data_5YJM # _model_server_result.job_id 4W_kOtqoO540dQB9NJwxEw _model_server_result.datetime_utc '2024-11-14 10:19:01' _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 5yjm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":304}' # _entry.id 5YJM # _exptl.entry_id 5YJM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 594.058 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-amino-4-((R)-1-((R,Z)-6-(5-chloro-2-methoxybenzyl)-7-oxo-3-(phenoxyimino)-1,4-diazepane-1-carboxamido)propyl)benzoic acid' _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 5YJM _cell.length_a 75.089 _cell.length_b 75.089 _cell.length_c 49.75 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YJM _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 E _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 disulf ? disulf1 A SG CYS 30 A CYS 42 1_555 A SG CYS 46 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf2 A SG CYS 123 A CYS 136 1_555 A SG CYS 188 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? disulf ? disulf3 A SG CYS 154 A CYS 168 1_555 A SG CYS 167 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? covale ? covale1 A ND2 ASN 59 A ASN 72 1_555 B C1 NAG . A NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale2 A ND2 ASN 82 A ASN 95 1_555 C C1 NAG . A NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? metalc ? metalc1 A NE2 HIS 10 A HIS 25 1_555 D ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc2 A OE2 GLU 64 A GLU 77 1_555 D ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.847 ? metalc ? metalc3 A OE2 GLU 71 A GLU 84 1_555 D ZN ZN . A ZN 303 2_544 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc4 A NZ LYS 96 A LYS 109 1_555 D ZN ZN . A ZN 303 2_544 ? ? ? ? ? ? ? ? ? ? ? ? 1.746 ? # _chem_comp.formula 'C30 H32 Cl N5 O6' _chem_comp.formula_weight 594.058 _chem_comp.id 8W3 _chem_comp.mon_nstd_flag . _chem_comp.name '2-amino-4-((R)-1-((R,Z)-6-(5-chloro-2-methoxybenzyl)-7-oxo-3-(phenoxyimino)-1,4-diazepane-1-carboxamido)propyl)benzoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '2-azanyl-4-[(1R)-1-[[(3Z,6R)-6-[(5-chloranyl-2-methoxy-phenyl)methyl]-7-oxidanylidene-3-phenoxyimino-1,4-diazepan-1-yl] carbonylamino]propyl]benzoic acid' # 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 C67 C66 8W3 doub 1 n y C67 C68 8W3 sing 2 n y C66 C65 8W3 sing 3 n y C68 C63 8W3 doub 4 n y C65 C64 8W3 doub 5 n y C63 C64 8W3 sing 6 n y C63 O62 8W3 sing 7 n n O18 C17 8W3 doub 8 n n N14 O62 8W3 sing 9 n n N14 C13 8W3 doub 10 z n C30 C20 8W3 sing 11 n n C30 C35 8W3 sing 12 n n C20 C21 8W3 sing 13 n n C20 N19 8W3 sing 14 n n C17 N19 8W3 sing 15 n n C17 N16 8W3 sing 16 n n C29 C21 8W3 doub 17 n y C29 C28 8W3 sing 18 n y C15 C13 8W3 sing 19 n n C15 N16 8W3 sing 20 n n C13 N12 8W3 sing 21 n n C21 C25 8W3 sing 22 n y C28 C27 8W3 doub 23 n y N16 C1 8W3 sing 24 n n N12 C11 8W3 sing 25 n n C25 C26 8W3 doub 26 n y C27 C26 8W3 sing 27 n y C27 C31 8W3 sing 28 n n O32 C31 8W3 doub 29 n n C1 O2 8W3 doub 30 n n C1 C3 8W3 sing 31 n n C26 N57 8W3 sing 32 n n C31 O33 8W3 sing 33 n n C11 C3 8W3 sing 34 n n C3 C4 8W3 sing 35 n n C24 O23 8W3 sing 36 n n O23 C6 8W3 sing 37 n n C4 C5 8W3 sing 38 n n C6 C5 8W3 doub 39 n y C6 C7 8W3 sing 40 n y C5 C10 8W3 sing 41 n y C7 C8 8W3 doub 42 n y C10 C9 8W3 doub 43 n y C8 C9 8W3 sing 44 n y C9 CL2 8W3 sing 45 n n C10 H1 8W3 sing 46 n n C8 H2 8W3 sing 47 n n C7 H3 8W3 sing 48 n n C24 H4 8W3 sing 49 n n C24 H5 8W3 sing 50 n n C24 H6 8W3 sing 51 n n C4 H7 8W3 sing 52 n n C4 H8 8W3 sing 53 n n C3 H9 8W3 sing 54 n n C11 H10 8W3 sing 55 n n C68 H11 8W3 sing 56 n n C67 H12 8W3 sing 57 n n C66 H13 8W3 sing 58 n n C65 H14 8W3 sing 59 n n C64 H15 8W3 sing 60 n n C15 H16 8W3 sing 61 n n C15 H17 8W3 sing 62 n n N19 H18 8W3 sing 63 n n C20 H19 8W3 sing 64 n n C30 H20 8W3 sing 65 n n C30 H21 8W3 sing 66 n n C35 H22 8W3 sing 67 n n C35 H23 8W3 sing 68 n n C35 H24 8W3 sing 69 n n C25 H25 8W3 sing 70 n n N57 H26 8W3 sing 71 n n N57 H27 8W3 sing 72 n n C29 H28 8W3 sing 73 n n C28 H29 8W3 sing 74 n n O33 H30 8W3 sing 75 n n C11 H31 8W3 sing 76 n n N12 H32 8W3 sing 77 n n # _atom_sites.entry_id 5YJM _atom_sites.fract_transf_matrix[1][1] 0.013318 _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] 0.013318 _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] 0.020101 _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 NAG A 1 301 301 NAG NAG . C 2 NAG A 1 302 302 NAG NAG . D 3 ZN A 1 303 303 ZN ZN . E 4 8W3 A 1 304 401 8W3 ASB . F 5 HOH A 1 401 34 HOH HOH . F 5 HOH A 2 402 78 HOH HOH . F 5 HOH A 3 403 52 HOH HOH . F 5 HOH A 4 404 45 HOH HOH . F 5 HOH A 5 405 16 HOH HOH . F 5 HOH A 6 406 59 HOH HOH . F 5 HOH A 7 407 4 HOH HOH . F 5 HOH A 8 408 56 HOH HOH . F 5 HOH A 9 409 17 HOH HOH . F 5 HOH A 10 410 20 HOH HOH . F 5 HOH A 11 411 42 HOH HOH . F 5 HOH A 12 412 67 HOH HOH . F 5 HOH A 13 413 3 HOH HOH . F 5 HOH A 14 414 60 HOH HOH . F 5 HOH A 15 415 77 HOH HOH . F 5 HOH A 16 416 68 HOH HOH . F 5 HOH A 17 417 24 HOH HOH . F 5 HOH A 18 418 43 HOH HOH . F 5 HOH A 19 419 27 HOH HOH . F 5 HOH A 20 420 30 HOH HOH . F 5 HOH A 21 421 10 HOH HOH . F 5 HOH A 22 422 9 HOH HOH . F 5 HOH A 23 423 35 HOH HOH . F 5 HOH A 24 424 6 HOH HOH . F 5 HOH A 25 425 11 HOH HOH . F 5 HOH A 26 426 47 HOH HOH . F 5 HOH A 27 427 8 HOH HOH . F 5 HOH A 28 428 19 HOH HOH . F 5 HOH A 29 429 50 HOH HOH . F 5 HOH A 30 430 53 HOH HOH . F 5 HOH A 31 431 84 HOH HOH . F 5 HOH A 32 432 15 HOH HOH . F 5 HOH A 33 433 29 HOH HOH . F 5 HOH A 34 434 1 HOH HOH . F 5 HOH A 35 435 87 HOH HOH . F 5 HOH A 36 436 58 HOH HOH . F 5 HOH A 37 437 51 HOH HOH . F 5 HOH A 38 438 70 HOH HOH . F 5 HOH A 39 439 12 HOH HOH . F 5 HOH A 40 440 44 HOH HOH . F 5 HOH A 41 441 49 HOH HOH . F 5 HOH A 42 442 55 HOH HOH . F 5 HOH A 43 443 14 HOH HOH . F 5 HOH A 44 444 48 HOH HOH . F 5 HOH A 45 445 2 HOH HOH . F 5 HOH A 46 446 25 HOH HOH . F 5 HOH A 47 447 64 HOH HOH . F 5 HOH A 48 448 40 HOH HOH . F 5 HOH A 49 449 37 HOH HOH . F 5 HOH A 50 450 13 HOH HOH . F 5 HOH A 51 451 32 HOH HOH . F 5 HOH A 52 452 33 HOH HOH . F 5 HOH A 53 453 7 HOH HOH . F 5 HOH A 54 454 23 HOH HOH . F 5 HOH A 55 455 63 HOH HOH . F 5 HOH A 56 456 71 HOH HOH . F 5 HOH A 57 457 5 HOH HOH . F 5 HOH A 58 458 36 HOH HOH . F 5 HOH A 59 459 31 HOH HOH . F 5 HOH A 60 460 21 HOH HOH . F 5 HOH A 61 461 81 HOH HOH . F 5 HOH A 62 462 65 HOH HOH . F 5 HOH A 63 463 74 HOH HOH . F 5 HOH A 64 464 38 HOH HOH . F 5 HOH A 65 465 86 HOH HOH . F 5 HOH A 66 466 88 HOH HOH . F 5 HOH A 67 467 66 HOH HOH . F 5 HOH A 68 468 28 HOH HOH . F 5 HOH A 69 469 73 HOH HOH . F 5 HOH A 70 470 18 HOH HOH . F 5 HOH A 71 471 57 HOH HOH . F 5 HOH A 72 472 72 HOH HOH . F 5 HOH A 73 473 22 HOH HOH . F 5 HOH A 74 474 80 HOH HOH . F 5 HOH A 75 475 76 HOH HOH . F 5 HOH A 76 476 39 HOH HOH . F 5 HOH A 77 477 26 HOH HOH . F 5 HOH A 78 478 83 HOH HOH . F 5 HOH A 79 479 79 HOH HOH . F 5 HOH A 80 480 75 HOH HOH . F 5 HOH A 81 481 46 HOH HOH . F 5 HOH A 82 482 69 HOH HOH . F 5 HOH A 83 483 41 HOH HOH . F 5 HOH A 84 484 54 HOH HOH . F 5 HOH A 85 485 62 HOH HOH . F 5 HOH A 86 486 85 HOH HOH . F 5 HOH A 87 487 61 HOH HOH . F 5 HOH A 88 488 82 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 C C1 8W3 . . . E 4 -9.519 -16.738 -6.085 1 23.58 ? C1 8W3 304 A 1 HETATM 2 O O2 8W3 . . . E 4 -8.567 -17.215 -5.481 1 23.03 ? O2 8W3 304 A 1 HETATM 3 CL CL2 8W3 . . . E 4 -14.062 -15.108 -0.439 1 25.96 ? CL2 8W3 304 A 1 HETATM 4 C C9 8W3 . . . E 4 -13.053 -14.495 -1.585 1 23.58 ? C9 8W3 304 A 1 HETATM 5 C C10 8W3 . . . E 4 -12.169 -15.319 -2.27 1 21.09 ? C10 8W3 304 A 1 HETATM 6 C C8 8W3 . . . E 4 -13.125 -13.122 -1.791 1 22.42 ? C8 8W3 304 A 1 HETATM 7 C C7 8W3 . . . E 4 -12.281 -12.579 -2.743 1 22.6 ? C7 8W3 304 A 1 HETATM 8 C C6 8W3 . . . E 4 -11.348 -13.364 -3.458 1 24.35 ? C6 8W3 304 A 1 HETATM 9 O O23 8W3 . . . E 4 -10.499 -12.984 -4.458 1 25.59 ? O23 8W3 304 A 1 HETATM 10 C C24 8W3 . . . E 4 -10.387 -11.634 -4.892 1 30.27 ? C24 8W3 304 A 1 HETATM 11 C C5 8W3 . . . E 4 -11.299 -14.725 -3.185 1 22.52 ? C5 8W3 304 A 1 HETATM 12 C C4 8W3 . . . E 4 -10.305 -15.535 -3.922 1 22.14 ? C4 8W3 304 A 1 HETATM 13 C C3 8W3 . . . E 4 -10.631 -16.043 -5.311 1 22.64 ? C3 8W3 304 A 1 HETATM 14 C C11 8W3 . . . E 4 -12.054 -16.59 -5.482 1 21.86 ? C11 8W3 304 A 1 HETATM 15 N N12 8W3 . . . E 4 -12.608 -16.851 -6.764 1 19.6 ? N12 8W3 304 A 1 HETATM 16 C C13 8W3 . . . E 4 -12.088 -16.614 -7.995 1 18.86 ? C13 8W3 304 A 1 HETATM 17 N N14 8W3 . . . E 4 -12.703 -16.899 -9.055 1 20.74 ? N14 8W3 304 A 1 HETATM 18 O O62 8W3 . . . E 4 -14.015 -17.369 -8.779 1 22.87 ? O62 8W3 304 A 1 HETATM 19 C C63 8W3 . . . E 4 -14.749 -17.859 -9.809 1 22.9 ? C63 8W3 304 A 1 HETATM 20 C C68 8W3 . . . E 4 -14.315 -17.949 -11.141 1 23.18 ? C68 8W3 304 A 1 HETATM 21 C C67 8W3 . . . E 4 -15.172 -18.528 -12.109 1 25.29 ? C67 8W3 304 A 1 HETATM 22 C C66 8W3 . . . E 4 -16.398 -19.091 -11.752 1 25.12 ? C66 8W3 304 A 1 HETATM 23 C C65 8W3 . . . E 4 -16.814 -19.012 -10.419 1 23.83 ? C65 8W3 304 A 1 HETATM 24 C C64 8W3 . . . E 4 -15.974 -18.443 -9.457 1 21.54 ? C64 8W3 304 A 1 HETATM 25 C C15 8W3 . . . E 4 -10.709 -16.034 -8.167 1 20.38 ? C15 8W3 304 A 1 HETATM 26 N N16 8W3 . . . E 4 -9.684 -16.825 -7.47 1 23.86 ? N16 8W3 304 A 1 HETATM 27 C C17 8W3 . . . E 4 -8.843 -17.556 -8.323 1 24.57 ? C17 8W3 304 A 1 HETATM 28 O O18 8W3 . . . E 4 -9.02 -17.589 -9.498 1 23.89 ? O18 8W3 304 A 1 HETATM 29 N N19 8W3 . . . E 4 -7.898 -18.313 -7.805 1 25.53 ? N19 8W3 304 A 1 HETATM 30 C C20 8W3 . . . E 4 -6.949 -19.097 -8.583 1 28.44 ? C20 8W3 304 A 1 HETATM 31 C C30 8W3 . . . E 4 -7.516 -20.522 -8.679 1 29.93 ? C30 8W3 304 A 1 HETATM 32 C C35 8W3 . . . E 4 -6.538 -21.571 -8.419 1 30.77 ? C35 8W3 304 A 1 HETATM 33 C C21 8W3 . . . E 4 -5.718 -18.627 -7.858 1 28.96 ? C21 8W3 304 A 1 HETATM 34 C C25 8W3 . . . E 4 -5.213 -19.22 -6.661 1 27.96 ? C25 8W3 304 A 1 HETATM 35 C C26 8W3 . . . E 4 -4.104 -18.697 -5.989 1 30.81 ? C26 8W3 304 A 1 HETATM 36 N N57 8W3 . . . E 4 -3.631 -19.383 -4.886 1 31.09 ? N57 8W3 304 A 1 HETATM 37 C C29 8W3 . . . E 4 -5.13 -17.428 -8.303 1 33.41 ? C29 8W3 304 A 1 HETATM 38 C C28 8W3 . . . E 4 -4.035 -16.873 -7.631 1 34.58 ? C28 8W3 304 A 1 HETATM 39 C C27 8W3 . . . E 4 -3.492 -17.492 -6.472 1 39.07 ? C27 8W3 304 A 1 HETATM 40 C C31 8W3 . . . E 4 -2.301 -16.822 -5.811 1 46.69 ? C31 8W3 304 A 1 HETATM 41 O O32 8W3 . . . E 4 -1.813 -15.744 -6.296 1 51.11 ? O32 8W3 304 A 1 HETATM 42 O O33 8W3 . . . E 4 -1.8 -17.364 -4.777 1 55.94 ? O33 8W3 304 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 42 #