data_5YJP # _model_server_result.job_id YV4EeGUMh8ChQJI_ZNJo2g _model_server_result.datetime_utc '2024-11-14 09:57:35' _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 5yjp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":304}' # _entry.id 5YJP # _exptl.entry_id 5YJP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 531.001 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '4-((R)-1-((R,Z)-6-(5-chloro-2-methoxybenzyl)-3-(ethoxyimino)-7-oxo-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 5YJP _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 5YJP _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 123 A CYS 136 1_555 A SG CYS 188 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf3 A SG CYS 154 A CYS 168 1_555 A SG CYS 167 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? covale ? covale1 A ND2 ASN 59 A ASN 72 1_555 B C1 NAG . A NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale2 A ND2 ASN 82 A ASN 95 1_555 C C1 NAG . A NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? metalc ? metalc1 A NE2 HIS 10 A HIS 25 1_555 D ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc2 A OE2 GLU 64 A GLU 77 1_555 D ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.854 ? metalc ? metalc3 A OE2 GLU 71 A GLU 84 1_555 D ZN ZN . A ZN 303 2_544 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc4 A NZ LYS 96 A LYS 109 1_555 D ZN ZN . A ZN 303 2_544 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? # _chem_comp.formula 'C26 H31 Cl N4 O6' _chem_comp.formula_weight 531.001 _chem_comp.id 8W6 _chem_comp.mon_nstd_flag . _chem_comp.name '4-((R)-1-((R,Z)-6-(5-chloro-2-methoxybenzyl)-3-(ethoxyimino)-7-oxo-1,4-diazepane-1-carboxamido)propyl)benzoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '4-[(1R)-1-[[(3Z,6R)-6-[(5-chloranyl-2-methoxy-phenyl)methyl]-3-ethoxyimino-7-oxidanylidene-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 C63 C64 8W6 sing 1 n n C63 O62 8W6 sing 2 n n O18 C17 8W6 doub 3 n n N14 O62 8W6 sing 4 n n N14 C13 8W6 doub 5 z n C35 C30 8W6 sing 6 n n C15 C13 8W6 sing 7 n n C15 N16 8W6 sing 8 n n C17 N19 8W6 sing 9 n n C17 N16 8W6 sing 10 n n C13 N12 8W6 sing 11 n n C20 C30 8W6 sing 12 n n C20 N19 8W6 sing 13 n n C20 C21 8W6 sing 14 n n C25 C21 8W6 doub 15 n y C25 C26 8W6 sing 16 n y N16 C1 8W6 sing 17 n n C21 C29 8W6 sing 18 n y C26 C27 8W6 doub 19 n y N12 C11 8W6 sing 20 n n C29 C28 8W6 doub 21 n y C1 C3 8W6 sing 22 n n C1 