data_8YXA # _model_server_result.job_id xsmIj3tqlV7as97lGYkFCA _model_server_result.datetime_utc '2024-11-17 01:56:01' _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 8yxa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 8YXA # _exptl.entry_id 8YXA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 454.507 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(6~{R},7~{R})-3-[(5-methyl-1,3,4-thiadiazol-2-yl)sulfanylmethyl]-8-oxidanylidene-7-[2-(1,2,3,4-tetrazol-1-yl)ethanoylamino]-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 105.19 _cell.angle_beta 101.78 _cell.angle_gamma 90.03 _cell.entry_id 8YXA _cell.length_a 38.801 _cell.length_b 94.351 _cell.length_c 94.461 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YXA _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall 'P 1' _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F 1 1 B,G,H,I 2 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 G N 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 disulf ? disulf1 A SG CYS 53 A CYS 53 1_555 A SG CYS 62 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 75 A CYS 75 1_555 A SG CYS 91 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf3 A SG CYS 90 A CYS 90 1_555 A SG CYS 101 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf4 A SG CYS 124 A CYS 124 1_555 A SG CYS 169 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 168 A CYS 168 1_555 A SG CYS 177 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 A SG CYS 200 A CYS 200 1_555 A SG CYS 246 A CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf7 A SG CYS 245 A CYS 245 1_555 A SG CYS 253 A CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf8 A SG CYS 265 A CYS 265 1_555 A SG CYS 279 A CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 A SG CYS 278 A CYS 278 1_555 A SG CYS 289 A CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf10 A SG CYS 316 A CYS 316 1_555 A SG CYS 361 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf11 A SG CYS 360 A CYS 360 1_555 A SG CYS 369 A CYS 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf12 A SG CYS 392 A CYS 392 1_555 A SG CYS 438 A CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf13 A SG CYS 437 A CYS 437 1_555 A SG CYS 448 A CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf14 A SG CYS 461 A CYS 461 1_555 A SG CYS 477 A CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf15 A SG CYS 476 A CYS 476 1_555 A SG CYS 487 A CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf16 A SG CYS 514 A CYS 514 1_555 A SG CYS 559 A CYS 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf17 A SG CYS 558 A CYS 558 1_555 A SG CYS 567 A CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf18 B SG CYS 53 B CYS 53 1_555 B SG CYS 62 B CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf19 B SG CYS 75 B CYS 75 1_555 B SG CYS 91 B CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf20 B SG CYS 90 B CYS 90 1_555 B SG CYS 101 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf21 B SG CYS 124 B CYS 124 1_555 B SG CYS 169 B CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf22 B SG CYS 168 B CYS 168 1_555 B SG CYS 177 B CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf23 B SG CYS 200 B CYS 200 1_555 B SG CYS 246 B CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf24 B SG CYS 245 B CYS 245 1_555 B SG CYS 253 B CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf25 B SG CYS 265 B CYS 265 1_555 B SG CYS 279 B CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf26 B SG CYS 278 B CYS 278 1_555 B SG CYS 289 B CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf27 B SG CYS 316 B CYS 316 1_555 B SG CYS 361 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf28 B SG CYS 360 B CYS 360 1_555 B SG CYS 369 B CYS 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf29 B SG CYS 392 B CYS 392 1_555 B SG CYS 438 B CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf30 B SG CYS 437 B CYS 437 1_555 B SG CYS 448 B CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf31 B SG CYS 461 B CYS 461 1_555 B SG CYS 477 B CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf32 B SG CYS 476 B CYS 476 1_555 B SG CYS 487 B CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf33 B SG CYS 514 B CYS 514 1_555 B SG CYS 559 B CYS 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf34 B SG CYS 558 B CYS 558 1_555 B SG CYS 567 B CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? # _chem_comp.formula 'C14 H14 N8 O4 S3' _chem_comp.formula_weight 454.507 _chem_comp.id X56 _chem_comp.mon_nstd_flag . _chem_comp.name '(6~{R},7~{R})-3-[(5-methyl-1,3,4-thiadiazol-2-yl)sulfanylmethyl]-8-oxidanylidene-7-[2-(1,2,3,4-tetrazol-1-yl)ethanoylamino]-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms cefazolin # 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 C1 C2 X56 sing 417 n n C1 S1 X56 sing 418 n n C1 N1 X56 sing 419 n n C2 N2 X56 sing 420 n n C2 C3 X56 sing 421 n n N2 C9 X56 sing 422 n n S1 C6 X56 sing 423 n n O2 C8 X56 doub 424 n n C6 C5 X56 sing 425 n n N1 C3 X56 sing 426 n n N1 C4 X56 sing 427 n n C3 O1 X56 doub 428 n n C12 N6 X56 doub 429 n y C12 N3 X56 sing 430 n y C8 O3 X56 sing 431 n n C8 C4 X56 sing 432 n n C9 O4 X56 doub 433 n n C9 C10 X56 sing 434 n n C4 C5 X56 doub 435 n n C10 N3 X56 sing 436 n n C5 C7 X56 sing 437 n n N6 N7 X56 sing 438 n y N3 N4 X56 sing 439 n y N7 N4 X56 doub 440 n y C7 S2 X56 sing 441 n n S2 C11 X56 sing 442 n n C11 S3 X56 sing 443 n y C11 N5 X56 doub 444 n y S3 C13 X56 sing 445 n y N5 N8 X56 sing 446 n y C13 N8 X56 doub 447 n y C13 C14 X56 sing 448 n n C1 H1 X56 sing 449 n n C2 H2 X56 sing 450 n n C6 H5 X56 sing 451 n n C6 H6 X56 sing 452 n n C7 H7 X56 sing 453 n n C7 H8 X56 sing 454 n n O3 H9 X56 sing 455 n n N2 H10 X56 sing 456 n n C10 H11 X56 sing 457 n n C10 H12 X56 sing 458 n n C12 H13 X56 sing 459 n n C14 H14 X56 sing 460 n n C14 H15 X56 sing 461 n n C14 H16 X56 sing 462 n n # _atom_sites.entry_id 8YXA _atom_sites.fract_transf_matrix[1][1] 0.025773 _atom_sites.fract_transf_matrix[1][2] 0.000013 _atom_sites.fract_transf_matrix[1][3] 0.005582 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010599 _atom_sites.fract_transf_matrix[2][3] 0.002946 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.011224 _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 X56 A 1 601 1 X56 LIG . D 3 MYR A 1 602 11 MYR MYR . E 3 MYR A 1 603 12 MYR MYR . F 3 MYR A 1 604 19 MYR MYR . G 2 X56 B 1 601 2 X56 LIG . H 3 MYR B 1 602 16 MYR MYR . I 3 MYR B 1 603 18 MYR MYR . # 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 S S1 X56 . . . C 2 -0.774 -13.899 -12.302 0.8 107.08 ? S1 X56 601 A 1 HETATM 2 C C1 X56 . . . C 2 0.874 -14.501 -11.94 0.8 98.78 ? C1 X56 601 A 1 HETATM 3 C C2 X56 . . . C 2 1.129 -16.067 -12.037 0.8 83.8 ? C2 X56 601 A 1 HETATM 4 C C3 X56 . . . C 2 1.417 -16.007 -10.522 0.8 90 ? C3 X56 601 A 1 HETATM 5 C C4 X56 . . . C 2 0.613 -13.85 -9.494 0.8 95.68 ? C4 X56 601 A 1 HETATM 6 C C5 X56 . . . C 2 -0.014 -12.709 -9.863 0.8 88.52 ? C5 X56 601 A 1 HETATM 7 O O1 X56 . . . C 2 1.816 -16.757 -9.668 0.8 99.55 ? O1 X56 601 A 1 HETATM 8 O O2 X56 . . . C 2 -0.078 -14.28 -7.303 0.8 86.7 ? O2 X56 601 A 1 HETATM 9 N N1 X56 . . . C 2 0.967 -14.728 -10.498 0.8 90.68 ? N1 X56 601 A 1 HETATM 10 C C6 X56 . . . C 2 -0.575 -12.443 -11.244 0.8 85.13 ? C6 X56 601 A 1 HETATM 11 C C7 X56 . . . C 2 -0.213 -11.566 -8.911 0.8 87.1 ? C7 X56 601 A 1 HETATM 12 C C8 X56 . . . C 2 0.886 -14.212 -8.041 0.8 90.65 ? C8 X56 601 A 1 HETATM 13 O O3 X56 . . . C 2 2.04 -14.463 -7.744 0.8 95.52 ? O3 X56 601 A 1 HETATM 14 N N2 X56 . . . C 2 0.043 -16.92 -12.424 0.8 87.64 ? N2 X56 601 A 1 HETATM 15 C C9 X56 . . . C 2 0.002 -17.515 -13.619 0.8 102.46 ? C9 X56 601 A 1 HETATM 16 O O4 X56 . . . C 2 -0.936 -18.227 -13.973 0.8 105.14 ? O4 X56 601 A 1 HETATM 17 C C10 X56 . . . C 2 1.195 -17.255 -14.53 0.8 89.76 ? C10 X56 601 A 1 HETATM 18 N N3 X56 . . . C 2 1.214 -18.178 -15.651 0.8 96.39 ? N3 X56 601 A 1 HETATM 19 C C11 X56 . . . C 2 -2.077 -9.736 -8.105 0.8 87.4 ? C11 X56 601 A 1 HETATM 20 C C12 X56 . . . C 2 1.69 -19.416 -15.732 0.8 99.82 ? C12 X56 601 A 1 HETATM 21 C C13 X56 . . . C 2 -2.717 -7.463 -8.049 0.8 90.79 ? C13 X56 601 A 1 HETATM 22 S S2 X56 . . . C 2 -1.964 -11.443 -8.444 0.8 107.79 ? S2 X56 601 A 1 HETATM 23 C C14 X56 . . . C 2 -3.373 -6.129 -8.197 0.8 84.92 ? C14 X56 601 A 1 HETATM 24 N N4 X56 . . . C 2 0.707 -17.844 -16.849 0.8 93.55 ? N4 X56 601 A 1 HETATM 25 N N5 X56 . . . C 2 -1.065 -8.953 -7.898 0.8 88.07 ? N5 X56 601 A 1 HETATM 26 N N6 X56 . . . C 2 1.494 -19.875 -16.944 0.8 104.61 ? N6 X56 601 A 1 HETATM 27 N N7 X56 . . . C 2 0.877 -18.868 -17.622 0.8 100.24 ? N7 X56 601 A 1 HETATM 28 N N8 X56 . . . C 2 -1.446 -7.618 -7.911 0.8 92.05 ? N8 X56 601 A 1 HETATM 29 S S3 X56 . . . C 2 -3.604 -8.945 -8.034 0.8 98.68 ? S3 X56 601 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 29 #