data_9DFU # _model_server_result.job_id MERBjzd96fkmKbfPaWicqA _model_server_result.datetime_utc '2025-02-23 09:55:05' _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 9dfu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 9DFU # _exptl.entry_id 9DFU _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 90 _cell.entry_id 9DFU _cell.length_a 37.137 _cell.length_b 55.959 _cell.length_c 152.81 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DFU _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 metalc ? metalc1 A SG CYS 38 A CYS 45 1_555 C FE4 SF4 . A SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc2 A SG CYS 42 A CYS 49 1_555 C FE1 SF4 . A SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? metalc ? metalc3 A SG CYS 45 A CYS 52 1_555 C FE3 SF4 . A SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc4 C FE2 SF4 . A SF4 402 1_555 D N SAM . A SAM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? metalc ? metalc5 C FE2 SF4 . A SF4 402 1_555 D OXT SAM . A SAM 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? # _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 323 n n N HN1 SAM sing 324 n n N HN2 SAM sing 325 n n CA C SAM sing 326 n n CA CB SAM sing 327 n n CA HA SAM sing 328 n n C O SAM doub 329 n n C OXT SAM sing 330 n n CB CG SAM sing 331 n n CB HB1 SAM sing 332 n n CB HB2 SAM sing 333 n n CG SD SAM sing 334 n n CG HG1 SAM sing 335 n n CG HG2 SAM sing 336 n n SD CE SAM sing 337 n n SD C5' SAM sing 338 n n CE HE1 SAM sing 339 n n CE HE2 SAM sing 340 n n CE HE3 SAM sing 341 n n C5' C4' SAM sing 342 n n C5' "H5'1" SAM sing 343 n n C5' "H5'2" SAM sing 344 n n C4' O4' SAM sing 345 n n C4' C3' SAM sing 346 n n C4' H4' SAM sing 347 n n O4' C1' SAM sing 348 n n C3' O3' SAM sing 349 n n C3' C2' SAM sing 350 n n C3' H3' SAM sing 351 n n O3' HO3' SAM sing 352 n n C2' O2' SAM sing 353 n n C2' C1' SAM sing 354 n n C2' H2' SAM sing 355 n n O2' HO2' SAM sing 356 n n C1' N9 SAM sing 357 n n C1' H1' SAM sing 358 n n N9 C8 SAM sing 359 n y N9 C4 SAM sing 360 n y C8 N7 SAM doub 361 n y C8 H8 SAM sing 362 n n N7 C5 SAM sing 363 n y C5 C6 SAM sing 364 n y C5 C4 SAM doub 365 n y C6 N6 SAM sing 366 n n C6 N1 SAM doub 367 n y N6 HN61 SAM sing 368 n n N6 HN62 SAM sing 369 n n N1 C2 SAM sing 370 n y C2 N3 SAM doub 371 n y C2 H2 SAM sing 372 n n N3 C4 SAM sing 373 n y # _atom_sites.entry_id 9DFU _atom_sites.fract_transf_matrix[1][1] 0.026927 _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] 0.01787 _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] 0.006544 _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 CTP A 1 401 401 CTP CTP . C 3 SF4 A 1 402 402 SF4 SF4 . D 4 SAM A 1 403 403 SAM SAM . E 5 CL A 1 404 1 CL CL . F 6 HOH A 1 501 91 HOH HOH . F 6 HOH A 2 502 131 HOH HOH . F 6 HOH A 3 503 12 HOH HOH . F 6 HOH A 4 504 9 HOH HOH . F 6 HOH A 5 505 77 HOH HOH . F 6 HOH A 6 506 52 HOH HOH . F 6 HOH A 7 507 3 HOH HOH . F 6 HOH A 8 508 85 HOH HOH . F 6 HOH A 9 509 59 HOH HOH . F 6 HOH A 10 510 61 HOH HOH . F 6 HOH A 11 511 4 HOH HOH . F 6 HOH A 12 512 68 HOH HOH . F 6 HOH A 13 513 48 HOH HOH . F 6 HOH A 14 514 18 HOH HOH . F 6 HOH A 15 515 32 HOH HOH . F 6 HOH A 16 516 126 HOH HOH . F 6 HOH A 17 517 54 HOH HOH . F 6 HOH A 18 518 117 HOH HOH . F 6 HOH A 19 519 5 HOH HOH . F 6 HOH A 20 520 13 HOH HOH . F 6 HOH A 21 521 1 HOH HOH . F 6 HOH A 22 522 64 HOH HOH . F 6 HOH A 23 523 60 HOH HOH . F 6 HOH A 24 524 31 HOH HOH . F 6 HOH A 25 525 10 HOH HOH . F 6 HOH A 26 526 19 HOH HOH . F 6 HOH A 27 527 58 HOH HOH . F 6 HOH A 28 528 41 HOH HOH . F 6 HOH A 29 529 35 HOH HOH . F 6 HOH A 30 530 25 HOH HOH . F 6 HOH A 31 531 42 HOH HOH . F 6 HOH A 32 532 6 HOH HOH . F 6 HOH A 33 533 8 HOH HOH . F 6 HOH A 34 534 11 HOH HOH . F 6 HOH A 35 535 2 HOH HOH . F 6 HOH A 36 536 27 HOH HOH . F 6 HOH A 37 537 39 HOH HOH . F 6 HOH A 38 538 34 HOH HOH . F 6 HOH A 39 539 90 HOH HOH . F 6 HOH A 40 540 36 HOH HOH . F 6 HOH A 41 541 24 HOH HOH . F 6 HOH A 42 542 22 HOH HOH . F 6 HOH A 43 543 51 HOH HOH . F 6 HOH A 44 544 40 HOH HOH . F 6 HOH A 45 545 21 HOH HOH . F 6 HOH A 46 546 110 HOH HOH . F 6 HOH A 47 547 20 HOH HOH . F 6 HOH A 48 548 16 HOH HOH . F 6 HOH A 49 549 109 HOH HOH . F 6 HOH A 50 550 74 HOH HOH . F 6 HOH A 51 551 49 HOH HOH . F 6 HOH A 52 552 46 HOH HOH . F 6 HOH A 53 553 76 HOH HOH . F 6 HOH A 54 554 69 HOH HOH . F 6 HOH A 55 555 55 HOH HOH . F 6 HOH A 56 556 28 HOH HOH . F 6 HOH A 57 557 15 HOH HOH . F 6 HOH A 58 558 72 HOH HOH . F 6 HOH A 59 559 71 HOH HOH . F 6 HOH A 60 560 98 HOH HOH . F 6 HOH A 61 561 70 HOH HOH . F 6 HOH A 62 562 23 HOH HOH . F 6 HOH A 63 563 33 HOH HOH . F 6 HOH A 64 564 7 HOH HOH . F 6 HOH A 65 565 38 HOH HOH . F 6 HOH A 66 566 14 HOH HOH . F 6 HOH A 67 567 63 HOH HOH . F 6 HOH A 68 568 80 HOH HOH . F 6 HOH A 69 569 100 HOH HOH . F 6 HOH A 70 570 62 HOH HOH . F 6 HOH A 71 571 95 HOH HOH . F 6 HOH A 72 572 50 HOH HOH . F 6 HOH A 73 573 89 HOH HOH . F 6 HOH A 74 574 67 HOH HOH . F 6 HOH A 75 575 53 HOH HOH . F 6 HOH A 76 576 114 HOH HOH . F 6 HOH A 77 577 30 HOH HOH . F 6 HOH A 78 578 82 HOH HOH . F 6 HOH A 79 579 81 HOH HOH . F 6 HOH A 80 580 94 HOH HOH . F 6 HOH A 81 581 105 HOH HOH . F 6 HOH A 82 582 43 HOH HOH . F 6 HOH A 83 583 47 HOH HOH . F 6 HOH A 84 584 102 HOH HOH . F 6 HOH A 85 585 124 HOH HOH . F 6 HOH A 86 586 45 HOH HOH . F 6 HOH A 87 587 57 HOH HOH . F 6 HOH A 88 588 122 HOH HOH . F 6 HOH A 89 589 127 HOH HOH . F 6 HOH A 90 590 119 HOH HOH . F 6 HOH A 91 591 118 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 -18.149 -9.879 26.101 1 15.6 ? N SAM 403 A 1 HETATM 2 C CA SAM . . . D 4 -16.835 -10.212 25.607 1 17.3 ? CA SAM 403 A 1 HETATM 3 C C SAM . . . D 4 -15.748 -9.899 26.603 1 14.35 ? C SAM 403 A 1 HETATM 4 O O SAM . . . D 4 -14.711 -10.504 26.554 1 18.99 ? O SAM 403 A 1 HETATM 5 O OXT SAM . . . D 4 -15.882 -9.09 27.43 1 14.96 ? OXT SAM 403 A 1 HETATM 6 C CB SAM . . . D 4 -16.647 -9.518 24.258 1 15.4 ? CB SAM 403 A 1 HETATM 7 C CG SAM . . . D 4 -17.097 -8.068 24.199 1 20.04 ? CG SAM 403 A 1 HETATM 8 S SD SAM . . . D 4 -15.953 -6.978 24.668 1 23.47 ? SD SAM 403 A 1 HETATM 9 C CE SAM . . . D 4 -16.461 -5.497 24.153 1 21.17 ? CE SAM 403 A 1 HETATM 10 C C5' SAM . . . D 4 -14.483 -7.34 23.966 1 20.81 ? C5' SAM 403 A 1 HETATM 11 C C4' SAM . . . D 4 -13.246 -6.775 24.671 1 17.86 ? C4' SAM 403 A 1 HETATM 12 O O4' SAM . . . D 4 -13.166 -5.352 24.594 1 18.86 ? O4' SAM 403 A 1 HETATM 13 C C3' SAM . . . D 4 -13.225 -7.125 26.147 1 18.76 ? C3' SAM 403 A 1 HETATM 14 O O3' SAM . . . D 4 -11.951 -7.65 26.477 1 12.69 ? O3' SAM 403 A 1 HETATM 15 C C2' SAM . . . D 4 -13.48 -5.818 26.854 1 14.52 ? C2' SAM 403 A 1 HETATM 16 O O2' SAM . . . D 4 -12.87 -5.79 28.132 1 20.21 ? O2' SAM 403 A 1 HETATM 17 C C1' SAM . . . D 4 -12.867 -4.827 25.887 1 15.31 ? C1' SAM 403 A 1 HETATM 18 N N9 SAM . . . D 4 -13.399 -3.451 26.005 1 16.74 ? N9 SAM 403 A 1 HETATM 19 C C8 SAM . . . D 4 -14.668 -3.075 26.14 1 13.65 ? C8 SAM 403 A 1 HETATM 20 N N7 SAM . . . D 4 -14.769 -1.735 26.205 1 14.18 ? N7 SAM 403 A 1 HETATM 21 C C5 SAM . . . D 4 -13.542 -1.229 26.101 1 14.48 ? C5 SAM 403 A 1 HETATM 22 C C6 SAM . . . D 4 -12.941 0.117 26.094 1 16.23 ? C6 SAM 403 A 1 HETATM 23 N N6 SAM . . . D 4 -13.71 1.211 26.207 1 14.89 ? N6 SAM 403 A 1 HETATM 24 N N1 SAM . . . D 4 -11.607 0.206 25.965 1 12.31 ? N1 SAM 403 A 1 HETATM 25 C C2 SAM . . . D 4 -10.847 -0.889 25.843 1 14.13 ? C2 SAM 403 A 1 HETATM 26 N N3 SAM . . . D 4 -11.324 -2.138 25.842 1 14.35 ? N3 SAM 403 A 1 HETATM 27 C C4 SAM . . . D 4 -12.641 -2.367 25.968 1 12.59 ? C4 SAM 403 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #