.877 0.798 1 A_DG1:DC7_B A 1 ? B 7 ? 19 1 1 A DC 2 1_555 B DG 6 1_555 0.248 -0.161 -0.092 10.135 -2.960 -0.853 2 A_DC2:DG6_B A 2 ? B 6 ? 19 1 1 A DG 3 1_555 B DA 4 1_555 6.718 -4.335 0.368 33.617 -5.499 -0.837 3 A_DG3:DA4_B A 3 ? B 4 ? 11 9 1 A DA 4 1_555 B DG 3 1_555 -6.684 -4.230 0.120 -33.062 2.366 -2.400 4 A_DA4:DG3_B A 4 ? B 3 ? 11 9 1 A DG 6 1_555 B DC 2 1_555 -0.334 -0.072 -0.055 -12.160 -1.291 2.399 5 A_DG6:DC2_B A 6 ? B 2 ? 19 1 1 A DC 7 1_555 B DG 1 1_555 0.175 -0.069 0.231 -5.782 -0.772 1.344 6 A_DC7:DG1_B A 7 ? B 1 ? 19 1 1 C DG 1 1_555 D DC 7 1_555 -0.170 -0.113 -0.095 -4.454 -0.568 -4.329 7 C_DG1:DC7_D C 1 ? D 7 ? 19 1 1 C DC 2 1_555 D DG 6 1_555 0.345 -0.136 -0.190 14.527 -3.406 1.076 8 C_DC2:DG6_D C 2 ? D 6 ? 19 1 1 C DG 3 1_555 D DA 4 1_555 6.783 -4.515 0.358 37.568 -2.464 -3.060 9 C_DG3:DA4_D C 3 ? D 4 ? 11 10 1 C DA 4 1_555 D DG 3 1_555 -6.586 -4.400 0.204 -38.518 -0.859 -1.251 10 C_DA4:DG3_D C 4 ? D 3 ? 11 9 1 C DG 6 1_555 D DC 2 1_555 -0.319 -0.033 -0.064 -16.140 -0.855 4.541 11 C_DG6:DC2_D C 6 ? D 2 ? 19 1 1 C DC 7 1_555 D DG 1 1_555 0.314 -0.092 0.324 -8.785 -0.255 0.688 12 C_DC7:DG1_D C 7 ? D 1 ? 19 1 1 E DG 1 1_555 F DC 7 1_555 -0.146 -0.108 0.051 -3.739 -2.019 -0.242 13 E_DG1:DC7_F E 1 ? F 7 ? 19 1 1 E DC 2 1_555 F DG 6 1_555 0.401 -0.150 0.026 10.980 -0.978 0.856 14 E_DC2:DG6_F E 2 ? F 6 ? 19 1 1 E DG 3 1_555 F DA 4 1_555 6.722 -4.303 0.246 36.796 -0.441 -1.142 15 E_DG3:DA4_F E 3 ? F 4 ? 11 9 1 E DA 4 1_555 F DG 3 1_555 -6.713 -4.267 0.280 -37.180 -1.343 -2.592 16 E_DA4:DG3_F E 4 ? F 3 ? 11 9 1 E DG 6 1_555 F DC 2 1_555 -0.224 -0.112 0.218 -5.788 -2.792 0.403 17 E_DG6:DC2_F E 6 ? F 2 ? 19 1 1 E DC 7 1_555 F DG 1 1_555 0.432 -0.148 0.316 -5.913 0.585 1.774 18 E_DC7:DG1_F E 7 ? F 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 DG 1 1_555 B DC 7 1_555 A DC 2 1_555 B DG 6 1_555 0.451 -0.319 3.291 2.331 -0.907 30.650 -0.422 -0.388 3.323 -1.713 -4.401 30.750 1 AA_DG1DC2:DG6DC7_BB A 1 ? B 7 ? A 2 ? B 6 ? 1 A DC 2 1_555 B DG 6 1_555 A DG 3 1_555 B DA 4 1_555 1.017 1.928 5.210 -10.479 25.758 80.921 0.424 -1.164 5.395 19.342 7.868 84.782 2 AA_DC2DG3:DA4DG6_BB A 2 ? B 6 ? A 3 ? B 4 ? 1 A DG 3 1_555 B DA 4 1_555 A DA 4 1_555 B DG 3 1_555 -0.107 -0.537 4.735 -0.566 -0.310 -6.731 6.383 -4.249 4.680 2.634 -4.804 -6.761 3 AA_DG3DA4:DG3DA4_BB A 3 ? B 4 ? A 4 ? B 3 ? 1 A DA 4 1_555 B DG 3 1_555 A DG 6 1_555 B DC 2 1_555 -0.904 1.780 5.192 12.832 22.261 70.581 0.321 1.408 5.280 18.663 -10.758 74.538 4 AA_DA4DG6:DC2DG3_BB A 4 ? B 3 ? A 6 ? B 2 ? 1 A DG 6 1_555 B DC 2 1_555 A DC 7 1_555 B DG 1 1_555 -0.428 -0.232 3.292 -1.943 -2.305 31.385 0.008 0.422 3.320 -4.249 3.582 31.526 5 AA_DG6DC7:DG1DC2_BB A 6 ? B 2 ? A 7 ? B 1 ? 1 C DG 1 1_555 D DC 7 1_555 C DC 2 1_555 D DG 6 1_555 0.375 0.146 2.946 0.477 2.654 27.688 -0.271 -0.676 2.952 5.529 -0.994 27.817 6 CC_DG1DC2:DG6DC7_DD C 1 ? D 7 ? C 2 ? D 6 ? 1 C DC 2 1_555 D DG 6 1_555 C DG 3 1_555 D DA 4 1_555 1.063 1.284 5.153 -14.001 27.057 74.331 -0.193 -1.450 5.083 21.549 11.150 79.490 7 CC_DC2DG3:DA4DG6_DD C 2 ? D 6 ? C 3 ? D 4 ? 1 C DG 3 1_555 D DA 4 1_555 C DA 4 1_555 D DG 3 1_555 0.101 -1.029 4.975 0.657 1.567 -5.306 -4.209 7.243 5.015 -16.381 6.870 -5.571 8 CC_DG3DA4:DG3DA4_DD C 3 ? D 4 ? C 4 ? D 3 ? 1 C DA 4 1_555 D DG 3 1_555 C DG 6 1_555 D DC 2 1_555 -1.056 1.531 5.136 13.176 23.561 75.486 0.162 1.405 5.155 18.688 -10.450 79.486 9 CC_DA4DG6:DC2DG3_DD C 4 ? D 3 ? C 6 ? D 2 ? 1 C DG 6 1_555 D DC 2 1_555 C DC 7 1_555 D DG 1 1_555 -0.624 0.054 3.234 -3.501 -1.144 35.279 0.256 0.513 3.276 -1.881 5.756 35.465 10 CC_DG6DC7:DG1DC2_DD C 6 ? D 2 ? C 7 ? D 1 ? 1 E DG 1 1_555 F DC 7 1_555 E DC 2 1_555 F DG 6 1_555 0.421 -0.022 3.010 -0.044 1.610 29.441 -0.359 -0.836 3.004 3.164 0.086 29.484 11 EE_DG1DC2:DG6DC7_FF E 1 ? F 7 ? E 2 ? F 6 ? 1 E DC 2 1_555 F DG 6 1_555 E DG 3 1_555 F DA 4 1_555 1.198 1.446 5.058 -13.181 22.623 74.380 0.137 -1.538 5.031 18.182 10.593 78.221 12 EE_DC2DG3:DA4DG6_FF E 2 ? F 6 ? E 3 ? F 4 ? 1 E DG 3 1_555 F DA 4 1_555 E DA 4 1_555 F DG 3 1_555 -0.178 -0.792 4.948 -0.296 0.773 -3.036 -8.125 -11.882 4.951 -14.250 -5.460 -3.147 13 EE_DG3DA4:DG3DA4_FF E 3 ? F 4 ? E 4 ? F 3 ? 1 E DA 4 1_555 F DG 3 1_555 E DG 6 1_555 F DC 2 1_555 -1.064 1.765 4.901 14.620 22.118 74.355 0.435 1.479 4.947 17.768 -11.745 78.293 14 EE_DA4DG6:DC2DG3_FF E 4 ? F 3 ? E 6 ? F 2 ? 1 E DG 6 1_555 F DC 2 1_555 E DC 7 1_555 F DG 1 1_555 0.314 -0.351 3.414 -0.694 -3.232 32.499 -0.038 -0.685 3.425 -5.756 1.236 32.662 15 EE_DG6DC7:DG1DC2_FF E 6 ? F 2 ? E 7 ? F 1 ? # _atom_sites.entry_id 1UB8 _atom_sites.fract_transf_matrix[1][1] 0.020544 _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] 0.020468 _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] 0.015684 _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 CO N O P # loop_