data_5ZW4 # _model_server_result.job_id i9T2CnZGIr0LaFnxm0AHhQ _model_server_result.datetime_utc '2024-11-12 20:50:49' _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 5zw4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 5ZW4 # _exptl.entry_id 5ZW4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYLMETHIONINE _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 120 _cell.entry_id 5ZW4 _cell.length_a 64.982 _cell.length_b 64.982 _cell.length_c 126.68 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZW4 _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 _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 hydrog WATSON-CRICK hydrog1 B N3 C 1 D C 27 1_555 B N1 G 17 D G 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 C 1 D C 27 1_555 B O6 G 17 D G 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 C 1 D C 27 1_555 B N2 G 17 D G 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 C 2 D C 28 1_555 B N1 G 16 D G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N4 C 2 D C 28 1_555 B O6 G 16 D G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O2 C 2 D C 28 1_555 B N2 G 16 D G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N3 U 3 D U 29 1_555 B N1 A 15 D A 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O4 U 3 D U 29 1_555 B N6 A 15 D A 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 G 4 D G 30 1_555 B N3 C 14 D C 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N2 G 4 D G 30 1_555 B O2 C 14 D C 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O6 G 4 D G 30 1_555 B N4 C 14 D C 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N3 C 5 D C 31 1_555 B N1 G 13 D G 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N4 C 5 D C 31 1_555 B O6 G 13 D G 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O2 C 5 D C 31 1_555 B N2 G 13 D G 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C15 H22 N6 O5 S' _chem_comp.formula_weight 398.437 _chem_comp.id SAM _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYLMETHIONINE _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 SAM sing 383 n n N HN1 SAM sing 384 n n N HN2 SAM sing 385 n n CA C SAM sing 386 n n CA CB SAM sing 387 n n CA HA SAM sing 388 n n C O SAM doub 389 n n C OXT SAM sing 390 n n CB CG SAM sing 391 n n CB HB1 SAM sing 392 n n CB HB2 SAM sing 393 n n CG SD SAM sing 394 n n CG HG1 SAM sing 395 n n CG HG2 SAM sing 396 n n SD CE SAM sing 397 n n SD C5' SAM sing 398 n n CE HE1 SAM sing 399 n n CE HE2 SAM sing 400 n n CE HE3 SAM sing 401 n n C5' C4' SAM sing 402 n n C5' "H5'1" SAM sing 403 n n C5' "H5'2" SAM sing 404 n n C4' O4' SAM sing 405 n n C4' C3' SAM sing 406 n n C4' H4' SAM sing 407 n n O4' C1' SAM sing 408 n n C3' O3' SAM sing 409 