data_1YPN # _model_server_result.job_id KCON2Ue6k2eTrl2Qr6SFVg _model_server_result.datetime_utc '2024-11-30 00:46:57' _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 1ypn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":314}' # _entry.id 1YPN # _exptl.entry_id 1YPN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 420.413 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic 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 1YPN _cell.length_a 88.47 _cell.length_b 76.15 _cell.length_c 50.79 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YPN _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 242 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 242 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id CHA _struct_conn.ptnr2_label_comp_id DPM _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id DPM _struct_conn.ptnr2_auth_seq_id 314 _struct_conn.ptnr2_symmetry 1_555 _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 1.821 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C20 H24 N2 O8' _chem_comp.formula_weight 420.413 _chem_comp.id DPM _chem_comp.mon_nstd_flag . _chem_comp.name '3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)-5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)-1H-pyrrol-3-yl]propanoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'DIPYRROMETHANE COFACTOR' # _atom_sites.entry_id 1YPN _atom_sites.fract_transf_matrix[1][1] 0.011303 _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] 0.013132 _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] 0.019689 _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 DPM A 1 314 314 DPM DPM . C 3 HOH A 1 322 322 HOH HOH . C 3 HOH A 2 323 323 HOH HOH . C 3 HOH A 3 324 324 HOH HOH . C 3 HOH A 4 325 325 HOH HOH . C 3 HOH A 5 326 326 HOH HOH . C 3 HOH A 6 327 327 HOH HOH . C 3 HOH A 7 328 328 HOH HOH . C 3 HOH A 8 329 329 HOH HOH . C 3 HOH A 9 330 330 HOH HOH . C 3 HOH A 10 331 331 HOH HOH . C 3 HOH A 11 332 332 HOH HOH . C 3 HOH A 12 333 333 HOH HOH . C 3 HOH A 13 334 334 HOH HOH . C 3 HOH A 14 335 335 HOH HOH . C 3 HOH A 15 336 336 HOH HOH . C 3 HOH A 16 337 337 HOH HOH . C 3 HOH A 17 338 338 HOH HOH . C 3 HOH A 18 339 339 HOH HOH . C 3 HOH A 19 340 340 HOH HOH . C 3 HOH A 20 341 341 HOH HOH . C 3 HOH A 21 342 342 HOH HOH . C 3 HOH A 22 343 343 HOH HOH . C 3 HOH A 23 344 344 HOH HOH . C 3 HOH A 24 345 345 HOH HOH . C 3 HOH A 25 346 346 HOH HOH . C 3 HOH A 26 347 347 HOH HOH . C 3 HOH A 27 348 348 HOH HOH . C 3 HOH A 28 349 349 HOH HOH . C 3 HOH A 29 350 350 HOH HOH . C 3 HOH A 30 351 351 HOH HOH . C 3 HOH A 31 352 352 HOH HOH . C 3 HOH A 32 353 353 HOH HOH . C 3 HOH A 33 354 354 HOH HOH . C 3 HOH A 34 355 355 HOH HOH . C 3 HOH A 35 356 356 HOH HOH . C 3 HOH A 36 357 357 HOH HOH . C 3 HOH A 37 358 358 HOH HOH . C 3 HOH A 38 359 359 HOH HOH . C 3 HOH A 39 360 360 HOH HOH . C 3 HOH A 40 361 361 HOH HOH . C 3 HOH A 41 362 362 HOH HOH . C 3 HOH A 42 363 363 HOH HOH . C 3 HOH A 43 364 364 HOH HOH . C 3 HOH A 44 365 365 HOH HOH . C 3 HOH A 45 366 366 HOH HOH . C 3 HOH A 46 367 367 HOH HOH . C 3 HOH A 47 368 368 HOH HOH . C 3 HOH A 48 369 369 HOH HOH . C 3 HOH A 49 370 370 HOH HOH . C 3 HOH A 50 371 371 HOH HOH . C 3 HOH A 51 372 372 HOH HOH . C 3 HOH A 52 373 373 HOH HOH . C 3 HOH A 53 374 374 HOH HOH . C 3 HOH A 54 375 375 HOH HOH . C 3 HOH A 55 376 376 HOH HOH . C 3 HOH A 56 377 377 HOH HOH . C 3 HOH A 57 378 378 HOH HOH . C 3 HOH A 58 379 379 HOH HOH . C 3 HOH A 59 380 380 HOH HOH . C 3 HOH A 60 381 381 HOH HOH . C 3 HOH A 61 382 382 HOH HOH . C 3 HOH A 62 383 383 HOH HOH . C 3 HOH A 63 384 384 HOH HOH . C 3 HOH A 64 385 385 HOH HOH . C 3 HOH A 65 386 386 HOH HOH . C 3 HOH A 66 387 387 HOH HOH . C 3 HOH A 67 388 388 HOH HOH . C 3 HOH A 68 389 389 HOH HOH . C 3 HOH A 69 390 390 HOH HOH . C 3 HOH A 70 391 391 HOH HOH . C 3 HOH A 71 392 392 HOH HOH . C 3 HOH A 72 393 393 HOH HOH . C 3 HOH A 73 394 394 HOH HOH . C 3 HOH A 74 395 395 HOH HOH . C 3 HOH A 75 396 396 HOH HOH . C 3 HOH A 76 397 397 HOH HOH . C 3 HOH A 77 398 398 HOH HOH . C 3 HOH A 78 399 399 HOH HOH . C 3 HOH A 79 400 400 HOH HOH . C 3 HOH A 80 401 401 HOH HOH . C 3 HOH A 81 402 402 HOH HOH . C 3 HOH A 82 403 403 HOH HOH . C 3 HOH A 83 404 404 HOH HOH . C 3 HOH A 84 405 405 HOH HOH . C 3 HOH A 85 406 406 HOH HOH . C 3 HOH A 86 407 407 HOH HOH . C 3 HOH A 87 408 408 HOH HOH . C 3 HOH A 88 409 409 HOH HOH . C 3 HOH A 89 410 410 HOH HOH . C 3 HOH A 90 411 411 HOH HOH . C 3 HOH A 91 412 412 HOH HOH . C 3 HOH A 92 413 413 HOH HOH . C 3 HOH A 93 414 414 HOH HOH . C 3 HOH A 94 415 415 HOH HOH . C 3 HOH A 95 416 416 HOH HOH . C 3 HOH A 96 417 417 HOH HOH . C 3 HOH A 97 418 418 HOH HOH . C 3 HOH A 98 419 419 HOH HOH . C 3 HOH A 99 420 420 HOH HOH . C 3 HOH A 100 421 421 HOH HOH . C 3 HOH A 101 422 422 HOH HOH . C 3 HOH A 102 423 423 HOH HOH . C 3 HOH A 103 424 424 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 C1A DPM . . . B 2 15.961 0.785 27.208 1 14 ? C1A DPM 314 A 1 HETATM 2 C C2A DPM . . . B 2 16.706 0.269 28.223 1 15.07 ? C2A DPM 314 A 1 HETATM 3 C C3A DPM . . . B 2 17.652 1.259 28.606 1 15.27 ? C3A DPM 314 A 1 HETATM 4 C C4A DPM . . . B 2 17.436 2.346 27.794 1 15.62 ? C4A DPM 314 A 1 HETATM 5 C C5A DPM . . . B 2 16.536 -1.122 28.804 1 16 ? C5A DPM 314 A 1 HETATM 6 C C6A DPM . . . B 2 17.595 -2.125 28.378 1 8.03 ? C6A DPM 314 A 1 HETATM 7 C C7A DPM . . . B 2 18.778 1.11 29.62 1 15.44 ? C7A DPM 314 A 1 HETATM 8 C C8A DPM . . . B 2 18.42 1.536 31.048 1 14.87 ? C8A DPM 314 A 1 HETATM 9 C C9A DPM . . . B 2 19.578 1.352 32.037 1 17.35 ? C9A DPM 314 A 1 HETATM 10 C CHA DPM . . . B 2 14.835 0.174 26.396 1 11.14 ? CHA DPM 314 A 1 HETATM 11 N NA DPM . . . B 2 16.382 2.063 26.967 1 14.72 ? NA DPM 314 A 1 HETATM 12 O O1A DPM . . . B 2 17.396 -3.323 28.655 1 14.72 ? O1A DPM 314 A 1 HETATM 13 O O2A DPM . . . B 2 18.623 -1.721 27.792 1 2.36 ? O2A DPM 314 A 1 HETATM 14 O O3A DPM . . . B 2 19.537 1.957 33.124 1 13.13 ? O3A DPM 314 A 1 HETATM 15 O O4A DPM . . . B 2 20.531 0.6 31.743 1 18.9 ? O4A DPM 314 A 1 HETATM 16 C C1B DPM . . . B 2 18.945 3.865 26.402 1 17.12 ? C1B DPM 314 A 1 HETATM 17 C C2B DPM . . . B 2 20.302 3.941 26.172 1 18.08 ? C2B DPM 314 A 1 HETATM 18 C C3B DPM . . . B 2 20.476 4.089 24.759 1 23.25 ? C3B DPM 314 A 1 HETATM 19 C C4B DPM . . . B 2 19.226 4.084 24.195 1 20.29 ? C4B DPM 314 A 1 HETATM 20 C C5B DPM . . . B 2 21.389 3.934 27.239 1 14.43 ? C5B DPM 314 A 1 HETATM 21 C C6B DPM . . . B 2 22.362 2.75 27.166 1 11.16 ? C6B DPM 314 A 1 HETATM 22 C C7B DPM . . . B 2 21.79 4.163 24.002 1 22.67 ? C7B DPM 314 A 1 HETATM 23 C C8B DPM . . . B 2 22.206 2.836 23.339 1 24.81 ? C8B DPM 314 A 1 HETATM 24 C C9B DPM . . . B 2 21.435 2.526 22.061 1 28.13 ? C9B DPM 314 A 1 HETATM 25 C CHB DPM . . . B 2 18.136 3.685 27.679 1 13.98 ? CHB DPM 314 A 1 HETATM 26 N NB DPM . . . B 2 18.299 3.953 25.196 1 17.6 ? NB DPM 314 A 1 HETATM 27 O O1B DPM . . . B 2 21.921 1.585 27.182 1 5.36 ? O1B DPM 314 A 1 HETATM 28 O O2B DPM . . . B 2 23.579 2.988 27.111 1 15.02 ? O2B DPM 314 A 1 HETATM 29 O O3B DPM . . . B 2 21.369 3.4 21.175 1 32.69 ? O3B DPM 314 A 1 HETATM 30 O O4B DPM . . . B 2 20.924 1.395 21.918 1 28.79 ? O4B DPM 314 A 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 30 #