data_5KOC # _model_server_result.job_id QJkkxznpAlf24lmThg-hbg _model_server_result.datetime_utc '2024-11-04 22:44:40' _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 5koc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 5KOC # _exptl.entry_id 5KOC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYLMETHIONINE _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 98.97 _cell.angle_gamma 90 _cell.entry_id 5KOC _cell.length_a 54.572 _cell.length_b 72.005 _cell.length_c 96.247 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KOC _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N # _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 277 n n N HN1 SAM sing 278 n n N HN2 SAM sing 279 n n CA C SAM sing 280 n n CA CB SAM sing 281 n n CA HA SAM sing 282 n n C O SAM doub 283 n n C OXT SAM sing 284 n n CB CG SAM sing 285 n n CB HB1 SAM sing 286 n n CB HB2 SAM sing 287 n n CG SD SAM sing 288 n n CG HG1 SAM sing 289 n n CG HG2 SAM sing 290 n n SD CE SAM sing 291 n n SD C5' SAM sing 292 n n CE HE1 SAM sing 293 n n CE HE2 SAM sing 294 n n CE HE3 SAM sing 295 n n C5' C4' SAM sing 296 n n C5' "H5'1" SAM sing 297 n n C5' "H5'2" SAM sing 298 n n C4' O4' SAM sing 299 n n C4' C3' SAM sing 300 n n C4' H4' SAM sing 301 n n O4' C1' SAM sing 302 n n C3' O3' SAM sing 303 n n C3' C2' SAM sing 304 n n C3' H3' SAM sing 305 n n O3' HO3' SAM sing 306 n n C2' O2' SAM sing 307 n n C2' C1' SAM sing 308 n n C2' H2' SAM sing 309 n n O2' HO2' SAM sing 310 n n C1' N9 SAM sing 311 n n C1' H1' SAM sing 312 n n N9 C8 SAM sing 313 n y N9 C4 SAM sing 314 n y C8 N7 SAM doub 315 n y C8 H8 SAM sing 316 n n N7 C5 SAM sing 317 n y C5 C6 SAM sing 318 n y C5 C4 SAM doub 319 n y C6 N6 SAM sing 320 n n C6 N1 SAM doub 321 n y N6 HN61 SAM sing 322 n n N6 HN62 SAM sing 323 n n N1 C2 SAM sing 324 n y C2 N3 SAM doub 325 n y C2 H2 SAM sing 326 n n N3 C4 SAM sing 327 n y # _atom_sites.entry_id 5KOC _atom_sites.fract_transf_matrix[1][1] 0.018324 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002892 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013888 _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] 0.010519 _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 2 SAM A 1 401 1 SAM SAM . D 2 SAM B 1 401 1 SAM SAM . E 3 HOH A 1 501 48 HOH HOH . E 3 HOH A 2 502 40 HOH HOH . E 3 HOH A 3 503 36 HOH HOH . E 3 HOH A 4 504 19 HOH HOH . E 3 HOH A 5 505 55 HOH HOH . E 3 HOH A 6 506 26 HOH HOH . E 3 HOH A 7 507 49 HOH HOH . E 3 HOH A 8 508 47 HOH HOH . E 3 HOH A 9 509 12 HOH HOH . E 3 HOH A 10 510 39 HOH HOH . E 3 HOH A 11 511 95 HOH HOH . E 3 HOH A 12 512 4 HOH HOH . E 3 HOH A 13 513 62 HOH HOH . E 3 HOH A 14 514 27 HOH HOH . E 3 HOH A 15 515 120 HOH HOH . E 3 HOH A 16 516 16 HOH HOH . E 3 HOH A 17 517 78 HOH HOH . E 3 HOH A 18 518 88 HOH HOH . E 3 HOH A 19 519 93 HOH HOH . E 3 HOH A 20 520 2 HOH HOH . E 3 HOH A 21 521 92 HOH HOH . E 3 HOH A 22 522 21 HOH HOH . E 3 HOH A 23 523 110 HOH HOH . E 3 HOH A 24 524 33 HOH HOH . E 3 HOH A 25 525 23 HOH HOH . E 3 HOH A 26 526 64 HOH HOH . E 3 HOH A 27 527 42 HOH HOH . E 3 HOH A 28 528 84 HOH HOH . E 3 HOH A 29 529 109 HOH HOH . E 3 HOH A 30 530 14 HOH HOH . E 3 HOH A 31 531 18 HOH HOH . E 3 HOH A 32 532 82 HOH HOH . E 3 HOH A 33 533 50 HOH HOH . E 3 HOH A 34 534 107 HOH HOH . E 3 HOH A 35 535 116 HOH HOH . E 3 HOH A 36 536 41 HOH HOH . E 3 HOH A 37 537 51 HOH HOH . E 3 HOH A 38 538 71 HOH HOH . E 3 HOH A 39 539 35 HOH HOH . E 3 HOH A 40 540 46 HOH HOH . E 3 HOH A 41 541 112 HOH HOH . E 3 HOH A 42 542 97 HOH HOH . E 3 HOH A 43 543 94 HOH HOH . E 3 HOH A 44 544 98 HOH HOH . E 3 HOH A 45 545 90 HOH HOH . E 3 HOH A 46 546 8 HOH HOH . E 3 HOH A 47 547 17 HOH HOH . E 3 HOH A 48 548 79 HOH HOH . E 3 HOH A 49 549 125 HOH HOH . F 3 HOH B 1 501 80 HOH HOH . F 3 HOH B 2 502 29 HOH HOH . F 3 HOH B 3 503 101 HOH HOH . F 3 HOH B 4 504 123 HOH HOH . F 3 HOH B 5 505 43 HOH HOH . F 3 HOH B 6 506 69 HOH HOH . F 3 HOH B 7 507 126 HOH HOH . F 3 HOH B 8 508 60 HOH HOH . F 3 HOH B 9 509 118 HOH HOH . F 3 HOH B 10 510 5 HOH HOH . F 3 HOH B 11 511 86 HOH HOH . F 3 HOH B 12 512 75 HOH HOH . F 3 HOH B 13 513 10 HOH HOH . F 3 HOH B 14 514 34 HOH HOH . F 3 HOH B 15 515 6 HOH HOH . F 3 HOH B 16 516 105 HOH HOH . F 3 HOH B 17 517 13 HOH HOH . F 3 HOH B 18 518 104 HOH HOH . F 3 HOH B 19 519 25 HOH HOH . F 3 HOH B 20 520 96 HOH HOH . F 3 HOH B 21 521 31 HOH HOH . F 3 HOH B 22 522 68 HOH HOH . F 3 HOH B 23 523 7 HOH HOH . F 3 HOH B 24 524 59 HOH HOH . F 3 HOH B 25 525 91 HOH HOH . F 3 HOH B 26 526 3 HOH HOH . F 3 HOH B 27 527 53 HOH HOH . F 3 HOH B 28 528 124 HOH HOH . F 3 HOH B 29 529 74 HOH HOH . F 3 HOH B 30 530 102 HOH HOH . F 3 HOH B 31 531 63 HOH HOH . F 3 HOH B 32 532 56 HOH HOH . F 3 HOH B 33 533 65 HOH HOH . F 3 HOH B 34 534 30 HOH HOH . F 3 HOH B 35 535 70 HOH HOH . F 3 HOH B 36 536 87 HOH HOH . F 3 HOH B 37 537 99 HOH HOH . F 3 HOH B 38 538 57 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 2 3.875 65.981 -35.89 1 51.52 ? N SAM 401 B 1 HETATM 2 C CA SAM . . . D 2 3.788 66.932 -37.029 1 54.91 ? CA SAM 401 B 1 HETATM 3 C C SAM . . . D 2 2.43 67.661 -36.994 1 55.12 ? C SAM 401 B 1 HETATM 4 O O SAM . . . D 2 2.247 68.627 -37.883 1 59.14 ? O SAM 401 B 1 HETATM 5 O OXT SAM . . . D 2 1.604 67.34 -36.141 1 54.66 ? OXT SAM 401 B 1 HETATM 6 C CB SAM . . . D 2 3.987 66.173 -38.358 1 56.22 ? CB SAM 401 B 1 HETATM 7 C CG SAM . . . D 2 2.746 65.864 -39.212 1 60.26 ? CG SAM 401 B 1 HETATM 8 S SD SAM . . . D 2 2.753 64.277 -39.91 1 70.59 ? SD SAM 401 B 1 HETATM 9 C CE SAM . . . D 2 1.177 63.969 -40.704 1 62.05 ? CE SAM 401 B 1 HETATM 10 C C5' SAM . . . D 2 3.902 63.894 -41.138 1 64.2 ? C5' SAM 401 B 1 HETATM 11 C C4' SAM . . . D 2 5.34 64.439 -40.932 1 62.22 ? C4' SAM 401 B 1 HETATM 12 O O4' SAM . . . D 2 6.328 63.384 -40.847 1 58.34 ? O4' SAM 401 B 1 HETATM 13 C C3' SAM . . . D 2 5.694 65.283 -42.161 1 60.67 ? C3' SAM 401 B 1 HETATM 14 O O3' SAM . . . D 2 5.933 66.638 -41.792 1 60.69 ? O3' SAM 401 B 1 HETATM 15 C C2' SAM . . . D 2 6.945 64.602 -42.743 1 62.32 ? C2' SAM 401 B 1 HETATM 16 O O2' SAM . . . D 2 7.899 65.551 -43.231 1 65.01 ? O2' SAM 401 B 1 HETATM 17 C C1' SAM . . . D 2 7.473 63.821 -41.539 1 60.44 ? C1' SAM 401 B 1 HETATM 18 N N9 SAM . . . D 2 8.305 62.664 -41.875 1 57.38 ? N9 SAM 401 B 1 HETATM 19 C C8 SAM . . . D 2 7.909 61.462 -42.407 1 53.33 ? C8 SAM 401 B 1 HETATM 20 N N7 SAM . . . D 2 8.895 60.621 -42.617 1 50.32 ? N7 SAM 401 B 1 HETATM 21 C C5 SAM . . . D 2 10.018 61.319 -42.196 1 55.41 ? C5 SAM 401 B 1 HETATM 22 C C6 SAM . . . D 2 11.386 60.983 -42.146 1 58.65 ? C6 SAM 401 B 1 HETATM 23 N N6 SAM . . . D 2 11.878 59.804 -42.541 1 58.23 ? N6 SAM 401 B 1 HETATM 24 N N1 SAM . . . D 2 12.245 61.915 -41.67 1 54.99 ? N1 SAM 401 B 1 HETATM 25 C C2 SAM . . . D 2 11.762 63.093 -41.271 1 55 ? C2 SAM 401 B 1 HETATM 26 N N3 SAM . . . D 2 10.497 63.518 -41.261 1 58.79 ? N3 SAM 401 B 1 HETATM 27 C C4 SAM . . . D 2 9.669 62.579 -41.737 1 58.32 ? C4 SAM 401 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #