data_5VAC # _model_server_result.job_id FW4JFDla2SOiM7jQ5G78Zw _model_server_result.datetime_utc '2024-10-12 12:26:59' _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 5vac # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 5VAC # _exptl.entry_id 5VAC _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 5VAC _cell.length_a 74.548 _cell.length_b 81.353 _cell.length_c 88.503 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VAC _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _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 # _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 # _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 286 n n N HN1 SAH sing 287 n n N HN2 SAH sing 288 n n CA CB SAH sing 289 n n CA C SAH sing 290 n n CA HA SAH sing 291 n n CB CG SAH sing 292 n n CB HB1 SAH sing 293 n n CB HB2 SAH sing 294 n n CG SD SAH sing 295 n n CG HG1 SAH sing 296 n n CG HG2 SAH sing 297 n n SD C5' SAH sing 298 n n C O SAH doub 299 n n C OXT SAH sing 300 n n OXT HXT SAH sing 301 n n C5' C4' SAH sing 302 n n C5' "H5'1" SAH sing 303 n n C5' "H5'2" SAH sing 304 n n C4' O4' SAH sing 305 n n C4' C3' SAH sing 306 n n C4' H4' SAH sing 307 n n O4' C1' SAH sing 308 n n C3' O3' SAH sing 309 n n C3' C2' SAH sing 310 n n C3' H3' SAH sing 311 n n O3' HO3' SAH sing 312 n n C2' O2' SAH sing 313 n n C2' C1' SAH sing 314 n n C2' H2' SAH sing 315 n n O2' HO2' SAH sing 316 n n C1' N9 SAH sing 317 n n C1' H1' SAH sing 318 n n N9 C8 SAH sing 319 n y N9 C4 SAH sing 320 n y C8 N7 SAH doub 321 n y C8 H8 SAH sing 322 n n N7 C5 SAH sing 323 n y C5 C6 SAH sing 324 n y C5 C4 SAH doub 325 n y C6 N6 SAH sing 326 n n C6 N1 SAH doub 327 n y N6 HN61 SAH sing 328 n n N6 HN62 SAH sing 329 n n N1 C2 SAH sing 330 n y C2 N3 SAH doub 331 n y C2 H2 SAH sing 332 n n N3 C4 SAH sing 333 n y # _atom_sites.entry_id 5VAC _atom_sites.fract_transf_matrix[1][1] 0.013414 _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] 0.012292 _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] 0.011299 _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 SAH A 1 401 120 SAH SAH . D 4 DMS A 1 402 3092 DMS DMS . E 5 HOH A 1 501 4 HOH HOH . E 5 HOH A 2 502 49 HOH HOH . E 5 HOH A 3 503 10 HOH HOH . E 5 HOH A 4 504 18 HOH HOH . E 5 HOH A 5 505 21 HOH HOH . E 5 HOH A 6 506 7 HOH HOH . E 5 HOH A 7 507 22 HOH HOH . E 5 HOH A 8 508 14 HOH HOH . E 5 HOH A 9 509 20 HOH HOH . E 5 HOH A 10 510 30 HOH HOH . E 5 HOH A 11 511 63 HOH HOH . E 5 HOH A 12 512 35 HOH HOH . E 5 HOH A 13 513 45 HOH HOH . E 5 HOH A 14 514 2 HOH HOH . E 5 HOH A 15 515 25 HOH HOH . E 5 HOH A 16 516 40 HOH HOH . E 5 HOH A 17 517 3 HOH HOH . E 5 HOH A 18 518 44 HOH HOH . E 5 HOH A 19 519 34 HOH HOH . E 5 HOH A 20 520 43 HOH HOH . E 5 HOH A 21 521 5 HOH HOH . E 5 HOH A 22 522 1 HOH HOH . E 5 HOH A 23 523 19 HOH HOH . E 5 HOH A 24 524 32 HOH HOH . E 5 HOH A 25 525 76 HOH HOH . E 5 HOH A 26 526 65 HOH HOH . E 5 HOH A 27 527 36 HOH HOH . E 5 HOH A 28 528 48 HOH HOH . E 5 HOH A 29 529 24 HOH HOH . E 5 HOH A 30 530 41 HOH HOH . E 5 HOH A 31 531 27 HOH HOH . E 5 HOH A 32 532 38 HOH HOH . E 5 HOH A 33 533 96 HOH HOH . E 5 HOH A 34 534 52 HOH HOH . E 5 HOH A 35 535 64 HOH HOH . E 5 HOH A 36 536 6 HOH HOH . E 5 HOH A 37 537 13 HOH HOH . E 5 HOH A 38 538 59 HOH HOH . E 5 HOH A 39 539 71 HOH HOH . E 5 HOH A 40 540 9 HOH HOH . E 5 HOH A 41 541 51 HOH HOH . E 5 HOH A 42 542 31 HOH HOH . E 5 HOH A 43 543 54 HOH HOH . E 5 HOH A 44 544 28 HOH HOH . E 5 HOH A 45 545 50 HOH HOH . E 5 HOH A 46 546 12 HOH HOH . E 5 HOH A 47 547 26 HOH HOH . E 5 HOH A 48 548 42 HOH HOH . E 5 HOH A 49 549 53 HOH HOH . E 5 HOH A 50 550 68 HOH HOH . E 5 HOH A 51 551 57 HOH HOH . E 5 HOH A 52 552 8 HOH HOH . E 5 HOH A 53 553 23 HOH HOH . E 5 HOH A 54 554 55 HOH HOH . E 5 HOH A 55 555 15 HOH HOH . E 5 HOH A 56 556 61 HOH HOH . E 5 HOH A 57 557 16 HOH HOH . E 5 HOH A 58 558 17 HOH HOH . E 5 HOH A 59 559 46 HOH HOH . E 5 HOH A 60 560 58 HOH HOH . E 5 HOH A 61 561 37 HOH HOH . E 5 HOH A 62 562 39 HOH HOH . E 5 HOH A 63 563 11 HOH HOH . E 5 HOH A 64 564 95 HOH HOH . E 5 HOH A 65 565 78 HOH HOH . E 5 HOH A 66 566 74 HOH HOH . E 5 HOH A 67 567 70 HOH HOH . E 5 HOH A 68 568 33 HOH HOH . E 5 HOH A 69 569 72 HOH HOH . E 5 HOH A 70 570 60 HOH HOH . E 5 HOH A 71 571 67 HOH HOH . E 5 HOH A 72 572 47 HOH HOH . E 5 HOH A 73 573 62 HOH HOH . E 5 HOH A 74 574 73 HOH HOH . E 5 HOH A 75 575 66 HOH HOH . E 5 HOH A 76 576 75 HOH HOH . E 5 HOH A 77 577 94 HOH HOH . F 5 HOH C 1 101 29 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 -27.007 -25.04 -24.744 1 35.95 ? N SAH 401 A 1 HETATM 2 C CA SAH . . . C 3 -27.723 -25.061 -23.472 1 38.08 ? CA SAH 401 A 1 HETATM 3 C CB SAH . . . C 3 -27.059 -24.12 -22.458 1 35.13 ? CB SAH 401 A 1 HETATM 4 C CG SAH . . . C 3 -25.814 -24.721 -21.807 1 31.61 ? CG SAH 401 A 1 HETATM 5 S SD SAH . . . C 3 -26.283 -26.022 -20.637 1 39.37 ? SD SAH 401 A 1 HETATM 6 C C SAH . . . C 3 -29.188 -24.718 -23.694 1 45.06 ? C SAH 401 A 1 HETATM 7 O O SAH . . . C 3 -29.65 -24.685 -24.832 1 45.48 ? O SAH 401 A 1 HETATM 8 O OXT SAH . . . C 3 -29.94 -24.46 -22.754 1 51.32 ? OXT SAH 401 A 1 HETATM 9 C C5' SAH . . . C 3 -25.16 -27.28 -21.333 1 39.24 ? C5' SAH 401 A 1 HETATM 10 C C4' SAH . . . C 3 -25.691 -27.98 -22.588 1 32.62 ? C4' SAH 401 A 1 HETATM 11 O O4' SAH . . . C 3 -25.46 -27.156 -23.727 1 32.25 ? O4' SAH 401 A 1 HETATM 12 C C3' SAH . . . C 3 -25.017 -29.318 -22.896 1 34.34 ? C3' SAH 401 A 1 HETATM 13 O O3' SAH . . . C 3 -25.683 -30.41 -22.312 1 32.19 ? O3' SAH 401 A 1 HETATM 14 C C2' SAH . . . C 3 -25.105 -29.399 -24.4 1 40.13 ? C2' SAH 401 A 1 HETATM 15 O O2' SAH . . . C 3 -26.35 -29.958 -24.755 1 38.96 ? O2' SAH 401 A 1 HETATM 16 C C1' SAH . . . C 3 -25.053 -27.939 -24.828 1 30.98 ? C1' SAH 401 A 1 HETATM 17 N N9 SAH . . . C 3 -23.657 -27.597 -25.156 1 30.72 ? N9 SAH 401 A 1 HETATM 18 C C8 SAH . . . C 3 -22.79 -26.873 -24.376 1 25.52 ? C8 SAH 401 A 1 HETATM 19 N N7 SAH . . . C 3 -21.596 -26.806 -25.011 1 26.37 ? N7 SAH 401 A 1 HETATM 20 C C5 SAH . . . C 3 -21.688 -27.488 -26.182 1 28.88 ? C5 SAH 401 A 1 HETATM 21 C C6 SAH . . . C 3 -20.782 -27.731 -27.209 1 35.96 ? C6 SAH 401 A 1 HETATM 22 N N6 SAH . . . C 3 -19.536 -27.259 -27.157 1 32.74 ? N6 SAH 401 A 1 HETATM 23 N N1 SAH . . . C 3 -21.178 -28.473 -28.302 1 39.04 ? N1 SAH 401 A 1 HETATM 24 C C2 SAH . . . C 3 -22.461 -28.972 -28.374 1 37.94 ? C2 SAH 401 A 1 HETATM 25 N N3 SAH . . . C 3 -23.354 -28.727 -27.358 1 31.33 ? N3 SAH 401 A 1 HETATM 26 C C4 SAH . . . C 3 -22.981 -27.986 -26.285 1 31.11 ? C4 SAH 401 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #