data_3MKF # _model_server_result.job_id wItQftBvpTxwkmoL_bs_bA _model_server_result.datetime_utc '2025-04-26 07:42:21' _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 3mkf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1}' # _entry.id 3MKF # _exptl.entry_id 3MKF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 390.156 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '({[(2R)-2-{[(4-ethyl-2,3-dioxo-3,4-dihydropyrazin-1(2H)-yl)carbonyl]amino}-2-(4-hydroxyphenyl)acetyl]amino}methyl)boronic 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 3MKF _cell.length_a 49.215 _cell.length_b 56.139 _cell.length_c 82.59 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3MKF _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 # 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 52 A CYS 77 1_555 A SG CYS 98 A CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? covale ? covale1 B BAY CZ7 . A CZ7 1 1_555 A OG SER 45 A SER 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.557 ? # _chem_comp.formula 'C16 H19 B N4 O7' _chem_comp.formula_weight 390.156 _chem_comp.id CZ7 _chem_comp.mon_nstd_flag . _chem_comp.name '({[(2R)-2-{[(4-ethyl-2,3-dioxo-3,4-dihydropyrazin-1(2H)-yl)carbonyl]amino}-2-(4-hydroxyphenyl)acetyl]amino}methyl)boronic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O C CZ7 doub 83 n n C CA CZ7 sing 84 n n C NAQ CZ7 sing 85 n n CA N CZ7 sing 86 n n N CAT CZ7 sing 87 n n N HN CZ7 sing 88 n n CAX CA CZ7 sing 89 n n CA HA CZ7 sing 90 n n CAM CAA CZ7 sing 91 n n CAA HAA CZ7 sing 92 n n CAA HAAA CZ7 sing 93 n n CAA HAAB CZ7 sing 94 n n CAT OAC CZ7 doub 95 n n OAD CAU CZ7 doub 96 n n OAE CAV CZ7 doub 97 n n OAF CAW CZ7 sing 98 n n OAF HOAF CZ7 sing 99 n n BAY OAG CZ7 sing 100 n n OAG HOAG CZ7 sing 101 n n BAY OAH CZ7 sing 102 n n OAH HOAH CZ7 sing 103 n n CAW CAI CZ7 doub 104 n y CAI CAK CZ7 sing 105 n y CAI HAI CZ7 sing 106 n n CAJ CAW CZ7 sing 107 n y CAJ CAL CZ7 doub 108 n y CAJ HAJ CZ7 sing 109 n n CAX CAK CZ7 doub 110 n y CAK HAK CZ7 sing 111 n n CAL CAX CZ7 sing 112 n y CAL HAL CZ7 sing 113 n n NBA CAM CZ7 sing 114 n n CAM HAM CZ7 sing 115 n n CAM HAMA CZ7 sing 116 n n CAN NAQ CZ7 sing 117 n n CAN BAY CZ7 sing 118 n n CAN HAN CZ7 sing 119 n n CAN HANA CZ7 sing 120 n n NBA CAO CZ7 sing 121 n n CAP CAO CZ7 doub 122 n n CAO HAO CZ7 sing 123 n n NBB CAP CZ7 sing 124 n n CAP HAP CZ7 sing 125 n n NAQ HNAQ CZ7 sing 126 n n CAT NBB CZ7 sing 127 n n CAV CAU CZ7 sing 128 n n CAU NBA CZ7 sing 129 n n CAV NBB CZ7 sing 130 n n # _atom_sites.entry_id 3MKF _atom_sites.fract_transf_matrix[1][1] 0.020319 _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] 0.017813 _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] 0.012108 _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 CZ7 A 1 1 1 CZ7 CZ7 . C 3 MA4 A 1 600 600 MA4 MA4 . D 3 MA4 A 1 601 601 MA4 MA4 . E 4 HOH A 1 2 2 HOH HOH . E 4 HOH A 2 3 3 HOH HOH . E 4 HOH A 3 4 4 HOH HOH . E 4 HOH A 4 5 5 HOH HOH . E 4 HOH A 5 6 6 HOH HOH . E 4 HOH A 6 7 7 HOH HOH . E 4 HOH A 7 8 8 HOH HOH . E 4 HOH A 8 9 9 HOH HOH . E 4 HOH A 9 10 10 HOH HOH . E 4 HOH A 10 11 11 HOH HOH . E 4 HOH A 11 12 12 HOH HOH . E 4 HOH A 12 13 13 HOH HOH . E 4 HOH A 13 14 14 HOH HOH . E 4 HOH A 14 15 15 HOH HOH . E 4 HOH A 15 16 16 HOH HOH . E 4 HOH A 16 17 17 HOH HOH . E 4 HOH A 17 18 18 HOH HOH . E 4 HOH A 18 19 19 HOH HOH . E 4 HOH A 19 20 20 HOH HOH . E 4 HOH A 20 21 21 HOH HOH . E 4 HOH A 21 22 22 HOH HOH . E 4 HOH A 22 23 23 HOH HOH . E 4 HOH A 23 24 24 HOH HOH . E 4 HOH A 24 25 25 HOH HOH . E 4 HOH A 25 293 1 HOH HOH . E 4 HOH A 26 294 26 HOH HOH . E 4 HOH A 27 295 27 HOH HOH . E 4 HOH A 28 296 28 HOH HOH . E 4 HOH A 29 297 29 HOH HOH . E 4 HOH A 30 298 30 HOH HOH . E 4 HOH A 31 299 31 HOH HOH . E 4 HOH A 32 300 32 HOH HOH . E 4 HOH A 33 301 33 HOH HOH . E 4 HOH A 34 302 34 HOH HOH . E 4 HOH A 35 303 35 HOH HOH . E 4 HOH A 36 304 36 HOH HOH . E 4 HOH A 37 305 37 HOH HOH . E 4 HOH A 38 306 38 HOH HOH . E 4 HOH A 39 307 39 HOH HOH . E 4 HOH A 40 308 40 HOH HOH . E 4 HOH A 41 309 41 HOH HOH . E 4 HOH A 42 310 42 HOH HOH . E 4 HOH A 43 311 43 HOH HOH . E 4 HOH A 44 312 44 HOH HOH . E 4 HOH A 45 313 45 HOH HOH . E 4 HOH A 46 314 46 HOH HOH . E 4 HOH A 47 315 47 HOH HOH . E 4 HOH A 48 316 48 HOH HOH . E 4 HOH A 49 317 49 HOH HOH . E 4 HOH A 50 318 50 HOH HOH . E 4 HOH A 51 319 51 HOH HOH . E 4 HOH A 52 320 52 HOH HOH . E 4 HOH A 53 321 53 HOH HOH . E 4 HOH A 54 322 54 HOH HOH . E 4 HOH A 55 323 55 HOH HOH . E 4 HOH A 56 324 56 HOH HOH . E 4 HOH A 57 325 57 HOH HOH . E 4 HOH A 58 326 58 HOH HOH . E 4 HOH A 59 327 59 HOH HOH . E 4 HOH A 60 328 60 HOH HOH . E 4 HOH A 61 329 61 HOH HOH . E 4 HOH A 62 330 62 HOH HOH . E 4 HOH A 63 331 63 HOH HOH . E 4 HOH A 64 332 64 HOH HOH . E 4 HOH A 65 333 65 HOH HOH . E 4 HOH A 66 334 66 HOH HOH . E 4 HOH A 67 335 67 HOH HOH . E 4 HOH A 68 336 68 HOH HOH . E 4 HOH A 69 337 69 HOH HOH . E 4 HOH A 70 338 70 HOH HOH . E 4 HOH A 71 339 71 HOH HOH . E 4 HOH A 72 340 72 HOH HOH . E 4 HOH A 73 341 73 HOH HOH . E 4 HOH A 74 342 74 HOH HOH . E 4 HOH A 75 343 75 HOH HOH . E 4 HOH A 76 344 76 HOH HOH . E 4 HOH A 77 345 77 HOH HOH . E 4 HOH A 78 346 78 HOH HOH . E 4 HOH A 79 347 79 HOH HOH . E 4 HOH A 80 348 80 HOH HOH . E 4 HOH A 81 349 81 HOH HOH . E 4 HOH A 82 350 82 HOH HOH . E 4 HOH A 83 351 83 HOH HOH . E 4 HOH A 84 352 84 HOH HOH . E 4 HOH A 85 353 85 HOH HOH . E 4 HOH A 86 354 86 HOH HOH . E 4 HOH A 87 355 87 HOH HOH . E 4 HOH A 88 356 88 HOH HOH . E 4 HOH A 89 357 89 HOH HOH . E 4 HOH A 90 358 90 HOH HOH . E 4 HOH A 91 359 91 HOH HOH . E 4 HOH A 92 360 92 HOH HOH . E 4 HOH A 93 361 93 HOH HOH . E 4 HOH A 94 362 94 HOH HOH . E 4 HOH A 95 363 95 HOH HOH . E 4 HOH A 96 364 96 HOH HOH . E 4 HOH A 97 365 97 HOH HOH . E 4 HOH A 98 366 98 HOH HOH . E 4 HOH A 99 367 99 HOH HOH . E 4 HOH A 100 368 100 HOH HOH . E 4 HOH A 101 369 101 HOH HOH . E 4 HOH A 102 370 102 HOH HOH . E 4 HOH A 103 371 103 HOH HOH . E 4 HOH A 104 372 104 HOH HOH . E 4 HOH A 105 373 105 HOH HOH . E 4 HOH A 106 374 106 HOH HOH . E 4 HOH A 107 375 107 HOH HOH . E 4 HOH A 108 376 108 HOH HOH . E 4 HOH A 109 377 109 HOH HOH . E 4 HOH A 110 378 110 HOH HOH . E 4 HOH A 111 379 111 HOH HOH . E 4 HOH A 112 380 112 HOH HOH . E 4 HOH A 113 381 113 HOH HOH . E 4 HOH A 114 382 114 HOH HOH . E 4 HOH A 115 383 115 HOH HOH . E 4 HOH A 116 384 116 HOH HOH . E 4 HOH A 117 385 117 HOH HOH . E 4 HOH A 118 386 118 HOH HOH . E 4 HOH A 119 387 119 HOH HOH . E 4 HOH A 120 388 120 HOH HOH . E 4 HOH A 121 389 121 HOH HOH . E 4 HOH A 122 390 122 HOH HOH . E 4 HOH A 123 391 123 HOH HOH . E 4 HOH A 124 392 124 HOH HOH . E 4 HOH A 125 393 125 HOH HOH . E 4 HOH A 126 394 126 HOH HOH . E 4 HOH A 127 395 127 HOH HOH . E 4 HOH A 128 396 128 HOH HOH . E 4 HOH A 129 397 129 HOH HOH . E 4 HOH A 130 398 130 HOH HOH . E 4 HOH A 131 399 131 HOH HOH . E 4 HOH A 132 400 132 HOH HOH . E 4 HOH A 133 401 133 HOH HOH . E 4 HOH A 134 402 134 HOH HOH . E 4 HOH A 135 403 135 HOH HOH . E 4 HOH A 136 404 136 HOH HOH . E 4 HOH A 137 405 137 HOH HOH . E 4 HOH A 138 406 138 HOH HOH . E 4 HOH A 139 407 139 HOH HOH . E 4 HOH A 140 408 140 HOH HOH . E 4 HOH A 141 409 141 HOH HOH . E 4 HOH A 142 410 142 HOH HOH . E 4 HOH A 143 411 143 HOH HOH . E 4 HOH A 144 412 144 HOH HOH . E 4 HOH A 145 413 145 HOH HOH . E 4 HOH A 146 414 146 HOH HOH . E 4 HOH A 147 415 147 HOH HOH . E 4 HOH A 148 416 148 HOH HOH . E 4 HOH A 149 417 149 HOH HOH . E 4 HOH A 150 418 150 HOH HOH . E 4 HOH A 151 419 151 HOH HOH . E 4 HOH A 152 420 152 HOH HOH . E 4 HOH A 153 421 153 HOH HOH . E 4 HOH A 154 422 154 HOH HOH . E 4 HOH A 155 423 155 HOH HOH . E 4 HOH A 156 424 156 HOH HOH . E 4 HOH A 157 425 157 HOH HOH . E 4 HOH A 158 426 158 HOH HOH . E 4 HOH A 159 427 159 HOH HOH . E 4 HOH A 160 428 160 HOH HOH . E 4 HOH A 161 429 161 HOH HOH . E 4 HOH A 162 430 162 HOH HOH . E 4 HOH A 163 431 163 HOH HOH . E 4 HOH A 164 432 164 HOH HOH . E 4 HOH A 165 433 165 HOH HOH . E 4 HOH A 166 434 166 HOH HOH . E 4 HOH A 167 435 167 HOH HOH . E 4 HOH A 168 436 168 HOH HOH . E 4 HOH A 169 437 169 HOH HOH . E 4 HOH A 170 438 170 HOH HOH . E 4 HOH A 171 439 171 HOH HOH . E 4 HOH A 172 440 172 HOH HOH . E 4 HOH A 173 441 173 HOH HOH . E 4 HOH A 174 442 174 HOH HOH . E 4 HOH A 175 443 175 HOH HOH . E 4 HOH A 176 444 176 HOH HOH . E 4 HOH A 177 445 177 HOH HOH . E 4 HOH A 178 446 178 HOH HOH . E 4 HOH A 179 447 179 HOH HOH . E 4 HOH A 180 448 180 HOH HOH . E 4 HOH A 181 449 181 HOH HOH . E 4 HOH A 182 450 182 HOH HOH . E 4 HOH A 183 451 183 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 C CZ7 . . . B 2 31.285 65.692 4.274 1 11.38 ? C CZ7 1 A 1 HETATM 2 N N CZ7 . . . B 2 30.882 68.089 4.61 1 12.64 ? N CZ7 1 A 1 HETATM 3 O O CZ7 . . . B 2 30.205 65.581 3.698 1 10.81 ? O CZ7 1 A 1 HETATM 4 C CA CZ7 . . . B 2 31.903 67.043 4.537 1 12.91 ? CA CZ7 1 A 1 HETATM 5 C CAA CZ7 . . . B 2 25.292 72.122 6.498 1 22.98 ? CAA CZ7 1 A 1 HETATM 6 O OAC CZ7 . . . B 2 31.878 69.172 6.275 1 13.47 ? OAC CZ7 1 A 1 HETATM 7 O OAD CZ7 . . . B 2 27.383 71.659 3.97 1 21.3 ? OAD CZ7 1 A 1 HETATM 8 O OAE CZ7 . . . B 2 28.765 69.312 3.741 1 15.78 ? OAE CZ7 1 A 1 HETATM 9 O OAF CZ7 . . . B 2 35.707 68.362 0.57 1 15.81 ? OAF CZ7 1 A 1 HETATM 10 O OAG CZ7 . . . B 2 31.219 62.702 7.161 1 11.2 ? OAG CZ7 1 A 1 HETATM 11 O OAH CZ7 . . . B 2 33.5 62.75 6.182 1 8.01 ? OAH CZ7 1 A 1 HETATM 12 C CAI CZ7 . . . B 2 35.148 68.058 2.876 1 14.25 ? CAI CZ7 1 A 1 HETATM 13 C CAJ CZ7 . . . B 2 33.489 67.707 1.162 1 14.83 ? CAJ CZ7 1 A 1 HETATM 14 C CAK CZ7 . . . B 2 34.221 67.733 3.863 1 13.24 ? CAK CZ7 1 A 1 HETATM 15 C CAL CZ7 . . . B 2 32.561 67.382 2.148 1 13.24 ? CAL CZ7 1 A 1 HETATM 16 C CAM CZ7 . . . B 2 26.717 72.541 6.28 1 22.05 ? CAM CZ7 1 A 1 HETATM 17 C CAN CZ7 . . . B 2 31.575 63.249 4.568 1 9.72 ? CAN CZ7 1 A 1 HETATM 18 C CAO CZ7 . . . B 2 28.622 71.442 7.08 1 19.95 ? CAO CZ7 1 A 1 HETATM 19 C CAP CZ7 . . . B 2 29.828 70.775 6.739 1 17.59 ? CAP CZ7 1 A 1 HETATM 20 N NAQ CZ7 . . . B 2 31.974 64.646 4.709 1 10.33 ? NAQ CZ7 1 A 1 HETATM 21 C CAT CZ7 . . . B 2 30.943 69.103 5.487 1 13.48 ? CAT CZ7 1 A 1 HETATM 22 C CAU CZ7 . . . B 2 27.902 71.096 4.929 1 18.55 ? CAU CZ7 1 A 1 HETATM 23 C CAV CZ7 . . . B 2 28.922 70.067 4.685 1 15.09 ? CAV CZ7 1 A 1 HETATM 24 C CAW CZ7 . . . B 2 34.789 68.042 1.53 1 14.06 ? CAW CZ7 1 A 1 HETATM 25 C CAX CZ7 . . . B 2 32.915 67.39 3.5 1 12.23 ? CAX CZ7 1 A 1 HETATM 26 B BAY CZ7 . . . B 2 32.026 62.476 5.885 1 11.09 ? BAY CZ7 1 A 1 HETATM 27 N NBA CZ7 . . . B 2 27.521 71.375 6.185 1 20.3 ? NBA CZ7 1 A 1 HETATM 28 N NBB CZ7 . . . B 2 29.972 70.044 5.526 1 14.57 ? NBB CZ7 1 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 355 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #