data_3SAY # _model_server_result.job_id Erlh2lUWY60gpt6VFtoHyg _model_server_result.datetime_utc '2025-04-02 22:54:31' _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 3say # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":432}' # _entry.id 3SAY # _exptl.entry_id 3SAY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 104.061 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MALONIC ACID' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 97.08 _cell.angle_gamma 90 _cell.entry_id 3SAY _cell.length_a 67.52 _cell.length_b 110.78 _cell.length_c 67.91 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SAY _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 software_defined_assembly 1 PISA monomeric 1 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 G N 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 covale ? covale1 A C SER 215 A SER 215 1_555 A N PTR 216 A PTR 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale2 A C PTR 216 A PTR 216 1_555 A N ILE 217 A ILE 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale3 B C SER 215 B SER 215 1_555 B N PTR 216 B PTR 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale4 B C PTR 216 B PTR 216 1_555 B N ILE 217 B ILE 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? # _chem_comp.formula 'C3 H4 O4' _chem_comp.formula_weight 104.061 _chem_comp.id MLA _chem_comp.mon_nstd_flag . _chem_comp.name 'MALONIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'DICARBOXYLIC ACID C3;PROPANEDIOLIC ACID;METHANEDICARBOXYLIC 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 C1 O1A MLA sing 241 n n C1 O1B MLA doub 242 n n C1 C2 MLA sing 243 n n O1A H1A MLA sing 244 n n C2 C3 MLA sing 245 n n C2 HC21 MLA sing 246 n n C2 HC22 MLA sing 247 n n C3 O3A MLA doub 248 n n C3 O3B MLA sing 249 n n O3B H3B MLA sing 250 n n # _atom_sites.entry_id 3SAY _atom_sites.fract_transf_matrix[1][1] 0.01481 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001839 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009027 _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] 0.014839 _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 C 2 OFT A 1 431 1 OFT OFT . D 3 MLA A 1 432 2 MLA MAL . E 4 FMT A 1 433 1 FMT FMT . F 2 OFT B 1 431 2 OFT OFT . G 3 MLA B 1 432 1 MLA MAL . H 5 MPD B 1 433 1 MPD MPD . I 6 HOH A 1 434 6 HOH HOH . I 6 HOH A 2 435 7 HOH HOH . I 6 HOH A 3 436 8 HOH HOH . I 6 HOH A 4 437 9 HOH HOH . I 6 HOH A 5 438 10 HOH HOH . I 6 HOH A 6 439 13 HOH HOH . I 6 HOH A 7 440 14 HOH HOH . I 6 HOH A 8 441 16 HOH HOH . I 6 HOH A 9 442 17 HOH HOH . I 6 HOH A 10 443 18 HOH HOH . I 6 HOH A 11 444 20 HOH HOH . I 6 HOH A 12 445 21 HOH HOH . I 6 HOH A 13 446 22 HOH HOH . I 6 HOH A 14 447 24 HOH HOH . I 6 HOH A 15 448 28 HOH HOH . I 6 HOH A 16 449 31 HOH HOH . I 6 HOH A 17 450 32 HOH HOH . I 6 HOH A 18 451 38 HOH HOH . I 6 HOH A 19 452 39 HOH HOH . I 6 HOH A 20 453 40 HOH HOH . I 6 HOH A 21 454 42 HOH HOH . I 6 HOH A 22 455 45 HOH HOH . I 6 HOH A 23 456 46 HOH HOH . I 6 HOH A 24 457 47 HOH HOH . I 6 HOH A 25 458 48 HOH HOH . I 6 HOH A 26 459 50 HOH HOH . I 6 HOH A 27 460 51 HOH HOH . I 6 HOH A 28 461 53 HOH HOH . I 6 HOH A 29 462 54 HOH HOH . I 6 HOH A 30 463 55 HOH HOH . I 6 HOH A 31 464 59 HOH HOH . I 6 HOH A 32 465 60 HOH HOH . I 6 HOH A 33 466 62 HOH HOH . I 6 HOH A 34 467 67 HOH HOH . I 6 HOH A 35 468 68 HOH HOH . I 6 HOH A 36 469 72 HOH HOH . I 6 HOH A 37 470 74 HOH HOH . I 6 HOH A 38 471 75 HOH HOH . I 6 HOH A 39 472 77 HOH HOH . I 6 HOH A 40 473 79 HOH HOH . I 6 HOH A 41 474 80 HOH HOH . I 6 HOH A 42 475 81 HOH HOH . I 6 HOH A 43 476 82 HOH HOH . I 6 HOH A 44 477 83 HOH HOH . I 6 HOH A 45 478 84 HOH HOH . I 6 HOH A 46 479 85 HOH HOH . I 6 HOH A 47 480 86 HOH HOH . I 6 HOH A 48 481 87 HOH HOH . I 6 HOH A 49 482 90 HOH HOH . I 6 HOH A 50 483 94 HOH HOH . I 6 HOH A 51 484 95 HOH HOH . I 6 HOH A 52 485 97 HOH HOH . I 6 HOH A 53 486 98 HOH HOH . I 6 HOH A 54 487 99 HOH HOH . I 6 HOH A 55 488 100 HOH HOH . I 6 HOH A 56 489 101 HOH HOH . I 6 HOH A 57 490 103 HOH HOH . I 6 HOH A 58 491 104 HOH HOH . I 6 HOH A 59 492 106 HOH HOH . I 6 HOH A 60 493 109 HOH HOH . I 6 HOH A 61 494 112 HOH HOH . I 6 HOH A 62 495 113 HOH HOH . I 6 HOH A 63 496 114 HOH HOH . I 6 HOH A 64 497 115 HOH HOH . I 6 HOH A 65 498 116 HOH HOH . I 6 HOH A 66 499 117 HOH HOH . I 6 HOH A 67 500 118 HOH HOH . I 6 HOH A 68 501 119 HOH HOH . I 6 HOH A 69 502 122 HOH HOH . I 6 HOH A 70 503 123 HOH HOH . I 6 HOH A 71 504 124 HOH HOH . I 6 HOH A 72 505 125 HOH HOH . I 6 HOH A 73 506 126 HOH HOH . I 6 HOH A 74 507 128 HOH HOH . I 6 HOH A 75 508 130 HOH HOH . I 6 HOH A 76 509 131 HOH HOH . I 6 HOH A 77 510 134 HOH HOH . I 6 HOH A 78 511 135 HOH HOH . I 6 HOH A 79 512 139 HOH HOH . I 6 HOH A 80 513 140 HOH HOH . I 6 HOH A 81 514 143 HOH HOH . I 6 HOH A 82 515 146 HOH HOH . I 6 HOH A 83 516 149 HOH HOH . I 6 HOH A 84 517 150 HOH HOH . I 6 HOH A 85 518 151 HOH HOH . I 6 HOH A 86 519 153 HOH HOH . I 6 HOH A 87 520 154 HOH HOH . I 6 HOH A 88 521 155 HOH HOH . I 6 HOH A 89 522 156 HOH HOH . I 6 HOH A 90 523 157 HOH HOH . I 6 HOH A 91 524 158 HOH HOH . I 6 HOH A 92 525 159 HOH HOH . I 6 HOH A 93 526 160 HOH HOH . I 6 HOH A 94 527 161 HOH HOH . I 6 HOH A 95 528 162 HOH HOH . I 6 HOH A 96 529 163 HOH HOH . I 6 HOH A 97 530 164 HOH HOH . I 6 HOH A 98 531 165 HOH HOH . I 6 HOH A 99 532 166 HOH HOH . I 6 HOH A 100 533 167 HOH HOH . I 6 HOH A 101 534 168 HOH HOH . I 6 HOH A 102 535 169 HOH HOH . I 6 HOH A 103 536 170 HOH HOH . I 6 HOH A 104 537 171 HOH HOH . I 6 HOH A 105 538 172 HOH HOH . I 6 HOH A 106 539 184 HOH HOH . I 6 HOH A 107 540 185 HOH HOH . I 6 HOH A 108 541 186 HOH HOH . I 6 HOH A 109 542 187 HOH HOH . I 6 HOH A 110 543 188 HOH HOH . I 6 HOH A 111 544 190 HOH HOH . I 6 HOH A 112 545 191 HOH HOH . I 6 HOH A 113 546 192 HOH HOH . I 6 HOH A 114 547 193 HOH HOH . I 6 HOH A 115 548 194 HOH HOH . I 6 HOH A 116 549 195 HOH HOH . I 6 HOH A 117 550 196 HOH HOH . I 6 HOH A 118 551 197 HOH HOH . I 6 HOH A 119 552 198 HOH HOH . I 6 HOH A 120 553 199 HOH HOH . I 6 HOH A 121 554 200 HOH HOH . I 6 HOH A 122 555 201 HOH HOH . I 6 HOH A 123 556 202 HOH HOH . I 6 HOH A 124 557 209 HOH HOH . I 6 HOH A 125 558 210 HOH HOH . I 6 HOH A 126 559 211 HOH HOH . I 6 HOH A 127 560 212 HOH HOH . I 6 HOH A 128 561 213 HOH HOH . I 6 HOH A 129 562 219 HOH HOH . J 6 HOH B 1 434 1 HOH HOH . J 6 HOH B 2 435 2 HOH HOH . J 6 HOH B 3 436 3 HOH HOH . J 6 HOH B 4 437 4 HOH HOH . J 6 HOH B 5 438 5 HOH HOH . J 6 HOH B 6 439 11 HOH HOH . J 6 HOH B 7 440 12 HOH HOH . J 6 HOH B 8 441 15 HOH HOH . J 6 HOH B 9 442 19 HOH HOH . J 6 HOH B 10 443 23 HOH HOH . J 6 HOH B 11 444 25 HOH HOH . J 6 HOH B 12 445 26 HOH HOH . J 6 HOH B 13 446 27 HOH HOH . J 6 HOH B 14 447 29 HOH HOH . J 6 HOH B 15 448 30 HOH HOH . J 6 HOH B 16 449 33 HOH HOH . J 6 HOH B 17 450 34 HOH HOH . J 6 HOH B 18 451 35 HOH HOH . J 6 HOH B 19 452 36 HOH HOH . J 6 HOH B 20 453 37 HOH HOH . J 6 HOH B 21 454 41 HOH HOH . J 6 HOH B 22 455 43 HOH HOH . J 6 HOH B 23 456 44 HOH HOH . J 6 HOH B 24 457 49 HOH HOH . J 6 HOH B 25 458 52 HOH HOH . J 6 HOH B 26 459 56 HOH HOH . J 6 HOH B 27 460 57 HOH HOH . J 6 HOH B 28 461 58 HOH HOH . J 6 HOH B 29 462 61 HOH HOH . J 6 HOH B 30 463 63 HOH HOH . J 6 HOH B 31 464 64 HOH HOH . J 6 HOH B 32 465 65 HOH HOH . J 6 HOH B 33 466 66 HOH HOH . J 6 HOH B 34 467 69 HOH HOH . J 6 HOH B 35 468 70 HOH HOH . J 6 HOH B 36 469 71 HOH HOH . J 6 HOH B 37 470 73 HOH HOH . J 6 HOH B 38 471 76 HOH HOH . J 6 HOH B 39 472 78 HOH HOH . J 6 HOH B 40 473 88 HOH HOH . J 6 HOH B 41 474 89 HOH HOH . J 6 HOH B 42 475 91 HOH HOH . J 6 HOH B 43 476 92 HOH HOH . J 6 HOH B 44 477 93 HOH HOH . J 6 HOH B 45 478 96 HOH HOH . J 6 HOH B 46 479 102 HOH HOH . J 6 HOH B 47 480 105 HOH HOH . J 6 HOH B 48 481 107 HOH HOH . J 6 HOH B 49 482 108 HOH HOH . J 6 HOH B 50 483 110 HOH HOH . J 6 HOH B 51 484 111 HOH HOH . J 6 HOH B 52 485 120 HOH HOH . J 6 HOH B 53 486 121 HOH HOH . J 6 HOH B 54 487 127 HOH HOH . J 6 HOH B 55 488 129 HOH HOH . J 6 HOH B 56 489 132 HOH HOH . J 6 HOH B 57 490 133 HOH HOH . J 6 HOH B 58 491 136 HOH HOH . J 6 HOH B 59 492 137 HOH HOH . J 6 HOH B 60 493 138 HOH HOH . J 6 HOH B 61 494 141 HOH HOH . J 6 HOH B 62 495 142 HOH HOH . J 6 HOH B 63 496 144 HOH HOH . J 6 HOH B 64 497 145 HOH HOH . J 6 HOH B 65 498 147 HOH HOH . J 6 HOH B 66 499 148 HOH HOH . J 6 HOH B 67 500 152 HOH HOH . J 6 HOH B 68 501 173 HOH HOH . J 6 HOH B 69 502 174 HOH HOH . J 6 HOH B 70 503 175 HOH HOH . J 6 HOH B 71 504 176 HOH HOH . J 6 HOH B 72 505 177 HOH HOH . J 6 HOH B 73 506 178 HOH HOH . J 6 HOH B 74 507 179 HOH HOH . J 6 HOH B 75 508 180 HOH HOH . J 6 HOH B 76 509 181 HOH HOH . J 6 HOH B 77 510 182 HOH HOH . J 6 HOH B 78 511 183 HOH HOH . J 6 HOH B 79 512 189 HOH HOH . J 6 HOH B 80 513 203 HOH HOH . J 6 HOH B 81 514 204 HOH HOH . J 6 HOH B 82 515 205 HOH HOH . J 6 HOH B 83 516 206 HOH HOH . J 6 HOH B 84 517 207 HOH HOH . J 6 HOH B 85 518 208 HOH HOH . J 6 HOH B 86 519 214 HOH HOH . J 6 HOH B 87 520 215 HOH HOH . J 6 HOH B 88 521 216 HOH HOH . J 6 HOH B 89 522 217 HOH HOH . J 6 HOH B 90 523 218 HOH HOH . J 6 HOH B 91 524 220 HOH HOH . J 6 HOH B 92 525 221 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 MLA . . . D 3 -11.546 -0.48 -11.01 1 50.98 ? C1 MLA 432 A 1 HETATM 2 O O1A MLA . . . D 3 -11.87 -1.654 -11.319 1 50.07 ? O1A MLA 432 A 1 HETATM 3 O O1B MLA . . . D 3 -11.428 0.456 -11.83 1 48.83 ? O1B MLA 432 A 1 HETATM 4 C C2 MLA . . . D 3 -11.285 -0.17 -9.554 1 52.39 ? C2 MLA 432 A 1 HETATM 5 C C3 MLA . . . D 3 -9.8 -0.032 -9.345 1 54.08 ? C3 MLA 432 A 1 HETATM 6 O O3A MLA . . . D 3 -9.024 -0.812 -9.941 1 52.53 ? O3A MLA 432 A 1 HETATM 7 O O3B MLA . . . D 3 -9.415 0.877 -8.577 1 56.68 ? O3B MLA 432 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 362 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 7 #