data_9J56 # _model_server_result.job_id sU6Fd3GkrqQ6Piq13dXytw _model_server_result.datetime_utc '2024-11-07 03:29:45' _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 9j56 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 9J56 # _exptl.entry_id 9J56 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _entity.pdbx_number_of_molecules 2 _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 120 _cell.entry_id 9J56 _cell.length_a 79.997 _cell.length_b 79.997 _cell.length_c 234.203 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9J56 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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,G,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N N # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _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 N CA SAH sing 349 n n N HN1 SAH sing 350 n n N HN2 SAH sing 351 n n CA CB SAH sing 352 n n CA C SAH sing 353 n n CA HA SAH sing 354 n n CB CG SAH sing 355 n n CB HB1 SAH sing 356 n n CB HB2 SAH sing 357 n n CG SD SAH sing 358 n n CG HG1 SAH sing 359 n n CG HG2 SAH sing 360 n n SD C5' SAH sing 361 n n C O SAH doub 362 n n C OXT SAH sing 363 n n OXT HXT SAH sing 364 n n C5' C4' SAH sing 365 n n C5' "H5'1" SAH sing 366 n n C5' "H5'2" SAH sing 367 n n C4' O4' SAH sing 368 n n C4' C3' SAH sing 369 n n C4' H4' SAH sing 370 n n O4' C1' SAH sing 371 n n C3' O3' SAH sing 372 n n C3' C2' SAH sing 373 n n C3' H3' SAH sing 374 n n O3' HO3' SAH sing 375 n n C2' O2' SAH sing 376 n n C2' C1' SAH sing 377 n n C2' H2' SAH sing 378 n n O2' HO2' SAH sing 379 n n C1' N9 SAH sing 380 n n C1' H1' SAH sing 381 n n N9 C8 SAH sing 382 n y N9 C4 SAH sing 383 n y C8 N7 SAH doub 384 n y C8 H8 SAH sing 385 n n N7 C5 SAH sing 386 n y C5 C6 SAH sing 387 n y C5 C4 SAH doub 388 n y C6 N6 SAH sing 389 n n C6 N1 SAH doub 390 n y N6 HN61 SAH sing 391 n n N6 HN62 SAH sing 392 n n N1 C2 SAH sing 393 n y C2 N3 SAH doub 394 n y C2 H2 SAH sing 395 n n N3 C4 SAH sing 396 n y # _atom_sites.entry_id 9J56 _atom_sites.fract_transf_matrix[1][1] 0.0125 _atom_sites.fract_transf_matrix[1][2] 0.007217 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014434 _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] 0.00427 _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 2 SAH A 1 401 401 SAH SAH . D 3 A1L3V A 1 402 501 A1L3V DOR . E 2 SAH B 1 401 403 SAH SAH . F 3 A1L3V B 1 402 501 A1L3V DOR . G 4 HOH A 1 501 146 HOH HOH . G 4 HOH A 2 502 47 HOH HOH . G 4 HOH A 3 503 33 HOH HOH . G 4 HOH A 4 504 66 HOH HOH . G 4 HOH A 5 505 86 HOH HOH . G 4 HOH A 6 506 139 HOH HOH . G 4 HOH A 7 507 151 HOH HOH . G 4 HOH A 8 508 51 HOH HOH . G 4 HOH A 9 509 170 HOH HOH . G 4 HOH A 10 510 17 HOH HOH . G 4 HOH A 11 511 99 HOH HOH . G 4 HOH A 12 512 215 HOH HOH . G 4 HOH A 13 513 188 HOH HOH . G 4 HOH A 14 514 190 HOH HOH . G 4 HOH A 15 515 203 HOH HOH . G 4 HOH A 16 516 32 HOH HOH . G 4 HOH A 17 517 75 HOH HOH . G 4 HOH A 18 518 94 HOH HOH . G 4 HOH A 19 519 103 HOH HOH . G 4 HOH A 20 520 159 HOH HOH . G 4 HOH A 21 521 77 HOH HOH . G 4 HOH A 22 522 163 HOH HOH . G 4 HOH A 23 523 55 HOH HOH . G 4 HOH A 24 524 232 HOH HOH . G 4 HOH A 25 525 58 HOH HOH . G 4 HOH A 26 526 189 HOH HOH . G 4 HOH A 27 527 28 HOH HOH . G 4 HOH A 28 528 54 HOH HOH . G 4 HOH A 29 529 212 HOH HOH . G 4 HOH A 30 530 231 HOH HOH . G 4 HOH A 31 531 21 HOH HOH . G 4 HOH A 32 532 29 HOH HOH . G 4 HOH A 33 533 152 HOH HOH . G 4 HOH A 34 534 242 HOH HOH . G 4 HOH A 35 535 13 HOH HOH . G 4 HOH A 36 536 36 HOH HOH . G 4 HOH A 37 537 38 HOH HOH . G 4 HOH A 38 538 3 HOH HOH . G 4 HOH A 39 539 45 HOH HOH . G 4 HOH A 40 540 131 HOH HOH . G 4 HOH A 41 541 168 HOH HOH . G 4 HOH A 42 542 10 HOH HOH . G 4 HOH A 43 543 132 HOH HOH . G 4 HOH A 44 544 141 HOH HOH . G 4 HOH A 45 545 16 HOH HOH . G 4 HOH A 46 546 92 HOH HOH . G 4 HOH A 47 547 210 HOH HOH . G 4 HOH A 48 548 81 HOH HOH . G 4 HOH A 49 549 18 HOH HOH . G 4 HOH A 50 550 62 HOH HOH . G 4 HOH A 51 551 128 HOH HOH . G 4 HOH A 52 552 4 HOH HOH . G 4 HOH A 53 553 19 HOH HOH . G 4 HOH A 54 554 5 HOH HOH . G 4 HOH A 55 555 2 HOH HOH . G 4 HOH A 56 556 230 HOH HOH . G 4 HOH A 57 557 44 HOH HOH . G 4 HOH A 58 558 59 HOH HOH . G 4 HOH A 59 559 239 HOH HOH . G 4 HOH A 60 560 192 HOH HOH . G 4 HOH A 61 561 9 HOH HOH . G 4 HOH A 62 562 237 HOH HOH . G 4 HOH A 63 563 156 HOH HOH . G 4 HOH A 64 564 108 HOH HOH . G 4 HOH A 65 565 34 HOH HOH . G 4 HOH A 66 566 118 HOH HOH . G 4 HOH A 67 567 11 HOH HOH . G 4 HOH A 68 568 222 HOH HOH . G 4 HOH A 69 569 165 HOH HOH . G 4 HOH A 70 570 240 HOH HOH . G 4 HOH A 71 571 31 HOH HOH . G 4 HOH A 72 572 41 HOH HOH . G 4 HOH A 73 573 154 HOH HOH . G 4 HOH A 74 574 95 HOH HOH . G 4 HOH A 75 575 64 HOH HOH . G 4 HOH A 76 576 233 HOH HOH . G 4 HOH A 77 577 113 HOH HOH . G 4 HOH A 78 578 195 HOH HOH . G 4 HOH A 79 579 69 HOH HOH . G 4 HOH A 80 580 123 HOH HOH . G 4 HOH A 81 581 70 HOH HOH . G 4 HOH A 82 582 68 HOH HOH . G 4 HOH A 83 583 80 HOH HOH . G 4 HOH A 84 584 150 HOH HOH . G 4 HOH A 85 585 76 HOH HOH . G 4 HOH A 86 586 23 HOH HOH . G 4 HOH A 87 587 90 HOH HOH . G 4 HOH A 88 588 209 HOH HOH . G 4 HOH A 89 589 26 HOH HOH . G 4 HOH A 90 590 50 HOH HOH . G 4 HOH A 91 591 169 HOH HOH . G 4 HOH A 92 592 74 HOH HOH . G 4 HOH A 93 593 101 HOH HOH . G 4 HOH A 94 594 218 HOH HOH . G 4 HOH A 95 595 142 HOH HOH . G 4 HOH A 96 596 124 HOH HOH . G 4 HOH A 97 597 53 HOH HOH . G 4 HOH A 98 598 6 HOH HOH . G 4 HOH A 99 599 65 HOH HOH . G 4 HOH A 100 600 72 HOH HOH . G 4 HOH A 101 601 206 HOH HOH . G 4 HOH A 102 602 42 HOH HOH . G 4 HOH A 103 603 48 HOH HOH . G 4 HOH A 104 604 20 HOH HOH . G 4 HOH A 105 605 79 HOH HOH . G 4 HOH A 106 606 225 HOH HOH . G 4 HOH A 107 607 73 HOH HOH . G 4 HOH A 108 608 219 HOH HOH . G 4 HOH A 109 609 46 HOH HOH . G 4 HOH A 110 610 236 HOH HOH . G 4 HOH A 111 611 173 HOH HOH . G 4 HOH A 112 612 166 HOH HOH . G 4 HOH A 113 613 129 HOH HOH . G 4 HOH A 114 614 148 HOH HOH . G 4 HOH A 115 615 114 HOH HOH . G 4 HOH A 116 616 52 HOH HOH . G 4 HOH A 117 617 238 HOH HOH . G 4 HOH A 118 618 204 HOH HOH . G 4 HOH A 119 619 78 HOH HOH . G 4 HOH A 120 620 93 HOH HOH . G 4 HOH A 121 621 122 HOH HOH . G 4 HOH A 122 622 149 HOH HOH . G 4 HOH A 123 623 191 HOH HOH . G 4 HOH A 124 624 214 HOH HOH . G 4 HOH A 125 625 155 HOH HOH . G 4 HOH A 126 626 221 HOH HOH . G 4 HOH A 127 627 199 HOH HOH . G 4 HOH A 128 628 82 HOH HOH . G 4 HOH A 129 629 91 HOH HOH . G 4 HOH A 130 630 181 HOH HOH . G 4 HOH A 131 631 133 HOH HOH . G 4 HOH A 132 632 84 HOH HOH . G 4 HOH A 133 633 171 HOH HOH . G 4 HOH A 134 634 89 HOH HOH . G 4 HOH A 135 635 138 HOH HOH . G 4 HOH A 136 636 174 HOH HOH . H 4 HOH B 1 501 37 HOH HOH . H 4 HOH B 2 502 111 HOH HOH . H 4 HOH B 3 503 25 HOH HOH . H 4 HOH B 4 504 22 HOH HOH . H 4 HOH B 5 505 247 HOH HOH . H 4 HOH B 6 506 88 HOH HOH . H 4 HOH B 7 507 60 HOH HOH . H 4 HOH B 8 508 202 HOH HOH . H 4 HOH B 9 509 127 HOH HOH . H 4 HOH B 10 510 63 HOH HOH . H 4 HOH B 11 511 67 HOH HOH . H 4 HOH B 12 512 83 HOH HOH . H 4 HOH B 13 513 160 HOH HOH . H 4 HOH B 14 514 109 HOH HOH . H 4 HOH B 15 515 14 HOH HOH . H 4 HOH B 16 516 153 HOH HOH . H 4 HOH B 17 517 8 HOH HOH . H 4 HOH B 18 518 57 HOH HOH . H 4 HOH B 19 519 211 HOH HOH . H 4 HOH B 20 520 56 HOH HOH . H 4 HOH B 21 521 119 HOH HOH . H 4 HOH B 22 522 137 HOH HOH . H 4 HOH B 23 523 27 HOH HOH . H 4 HOH B 24 524 102 HOH HOH . H 4 HOH B 25 525 40 HOH HOH . H 4 HOH B 26 526 245 HOH HOH . H 4 HOH B 27 527 134 HOH HOH . H 4 HOH B 28 528 164 HOH HOH . H 4 HOH B 29 529 244 HOH HOH . H 4 HOH B 30 530 179 HOH HOH . H 4 HOH B 31 531 143 HOH HOH . H 4 HOH B 32 532 105 HOH HOH . H 4 HOH B 33 533 208 HOH HOH . H 4 HOH B 34 534 162 HOH HOH . H 4 HOH B 35 535 229 HOH HOH . H 4 HOH B 36 536 196 HOH HOH . H 4 HOH B 37 537 100 HOH HOH . H 4 HOH B 38 538 96 HOH HOH . H 4 HOH B 39 539 24 HOH HOH . H 4 HOH B 40 540 35 HOH HOH . H 4 HOH B 41 541 144 HOH HOH . H 4 HOH B 42 542 49 HOH HOH . H 4 HOH B 43 543 161 HOH HOH . H 4 HOH B 44 544 145 HOH HOH . H 4 HOH B 45 545 194 HOH HOH . H 4 HOH B 46 546 158 HOH HOH . H 4 HOH B 47 547 147 HOH HOH . H 4 HOH B 48 548 97 HOH HOH . H 4 HOH B 49 549 178 HOH HOH . H 4 HOH B 50 550 121 HOH HOH . H 4 HOH B 51 551 104 HOH HOH . H 4 HOH B 52 552 235 HOH HOH . H 4 HOH B 53 553 167 HOH HOH . H 4 HOH B 54 554 115 HOH HOH . H 4 HOH B 55 555 243 HOH HOH . H 4 HOH B 56 556 85 HOH HOH . H 4 HOH B 57 557 112 HOH HOH . H 4 HOH B 58 558 228 HOH HOH . H 4 HOH B 59 559 217 HOH HOH . H 4 HOH B 60 560 120 HOH HOH . H 4 HOH B 61 561 71 HOH HOH . H 4 HOH B 62 562 207 HOH HOH . H 4 HOH B 63 563 98 HOH HOH . H 4 HOH B 64 564 187 HOH HOH . H 4 HOH B 65 565 7 HOH HOH . H 4 HOH B 66 566 15 HOH HOH . H 4 HOH B 67 567 87 HOH HOH . H 4 HOH B 68 568 125 HOH HOH . H 4 HOH B 69 569 180 HOH HOH . H 4 HOH B 70 570 157 HOH HOH . H 4 HOH B 71 571 205 HOH HOH . H 4 HOH B 72 572 224 HOH HOH . H 4 HOH B 73 573 227 HOH HOH . H 4 HOH B 74 574 172 HOH HOH . H 4 HOH B 75 575 117 HOH HOH . H 4 HOH B 76 576 198 HOH HOH . H 4 HOH B 77 577 234 HOH HOH . H 4 HOH B 78 578 220 HOH HOH . H 4 HOH B 79 579 246 HOH HOH . H 4 HOH B 80 580 226 HOH HOH . H 4 HOH B 81 581 106 HOH HOH . H 4 HOH B 82 582 107 HOH HOH . H 4 HOH B 83 583 61 HOH HOH . H 4 HOH B 84 584 201 HOH HOH . H 4 HOH B 85 585 216 HOH HOH . H 4 HOH B 86 586 223 HOH HOH . H 4 HOH B 87 587 200 HOH HOH . H 4 HOH B 88 588 136 HOH HOH . H 4 HOH B 89 589 126 HOH HOH . H 4 HOH B 90 590 183 HOH HOH . H 4 HOH B 91 591 241 HOH HOH . H 4 HOH B 92 592 197 HOH HOH . H 4 HOH B 93 593 182 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 N N SAH . . . C 2 46.2 44.903 116.662 1 34.44 ? N SAH 401 A 1 HETATM 2 C CA SAH . . . C 2 45.209 43.98 116.131 1 39.25 ? CA SAH 401 A 1 HETATM 3 C CB SAH . . . C 2 45.4 43.846 114.624 1 39.29 ? CB SAH 401 A 1 HETATM 4 C CG SAH . . . C 2 44.046 43.955 113.983 1 41.47 ? CG SAH 401 A 1 HETATM 5 S SD SAH . . . C 2 44.395 43.944 112.198 1 37.5 ? SD SAH 401 A 1 HETATM 6 C C SAH . . . C 2 45.294 42.591 116.773 1 41.27 ? C SAH 401 A 1 HETATM 7 O O SAH . . . C 2 44.236 41.936 117 1 41.94 ? O SAH 401 A 1 HETATM 8 O OXT SAH . . . C 2 46.425 42.099 117.056 1 39.16 -1 OXT SAH 401 A 1 HETATM 9 C C5' SAH . . . C 2 44.963 45.587 111.644 1 35.29 ? C5' SAH 401 A 1 HETATM 10 C C4' SAH . . . C 2 44.112 46.754 112.235 1 36.55 ? C4' SAH 401 A 1 HETATM 11 O O4' SAH . . . C 2 44.442 47.883 111.624 1 33.71 ? O4' SAH 401 A 1 HETATM 12 C C3' SAH . . . C 2 42.585 46.547 112.037 1 37.93 ? C3' SAH 401 A 1 HETATM 13 O O3' SAH . . . C 2 41.925 46.453 113.233 1 37.68 ? O3' SAH 401 A 1 HETATM 14 C C2' SAH . . . C 2 42.204 47.84 111.288 1 33.91 ? C2' SAH 401 A 1 HETATM 15 O O2' SAH . . . C 2 40.924 48.411 111.767 1 38.38 ? O2' SAH 401 A 1 HETATM 16 C C1' SAH . . . C 2 43.34 48.766 111.701 1 35.45 ? C1' SAH 401 A 1 HETATM 17 N N9 SAH . . . C 2 43.505 49.868 110.784 1 38.63 ? N9 SAH 401 A 1 HETATM 18 C C8 SAH . . . C 2 43.594 49.801 109.448 1 35.35 ? C8 SAH 401 A 1 HETATM 19 N N7 SAH . . . C 2 43.764 51.039 108.987 1 37.76 ? N7 SAH 401 A 1 HETATM 20 C C5 SAH . . . C 2 43.782 51.883 110.02 1 38.15 ? C5 SAH 401 A 1 HETATM 21 C C6 SAH . . . C 2 43.92 53.252 110.083 1 39.13 ? C6 SAH 401 A 1 HETATM 22 N N6 SAH . . . C 2 44.096 54.172 108.979 1 37.07 ? N6 SAH 401 A 1 HETATM 23 N N1 SAH . . . C 2 43.908 53.871 111.265 1 38.31 ? N1 SAH 401 A 1 HETATM 24 C C2 SAH . . . C 2 43.753 53.146 112.392 1 37.42 ? C2 SAH 401 A 1 HETATM 25 N N3 SAH . . . C 2 43.606 51.8 112.332 1 37.35 ? N3 SAH 401 A 1 HETATM 26 C C4 SAH . . . C 2 43.619 51.164 111.142 1 38.1 ? C4 SAH 401 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 26 #