data_6YNB # _model_server_result.job_id A9-dE4NGTBaJS0TzpFDi5g _model_server_result.datetime_utc '2024-10-13 02:26:28' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 6ynb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 6YNB # _exptl.entry_id 6YNB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 78.133 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIMETHYL SULFOXIDE' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 6YNB _cell.length_a 58.071 _cell.length_b 72.343 _cell.length_c 108.76 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YNB _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _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 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_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_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A C GLY 12 A GLY 9 1_555 A N SEP 13 A SEP 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C SEP 13 A SEP 10 1_555 A N GLU 14 A GLU 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale3 A C PHE 141 A PHE 138 1_555 A N SEP 142 A SEP 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 A C SEP 142 A SEP 139 1_555 A N GLU 143 A GLU 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale5 A C TRP 199 A TRP 196 1_555 A N TPO 200 A TPO 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale6 A C TPO 200 A TPO 197 1_555 A N LEU 201 A LEU 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale7 A C VAL 340 A VAL 337 1_555 A N SEP 341 A SEP 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 A C SEP 341 A SEP 338 1_555 A N ILE 342 A ILE 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? # _chem_comp.formula 'C2 H6 O S' _chem_comp.formula_weight 78.133 _chem_comp.id DMS _chem_comp.mon_nstd_flag . _chem_comp.name 'DIMETHYL SULFOXIDE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag S O DMS doub 83 n n S C1 DMS sing 84 n n S C2 DMS sing 85 n n C1 H11 DMS sing 86 n n C1 H12 DMS sing 87 n n C1 H13 DMS sing 88 n n C2 H21 DMS sing 89 n n C2 H22 DMS sing 90 n n C2 H23 DMS sing 91 n n # _atom_sites.entry_id 6YNB _atom_sites.fract_transf_matrix[1][1] 0.01722 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013823 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.009195 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code C 3 IQU A 1 401 1 IQU C05 . D 4 DMS A 1 402 1 DMS DMS . E 5 HOH A 1 501 307 HOH HOH . E 5 HOH A 2 502 229 HOH HOH . E 5 HOH A 3 503 206 HOH HOH . E 5 HOH A 4 504 188 HOH HOH . E 5 HOH A 5 505 111 HOH HOH . E 5 HOH A 6 506 275 HOH HOH . E 5 HOH A 7 507 156 HOH HOH . E 5 HOH A 8 508 167 HOH HOH . E 5 HOH A 9 509 319 HOH HOH . E 5 HOH A 10 510 177 HOH HOH . E 5 HOH A 11 511 171 HOH HOH . E 5 HOH A 12 512 273 HOH HOH . E 5 HOH A 13 513 20 HOH HOH . E 5 HOH A 14 514 144 HOH HOH . E 5 HOH A 15 515 55 HOH HOH . E 5 HOH A 16 516 158 HOH HOH . E 5 HOH A 17 517 305 HOH HOH . E 5 HOH A 18 518 130 HOH HOH . E 5 HOH A 19 519 312 HOH HOH . E 5 HOH A 20 520 106 HOH HOH . E 5 HOH A 21 521 309 HOH HOH . E 5 HOH A 22 522 150 HOH HOH . E 5 HOH A 23 523 242 HOH HOH . E 5 HOH A 24 524 27 HOH HOH . E 5 HOH A 25 525 100 HOH HOH . E 5 HOH A 26 526 209 HOH HOH . E 5 HOH A 27 527 227 HOH HOH . E 5 HOH A 28 528 170 HOH HOH . E 5 HOH A 29 529 217 HOH HOH . E 5 HOH A 30 530 326 HOH HOH . E 5 HOH A 31 531 134 HOH HOH . E 5 HOH A 32 532 138 HOH HOH . E 5 HOH A 33 533 10 HOH HOH . E 5 HOH A 34 534 214 HOH HOH . E 5 HOH A 35 535 317 HOH HOH . E 5 HOH A 36 536 29 HOH HOH . E 5 HOH A 37 537 126 HOH HOH . E 5 HOH A 38 538 137 HOH HOH . E 5 HOH A 39 539 198 HOH HOH . E 5 HOH A 40 540 224 HOH HOH . E 5 HOH A 41 541 129 HOH HOH . E 5 HOH A 42 542 316 HOH HOH . E 5 HOH A 43 543 99 HOH HOH . E 5 HOH A 44 544 287 HOH HOH . E 5 HOH A 45 545 51 HOH HOH . E 5 HOH A 46 546 96 HOH HOH . E 5 HOH A 47 547 18 HOH HOH . E 5 HOH A 48 548 203 HOH HOH . E 5 HOH A 49 549 255 HOH HOH . E 5 HOH A 50 550 175 HOH HOH . E 5 HOH A 51 551 35 HOH HOH . E 5 HOH A 52 552 236 HOH HOH . E 5 HOH A 53 553 89 HOH HOH . E 5 HOH A 54 554 98 HOH HOH . E 5 HOH A 55 555 44 HOH HOH . E 5 HOH A 56 556 127 HOH HOH . E 5 HOH A 57 557 187 HOH HOH . E 5 HOH A 58 558 36 HOH HOH . E 5 HOH A 59 559 228 HOH HOH . E 5 HOH A 60 560 21 HOH HOH . E 5 HOH A 61 561 234 HOH HOH . E 5 HOH A 62 562 143 HOH HOH . E 5 HOH A 63 563 306 HOH HOH . E 5 HOH A 64 564 153 HOH HOH . E 5 HOH A 65 565 163 HOH HOH . E 5 HOH A 66 566 5 HOH HOH . E 5 HOH A 67 567 107 HOH HOH . E 5 HOH A 68 568 208 HOH HOH . E 5 HOH A 69 569 14 HOH HOH . E 5 HOH A 70 570 149 HOH HOH . E 5 HOH A 71 571 103 HOH HOH . E 5 HOH A 72 572 118 HOH HOH . E 5 HOH A 73 573 162 HOH HOH . E 5 HOH A 74 574 101 HOH HOH . E 5 HOH A 75 575 94 HOH HOH . E 5 HOH A 76 576 7 HOH HOH . E 5 HOH A 77 577 104 HOH HOH . E 5 HOH A 78 578 202 HOH HOH . E 5 HOH A 79 579 48 HOH HOH . E 5 HOH A 80 580 46 HOH HOH . E 5 HOH A 81 581 45 HOH HOH . E 5 HOH A 82 582 31 HOH HOH . E 5 HOH A 83 583 141 HOH HOH . E 5 HOH A 84 584 301 HOH HOH . E 5 HOH A 85 585 122 HOH HOH . E 5 HOH A 86 586 302 HOH HOH . E 5 HOH A 87 587 244 HOH HOH . E 5 HOH A 88 588 97 HOH HOH . E 5 HOH A 89 589 32 HOH HOH . E 5 HOH A 90 590 15 HOH HOH . E 5 HOH A 91 591 92 HOH HOH . E 5 HOH A 92 592 240 HOH HOH . E 5 HOH A 93 593 4 HOH HOH . E 5 HOH A 94 594 220 HOH HOH . E 5 HOH A 95 595 183 HOH HOH . E 5 HOH A 96 596 181 HOH HOH . E 5 HOH A 97 597 269 HOH HOH . E 5 HOH A 98 598 19 HOH HOH . E 5 HOH A 99 599 254 HOH HOH . E 5 HOH A 100 600 77 HOH HOH . E 5 HOH A 101 601 57 HOH HOH . E 5 HOH A 102 602 282 HOH HOH . E 5 HOH A 103 603 161 HOH HOH . E 5 HOH A 104 604 125 HOH HOH . E 5 HOH A 105 605 133 HOH HOH . E 5 HOH A 106 606 30 HOH HOH . E 5 HOH A 107 607 142 HOH HOH . E 5 HOH A 108 608 132 HOH HOH . E 5 HOH A 109 609 116 HOH HOH . E 5 HOH A 110 610 241 HOH HOH . E 5 HOH A 111 611 151 HOH HOH . E 5 HOH A 112 612 109 HOH HOH . E 5 HOH A 113 613 205 HOH HOH . E 5 HOH A 114 614 136 HOH HOH . E 5 HOH A 115 615 28 HOH HOH . E 5 HOH A 116 616 191 HOH HOH . E 5 HOH A 117 617 271 HOH HOH . E 5 HOH A 118 618 323 HOH HOH . E 5 HOH A 119 619 75 HOH HOH . E 5 HOH A 120 620 178 HOH HOH . E 5 HOH A 121 621 292 HOH HOH . E 5 HOH A 122 622 80 HOH HOH . E 5 HOH A 123 623 124 HOH HOH . E 5 HOH A 124 624 74 HOH HOH . E 5 HOH A 125 625 64 HOH HOH . E 5 HOH A 126 626 190 HOH HOH . E 5 HOH A 127 627 128 HOH HOH . E 5 HOH A 128 628 71 HOH HOH . E 5 HOH A 129 629 285 HOH HOH . E 5 HOH A 130 630 90 HOH HOH . E 5 HOH A 131 631 238 HOH HOH . E 5 HOH A 132 632 160 HOH HOH . E 5 HOH A 133 633 192 HOH HOH . E 5 HOH A 134 634 182 HOH HOH . E 5 HOH A 135 635 300 HOH HOH . E 5 HOH A 136 636 119 HOH HOH . E 5 HOH A 137 637 283 HOH HOH . E 5 HOH A 138 638 115 HOH HOH . E 5 HOH A 139 639 40 HOH HOH . E 5 HOH A 140 640 286 HOH HOH . E 5 HOH A 141 641 324 HOH HOH . E 5 HOH A 142 642 184 HOH HOH . E 5 HOH A 143 643 179 HOH HOH . E 5 HOH A 144 644 193 HOH HOH . E 5 HOH A 145 645 267 HOH HOH . E 5 HOH A 146 646 159 HOH HOH . E 5 HOH A 147 647 210 HOH HOH . E 5 HOH A 148 648 294 HOH HOH . E 5 HOH A 149 649 250 HOH HOH . E 5 HOH A 150 650 117 HOH HOH . E 5 HOH A 151 651 95 HOH HOH . E 5 HOH A 152 652 131 HOH HOH . E 5 HOH A 153 653 73 HOH HOH . E 5 HOH A 154 654 87 HOH HOH . E 5 HOH A 155 655 13 HOH HOH . E 5 HOH A 156 656 197 HOH HOH . E 5 HOH A 157 657 270 HOH HOH . E 5 HOH A 158 658 189 HOH HOH . E 5 HOH A 159 659 252 HOH HOH . E 5 HOH A 160 660 145 HOH HOH . E 5 HOH A 161 661 147 HOH HOH . E 5 HOH A 162 662 185 HOH HOH . E 5 HOH A 163 663 102 HOH HOH . E 5 HOH A 164 664 42 HOH HOH . E 5 HOH A 165 665 154 HOH HOH . E 5 HOH A 166 666 232 HOH HOH . E 5 HOH A 167 667 231 HOH HOH . E 5 HOH A 168 668 110 HOH HOH . E 5 HOH A 169 669 34 HOH HOH . E 5 HOH A 170 670 172 HOH HOH . E 5 HOH A 171 671 180 HOH HOH . E 5 HOH A 172 672 53 HOH HOH . E 5 HOH A 173 673 230 HOH HOH . E 5 HOH A 174 674 33 HOH HOH . E 5 HOH A 175 675 315 HOH HOH . E 5 HOH A 176 676 50 HOH HOH . E 5 HOH A 177 677 288 HOH HOH . E 5 HOH A 178 678 281 HOH HOH . E 5 HOH A 179 679 245 HOH HOH . E 5 HOH A 180 680 194 HOH HOH . E 5 HOH A 181 681 226 HOH HOH . E 5 HOH A 182 682 174 HOH HOH . E 5 HOH A 183 683 308 HOH HOH . E 5 HOH A 184 684 279 HOH HOH . E 5 HOH A 185 685 265 HOH HOH . E 5 HOH A 186 686 280 HOH HOH . E 5 HOH A 187 687 186 HOH HOH . E 5 HOH A 188 688 320 HOH HOH . E 5 HOH A 189 689 264 HOH HOH . E 5 HOH A 190 690 78 HOH HOH . E 5 HOH A 191 691 221 HOH HOH . E 5 HOH A 192 692 284 HOH HOH . E 5 HOH A 193 693 225 HOH HOH . E 5 HOH A 194 694 322 HOH HOH . E 5 HOH A 195 695 256 HOH HOH . E 5 HOH A 196 696 218 HOH HOH . E 5 HOH A 197 697 139 HOH HOH . E 5 HOH A 198 698 291 HOH HOH . E 5 HOH A 199 699 47 HOH HOH . E 5 HOH A 200 700 268 HOH HOH . E 5 HOH A 201 701 54 HOH HOH . E 5 HOH A 202 702 155 HOH HOH . E 5 HOH A 203 703 212 HOH HOH . E 5 HOH A 204 704 272 HOH HOH . E 5 HOH A 205 705 261 HOH HOH . E 5 HOH A 206 706 85 HOH HOH . E 5 HOH A 207 707 289 HOH HOH . E 5 HOH A 208 708 200 HOH HOH . E 5 HOH A 209 709 304 HOH HOH . E 5 HOH A 210 710 113 HOH HOH . E 5 HOH A 211 711 253 HOH HOH . E 5 HOH A 212 712 173 HOH HOH . E 5 HOH A 213 713 211 HOH HOH . E 5 HOH A 214 714 311 HOH HOH . E 5 HOH A 215 715 296 HOH HOH . E 5 HOH A 216 716 325 HOH HOH . E 5 HOH A 217 717 276 HOH HOH . E 5 HOH A 218 718 277 HOH HOH . E 5 HOH A 219 719 303 HOH HOH . E 5 HOH A 220 720 196 HOH HOH . E 5 HOH A 221 721 195 HOH HOH . E 5 HOH A 222 722 260 HOH HOH . E 5 HOH A 223 723 278 HOH HOH . E 5 HOH A 224 724 237 HOH HOH . E 5 HOH A 225 725 216 HOH HOH . E 5 HOH A 226 726 293 HOH HOH . E 5 HOH A 227 727 274 HOH HOH . E 5 HOH A 228 728 258 HOH HOH . E 5 HOH A 229 729 257 HOH HOH . E 5 HOH A 230 730 248 HOH HOH . E 5 HOH A 231 731 249 HOH HOH . F 5 HOH B 1 101 146 HOH HOH . F 5 HOH B 2 102 235 HOH HOH . F 5 HOH B 3 103 88 HOH HOH . F 5 HOH B 4 104 93 HOH HOH . F 5 HOH B 5 105 121 HOH HOH . F 5 HOH B 6 106 247 HOH HOH . F 5 HOH B 7 107 233 HOH HOH . F 5 HOH B 8 108 120 HOH HOH . F 5 HOH B 9 109 239 HOH HOH . F 5 HOH B 10 110 222 HOH HOH . F 5 HOH B 11 111 157 HOH HOH . F 5 HOH B 12 112 266 HOH HOH . F 5 HOH B 13 113 169 HOH HOH . F 5 HOH B 14 114 259 HOH HOH . F 5 HOH B 15 115 168 HOH HOH . F 5 HOH B 16 116 91 HOH HOH . F 5 HOH B 17 117 299 HOH HOH . F 5 HOH B 18 118 215 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 S S DMS . . . D 4 -10.21 -14.566 3.05 1 80.18 ? S DMS 402 A 1 HETATM 2 O O DMS . . . D 4 -9.179 -13.66 2.455 1 78.73 ? O DMS 402 A 1 HETATM 3 C C1 DMS . . . D 4 -10.47 -14.107 4.782 1 79.82 ? C1 DMS 402 A 1 HETATM 4 C C2 DMS . . . D 4 -11.85 -14.167 2.382 1 78.64 ? C2 DMS 402 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 4 #