data_5PA4 # _model_server_result.job_id kGs8XAKFdlibvBQ-shzvgA _model_server_result.datetime_utc '2024-11-27 19:18:07' _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 5pa4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 5PA4 # _exptl.entry_id 5PA4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _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 5PA4 _cell.length_a 49.676 _cell.length_b 54.204 _cell.length_c 81.426 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5PA4 _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 PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 3 _struct_asym.id C _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 OD1 ASP 141 A ASP 141 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc2 A OD2 ASP 169 A ASP 169 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc3 A OD1 ASN 170 A ASN 170 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc4 B MG MG . A MG 301 1_555 D O12 7JD . A 7JD 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc5 B MG MG . A MG 301 1_555 F O HOH . A HOH 441 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag n _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type 'l-peptide linking' _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 SAH sing 307 n n N HN1 SAH sing 308 n n N HN2 SAH sing 309 n n CA CB SAH sing 310 n n CA C SAH sing 311 n n CA HA SAH sing 312 n n CB CG SAH sing 313 n n CB HB1 SAH sing 314 n n CB HB2 SAH sing 315 n n CG SD SAH sing 316 n n CG HG1 SAH sing 317 n n CG HG2 SAH sing 318 n n SD C5' SAH sing 319 n n C O SAH doub 320 n n C OXT SAH sing 321 n n OXT HXT SAH sing 322 n n C5' C4' SAH sing 323 n n C5' "H5'1" SAH sing 324 n n C5' "H5'2" SAH sing 325 n n C4' O4' SAH sing 326 n n C4' C3' SAH sing 327 n n C4' H4' SAH sing 328 n n O4' C1' SAH sing 329 n n C3' O3' SAH sing 330 n n C3' C2' SAH sing 331 n n C3' H3' SAH sing 332 n n O3' HO3' SAH sing 333 n n C2' O2' SAH sing 334 n n C2' C1' SAH sing 335 n n C2' H2' SAH sing 336 n n O2' HO2' SAH sing 337 n n C1' N9 SAH sing 338 n n C1' H1' SAH sing 339 n n N9 C8 SAH sing 340 n y N9 C4 SAH sing 341 n y C8 N7 SAH doub 342 n y C8 H8 SAH sing 343 n n N7 C5 SAH sing 344 n y C5 C6 SAH sing 345 n y C5 C4 SAH doub 346 n y C6 N6 SAH sing 347 n n C6 N1 SAH doub 348 n y N6 HN61 SAH sing 349 n n N6 HN62 SAH sing 350 n n N1 C2 SAH sing 351 n y C2 N3 SAH doub 352 n y C2 H2 SAH sing 353 n n N3 C4 SAH sing 354 n y # _atom_sites.entry_id 5PA4 _atom_sites.fract_transf_matrix[1][1] 0.02013 _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] 0.018449 _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] 0.012281 _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 MG A 1 301 1 MG MG . C 3 SAH A 1 302 1 SAH SAH . D 4 7JD A 1 303 1 7JD LIG . E 5 SO4 A 1 304 1 SO4 SO4 . F 6 HOH A 1 401 84 HOH HOH . F 6 HOH A 2 402 30 HOH HOH . F 6 HOH A 3 403 60 HOH HOH . F 6 HOH A 4 404 95 HOH HOH . F 6 HOH A 5 405 51 HOH HOH . F 6 HOH A 6 406 97 HOH HOH . F 6 HOH A 7 407 94 HOH HOH . F 6 HOH A 8 408 48 HOH HOH . F 6 HOH A 9 409 5 HOH HOH . F 6 HOH A 10 410 54 HOH HOH . F 6 HOH A 11 411 78 HOH HOH . F 6 HOH A 12 412 83 HOH HOH . F 6 HOH A 13 413 17 HOH HOH . F 6 HOH A 14 414 93 HOH HOH . F 6 HOH A 15 415 33 HOH HOH . F 6 HOH A 16 416 14 HOH HOH . F 6 HOH A 17 417 65 HOH HOH . F 6 HOH A 18 418 22 HOH HOH . F 6 HOH A 19 419 12 HOH HOH . F 6 HOH A 20 420 35 HOH HOH . F 6 HOH A 21 421 88 HOH HOH . F 6 HOH A 22 422 61 HOH HOH . F 6 HOH A 23 423 47 HOH HOH . F 6 HOH A 24 424 9 HOH HOH . F 6 HOH A 25 425 80 HOH HOH . F 6 HOH A 26 426 11 HOH HOH . F 6 HOH A 27 427 67 HOH HOH . F 6 HOH A 28 428 59 HOH HOH . F 6 HOH A 29 429 49 HOH HOH . F 6 HOH A 30 430 52 HOH HOH . F 6 HOH A 31 431 13 HOH HOH . F 6 HOH A 32 432 56 HOH HOH . F 6 HOH A 33 433 57 HOH HOH . F 6 HOH A 34 434 79 HOH HOH . F 6 HOH A 35 435 41 HOH HOH . F 6 HOH A 36 436 42 HOH HOH . F 6 HOH A 37 437 73 HOH HOH . F 6 HOH A 38 438 29 HOH HOH . F 6 HOH A 39 439 92 HOH HOH . F 6 HOH A 40 440 6 HOH HOH . F 6 HOH A 41 441 1 HOH HOH . F 6 HOH A 42 442 7 HOH HOH . F 6 HOH A 43 443 38 HOH HOH . F 6 HOH A 44 444 20 HOH HOH . F 6 HOH A 45 445 75 HOH HOH . F 6 HOH A 46 446 4 HOH HOH . F 6 HOH A 47 447 71 HOH HOH . F 6 HOH A 48 448 44 HOH HOH . F 6 HOH A 49 449 77 HOH HOH . F 6 HOH A 50 450 37 HOH HOH . F 6 HOH A 51 451 16 HOH HOH . F 6 HOH A 52 452 15 HOH HOH . F 6 HOH A 53 453 72 HOH HOH . F 6 HOH A 54 454 82 HOH HOH . F 6 HOH A 55 455 70 HOH HOH . F 6 HOH A 56 456 26 HOH HOH . F 6 HOH A 57 457 10 HOH HOH . F 6 HOH A 58 458 45 HOH HOH . F 6 HOH A 59 459 2 HOH HOH . F 6 HOH A 60 460 8 HOH HOH . F 6 HOH A 61 461 46 HOH HOH . F 6 HOH A 62 462 36 HOH HOH . F 6 HOH A 63 463 25 HOH HOH . F 6 HOH A 64 464 58 HOH HOH . F 6 HOH A 65 465 3 HOH HOH . F 6 HOH A 66 466 81 HOH HOH . F 6 HOH A 67 467 43 HOH HOH . F 6 HOH A 68 468 34 HOH HOH . F 6 HOH A 69 469 28 HOH HOH . F 6 HOH A 70 470 53 HOH HOH . F 6 HOH A 71 471 23 HOH HOH . F 6 HOH A 72 472 55 HOH HOH . F 6 HOH A 73 473 64 HOH HOH . F 6 HOH A 74 474 27 HOH HOH . F 6 HOH A 75 475 21 HOH HOH . F 6 HOH A 76 476 90 HOH HOH . F 6 HOH A 77 477 19 HOH HOH . F 6 HOH A 78 478 87 HOH HOH . F 6 HOH A 