n n C3' C2' SAM sing 410 n n C3' H3' SAM sing 411 n n O3' HO3' SAM sing 412 n n C2' O2' SAM sing 413 n n C2' C1' SAM sing 414 n n C2' H2' SAM sing 415 n n O2' HO2' SAM sing 416 n n C1' N9 SAM sing 417 n n C1' H1' SAM sing 418 n n N9 C8 SAM sing 419 n y N9 C4 SAM sing 420 n y C8 N7 SAM doub 421 n y C8 H8 SAM sing 422 n n N7 C5 SAM sing 423 n y C5 C6 SAM sing 424 n y C5 C4 SAM doub 425 n y C6 N6 SAM sing 426 n n C6 N1 SAM doub 427 n y N6 HN61 SAM sing 428 n n N6 HN62 SAM sing 429 n n N1 C2 SAM sing 430 n y C2 N3 SAM doub 431 n y C2 H2 SAM sing 432 n n N3 C4 SAM sing 433 n y # _atom_sites.entry_id 5ZW4 _atom_sites.fract_transf_matrix[1][1] 0.015389 _atom_sites.fract_transf_matrix[1][2] 0.008885 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01777 _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] 0.007894 _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 PO4 A 1 301 1 PO4 PO4 . D 4 SAM A 1 302 1 SAM SAM . E 5 HOH A 1 401 77 HOH HOH . E 5 HOH A 2 402 173 HOH HOH . E 5 HOH A 3 403 164 HOH HOH . E 5 HOH A 4 404 36 HOH HOH . E 5 HOH A 5 405 19 HOH HOH . E 5 HOH A 6 406 65 HOH HOH . E 5 HOH A 7 407 124 HOH HOH . E 5 HOH A 8 408 146 HOH HOH . E 5 HOH A 9 409 153 HOH HOH . E 5 HOH A 10 410 101 HOH HOH . E 5 HOH A 11 411 127 HOH HOH . E 5 HOH A 12 412 12 HOH HOH . E 5 HOH A 13 413 106 HOH HOH . E 5 HOH A 14 414 94 HOH HOH . E 5 HOH A 15 415 50 HOH HOH . E 5 HOH A 16 416 42 HOH HOH . E 5 HOH A 17 417 69 HOH HOH . E 5 HOH A 18 418 119 HOH HOH . E 5 HOH A 19 419 64 HOH HOH . E 5 HOH A 20 420 17 HOH HOH . E 5 HOH A 21 421 48 HOH HOH . E 5 HOH A 22 422 92 HOH HOH . E 5 HOH A 23 423 55 HOH HOH . E 5 HOH A 24 424 73 HOH HOH . E 5 HOH A 25 425 5 HOH HOH . E 5 HOH A 26 426 166 HOH HOH . E 5 HOH A 27 427 74 HOH HOH . E 5 HOH A 28 428 27 HOH HOH . E 5 HOH A 29 429 56 HOH HOH . E 5 HOH A 30 430 207 HOH HOH . E 5 HOH A 31 431 140 HOH HOH . E 5 HOH A 32 432 1 HOH HOH . E 5 HOH A 33 433 136 HOH HOH . E 5 HOH A 34 434 91 HOH HOH . E 5 HOH A 35 435 52 HOH HOH . E 5 HOH A 36 436 16 HOH HOH . E 5 HOH A 37 437 11 HOH HOH . E 5 HOH A 38 438 22 HOH HOH . E 5 HOH A 39 439 86 HOH HOH . E 5 HOH A 40 440 24 HOH HOH . E 5 HOH A 41 441 72 HOH HOH . E 5 HOH A 42 442 40 HOH HOH . E 5 HOH A 43 443 117 HOH HOH . E 5 HOH A 44 444 87 HOH HOH . E 5 HOH A 45 445 61 HOH HOH . E 5 HOH A 46 446 13 HOH HOH . E 5 HOH A 47 447 122 HOH HOH . E 5 HOH A 48 448 37 HOH HOH . E 5 HOH A 49 449 58 HOH HOH . E 5 HOH A 50 450 134 HOH HOH . E 5 HOH A 51 451 198 HOH HOH . E 5 HOH A 52 452 28 HOH HOH . E 5 HOH A 53 453 113 HOH HOH . E 5 HOH A 54 454 30 HOH HOH . E 5 HOH A 55 455 45 HOH HOH . E 5 HOH A 56 456 90 HOH HOH . E 5 HOH A 57 457 114 HOH HOH . E 5 HOH A 58 458 31 HOH HOH . E 5 HOH A 59 459 60 HOH HOH . E 5 HOH A 60 460 118 HOH HOH . E 5 HOH A 61 461 191 HOH HOH . E 5 HOH A 62 462 53 HOH HOH . E 5 HOH A 63 463 185 HOH HOH . E 5 HOH A 64 464 10 HOH HOH . E 5 HOH A 65 465 26 HOH HOH . E 5 HOH A 66 466 96 HOH HOH . E 5 HOH A 67 467 105 HOH HOH . E 5 HOH A 68 468 21 HOH HOH . E 5 HOH A 69 469 139 HOH HOH . E 5 HOH A 70 470 151 HOH HOH . E 5 HOH A 71 471 68 HOH HOH . E 5 HOH A 72 472 44 HOH HOH . E 5 HOH A 73 473 4 HOH HOH . E 5 HOH A 74 474 152 HOH HOH . E 5 HOH A 75 475 206 HOH HOH . E 5 HOH A 76 476 3 HOH HOH . E 5 HOH A 77 477 25 HOH HOH . E 5 HOH A 78 478 71 HOH HOH . E 5 HOH A 79 479 33 HOH HOH . E 5 HOH A 80 480 97 HOH HOH . E 5 HOH A 81 481 23 HOH HOH . E 5 HOH A 82 482 137 HOH HOH . E 5 HOH A 83 483 29 HOH HOH . E 5 HOH A 84 484 34 HOH HOH . E 5 HOH A 85 485 179 HOH HOH . E 5 HOH A 86 486 84 HOH HOH . E 5 HOH A 87 487 8 HOH HOH . E 5 HOH A 88 488 57 HOH HOH . E 5 HOH A 89 489 39 HOH HOH . E 5 HOH A 90 490 46 HOH HOH . E 5 HOH A 91 491 161 HOH HOH . E 5 HOH A 92 492 88 HOH HOH . E 5 HOH A 93 493 7 HOH HOH . E 5 HOH A 94 494 41 HOH HOH . E 5 HOH A 95 495 67 HOH HOH . E 5 HOH A 96 496 103 HOH HOH . E 5 HOH A 97 497 43 HOH HOH . E 5 HOH A 98 498 20 HOH HOH . E 5 HOH A 99 499 98 HOH HOH . E 5 HOH A 100 500 6 HOH HOH . E 5 HOH A 101 501 18 HOH HOH . E 5 HOH A 102 502 35 HOH HOH . E 5 HOH A 103 503 89 HOH HOH . E 5 HOH A 104 504 110 HOH HOH . E 5 HOH A 105 505 78 HOH HOH . E 5 HOH A 106 506 9 HOH HOH . E 5 HOH A 107 507 199 HOH HOH . E 5 HOH A 108 508 82 HOH HOH . E 5 HOH A 109 509 133 HOH HOH . E 5 HOH A 110 510 32 HOH HOH . E 5 HOH A 111 511 47 HOH HOH . E 5 HOH A 112 512 83 HOH HOH . E 5 HOH A 113 513 205 HOH HOH . E 5 HOH A 114 514 128 HOH HOH . E 5 HOH A 115 515 138 HOH HOH . E 5 HOH A 116 516 177 HOH HOH . E 5 HOH A 117 517 157 HOH HOH . E 5 HOH A 118 518 2 HOH HOH . E 5 HOH A 119 519 49 HOH HOH . E 5 HOH A 120 520 158 HOH HOH . E 5 HOH A 121 521 66 HOH HOH . E 5 HOH A 122 522 62 HOH HOH . E 5 HOH A 123 523 186 HOH HOH . E 5 HOH A 124 524 203 HOH HOH . E 5 HOH A 125 525 102 HOH HOH . E 5 HOH A 126 526 175 HOH HOH . E 5 HOH A 127 527 184 HOH HOH . E 5 HOH A 128 528 193 HOH HOH . E 5 HOH A 129 529 201 HOH HOH . E 5 HOH A 130 530 79 HOH HOH . E 5 HOH A 131 531 211 HOH HOH . E 5 HOH A 132 532 208 HOH HOH . E 5 HOH A 133 533 135 HOH HOH . E 5 HOH A 134 534 202 HOH HOH . E 5 HOH A 135 535 149 HOH HOH . E 5 HOH A 136 536 167 HOH HOH . E 5 HOH A 137 537 109 HOH HOH . E 5 HOH A 138 538 210 HOH HOH . E 5 HOH A 139 539 80 HOH HOH . E 5 HOH A 140 540 104 HOH HOH . E 5 HOH A 141 541 51 HOH HOH . E 5 HOH A 142 542 209 HOH HOH . E 5 HOH A 143 543 130 HOH HOH . E 5 HOH A 144 544 183 HOH HOH . E 5 HOH A 145 545 70 HOH HOH . E 5 HOH A 146 546 54 HOH HOH . E 5 HOH A 147 547 144 HOH HOH . E 5 HOH A 148 548 172 HOH HOH . E 5 HOH A 149 549 192 HOH HOH . E 5 HOH A 150 550 123 HOH HOH . E 5 HOH A 151 551 38 HOH HOH . E 5 HOH A 152 552 142 HOH HOH . E 5 HOH A 153 553 171 HOH HOH . E 5 HOH A 154 554 76 HOH HOH . E 5 HOH A 155 555 15 HOH HOH . E 5 HOH A 156 556 204 HOH HOH . E 5 HOH A 157 557 190 HOH HOH . E 5 HOH A 158 558 85 HOH HOH . F 5 HOH D 1 101 194 HOH HOH . F 5 HOH D 2 102 180 HOH HOH . F 5 HOH D 3 103 195 HOH HOH . F 5 HOH D 4 104 196 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 SAM . . . D 4 -27.698 11.594 -29.093 1 36.06 ? N SAM 302 A 1 HETATM 2 C CA SAM . . . D 4 -26.761 12.687 -28.911 1 40.49 ? CA SAM 302 A 1 HETATM 3 C C SAM . . . D 4 -26.711 13.392 -30.242 1 46.56 ? C SAM 302 A 1 HETATM 4 O O SAM . . . D 4 -26.266 12.8 -31.245 1 41.09 ? O SAM 302 A 1 HETATM 5 O OXT SAM . . . D 4 -27.124 14.569 -30.341 1 43.26 ? OXT SAM 302 A 1 HETATM 6 C CB SAM . . . D 4 -25.385 12.224 -28.411 1 43.79 ? CB SAM 302 A 1 HETATM 7 C CG SAM . . . D 4 -25.352 11.937 -26.902 1 50.44 ? CG SAM 302 A 1 HETATM 8 S SD SAM . . . D 4 -23.866 11.746 -26.133 1 37.99 ? SD SAM 302 A 1 HETATM 9 C CE SAM . . . D 4 -22.929 10.686 -27.026 1 52.59 ? CE SAM 302 A 1 HETATM 10 C C5' SAM . . . D 4 -24.149 10.939 -24.683 1 32.05 ? C5' SAM 302 A 1 HETATM 11 C C4' SAM . . . D 4 -24.987 11.723 -23.676 1 34.67 ? C4' SAM 302 A 1 HETATM 12 O O4' SAM . . . D 4 -25.577 10.806 -22.736 1 30.5 ? O4' SAM 302 A 1 HETATM 13 C C3' SAM . . . D 4 -24.214 12.747 -22.833 1 28.56 ? C3' SAM 302 A 1 HETATM 14 O O3' SAM . . . D 4 -24.771 14.058 -22.998 1 28.83 ? O3' SAM 302 A 1 HETATM 15 C C2' SAM . . . D 4 -24.347 12.259 -21.399 1 36.78 ? C2' SAM 302 A 1 HETATM 16 O O2' SAM . . . D 4 -24.472 13.347 -20.474 1 33.81 ? O2' SAM 302 A 1 HETATM 17 C C1' SAM . . . D 4 -25.619 11.423 -21.44 1 29.88 ? C1' SAM 302 A 1 HETATM 18 N N9 SAM . . . D 4 -25.661 10.297 -20.478 1 28.51 ? N9 SAM 302 A 1 HETATM 19 C C8 SAM . . . D 4 -24.66 9.478 -20.11 1 27.78 ? C8 SAM 302 A 1 HETATM 20 N N7 SAM . . . D 4 -25.07 8.533 -19.238 1 32.68 ? N7 SAM 302 A 1 HETATM 21 C C5 SAM . . . D 4 -26.382 8.767 -19.016 1 27.06 ? C5 SAM 302 A 1 HETATM 22 C C6 SAM . . . D 4 -27.454 8.187 -18.177 1 26.58 ? C6 SAM 302 A 1 HETATM 23 N N6 SAM . . . D 4 -27.22 7.127 -17.372 1 28.94 ? N6 SAM 302 A 1 HETATM 24 N N1 SAM . . . D 4 -28.678 8.756 -18.255 1 26.64 ? N1 SAM 302 A 1 HETATM 25 C C2 SAM . . . D 4 -28.943 9.812 -19.027 1 28.99 ? C2 SAM 302 A 1 HETATM 26 N N3 SAM . . . D 4 -28.032 10.414 -19.794 1 29.83 ? N3 SAM 302 A 1 HETATM 27 C C4 SAM . . . D 4 -26.769 9.936 -19.828 1 29.64 ? C4 SAM 302 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 234 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #