data_5PA6 # _model_server_result.job_id Nvmb6AYNFi52uB7GFRKQHg _model_server_result.datetime_utc '2024-11-23 12:07:06' _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 5pa6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5PA6 # _exptl.entry_id 5PA6 _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 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 5PA6 _cell.length_a 50.743 _cell.length_b 55.863 _cell.length_c 78.779 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5PA6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 metalc ? metalc1 A OD1 ASP 141 A ASP 141 1_555 G MG MG . A MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc2 A OD2 ASP 169 A ASP 169 1_555 G MG MG . A MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc3 A OD1 ASN 170 A ASN 170 1_555 G MG MG . A MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc4 C O12 7JW . A 7JW 302 1_555 G MG MG . A MG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc5 G MG MG . A MG 306 1_555 H O HOH . A HOH 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag n _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type 'l-peptide linking' _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 336 n n N HN1 SAH sing 337 n n N HN2 SAH sing 338 n n CA CB SAH sing 339 n n CA C SAH sing 340 n n CA HA SAH sing 341 n n CB CG SAH sing 342 n n CB HB1 SAH sing 343 n n CB HB2 SAH sing 344 n n CG SD SAH sing 345 n n CG HG1 SAH sing 346 n n CG HG2 SAH sing 347 n n SD C5' SAH sing 348 n n C O SAH doub 349 n n C OXT SAH sing 350 n n OXT HXT SAH sing 351 n n C5' C4' SAH sing 352 n n C5' "H5'1" SAH sing 353 n n C5' "H5'2" SAH sing 354 n n C4' O4' SAH sing 355 n n C4' C3' SAH sing 356 n n C4' H4' SAH sing 357 n n O4' C1' SAH sing 358 n n C3' O3' SAH sing 359 n n C3' C2' SAH sing 360 n n C3' H3' SAH sing 361 n n O3' HO3' SAH sing 362 n n C2' O2' SAH sing 363 n n C2' C1' SAH sing 364 n n C2' H2' SAH sing 365 n n O2' HO2' SAH sing 366 n n C1' N9 SAH sing 367 n n C1' H1' SAH sing 368 n n N9 C8 SAH sing 369 n y N9 C4 SAH sing 370 n y C8 N7 SAH doub 371 n y C8 H8 SAH sing 372 n n N7 C5 SAH sing 373 n y C5 C6 SAH sing 374 n y C5 C4 SAH doub 375 n y C6 N6 SAH sing 376 n n C6 N1 SAH doub 377 n y N6 HN61 SAH sing 378 n n N6 HN62 SAH sing 379 n n N1 C2 SAH sing 380 n y C2 N3 SAH doub 381 n y C2 H2 SAH sing 382 n n N3 C4 SAH sing 383 n y # _atom_sites.entry_id 5PA6 _atom_sites.fract_transf_matrix[1][1] 0.019707 _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] 0.017901 _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] 0.012694 _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 B 2 SAH A 1 301 1 SAH SAH . C 3 7JW A 1 302 1 7JW LIG . D 4 CL A 1 303 1 CL CL . E 5 NHE A 1 304 1 NHE NHE . F 6 SO4 A 1 305 1 SO4 SO4 . G 7 MG A 1 306 1 MG MG . H 8 HOH A 1 401 21 HOH HOH . H 8 HOH A 2 402 22 HOH HOH . H 8 HOH A 3 403 73 HOH HOH . H 8 HOH A 4 404 62 HOH HOH . H 8 HOH A 5 405 93 HOH HOH . H 8 HOH A 6 406 74 HOH HOH . H 8 HOH A 7 407 186 HOH HOH . H 8 HOH A 8 408 4 HOH HOH . H 8 HOH A 9 409 6 HOH HOH . H 8 HOH A 10 410 3 HOH HOH . H 8 HOH A 11 411 98 HOH HOH . H 8 HOH A 12 412 114 HOH HOH . H 8 HOH A 13 413 77 HOH HOH . H 8 HOH A 14 414 124 HOH HOH . H 8 HOH A 15 415 105 HOH HOH . H 8 HOH A 16 416 164 HOH HOH . H 8 HOH A 17 417 8 HOH HOH . H 8 HOH A 18 418 96 HOH HOH . H 8 HOH A 19 419 5 HOH HOH . H 8 HOH A 20 420 159 HOH HOH . H 8 HOH A 21 421 55 HOH HOH . H 8 HOH A 22 422 41 HOH HOH . H 8 HOH A 23 423 147 HOH HOH . H 8 HOH A 24 424 67 HOH HOH . H 8 HOH A 25 425 36 HOH HOH . H 8 HOH A 26 426 134 HOH HOH . H 8 HOH A 27 427 33 HOH HOH . H 8 HOH A 28 428 19 HOH HOH . H 8 HOH A 29 429 122 HOH HOH . H 8 HOH A 30 430 38 HOH HOH . H 8 HOH A 31 431 1 HOH HOH . H 8 HOH A 32 432 27 HOH HOH . H 8 HOH A 33 433 100 HOH HOH . H 8 HOH A 34 434 78 HOH HOH . H 8 HOH A 35 435 177 HOH HOH . H 8 HOH A 36 436 25 HOH HOH . H 8 HOH A 37 437 144 HOH HOH . H 8 HOH A 38 438 26 HOH HOH . H 8 HOH A 39 439 131 HOH HOH . H 8 HOH A 40 440 12 HOH HOH . H 8 HOH A 41 441 57 HOH HOH . H 8 HOH A 42 442 34 HOH HOH . H 8 HOH A 43 443 35 HOH HOH . H 8 HOH A 44 444 10 HOH HOH . H 8 HOH A 45 445 52 HOH HOH . H 8 HOH A 46 446 137 HOH HOH . H 8 HOH A 47 447 143 HOH HOH . H 8 HOH A 48 448 28 HOH HOH . H 8 HOH A 49 449 29 HOH HOH . H 8 HOH A 50 450 16 HOH HOH . H 8 HOH A 51 451 15 HOH HOH . H 8 HOH A 52 452 135 HOH HOH . H 8 HOH A 53 453 32 HOH HOH . H 8 HOH A 54 454 24 HOH HOH . H 8 HOH A 55 455 87 HOH HOH . H 8 HOH A 56 456 157 HOH HOH . H 8 HOH A 57 457 65 HOH HOH . H 8 HOH A 58 458 99 HOH HOH . H 8 HOH A 59 459 104 HOH HOH . H 8 HOH A 60 460 128 HOH HOH . H 8 HOH A 61 461 153 HOH HOH . H 8 HOH A 62 462 7 HOH HOH . H 8 HOH A 63 463 83 HOH HOH . H 8 HOH A 64 464 51 HOH HOH . H 8 HOH A 65 465 85 HOH HOH . H 8 HOH A 66 466 59 HOH HOH . H 8 HOH A 67 467 20 HOH HOH . H 8 HOH A 68 468 108 HOH HOH . H 8 HOH A 69 469 49 HOH HOH . H 8 HOH A 70 470 116 HOH HOH . H 8 HOH A 71 471 17 HOH HOH . H 8 HOH A 72 472 2 HOH HOH . H 8 HOH A 73 473 132 HOH HOH . H 8 HOH A 74 474 84 HOH HOH . H 8 HOH A 75 475 66 HOH HOH . H 8 HOH A 76 476 61 HOH HOH . H 8 HOH A 77 477 163 HOH HOH . H 8 HOH A 78 478 176 HOH HOH . H 8 HOH A 79 479 13 HOH HOH . H 8 HOH A 80 480 56 HOH HOH . H 8 HOH A 81 481 75 HOH HOH . H 8 HOH A 82 482 14 HOH HOH . H 8 HOH A 83 483 23 HOH HOH . H 8 HOH A 84 484 130 HOH HOH . H 8 HOH A 85 485 30 HOH HOH . H 8 HOH A 86 486 48 HOH HOH . H 8 HOH A 87 487 129 HOH HOH . H 8 HOH A 88 488 82 HOH HOH . H 8 HOH A 89 489 37 HOH HOH . H 8 HOH A 90 490 47 HOH HOH . H 8 HOH A 91 491 182 HOH HOH . H 8 HOH A 92 492 150 HOH HOH . H 8 HOH A 93 493 181 HOH HOH . H 8 HOH A 94 494 156 HOH HOH . H 8 HOH A 95 495 136 HOH HOH . H 8 HOH A 96 496 166 HOH HOH . H 8 HOH A 97 497 50 HOH HOH . H 8 HOH A 98 498 117 HOH HOH . H 8 HOH A 99 499 109 HOH HOH . H 8 HOH A 100 500 141 HOH HOH . H 8 HOH A 101 501 11 HOH HOH . H 8 HOH A 102 502 40 HOH HOH . H 8 HOH A 103 503 53 HOH HOH . H 8 HOH A 104 504 133 HOH HOH . H 8 HOH A 105 505 175 HOH HOH . H 8 HOH A 106 506 76 HOH HOH . H 8 HOH A 107 507 165 HOH HOH . H 8 HOH A 108 508 69 HOH HOH . H 8 HOH A 109 509 88 HOH HOH . H 8 HOH A 110 510 94 HOH HOH . H 8 HOH A 111 511 97 HOH HOH . H 8 HOH A 112 512 179 HOH HOH . H 8 HOH A 113 513 167 HOH HOH . H 8 HOH A 114 514 139 HOH HOH . H 8 HOH A 115 515 142 HOH HOH . H 8 HOH A 116 516 115 HOH HOH . H 8 HOH A 117 517 45 HOH HOH . H 8 HOH A 118 518 39 HOH HOH . H 8 HOH A 119 519 123 HOH HOH . H 8 HOH A 120 520 169 HOH HOH . H 8 HOH A 121 521 95 HOH HOH . H 8 HOH A 122 522 126 HOH HOH . H 8 HOH A 123 523 46 HOH HOH . H 8 HOH A 124 524 127 HOH HOH . H 8 HOH A 125 525 63 HOH HOH . H 8 HOH A 126 526 148 HOH HOH . H 8 HOH A 127 527 119 HOH HOH . H 8 HOH A 128 528 102 HOH HOH . H 8 HOH A 129 529 107 HOH HOH . H 8 HOH A 130 530 31 HOH HOH . H 8 HOH A 131 531 43 HOH HOH . H 8 HOH A 132 532 9 HOH HOH . H 8 HOH A 133 533 161 HOH HOH . H 8 HOH A 134 534 173 HOH HOH . H 8 HOH A 135 535 162 HOH HOH . H 8 HOH A 136 536 106 HOH HOH . H 8 HOH A 137 537 145 HOH HOH . H 8 HOH A 138 538 140 HOH HOH . H 8 HOH A 139 539 58 HOH HOH . H 8 HOH A 140 540 138 HOH HOH . H 8 HOH A 141 541 91 HOH HOH . H 8 HOH A 142 542 113 HOH HOH . H 8 HOH A 143 543 111 HOH HOH . H 8 HOH A 144 544 68 HOH HOH . H 8 HOH A 145 545 92 HOH HOH . H 8 HOH A 146 546 149 HOH HOH . H 8 HOH A 147 547 79 HOH HOH . H 8 HOH A 148 548 70 HOH HOH . H 8 HOH A 149 549 152 HOH HOH . H 8 HOH A 150 550 146 HOH HOH . H 8 HOH A 151 551 18 HOH HOH . H 8 HOH A 152 552 160 HOH HOH . H 8 HOH A 153 553 60 HOH HOH . H 8 HOH A 154 554 120 HOH HOH . H 8 HOH A 155 555 42 HOH HOH . H 8 HOH A 156 556 103 HOH HOH . H 8 HOH A 157 557 151 HOH HOH . H 8 HOH A 158 558 155 HOH HOH . H 8 HOH A 159 559 168 HOH HOH . H 8 HOH A 160 560 110 HOH HOH . H 8 HOH A 161 561 89 HOH HOH . H 8 HOH A 162 562 80 HOH HOH . H 8 HOH A 163 563 101 HOH HOH . H 8 HOH A 164 564 172 HOH HOH . H 8 HOH A 165 565 86 HOH HOH . H 8 HOH A 166 566 183 HOH HOH . H 8 HOH A 167 567 185 HOH HOH . H 8 HOH A 168 568 90 HOH HOH . H 8 HOH A 169 569 188 HOH HOH . H 8 HOH A 170 570 81 HOH HOH . H 8 HOH A 171 571 54 HOH HOH . H 8 HOH A 172 572 171 HOH HOH . H 8 HOH A 173 573 174 HOH HOH . H 8 HOH A 174 574 112 HOH HOH . H 8 HOH A 175 575 170 HOH HOH . H 8 HOH A 176 576 125 HOH HOH . H 8 HOH A 177 577 184 HOH HOH . H 8 HOH A 178 578 71 HOH HOH . H 8 HOH A 179 579 187 HOH HOH . H 8 HOH A 180 580 44 HOH HOH . H 8 HOH A 181 581 154 HOH HOH . H 8 HOH A 182 582 64 HOH HOH . H 8 HOH A 183 583 121 HOH HOH . H 8 HOH A 184 584 118 HOH HOH . H 8 HOH A 185 585 178 HOH HOH . H 8 HOH A 186 586 189 HOH HOH . H 8 HOH A 187 587 72 HOH HOH . H 8 HOH A 188 588 190 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 . . . B 2 22.264 -6.374 -12.411 1 12.23 ? N SAH 301 A 1 HETATM 2 C CA SAH . . . B 2 22.186 -6.486 -13.898 1 12.21 ? CA SAH 301 A 1 HETATM 3 C CB SAH . . . B 2 23.057 -7.608 -14.465 1 11.65 ? CB SAH 301 A 1 HETATM 4 C CG SAH . . . B 2 24.53 -7.453 -14.105 1 10.91 ? CG SAH 301 A 1 HETATM 5 S SD SAH . . . B 2 25.511 -8.58 -15.05 1 11.28 ? SD SAH 301 A 1 HETATM 6 C C SAH . . . B 2 20.761 -6.754 -14.266 1 12.87 ? C SAH 301 A 1 HETATM 7 O O SAH . . . B 2 20.231 -6.121 -15.172 1 14.56 ? O SAH 301 A 1 HETATM 8 O OXT SAH . . . B 2 20.087 -7.587 -13.657 1 13.24 ? OXT SAH 301 A 1 HETATM 9 C C5' SAH . . . B 2 27.078 -8.481 -14.23 1 11.09 ? C5' SAH 301 A 1 HETATM 10 C C4' SAH . . . B 2 27.787 -7.136 -14.413 1 10.8 ? C4' SAH 301 A 1 HETATM 11 O O4' SAH . . . B 2 28.728 -6.961 -13.347 1 10.55 ? O4' SAH 301 A 1 HETATM 12 C C3' SAH . . . B 2 28.589 -7.013 -15.711 1 10.61 ? C3' SAH 301 A 1 HETATM 13 O O3' SAH . . . B 2 28.139 -5.895 -16.495 1 11.69 ? O3' SAH 301 A 1 HETATM 14 C C2' SAH . . . B 2 30.035 -6.852 -15.252 1 10.19 ? C2' SAH 301 A 1 HETATM 15 O O2' SAH . . . B 2 30.844 -6.021 -16.085 1 11.09 ? O2' SAH 301 A 1 HETATM 16 C C1' SAH . . . B 2 29.854 -6.26 -13.868 1 10.12 ? C1' SAH 301 A 1 HETATM 17 N N9 SAH . . . B 2 30.968 -6.437 -12.925 1 10.12 ? N9 SAH 301 A 1 HETATM 18 C C8 SAH . . . B 2 31.705 -7.532 -12.75 1 10.64 ? C8 SAH 301 A 1 HETATM 19 N N7 SAH . . . B 2 32.621 -7.353 -11.777 1 10.69 ? N7 SAH 301 A 1 HETATM 20 C C5 SAH . . . B 2 32.439 -6.116 -11.302 1 10.28 ? C5 SAH 301 A 1 HETATM 21 C C6 SAH . . . B 2 33.067 -5.27 -10.276 1 10.75 ? C6 SAH 301 A 1 HETATM 22 N N6 SAH . . . B 2 34.08 -5.755 -9.537 1 11.59 ? N6 SAH 301 A 1 HETATM 23 N N1 SAH . . . B 2 32.581 -4.014 -10.096 1 11.08 ? N1 SAH 301 A 1 HETATM 24 C C2 SAH . . . B 2 31.562 -3.526 -10.836 1 11.05 ? C2 SAH 301 A 1 HETATM 25 N N3 SAH . . . B 2 30.951 -4.24 -11.796 1 10.62 ? N3 SAH 301 A 1 HETATM 26 C C4 SAH . . . B 2 31.345 -5.512 -12.061 1 10.17 ? C4 SAH 301 A 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 220 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 26 #