O2 8W6 doub 23 n n C27 C28 8W6 sing 24 n y C27 C31 8W6 sing 25 n n O33 C31 8W6 doub 26 n n C11 C3 8W6 sing 27 n n C3 C4 8W6 sing 28 n n C31 O32 8W6 sing 29 n n C24 O23 8W6 sing 30 n n O23 C6 8W6 sing 31 n n C4 C5 8W6 sing 32 n n C6 C5 8W6 doub 33 n y C6 C7 8W6 sing 34 n y C5 C10 8W6 sing 35 n y C7 C8 8W6 doub 36 n y C10 C9 8W6 doub 37 n y C8 C9 8W6 sing 38 n y C9 CL2 8W6 sing 39 n n C8 H1 8W6 sing 40 n n C7 H2 8W6 sing 41 n n C24 H3 8W6 sing 42 n n C24 H4 8W6 sing 43 n n C24 H5 8W6 sing 44 n n C10 H6 8W6 sing 45 n n C4 H7 8W6 sing 46 n n C4 H8 8W6 sing 47 n n C3 H9 8W6 sing 48 n n C11 H10 8W6 sing 49 n n C11 H11 8W6 sing 50 n n N12 H12 8W6 sing 51 n n C63 H13 8W6 sing 52 n n C63 H14 8W6 sing 53 n n C64 H15 8W6 sing 54 n n C64 H16 8W6 sing 55 n n C64 H17 8W6 sing 56 n n C15 H18 8W6 sing 57 n n C15 H19 8W6 sing 58 n n N19 H20 8W6 sing 59 n n C20 H21 8W6 sing 60 n n C30 H22 8W6 sing 61 n n C30 H23 8W6 sing 62 n n C35 H24 8W6 sing 63 n n C35 H25 8W6 sing 64 n n C35 H26 8W6 sing 65 n n C29 H27 8W6 sing 66 n n C28 H28 8W6 sing 67 n n C25 H29 8W6 sing 68 n n C26 H30 8W6 sing 69 n n O32 H31 8W6 sing 70 n n # _atom_sites.entry_id 5YJP _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 8W6 A 1 304 401 8W6 ASB . F 5 HOH A 1 401 89 HOH HOH . F 5 HOH A 2 402 59 HOH HOH . F 5 HOH A 3 403 70 HOH HOH . F 5 HOH A 4 404 32 HOH HOH . F 5 HOH A 5 405 14 HOH HOH . F 5 HOH A 6 406 58 HOH HOH . F 5 HOH A 7 407 50 HOH HOH . F 5 HOH A 8 408 68 HOH HOH . F 5 HOH A 9 409 41 HOH HOH . F 5 HOH A 10 410 46 HOH HOH . F 5 HOH A 11 411 42 HOH HOH . F 5 HOH A 12 412 49 HOH HOH . F 5 HOH A 13 413 5 HOH HOH . F 5 HOH A 14 414 63 HOH HOH . F 5 HOH A 15 415 62 HOH HOH . F 5 HOH A 16 416 91 HOH HOH . F 5 HOH A 17 417 8 HOH HOH . F 5 HOH A 18 418 10 HOH HOH . F 5 HOH A 19 419 86 HOH HOH . F 5 HOH A 20 420 39 HOH HOH . F 5 HOH A 21 421 35 HOH HOH . F 5 HOH A 22 422 61 HOH HOH . F 5 HOH A 23 423 11 HOH HOH . F 5 HOH A 24 424 55 HOH HOH . F 5 HOH A 25 425 25 HOH HOH . F 5 HOH A 26 426 47 HOH HOH . F 5 HOH A 27 427 64 HOH HOH . F 5 HOH A 28 428 9 HOH HOH . F 5 HOH A 29 429 45 HOH HOH . F 5 HOH A 30 430 83 HOH HOH . F 5 HOH A 31 431 2 HOH HOH . F 5 HOH A 32 432 93 HOH HOH . F 5 HOH A 33 433 15 HOH HOH . F 5 HOH A 34 434 24 HOH HOH . F 5 HOH A 35 435 30 HOH HOH . F 5 HOH A 36 436 57 HOH HOH . F 5 HOH A 37 437 19 HOH HOH . F 5 HOH A 38 438 99 HOH HOH . F 5 HOH A 39 439 71 HOH HOH . F 5 HOH A 40 440 28 HOH HOH . F 5 HOH A 41 441 37 HOH HOH . F 5 HOH A 42 442 69 HOH HOH . F 5 HOH A 43 443 36 HOH HOH . F 5 HOH A 44 444 98 HOH HOH . F 5 HOH A 45 445 97 HOH HOH . F 5 HOH A 46 446 54 HOH HOH . F 5 HOH A 47 447 56 HOH HOH . F 5 HOH A 48 448 3 HOH HOH . F 5 HOH A 49 449 48 HOH HOH . F 5 HOH A 50 450 1 HOH HOH . F 5 HOH A 51 451 84 HOH HOH . F 5 HOH A 52 452 72 HOH HOH . F 5 HOH A 53 453 7 HOH HOH . F 5 HOH A 54 454 17 HOH HOH . F 5 HOH A 55 455 82 HOH HOH . F 5 HOH A 56 456 43 HOH HOH . F 5 HOH A 57 457 18 HOH HOH . F 5 HOH A 58 458 74 HOH HOH . F 5 HOH A 59 459 12 HOH HOH . F 5 HOH A 60 460 26 HOH HOH . F 5 HOH A 61 461 76 HOH HOH . F 5 HOH A 62 462 80 HOH HOH . F 5 HOH A 63 463 22 HOH HOH . F 5 HOH A 64 464 4 HOH HOH . F 5 HOH A 65 465 33 HOH HOH . F 5 HOH A 66 466 20 HOH HOH . F 5 HOH A 67 467 100 HOH HOH . F 5 HOH A 68 468 53 HOH HOH . F 5 HOH A 69 469 21 HOH HOH . F 5 HOH A 70 470 29 HOH HOH . F 5 HOH A 71 471 101 HOH HOH . F 5 HOH A 72 472 40 HOH HOH . F 5 HOH A 73 473 102 HOH HOH . F 5 HOH A 74 474 31 HOH HOH . F 5 HOH A 75 475 6 HOH HOH . F 5 HOH A 76 476 34 HOH HOH . F 5 HOH A 77 477 79 HOH HOH . F 5 HOH A 78 478 60 HOH HOH . F 5 HOH A 79 479 44 HOH HOH . F 5 HOH A 80 480 23 HOH HOH . F 5 HOH A 81 481 87 HOH HOH . F 5 HOH A 82 482 81 HOH HOH . F 5 HOH A 83 483 38 HOH HOH . F 5 HOH A 84 484 16 HOH HOH . F 5 HOH A 85 485 13 HOH HOH . F 5 HOH A 86 486 95 HOH HOH . F 5 HOH A 87 487 88 HOH HOH . F 5 HOH A 88 488 66 HOH HOH . F 5 HOH A 89 489 85 HOH HOH . F 5 HOH A 90 490 27 HOH HOH . F 5 HOH A 91 491 96 HOH HOH . F 5 HOH A 92 492 52 HOH HOH . F 5 HOH A 93 493 51 HOH HOH . F 5 HOH A 94 494 90 HOH HOH . F 5 HOH A 95 495 65 HOH HOH . F 5 HOH A 96 496 77 HOH HOH . F 5 HOH A 97 497 73 HOH HOH . F 5 HOH A 98 498 67 HOH HOH . F 5 HOH A 99 499 78 HOH HOH . F 5 HOH A 100 500 94 HOH HOH . F 5 HOH A 101 501 75 HOH HOH . F 5 HOH A 102 502 92 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 8W6 . . . E 4 -9.411 -16.629 -5.935 1 19.77 ? C1 8W6 304 A 1 HETATM 2 O O2 8W6 . . . E 4 -8.499 -17.044 -5.205 1 16.87 ? O2 8W6 304 A 1 HETATM 3 CL CL2 8W6 . . . E 4 -14.07 -15.078 -0.457 1 20.75 ? CL2 8W6 304 A 1 HETATM 4 C C9 8W6 . . . E 4 -12.995 -14.377 -1.566 1 16.74 ? C9 8W6 304 A 1 HETATM 5 C C8 8W6 . . . E 4 -12.982 -13.012 -1.786 1 16.35 ? C8 8W6 304 A 1 HETATM 6 C C7 8W6 . . . E 4 -12.13 -12.454 -2.703 1 18.78 ? C7 8W6 304 A 1 HETATM 7 C C6 8W6 . . . E 4 -11.186 -13.277 -3.423 1 18.01 ? C6 8W6 304 A 1 HETATM 8 O O23 8W6 . . . E 4 -10.265 -12.88 -4.35 1 18.42 ? O23 8W6 304 A 1 HETATM 9 C C24 8W6 . . . E 4 -10.086 -11.519 -4.773 1 23.73 ? C24 8W6 304 A 1 HETATM 10 C C10 8W6 . . . E 4 -12.086 -15.204 -2.213 1 16.05 ? C10 8W6 304 A 1 HETATM 11 C C5 8W6 . . . E 4 -11.155 -14.633 -3.119 1 16.59 ? C5 8W6 304 A 1 HETATM 12 C C4 8W6 . . . E 4 -10.188 -15.515 -3.84 1 17.26 ? C4 8W6 304 A 1 HETATM 13 C C3 8W6 . . . E 4 -10.528 -15.78 -5.28 1 17.66 ? C3 8W6 304 A 1 HETATM 14 C C11 8W6 . . . E 4 -11.829 -16.617 -5.434 1 18.06 ? C11 8W6 304 A 1 HETATM 15 N N12 8W6 . . . E 4 -12.407 -16.726 -6.746 1 17.33 ? N12 8W6 304 A 1 HETATM 16 C C13 8W6 . . . E 4 -11.89 -16.53 -8.005 1 17.22 ? C13 8W6 304 A 1 HETATM 17 N N14 8W6 . . . E 4 -12.627 -16.771 -9.018 1 16.32 ? N14 8W6 304 A 1 HETATM 18 O O62 8W6 . . . E 4 -13.919 -17.207 -8.755 1 18.7 ? O62 8W6 304 A 1 HETATM 19 C C63 8W6 . . . E 4 -14.475 -17.814 -9.936 1 17.6 ? C63 8W6 304 A 1 HETATM 20 C C64 8W6 . . . E 4 -15.88 -18.301 -9.604 1 17.69 ? C64 8W6 304 A 1 HETATM 21 C C15 8W6 . . . E 4 -10.443 -16.071 -8.163 1 18.58 ? C15 8W6 304 A 1 HETATM 22 N N16 8W6 . . . E 4 -9.417 -16.774 -7.322 1 19.1 ? N16 8W6 304 A 1 HETATM 23 C C17 8W6 . . . E 4 -8.456 -17.49 -8.084 1 22.45 ? C17 8W6 304 A 1 HETATM 24 O O18 8W6 . . . E 4 -8.535 -17.551 -9.307 1 23.77 ? O18 8W6 304 A 1 HETATM 25 N N19 8W6 . . . E 4 -7.522 -18.196 -7.407 1 22.78 ? N19 8W6 304 A 1 HETATM 26 C C20 8W6 . . . E 4 -6.383 -18.966 -7.992 1 27 ? C20 8W6 304 A 1 HETATM 27 C C30 8W6 . . . E 4 -6.474 -20.468 -7.751 1 26.65 ? C30 8W6 304 A 1 HETATM 28 C C35 8W6 . . . E 4 -7.384 -21.156 -8.685 1 25.69 ? C35 8W6 304 A 1 HETATM 29 C C21 8W6 . . . E 4 -5.239 -18.213 -7.255 1 26.87 ? C21 8W6 304 A 1 HETATM 30 C C29 8W6 . . . E 4 -4.834 -18.569 -5.945 1 28.35 ? C29 8W6 304 A 1 HETATM 31 C C28 8W6 . . . E 4 -3.864 -17.827 -5.257 1 29.73 ? C28 8W6 304 A 1 HETATM 32 C C25 8W6 . . . E 4 -4.603 -17.129 -7.876 1 30.79 ? C25 8W6 304 A 1 HETATM 33 C C26 8W6 . . . E 4 -3.612 -16.374 -7.196 1 29.68 ? C26 8W6 304 A 1 HETATM 34 C C27 8W6 . . . E 4 -3.239 -16.704 -5.87 1 30.01 ? C27 8W6 304 A 1 HETATM 35 C C31 8W6 . . . E 4 -2.165 -15.928 -5.183 1 35.49 ? C31 8W6 304 A 1 HETATM 36 O O33 8W6 . . . E 4 -1.65 -14.922 -5.838 1 35.31 ? O33 8W6 304 A 1 HETATM 37 O O32 8W6 . . . E 4 -1.852 -16.252 -3.974 1 38.55 ? O32 8W6 304 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 238 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 37 #