79 479 18 HOH HOH . F 6 HOH A 80 480 24 HOH HOH . F 6 HOH A 81 481 62 HOH HOH . F 6 HOH A 82 482 86 HOH HOH . F 6 HOH A 83 483 32 HOH HOH . F 6 HOH A 84 484 89 HOH HOH . F 6 HOH A 85 485 85 HOH HOH . F 6 HOH A 86 486 50 HOH HOH . F 6 HOH A 87 487 63 HOH HOH . F 6 HOH A 88 488 66 HOH HOH . F 6 HOH A 89 489 68 HOH HOH . F 6 HOH A 90 490 40 HOH HOH . F 6 HOH A 91 491 39 HOH HOH . F 6 HOH A 92 492 74 HOH HOH . F 6 HOH A 93 493 91 HOH HOH . F 6 HOH A 94 494 76 HOH HOH . F 6 HOH A 95 495 96 HOH HOH . F 6 HOH A 96 496 69 HOH HOH . F 6 HOH A 97 497 31 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 SAH . . . C 3 3.118 5.724 28.091 1 27.91 ? N SAH 302 A 1 HETATM 2 C CA SAH . . . C 3 3.274 5.9 26.599 1 31.69 ? CA SAH 302 A 1 HETATM 3 C CB SAH . . . C 3 2.458 7.072 26.065 1 30.67 ? CB SAH 302 A 1 HETATM 4 C CG SAH . . . C 3 0.974 6.883 26.342 1 28.42 ? CG SAH 302 A 1 HETATM 5 S SD SAH . . . C 3 0.119 8.061 25.355 1 23.18 ? SD SAH 302 A 1 HETATM 6 C C SAH . . . C 3 4.711 6.143 26.198 1 31.69 ? C SAH 302 A 1 HETATM 7 O O SAH . . . C 3 5.2 5.523 25.25 1 33.73 ? O SAH 302 A 1 HETATM 8 O OXT SAH . . . C 3 5.421 6.964 26.773 1 30.67 ? OXT SAH 302 A 1 HETATM 9 C C5' SAH . . . C 3 -1.531 8.047 26.028 1 26.08 ? C5' SAH 302 A 1 HETATM 10 C C4' SAH . . . C 3 -2.209 6.681 25.874 1 25.95 ? C4' SAH 302 A 1 HETATM 11 O O4' SAH . . . C 3 -3.13 6.425 26.964 1 27 ? O4' SAH 302 A 1 HETATM 12 C C3' SAH . . . C 3 -3.007 6.524 24.569 1 25.69 ? C3' SAH 302 A 1 HETATM 13 O O3' SAH . . . C 3 -2.553 5.343 23.888 1 24.36 ? O3' SAH 302 A 1 HETATM 14 C C2' SAH . . . C 3 -4.467 6.345 25.019 1 26.22 ? C2' SAH 302 A 1 HETATM 15 O O2' SAH . . . C 3 -5.165 5.422 24.204 1 23.15 ? O2' SAH 302 A 1 HETATM 16 C C1' SAH . . . C 3 -4.339 5.811 26.452 1 25.48 ? C1' SAH 302 A 1 HETATM 17 N N9 SAH . . . C 3 -5.471 6.094 27.373 1 22.08 ? N9 SAH 302 A 1 HETATM 18 C C8 SAH . . . C 3 -6.168 7.256 27.498 1 24.29 ? C8 SAH 302 A 1 HETATM 19 N N7 SAH . . . C 3 -7.102 7.169 28.469 1 24.26 ? N7 SAH 302 A 1 HETATM 20 C C5 SAH . . . C 3 -6.974 5.913 28.988 1 23.43 ? C5 SAH 302 A 1 HETATM 21 C C6 SAH . . . C 3 -7.639 5.124 30.035 1 23.75 ? C6 SAH 302 A 1 HETATM 22 N N6 SAH . . . C 3 -8.636 5.657 30.758 1 23.56 ? N6 SAH 302 A 1 HETATM 23 N N1 SAH . . . C 3 -7.226 3.854 30.234 1 25.95 ? N1 SAH 302 A 1 HETATM 24 C C2 SAH . . . C 3 -6.229 3.287 29.545 1 23.22 ? C2 SAH 302 A 1 HETATM 25 N N3 SAH . . . C 3 -5.581 3.936 28.574 1 24.17 ? N3 SAH 302 A 1 HETATM 26 C C4 SAH . . . C 3 -5.909 5.222 28.259 1 21.53 ? C4 SAH 302 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #