data_4RTM # _model_server_result.job_id uX--100EZvZcv1ouFJeLZQ _model_server_result.datetime_utc '2024-10-12 19:28:57' _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 4rtm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 4RTM # _exptl.entry_id 4RTM _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 4RTM _cell.length_a 36.376 _cell.length_b 63.073 _cell.length_c 143.216 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RTM _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,G _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 DC 2 F DC 2 1_555 C N1 DG 11 G DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 2 F DC 2 1_555 C O6 DG 11 G DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 2 F DC 2 1_555 C N2 DG 11 G DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DT 3 F DT 3 1_555 C N1 DA 10 G DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O4 DT 3 F DT 3 1_555 C N6 DA 10 G DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 DA 4 F DA 4 1_555 C N3 DT 9 G DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N6 DA 4 F DA 4 1_555 C O4 DT 9 G DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N1 DA 5 F DA 5 1_555 C N3 DT 8 G DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N6 DA 5 F DA 5 1_555 C O4 DT 8 G DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N1 DA 6 F DA 6 1_555 C N3 DT 7 G DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N6 DA 6 F DA 6 1_555 C O4 DT 7 G DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 DG 7 F DG 7 1_555 C N3 DC 6 G DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N2 DG 7 F DG 7 1_555 C O2 DC 6 G DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B O6 DG 7 F DG 7 1_555 C N4 DC 6 G DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog15 B N1 DA 8 F DA 8 1_555 C N3 DT 5 G DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 DT 9 F DT 9 1_555 C N1 DA 4 G DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B O4 DT 9 F DT 9 1_555 C N6 DA 4 G DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N3 DC 10 F DC 10 1_555 C N1 DG 3 G DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N4 DC 10 F DC 10 1_555 C O6 DG 3 G DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O2 DC 10 F DC 10 1_555 C N2 DG 3 G DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N1 DG 11 F DG 11 1_555 C N3 DC 2 G DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N2 DG 11 F DG 11 1_555 C O2 DC 2 G DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O6 DG 11 F DG 11 1_555 C N4 DC 2 G DC 2 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 426 n n N HN1 SAM sing 427 n n N HN2 SAM sing 428 n n CA C SAM sing 429 n n CA CB SAM sing 430 n n CA HA SAM sing 431 n n C O SAM doub 432 n n C OXT SAM sing 433 n n CB CG SAM sing 434 n n CB HB1 SAM sing 435 n n CB HB2 SAM sing 436 n n CG SD SAM sing 437 n n CG HG1 SAM sing 438 n n CG HG2 SAM sing 439 n n SD CE SAM sing 440 n n SD C5' SAM sing 441 n n CE HE1 SAM sing 442 n n CE HE2 SAM sing 443 n n CE HE3 SAM sing 444 n n C5' C4' SAM sing 445 n n C5' "H5'1" SAM sing 446 n n C5' "H5'2" SAM sing 447 n n C4' O4' SAM sing 448 n n C4' C3' SAM sing 449 n n C4' H4' SAM sing 450 n n O4' C1' SAM sing 451 n n C3' O3' SAM sing 452 n n C3' C2' SAM sing 453 n n C3' H3' SAM sing 454 n n O3' HO3' SAM sing 455 n n C2' O2' SAM sing 456 n n C2' C1' SAM sing 457 n n C2' H2' SAM sing 458 n n O2' HO2' SAM sing 459 n n C1' N9 SAM sing 460 n n C1' H1' SAM sing 461 n n N9 C8 SAM sing 462 n y N9 C4 SAM sing 463 n y C8 N7 SAM doub 464 n y C8 H8 SAM sing 465 n n N7 C5 SAM sing 466 n y C5 C6 SAM sing 467 n y C5 C4 SAM doub 468 n y C6 N6 SAM sing 469 n n C6 N1 SAM doub 470 n y N6 HN61 SAM sing 471 n n N6 HN62 SAM sing 472 n n N1 C2 SAM sing 473 n y C2 N3 SAM doub 474 n y C2 H2 SAM sing 475 n n N3 C4 SAM sing 476 n y # _atom_sites.entry_id 4RTM _atom_sites.fract_transf_matrix[1][1] 0.027491 _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] 0.015855 _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] 0.006982 _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 D 4 SAM A 1 301 301 SAM SAM . E 5 HOH A 1 401 1 HOH HOH . E 5 HOH A 2 402 2 HOH HOH . E 5 HOH A 3 403 3 HOH HOH . E 5 HOH A 4 404 4 HOH HOH . E 5 HOH A 5 405 5 HOH HOH . E 5 HOH A 6 406 6 HOH HOH . E 5 HOH A 7 407 7 HOH HOH . E 5 HOH A 8 408 8 HOH HOH . E 5 HOH A 9 409 9 HOH HOH . E 5 HOH A 10 410 10 HOH HOH . E 5 HOH A 11 411 11 HOH HOH . E 5 HOH A 12 412 12 HOH HOH . E 5 HOH A 13 413 13 HOH HOH . E 5 HOH A 14 414 14 HOH HOH . E 5 HOH A 15 415 15 HOH HOH . E 5 HOH A 16 416 17 HOH HOH . E 5 HOH A 17 417 18 HOH HOH . E 5 HOH A 18 418 19 HOH HOH . E 5 HOH A 19 419 20 HOH HOH . E 5 HOH A 20 420 21 HOH HOH . E 5 HOH A 21 421 22 HOH HOH . E 5 HOH A 22 422 23 HOH HOH . E 5 HOH A 23 423 24 HOH HOH . E 5 HOH A 24 424 25 HOH HOH . E 5 HOH A 25 425 26 HOH HOH . E 5 HOH A 26 426 27 HOH HOH . E 5 HOH A 27 427 28 HOH HOH . E 5 HOH A 28 428 29 HOH HOH . E 5 HOH A 29 429 31 HOH HOH . E 5 HOH A 30 430 36 HOH HOH . E 5 HOH A 31 431 37 HOH HOH . E 5 HOH A 32 432 39 HOH HOH . E 5 HOH A 33 433 40 HOH HOH . E 5 HOH A 34 434 41 HOH HOH . E 5 HOH A 35 435 43 HOH HOH . E 5 HOH A 36 436 45 HOH HOH . E 5 HOH A 37 437 46 HOH HOH . E 5 HOH A 38 438 47 HOH HOH . E 5 HOH A 39 439 48 HOH HOH . E 5 HOH A 40 440 50 HOH HOH . F 5 HOH F 1 101 16 HOH HOH . F 5 HOH F 2 102 32 HOH HOH . F 5 HOH F 3 103 33 HOH HOH . F 5 HOH F 4 104 34 HOH HOH . F 5 HOH F 5 105 44 HOH HOH . G 5 HOH G 1 101 30 HOH HOH . G 5 HOH G 2 102 35 HOH HOH . G 5 HOH G 3 103 38 HOH HOH . G 5 HOH G 4 104 42 HOH HOH . G 5 HOH G 5 105 49 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 . A . D 4 -7.591 -1.537 88.042 0.56 48.87 ? N SAM 301 A 1 HETATM 2 N N SAM . B . D 4 -4.953 1.399 83.228 0.44 49.44 ? N SAM 301 A 1 HETATM 3 C CA SAM . A . D 4 -7.292 -0.847 89.292 0.56 48.58 ? CA SAM 301 A 1 HETATM 4 C CA SAM . B . D 4 -4.79 2.231 84.414 0.44 49.59 ? CA SAM 301 A 1 HETATM 5 C C SAM . A . D 4 -8.454 0.021 89.77 0.56 50.33 ? C SAM 301 A 1 HETATM 6 C C SAM . B . D 4 -4.222 3.608 84.088 0.44 50.48 ? C SAM 301 A 1 HETATM 7 O O SAM . A . D 4 -9.611 -0.228 89.431 0.56 51.7 ? O SAM 301 A 1 HETATM 8 O O SAM . B . D 4 -3.09 3.735 83.622 0.44 49.3 ? O SAM 301 A 1 HETATM 9 O OXT SAM . A . D 4 -8.262 0.981 90.517 0.56 48.29 ? OXT SAM 301 A 1 HETATM 10 O OXT SAM . B . D 4 -4.88 4.628 84.297 0.44 55.03 ? OXT SAM 301 A 1 HETATM 11 C CB SAM . A . D 4 -6.007 -0.031 89.182 0.56 48.72 ? CB SAM 301 A 1 HETATM 12 C CB SAM . B . D 4 -3.889 1.543 85.43 0.44 49.92 ? CB SAM 301 A 1 HETATM 13 C CG SAM . A . D 4 -5.35 -0.013 87.809 0.56 48.93 ? CG SAM 301 A 1 HETATM 14 C CG SAM . B . D 4 -4.623 0.721 86.48 0.44 50.8 ? CG SAM 301 A 1 HETATM 15 S SD SAM . A . D 4 -3.873 1.032 87.808 0.56 54.09 ? SD SAM 301 A 1 HETATM 16 S SD SAM . B . D 4 -3.933 1.009 88.128 0.44 52.43 ? SD SAM 301 A 1 HETATM 17 C CE SAM . A . D 4 -3.865 1.601 86.089 0.56 51.98 ? CE SAM 301 A 1 HETATM 18 C CE SAM . B . D 4 -3.28 2.69 87.951 0.44 49.38 ? CE SAM 301 A 1 HETATM 19 C C5' SAM . A . D 4 -2.555 -0.209 87.761 0.56 43.86 ? C5' SAM 301 A 1 HETATM 20 C C5' SAM . B . D 4 -2.411 0.04 88.004 0.44 43.96 ? C5' SAM 301 A 1 HETATM 21 C C4' SAM . A . D 4 -1.992 -0.54 89.139 0.56 40.74 ? C4' SAM 301 A 1 HETATM 22 C C4' SAM . B . D 4 -1.902 -0.46 89.348 0.44 40.78 ? C4' SAM 301 A 1 HETATM 23 O O4' SAM . A . D 4 -1.002 -1.539 89.002 0.56 41.79 ? O4' SAM 301 A 1 HETATM 24 O O4' SAM . B . D 4 -0.948 -1.474 89.116 0.44 41.55 ? O4' SAM 301 A 1 HETATM 25 C C3' SAM . A . D 4 -1.333 0.657 89.809 0.56 41.04 ? C3' SAM 301 A 1 HETATM 26 C C3' SAM . B . D 4 -1.212 0.637 90.145 0.44 41.16 ? C3' SAM 301 A 1 HETATM 27 O O3' SAM . A . D 4 -2.029 0.985 90.989 0.56 40.2 ? O3' SAM 301 A 1 HETATM 28 O O3' SAM . B . D 4 -1.874 0.826 91.374 0.44 39.65 ? O3' SAM 301 A 1 HETATM 29 C C2' SAM . A . D 4 0.076 0.211 90.15 0.56 39.73 ? C2' SAM 301 A 1 HETATM 30 C C2' SAM . B . D 4 0.197 0.139 90.394 0.44 39.57 ? C2' SAM 301 A 1 HETATM 31 O O2' SAM . A . D 4 0.353 0.45 91.51 0.56 37.15 ? O2' SAM 301 A 1 HETATM 32 O O2' SAM . B . D 4 0.521 0.252 91.76 0.44 37.11 ? O2' SAM 301 A 1 HETATM 33 C C1' SAM . A . D 4 0.1 -1.279 89.848 0.56 40.06 ? C1' SAM 301 A 1 HETATM 34 C C1' SAM . B . D 4 0.171 -1.32 89.965 0.44 40.28 ? C1' SAM 301 A 1 HETATM 35 N N9 SAM . A . D 4 1.354 -1.66 89.174 0.56 36.35 ? N9 SAM 301 A 1 HETATM 36 N N9 SAM . B . D 4 1.399 -1.693 89.241 0.44 36.85 ? N9 SAM 301 A 1 HETATM 37 C C8 SAM . A . D 4 2.145 -0.847 88.405 0.56 37.28 ? C8 SAM 301 A 1 HETATM 38 C C8 SAM . B . D 4 2.166 -0.873 88.456 0.44 37.3 ? C8 SAM 301 A 1 HETATM 39 N N7 SAM . A . D 4 3.203 -1.567 87.967 0.56 35.58 ? N7 SAM 301 A 1 HETATM 40 N N7 SAM . B . D 4 3.204 -1.593 87.971 0.44 36.29 ? N7 SAM 301 A 1 HETATM 41 C C5 SAM . A . D 4 3.099 -2.826 88.443 0.56 38.03 ? C5 SAM 301 A 1 HETATM 42 C C5 SAM . B . D 4 3.109 -2.858 88.434 0.44 38 ? C5 SAM 301 A 1 HETATM 43 C C6 SAM . A . D 4 3.903 -3.95 88.297 0.56 38.5 ? C6 SAM 301 A 1 HETATM 44 C C6 SAM . B . D 4 3.9 -3.985 88.246 0.44 38.35 ? C6 SAM 301 A 1 HETATM 45 N N6 SAM . A . D 4 5.015 -3.887 87.569 0.56 39.31 ? N6 SAM 301 A 1 HETATM 46 N N6 SAM . B . D 4 4.986 -3.92 87.481 0.44 39.2 ? N6 SAM 301 A 1 HETATM 47 N N1 SAM . A . D 4 3.541 -5.13 88.912 0.56 37.85 ? N1 SAM 301 A 1 HETATM 48 N N1 SAM . B . D 4 3.551 -5.171 88.858 0.44 37.87 ? N1 SAM 301 A 1 HETATM 49 C C2 SAM . A . D 4 2.384 -5.185 89.665 0.56 36.31 ? C2 SAM 301 A 1 HETATM 50 C C2 SAM . B . D 4 2.422 -5.23 89.65 0.44 36.39 ? C2 SAM 301 A 1 HETATM 51 N N3 SAM . A . D 4 1.59 -4.064 89.805 0.56 36.42 ? N3 SAM 301 A 1 HETATM 52 N N3 SAM . B . D 4 1.641 -4.106 89.832 0.44 36.19 ? N3 SAM 301 A 1 HETATM 53 C C4 SAM . A . D 4 1.942 -2.9 89.205 0.56 36.54 ? C4 SAM 301 A 1 HETATM 54 C C4 SAM . B . D 4 1.979 -2.936 89.235 0.44 36.78 ? C4 SAM 301 A 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 54 #