data_7JPE # _model_server_result.job_id '_Ku15FNqtkixAYYExdXDKg' _model_server_result.datetime_utc '2024-11-21 11:21:22' _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 7jpe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 7JPE # _exptl.entry_id 7JPE _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 7JPE _cell.length_a 170.93 _cell.length_b 170.93 _cell.length_c 52.786 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7JPE _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 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,I _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 B SG CYS 77 B CYS 74 1_555 F ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc2 B SG CYS 80 B CYS 77 1_555 F ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc3 B NE2 HIS 86 B HIS 83 1_555 F ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc4 B SG CYS 93 B CYS 90 1_555 F ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc5 B SG CYS 120 B CYS 117 1_555 G ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc6 B SG CYS 123 B CYS 120 1_555 G ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc7 B SG CYS 131 B CYS 128 1_555 G ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc8 B SG CYS 133 B CYS 130 1_555 G ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? # _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 412 n n N HN1 SAM sing 413 n n N HN2 SAM sing 414 n n CA C SAM sing 415 n n CA CB SAM sing 416 n n CA HA SAM sing 417 n n C O SAM doub 418 n n C OXT SAM sing 419 n n CB CG SAM sing 420 n n CB HB1 SAM sing 421 n n CB HB2 SAM sing 422 n n CG SD SAM sing 423 n n CG HG1 SAM sing 424 n n CG HG2 SAM sing 425 n n SD CE SAM sing 426 n n SD C5' SAM sing 427 n n CE HE1 SAM sing 428 n n CE HE2 SAM sing 429 n n CE HE3 SAM sing 430 n n C5' C4' SAM sing 431 n n C5' "H5'1" SAM sing 432 n n C5' "H5'2" SAM sing 433 n n C4' O4' SAM sing 434 n n C4' C3' SAM sing 435 n n C4' H4' SAM sing 436 n n O4' C1' SAM sing 437 n n C3' O3' SAM sing 438 n n C3' C2' SAM sing 439 n n C3' H3' SAM sing 440 n n O3' HO3' SAM sing 441 n n C2' O2' SAM sing 442 n n C2' C1' SAM sing 443 n n C2' H2' SAM sing 444 n n O2' HO2' SAM sing 445 n n C1' N9 SAM sing 446 n n C1' H1' SAM sing 447 n n N9 C8 SAM sing 448 n y N9 C4 SAM sing 449 n y C8 N7 SAM doub 450 n y C8 H8 SAM sing 451 n n N7 C5 SAM sing 452 n y C5 C6 SAM sing 453 n y C5 C4 SAM doub 454 n y C6 N6 SAM sing 455 n n C6 N1 SAM doub 456 n y N6 HN61 SAM sing 457 n n N6 HN62 SAM sing 458 n n N1 C2 SAM sing 459 n y C2 N3 SAM doub 460 n y C2 H2 SAM sing 461 n n N3 C4 SAM sing 462 n y # _atom_sites.entry_id 7JPE _atom_sites.fract_transf_matrix[1][1] 0.00585 _atom_sites.fract_transf_matrix[1][2] 0.003378 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006755 _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] 0.018944 _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 GTA A 1 301 303 GTA GTA . D 4 SAM A 1 302 403 SAM SAM . E 5 M7G A 1 303 503 M7G 8NK . F 6 ZN B 1 201 148 ZN ZN . G 6 ZN B 1 202 149 ZN ZN . H 7 HOH A 1 401 71 HOH HOH . H 7 HOH A 2 402 14 HOH HOH . H 7 HOH A 3 403 33 HOH HOH . H 7 HOH A 4 404 107 HOH HOH . H 7 HOH A 5 405 42 HOH HOH . H 7 HOH A 6 406 60 HOH HOH . H 7 HOH A 7 407 13 HOH HOH . H 7 HOH A 8 408 23 HOH HOH . H 7 HOH A 9 409 39 HOH HOH . H 7 HOH A 10 410 104 HOH HOH . H 7 HOH A 11 411 117 HOH HOH . H 7 HOH A 12 412 11 HOH HOH . H 7 HOH A 13 413 50 HOH HOH . H 7 HOH A 14 414 55 HOH HOH . H 7 HOH A 15 415 86 HOH HOH . H 7 HOH A 16 416 127 HOH HOH . H 7 HOH A 17 417 125 HOH HOH . H 7 HOH A 18 418 28 HOH HOH . H 7 HOH A 19 419 52 HOH HOH . H 7 HOH A 20 420 45 HOH HOH . H 7 HOH A 21 421 8 HOH HOH . H 7 HOH A 22 422 122 HOH HOH . H 7 HOH A 23 423 7 HOH HOH . H 7 HOH A 24 424 27 HOH HOH . H 7 HOH A 25 425 6 HOH HOH . H 7 HOH A 26 426 12 HOH HOH . H 7 HOH A 27 427 99 HOH HOH . H 7 HOH A 28 428 111 HOH HOH . H 7 HOH A 29 429 38 HOH HOH . H 7 HOH A 30 430 124 HOH HOH . H 7 HOH A 31 431 44 HOH HOH . H 7 HOH A 32 432 26 HOH HOH . H 7 HOH A 33 433 5 HOH HOH . H 7 HOH A 34 434 70 HOH HOH . H 7 HOH A 35 435 2 HOH HOH . H 7 HOH A 36 436 97 HOH HOH . H 7 HOH A 37 437 56 HOH HOH . H 7 HOH A 38 438 25 HOH HOH . H 7 HOH A 39 439 90 HOH HOH . H 7 HOH A 40 440 67 HOH HOH . H 7 HOH A 41 441 3 HOH HOH . H 7 HOH A 42 442 94 HOH HOH . H 7 HOH A 43 443 49 HOH HOH . H 7 HOH A 44 444 20 HOH HOH . H 7 HOH A 45 445 73 HOH HOH . H 7 HOH A 46 446 53 HOH HOH . H 7 HOH A 47 447 29 HOH HOH . H 7 HOH A 48 448 84 HOH HOH . H 7 HOH A 49 449 1 HOH HOH . H 7 HOH A 50 450 103 HOH HOH . H 7 HOH A 51 451 102 HOH HOH . H 7 HOH A 52 452 62 HOH HOH . H 7 HOH A 53 453 16 HOH HOH . H 7 HOH A 54 454 48 HOH HOH . H 7 HOH A 55 455 4 HOH HOH . H 7 HOH A 56 456 31 HOH HOH . H 7 HOH A 57 457 43 HOH HOH . H 7 HOH A 58 458 35 HOH HOH . H 7 HOH A 59 459 96 HOH HOH . H 7 HOH A 60 460 9 HOH HOH . H 7 HOH A 61 461 88 HOH HOH . H 7 HOH A 62 462 123 HOH HOH . H 7 HOH A 63 463 61 HOH HOH . H 7 HOH A 64 464 15 HOH HOH . H 7 HOH A 65 465 34 HOH HOH . H 7 HOH A 66 466 83 HOH HOH . H 7 HOH A 67 467 59 HOH HOH . H 7 HOH A 68 468 66 HOH HOH . H 7 HOH A 69 469 78 HOH HOH . H 7 HOH A 70 470 24 HOH HOH . H 7 HOH A 71 471 121 HOH HOH . H 7 HOH A 72 472 65 HOH HOH . H 7 HOH A 73 473 120 HOH HOH . H 7 HOH A 74 474 40 HOH HOH . H 7 HOH A 75 475 106 HOH HOH . H 7 HOH A 76 476 95 HOH HOH . H 7 HOH A 77 477 58 HOH HOH . H 7 HOH A 78 478 85 HOH HOH . H 7 HOH A 79 479 119 HOH HOH . H 7 HOH A 80 480 63 HOH HOH . H 7 HOH A 81 481 37 HOH HOH . H 7 HOH A 82 482 21 HOH HOH . H 7 HOH A 83 483 89 HOH HOH . H 7 HOH A 84 484 92 HOH HOH . H 7 HOH A 85 485 116 HOH HOH . H 7 HOH A 86 486 93 HOH HOH . H 7 HOH A 87 487 77 HOH HOH . H 7 HOH A 88 488 110 HOH HOH . H 7 HOH A 89 489 74 HOH HOH . H 7 HOH A 90 490 64 HOH HOH . H 7 HOH A 91 491 108 HOH HOH . H 7 HOH A 92 492 54 HOH HOH . H 7 HOH A 93 493 91 HOH HOH . H 7 HOH A 94 494 100 HOH HOH . H 7 HOH A 95 495 47 HOH HOH . H 7 HOH A 96 496 109 HOH HOH . H 7 HOH A 97 497 98 HOH HOH . H 7 HOH A 98 498 69 HOH HOH . H 7 HOH A 99 499 101 HOH HOH . H 7 HOH A 100 500 105 HOH HOH . H 7 HOH A 101 501 115 HOH HOH . H 7 HOH A 102 502 118 HOH HOH . H 7 HOH A 103 503 46 HOH HOH . H 7 HOH A 104 504 76 HOH HOH . I 7 HOH B 1 301 114 HOH HOH . I 7 HOH B 2 302 79 HOH HOH . I 7 HOH B 3 303 10 HOH HOH . I 7 HOH B 4 304 36 HOH HOH . I 7 HOH B 5 305 75 HOH HOH . I 7 HOH B 6 306 126 HOH HOH . I 7 HOH B 7 307 30 HOH HOH . I 7 HOH B 8 308 18 HOH HOH . I 7 HOH B 9 309 19 HOH HOH . I 7 HOH B 10 310 68 HOH HOH . I 7 HOH B 11 311 22 HOH HOH . I 7 HOH B 12 312 51 HOH HOH . I 7 HOH B 13 313 82 HOH HOH . I 7 HOH B 14 314 57 HOH HOH . I 7 HOH B 15 315 80 HOH HOH . I 7 HOH B 16 316 17 HOH HOH . I 7 HOH B 17 317 112 HOH HOH . I 7 HOH B 18 318 81 HOH HOH . I 7 HOH B 19 319 113 HOH HOH . I 7 HOH B 20 320 41 HOH HOH . I 7 HOH B 21 321 87 HOH HOH . I 7 HOH B 22 322 72 HOH HOH . I 7 HOH B 23 323 32 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 60.996 -65.776 2.355 1 25.37 ? N SAM 302 A 1 HETATM 2 C CA SAM . . . D 4 61.069 -67.193 1.888 1 24.45 ? CA SAM 302 A 1 HETATM 3 C C SAM . . . D 4 62.309 -67.86 2.502 1 24.35 ? C SAM 302 A 1 HETATM 4 O O SAM . . . D 4 62.691 -67.522 3.623 1 23.44 ? O SAM 302 A 1 HETATM 5 O OXT SAM . . . D 4 62.953 -68.74 1.926 1 24.75 ? OXT SAM 302 A 1 HETATM 6 C CB SAM . . . D 4 61.122 -67.266 0.355 1 23.4 ? CB SAM 302 A 1 HETATM 7 C CG SAM . . . D 4 59.849 -66.761 -0.318 1 23.53 ? CG SAM 302 A 1 HETATM 8 S SD SAM . . . D 4 59.892 -66.988 -2.11 1 23.73 ? SD SAM 302 A 1 HETATM 9 C CE SAM . . . D 4 61.113 -65.768 -2.563 1 25.06 ? CE SAM 302 A 1 HETATM 10 C C5' SAM . . . D 4 58.372 -66.126 -2.563 1 22.3 ? C5' SAM 302 A 1 HETATM 11 C C4' SAM . . . D 4 57.125 -66.777 -2 1 22.43 ? C4' SAM 302 A 1 HETATM 12 O O4' SAM . . . D 4 55.986 -65.934 -2.274 1 21.61 ? O4' SAM 302 A 1 HETATM 13 C C3' SAM . . . D 4 56.773 -68.153 -2.583 1 22.71 ? C3' SAM 302 A 1 HETATM 14 O O3' SAM . . . D 4 56.968 -69.171 -1.606 1 22.05 ? O3' SAM 302 A 1 HETATM 15 C C2' SAM . . . D 4 55.299 -68.021 -3.007 1 22.79 ? C2' SAM 302 A 1 HETATM 16 O O2' SAM . . . D 4 54.509 -69.131 -2.635 1 22.57 ? O2' SAM 302 A 1 HETATM 17 C C1' SAM . . . D 4 54.857 -66.764 -2.267 1 22.6 ? C1' SAM 302 A 1 HETATM 18 N N9 SAM . . . D 4 53.736 -66.073 -2.891 1 24.03 ? N9 SAM 302 A 1 HETATM 19 C C8 SAM . . . D 4 53.665 -65.605 -4.18 1 25.54 ? C8 SAM 302 A 1 HETATM 20 N N7 SAM . . . D 4 52.515 -65.049 -4.472 1 25.04 ? N7 SAM 302 A 1 HETATM 21 C C5 SAM . . . D 4 51.773 -65.164 -3.306 1 25.95 ? C5 SAM 302 A 1 HETATM 22 C C6 SAM . . . D 4 50.461 -64.767 -2.975 1 25.87 ? C6 SAM 302 A 1 HETATM 23 N N6 SAM . . . D 4 49.632 -64.169 -3.827 1 24.86 ? N6 SAM 302 A 1 HETATM 24 N N1 SAM . . . D 4 50.026 -65.036 -1.72 1 25.33 ? N1 SAM 302 A 1 HETATM 25 C C2 SAM . . . D 4 50.864 -65.648 -0.872 1 24.92 ? C2 SAM 302 A 1 HETATM 26 N N3 SAM . . . D 4 52.111 -66.068 -1.071 1 23.62 ? N3 SAM 302 A 1 HETATM 27 C C4 SAM . . . D 4 52.515 -65.794 -2.323 1 24.93 ? C4 SAM 302 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #