data_2YPN # _model_server_result.job_id DV_58FUi2-8zmCMgXiUGvA _model_server_result.datetime_utc '2024-12-02 01:30:20' _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 2ypn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":314}' # _entry.id 2YPN # _exptl.entry_id 2YPN _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 2YPN _cell.length_a 88.06 _cell.length_b 75.73 _cell.length_c 50.35 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YPN _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 1.82 _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' # 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 C1A C2A DPM doub 83 n y C1A CHA DPM sing 84 n n C1A NA DPM sing 85 n y C2A C3A DPM sing 86 n y C2A C5A DPM sing 87 n n C3A C4A DPM doub 88 n y C3A C7A DPM sing 89 n n C4A NA DPM sing 90 n y C4A CHB DPM sing 91 n n C5A C6A DPM sing 92 n n C6A O1A DPM doub 93 n n C6A O2A DPM sing 94 n n C7A C8A DPM sing 95 n n C8A C9A DPM sing 96 n n C9A O3A DPM doub 97 n n C9A O4A DPM sing 98 n n C1B C2B DPM doub 99 n y C1B CHB DPM sing 100 n n C1B NB DPM sing 101 n y C2B C3B DPM sing 102 n y C2B C5B DPM sing 103 n n C3B C4B DPM doub 104 n y C3B C7B DPM sing 105 n n C4B NB DPM sing 106 n y C5B C6B DPM sing 107 n n C6B O1B DPM doub 108 n n C6B O2B DPM sing 109 n n C7B C8B DPM sing 110 n n C8B C9B DPM sing 111 n n C9B O3B DPM doub 112 n n C9B O4B DPM sing 113 n n C5A H5A1 DPM sing 114 n n C5A H5A2 DPM sing 115 n n C7A H7A1 DPM sing 116 n n C7A H7A2 DPM sing 117 n n C8A H8A1 DPM sing 118 n n C8A H8A2 DPM sing 119 n n CHA HCA1 DPM sing 120 n n CHA HCA2 DPM sing 121 n n CHA HCA3 DPM sing 122 n n NA H10 DPM sing 123 n n O2A HOA2 DPM sing 124 n n O4A HOA4 DPM sing 125 n n C4B H4B1 DPM sing 126 n n C5B H5B1 DPM sing 127 n n C5B H5B2 DPM sing 128 n n C7B H7B1 DPM sing 129 n n C7B H7B2 DPM sing 130 n n C8B H8B1 DPM sing 131 n n C8B H8B2 DPM sing 132 n n CHB HCB1 DPM sing 133 n n CHB HCB2 DPM sing 134 n n NB H22 DPM sing 135 n n O2B HOB2 DPM sing 136 n n O4B HOB4 DPM sing 137 n n # _atom_sites.entry_id 2YPN _atom_sites.fract_transf_matrix[1][1] 0.011356 _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] 0.013205 _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] 0.019861 _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 1 318 318 HOH HOH . C 3 HOH A 2 319 319 HOH HOH . C 3 HOH A 3 320 320 HOH HOH . C 3 HOH A 4 321 321 HOH HOH . C 3 HOH A 5 322 322 HOH HOH . C 3 HOH A 6 323 323 HOH HOH . C 3 HOH A 7 324 324 HOH HOH . C 3 HOH A 8 325 325 HOH HOH . C 3 HOH A 9 326 326 HOH HOH . C 3 HOH A 10 327 327 HOH HOH . C 3 HOH A 11 328 328 HOH HOH . C 3 HOH A 12 329 329 HOH HOH . C 3 HOH A 13 330 330 HOH HOH . C 3 HOH A 14 331 331 HOH HOH . C 3 HOH A 15 332 332 HOH HOH . C 3 HOH A 16 333 333 HOH HOH . C 3 HOH A 17 334 334 HOH HOH . C 3 HOH A 18 335 335 HOH HOH . C 3 HOH A 19 336 336 HOH HOH . C 3 HOH A 20 337 337 HOH HOH . C 3 HOH A 21 338 338 HOH HOH . C 3 HOH A 22 339 339 HOH HOH . C 3 HOH A 23 340 340 HOH HOH . C 3 HOH A 24 341 341 HOH HOH . C 3 HOH A 25 342 342 HOH HOH . C 3 HOH A 26 343 343 HOH HOH . C 3 HOH A 27 344 344 HOH HOH . C 3 HOH A 28 345 345 HOH HOH . C 3 HOH A 29 346 346 HOH HOH . C 3 HOH A 30 347 347 HOH HOH . C 3 HOH A 31 348 348 HOH HOH . C 3 HOH A 32 349 349 HOH HOH . C 3 HOH A 33 350 350 HOH HOH . C 3 HOH A 34 351 351 HOH HOH . C 3 HOH A 35 352 352 HOH HOH . C 3 HOH A 36 353 353 HOH HOH . C 3 HOH A 37 354 354 HOH HOH . C 3 HOH A 38 355 355 HOH HOH . C 3 HOH A 39 356 356 HOH HOH . C 3 HOH A 40 357 357 HOH HOH . C 3 HOH A 41 358 358 HOH HOH . C 3 HOH A 42 359 359 HOH HOH . C 3 HOH A 43 360 360 HOH HOH . C 3 HOH A 44 361 361 HOH HOH . C 3 HOH A 45 362 362 HOH HOH . C 3 HOH A 46 363 363 HOH HOH . C 3 HOH A 47 364 364 HOH HOH . C 3 HOH A 48 365 365 HOH HOH . C 3 HOH A 49 366 366 HOH HOH . C 3 HOH A 50 367 367 HOH HOH . C 3 HOH A 51 368 368 HOH HOH . C 3 HOH A 52 369 369 HOH HOH . C 3 HOH A 53 370 370 HOH HOH . C 3 HOH A 54 371 371 HOH HOH . C 3 HOH A 55 372 372 HOH HOH . C 3 HOH A 56 373 373 HOH HOH . C 3 HOH A 57 374 374 HOH HOH . C 3 HOH A 58 375 375 HOH HOH . C 3 HOH A 59 376 376 HOH HOH . C 3 HOH A 60 377 377 HOH HOH . C 3 HOH A 61 378 378 HOH HOH . C 3 HOH A 62 379 379 HOH HOH . C 3 HOH A 63 380 380 HOH HOH . C 3 HOH A 64 381 381 HOH HOH . C 3 HOH A 65 382 382 HOH HOH . C 3 HOH A 66 383 383 HOH HOH . C 3 HOH A 67 384 384 HOH HOH . C 3 HOH A 68 385 385 HOH HOH . C 3 HOH A 69 386 386 HOH HOH . C 3 HOH A 70 387 387 HOH HOH . C 3 HOH A 71 388 388 HOH HOH . C 3 HOH A 72 389 389 HOH HOH . C 3 HOH A 73 390 390 HOH HOH . C 3 HOH A 74 391 391 HOH HOH . C 3 HOH A 75 392 392 HOH HOH . C 3 HOH A 76 393 393 HOH HOH . C 3 HOH A 77 394 394 HOH HOH . C 3 HOH A 78 395 395 HOH HOH . C 3 HOH A 79 396 396 HOH HOH . C 3 HOH A 80 397 397 HOH HOH . C 3 HOH A 81 398 398 HOH HOH . C 3 HOH A 82 399 399 HOH HOH . C 3 HOH A 83 400 400 HOH HOH . C 3 HOH A 84 401 401 HOH HOH . C 3 HOH A 85 402 402 HOH HOH . C 3 HOH A 86 403 403 HOH HOH . C 3 HOH A 87 404 404 HOH HOH . C 3 HOH A 88 405 405 HOH HOH . C 3 HOH A 89 406 406 HOH HOH . C 3 HOH A 90 407 407 HOH HOH . C 3 HOH A 91 408 408 HOH HOH . C 3 HOH A 92 409 409 HOH HOH . C 3 HOH A 93 410 410 HOH HOH . C 3 HOH A 94 411 411 HOH HOH . C 3 HOH A 95 412 412 HOH HOH . C 3 HOH A 96 413 413 HOH HOH . C 3 HOH A 97 414 414 HOH HOH . C 3 HOH A 98 415 415 HOH HOH . C 3 HOH A 99 416 416 HOH HOH . C 3 HOH A 100 417 417 HOH HOH . C 3 HOH A 101 418 418 HOH HOH . C 3 HOH A 102 419 419 HOH HOH . C 3 HOH A 103 420 420 HOH HOH . C 3 HOH A 104 421 421 HOH HOH . C 3 HOH A 105 422 422 HOH HOH . C 3 HOH A 106 423 423 HOH HOH . C 3 HOH A 107 424 424 HOH HOH . C 3 HOH A 108 425 425 HOH HOH . C 3 HOH A 109 426 426 HOH HOH . C 3 HOH A 110 427 427 HOH HOH . C 3 HOH A 111 428 428 HOH HOH . C 3 HOH A 112 429 429 HOH HOH . C 3 HOH A 113 430 430 HOH HOH . C 3 HOH A 114 431 431 HOH HOH . C 3 HOH A 115 432 432 HOH HOH . C 3 HOH A 116 433 433 HOH HOH . C 3 HOH A 117 434 434 HOH HOH . C 3 HOH A 118 435 435 HOH HOH . C 3 HOH A 119 436 436 HOH HOH . C 3 HOH A 120 437 437 HOH HOH . C 3 HOH A 121 438 438 HOH HOH . C 3 HOH A 122 439 439 HOH HOH . C 3 HOH A 123 440 440 HOH HOH . C 3 HOH A 124 441 441 HOH HOH . C 3 HOH A 125 442 442 HOH HOH . C 3 HOH A 126 443 443 HOH HOH . C 3 HOH A 127 444 444 HOH HOH . C 3 HOH A 128 445 445 HOH HOH . C 3 HOH A 129 446 446 HOH HOH . C 3 HOH A 130 447 447 HOH HOH . C 3 HOH A 131 448 448 HOH HOH . C 3 HOH A 132 449 449 HOH HOH . C 3 HOH A 133 450 450 HOH HOH . C 3 HOH A 134 451 451 HOH HOH . C 3 HOH A 135 452 452 HOH HOH . C 3 HOH A 136 453 453 HOH HOH . C 3 HOH A 137 454 454 HOH HOH . C 3 HOH A 138 455 455 HOH HOH . C 3 HOH A 139 456 456 HOH HOH . C 3 HOH A 140 457 457 HOH HOH . C 3 HOH A 141 458 458 HOH HOH . C 3 HOH A 142 459 459 HOH HOH . C 3 HOH A 143 460 460 HOH HOH . C 3 HOH A 144 461 461 HOH HOH . C 3 HOH A 145 462 462 HOH HOH . C 3 HOH A 146 463 463 HOH HOH . C 3 HOH A 147 464 464 HOH HOH . C 3 HOH A 148 465 465 HOH HOH . C 3 HOH A 149 466 466 HOH HOH . C 3 HOH A 150 467 467 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 16.159 0.809 27.147 1 12.01 ? C1A DPM 314 A 1 HETATM 2 C C2A DPM . . . B 2 16.946 0.408 28.186 1 13.42 ? C2A DPM 314 A 1 HETATM 3 C C3A DPM . . . B 2 17.854 1.464 28.457 1 15.08 ? C3A DPM 314 A 1 HETATM 4 C C4A DPM . . . B 2 17.574 2.465 27.571 1 16.01 ? C4A DPM 314 A 1 HETATM 5 C C5A DPM . . . B 2 16.838 -0.912 28.916 1 13.31 ? C5A DPM 314 A 1 HETATM 6 C C6A DPM . . . B 2 17.689 -2.03 28.33 1 9.75 ? C6A DPM 314 A 1 HETATM 7 C C7A DPM . . . B 2 18.98 1.463 29.463 1 8.27 ? C7A DPM 314 A 1 HETATM 8 C C8A DPM . . . B 2 18.515 1.536 30.898 1 9.54 ? C8A DPM 314 A 1 HETATM 9 C C9A DPM . . . B 2 19.663 1.511 31.891 1 10.32 ? C9A DPM 314 A 1 HETATM 10 C CHA DPM . . . B 2 15.06 0.107 26.402 1 16.24 ? CHA DPM 314 A 1 HETATM 11 N NA DPM . . . B 2 16.544 2.058 26.77 1 10.71 ? NA DPM 314 A 1 HETATM 12 O O1A DPM . . . B 2 17.399 -3.203 28.626 1 16.06 ? O1A DPM 314 A 1 HETATM 13 O O2A DPM . . . B 2 18.644 -1.747 27.581 1 10.27 ? O2A DPM 314 A 1 HETATM 14 O O3A DPM . . . B 2 19.537 2.153 32.945 1 15.85 ? O3A DPM 314 A 1 HETATM 15 O O4A DPM . . . B 2 20.695 0.852 31.636 1 15.07 ? O4A DPM 314 A 1 HETATM 16 C C1B DPM . . . B 2 19.032 3.946 26.073 1 17.3 ? C1B DPM 314 A 1 HETATM 17 C C2B DPM . . . B 2 20.381 3.915 25.862 1 16.88 ? C2B DPM 314 A 1 HETATM 18 C C3B DPM . . . B 2 20.58 4.019 24.448 1 18.86 ? C3B DPM 314 A 1 HETATM 19 C C4B DPM . . . B 2 19.345 4.119 23.876 1 14.48 ? C4B DPM 314 A 1 HETATM 20 C C5B DPM . . . B 2 21.429 3.904 26.967 1 20.8 ? C5B DPM 314 A 1 HETATM 21 C C6B DPM . . . B 2 22.406 2.734 26.956 1 19.97 ? C6B DPM 314 A 1 HETATM 22 C C7B DPM . . . B 2 21.885 3.968 23.69 1 20.66 ? C7B DPM 314 A 1 HETATM 23 C C8B DPM . . . B 2 22.168 2.614 23.002 1 22.54 ? C8B DPM 314 A 1 HETATM 24 C C9B DPM . . . B 2 21.397 2.391 21.7 1 21.99 ? C9B DPM 314 A 1 HETATM 25 C CHB DPM . . . B 2 18.205 3.825 27.345 1 17.87 ? CHB DPM 314 A 1 HETATM 26 N NB DPM . . . B 2 18.407 4.069 24.864 1 17.88 ? NB DPM 314 A 1 HETATM 27 O O1B DPM . . . B 2 21.972 1.566 26.935 1 12.29 ? O1B DPM 314 A 1 HETATM 28 O O2B DPM . . . B 2 23.621 2.988 26.998 1 20.49 ? O2B DPM 314 A 1 HETATM 29 O O3B DPM . . . B 2 21.261 1.228 21.279 1 19.81 ? O3B DPM 314 A 1 HETATM 30 O O4B DPM . . . B 2 20.955 3.372 21.072 1 31.42 ? O4B DPM 314 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 349 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 30 #