data_3QQV # _model_server_result.job_id oYw1um7N7ft9C7AadBsa0A _model_server_result.datetime_utc '2024-11-23 16:02:27' _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 3qqv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":383}' # _entry.id 3QQV # _exptl.entry_id 3QQV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 246.092 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIMETHYLALLYL DIPHOSPHATE' _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 90 _cell.angle_gamma 120 _cell.entry_id 3QQV _cell.length_a 123.636 _cell.length_b 123.636 _cell.length_c 51.82 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3QQV _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_554 x-y,-y,-z-1/3 1 0 0 0 -1 0 0 0 -1 0 0 -17.273333 # 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 E 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 ASP 153 A ASP 153 1_555 A N MSE 154 A MSE 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C MSE 154 A MSE 154 1_555 A N ALA 155 A ALA 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale3 A C ASP 161 A ASP 161 1_555 A N MSE 162 A MSE 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale4 A C MSE 162 A MSE 162 1_555 A N LEU 163 A LEU 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale5 A C GLY 182 A GLY 182 1_555 A N MSE 183 A MSE 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 A C MSE 183 A MSE 183 1_555 A N ARG 184 A ARG 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A OD2 ASP 108 A ASP 108 1_555 B MG MG . A MG 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc2 A OD1 ASP 108 A ASP 108 1_555 C MG MG . A MG 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc3 A OD2 ASP 112 A ASP 112 1_555 B MG MG . A MG 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc4 A OD2 ASP 112 A ASP 112 1_555 C MG MG . A MG 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? metalc ? metalc5 B MG MG . A MG 381 1_555 E O1A DMA . A DMA 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc6 B MG MG . A MG 381 1_555 H O HOH . A HOH 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc7 B MG MG . A MG 381 1_555 H O HOH . A HOH 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.897 ? metalc ? metalc8 C MG MG . A MG 382 1_555 E O3B DMA . A DMA 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.928 ? metalc ? metalc9 C MG MG . A MG 382 1_555 E O1A DMA . A DMA 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc10 C MG MG . A MG 382 1_555 H O HOH . A HOH 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? metalc ? metalc11 C MG MG . A MG 382 1_555 H O HOH . A HOH 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? # _chem_comp.formula 'C5 H12 O7 P2' _chem_comp.formula_weight 246.092 _chem_comp.id DMA _chem_comp.mon_nstd_flag . _chem_comp.name 'DIMETHYLALLYL DIPHOSPHATE' _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 C1 O1 DMA sing 83 n n C1 C2 DMA sing 84 n n C1 H11 DMA sing 85 n n C1 H12 DMA sing 86 n n O1 PA DMA sing 87 n n C2 C3 DMA doub 88 n n C2 H2 DMA sing 89 n n C3 C4 DMA sing 90 n n C3 C5 DMA sing 91 n n C4 H41 DMA sing 92 n n C4 H42 DMA sing 93 n n C4 H43 DMA sing 94 n n C5 H51 DMA sing 95 n n C5 H52 DMA sing 96 n n C5 H53 DMA sing 97 n n PA O1A DMA doub 98 n n PA O2A DMA sing 99 n n PA O3A DMA sing 100 n n O2A HOA2 DMA sing 101 n n O3A PB DMA sing 102 n n PB O1B DMA doub 103 n n PB O2B DMA sing 104 n n PB O3B DMA sing 105 n n O2B HOB2 DMA sing 106 n n O3B HOB3 DMA sing 107 n n # _atom_sites.entry_id 3QQV _atom_sites.fract_transf_matrix[1][1] 0.008088 _atom_sites.fract_transf_matrix[1][2] 0.00467 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00934 _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] 0.019298 _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 MG A 1 381 1 MG MG . C 2 MG A 1 382 1 MG MG . D 3 DMA A 1 383 1 DMA IPE . E 3 DMA A 1 384 1 DMA IPE . F 4 UNL A 1 385 2 UNL UNX . G 5 GOL A 1 386 1 GOL GOL . H 6 HOH A 1 387 3 HOH HOH . H 6 HOH A 2 388 4 HOH HOH . H 6 HOH A 3 389 5 HOH HOH . H 6 HOH A 4 390 6 HOH HOH . H 6 HOH A 5 391 7 HOH HOH . H 6 HOH A 6 392 8 HOH HOH . H 6 HOH A 7 393 9 HOH HOH . H 6 HOH A 8 394 10 HOH HOH . H 6 HOH A 9 395 11 HOH HOH . H 6 HOH A 10 396 12 HOH HOH . H 6 HOH A 11 397 13 HOH HOH . H 6 HOH A 12 398 15 HOH HOH . H 6 HOH A 13 399 18 HOH HOH . H 6 HOH A 14 400 19 HOH HOH . H 6 HOH A 15 401 20 HOH HOH . H 6 HOH A 16 402 21 HOH HOH . H 6 HOH A 17 403 22 HOH HOH . H 6 HOH A 18 404 23 HOH HOH . H 6 HOH A 19 405 24 HOH HOH . H 6 HOH A 20 406 25 HOH HOH . H 6 HOH A 21 407 26 HOH HOH . H 6 HOH A 22 408 27 HOH HOH . H 6 HOH A 23 409 28 HOH HOH . H 6 HOH A 24 410 29 HOH HOH . H 6 HOH A 25 411 30 HOH HOH . H 6 HOH A 26 412 31 HOH HOH . H 6 HOH A 27 413 32 HOH HOH . H 6 HOH A 28 414 33 HOH HOH . H 6 HOH A 29 415 34 HOH HOH . H 6 HOH A 30 416 35 HOH HOH . H 6 HOH A 31 417 36 HOH HOH . H 6 HOH A 32 418 37 HOH HOH . H 6 HOH A 33 419 38 HOH HOH . H 6 HOH A 34 420 39 HOH HOH . H 6 HOH A 35 421 40 HOH HOH . H 6 HOH A 36 422 42 HOH HOH . H 6 HOH A 37 423 43 HOH HOH . H 6 HOH A 38 424 44 HOH HOH . H 6 HOH A 39 425 45 HOH HOH . H 6 HOH A 40 426 46 HOH HOH . H 6 HOH A 41 427 47 HOH HOH . H 6 HOH A 42 428 48 HOH HOH . H 6 HOH A 43 429 49 HOH HOH . H 6 HOH A 44 430 50 HOH HOH . H 6 HOH A 45 431 52 HOH HOH . H 6 HOH A 46 432 53 HOH HOH . H 6 HOH A 47 433 54 HOH HOH . H 6 HOH A 48 434 55 HOH HOH . H 6 HOH A 49 435 56 HOH HOH . H 6 HOH A 50 436 57 HOH HOH . H 6 HOH A 51 437 58 HOH HOH . H 6 HOH A 52 438 59 HOH HOH . H 6 HOH A 53 439 60 HOH HOH . H 6 HOH A 54 440 61 HOH HOH . H 6 HOH A 55 441 62 HOH HOH . H 6 HOH A 56 442 63 HOH HOH . H 6 HOH A 57 443 64 HOH HOH . H 6 HOH A 58 444 65 HOH HOH . H 6 HOH A 59 445 66 HOH HOH . H 6 HOH A 60 446 67 HOH HOH . H 6 HOH A 61 447 68 HOH HOH . H 6 HOH A 62 448 69 HOH HOH . H 6 HOH A 63 449 70 HOH HOH . H 6 HOH A 64 450 71 HOH HOH . H 6 HOH A 65 451 72 HOH HOH . H 6 HOH A 66 452 73 HOH HOH . H 6 HOH A 67 453 74 HOH HOH . H 6 HOH A 68 454 75 HOH HOH . H 6 HOH A 69 455 77 HOH HOH . H 6 HOH A 70 456 78 HOH HOH . H 6 HOH A 71 457 79 HOH HOH . H 6 HOH A 72 458 80 HOH HOH . H 6 HOH A 73 459 81 HOH HOH . H 6 HOH A 74 460 83 HOH HOH . H 6 HOH A 75 461 84 HOH HOH . H 6 HOH A 76 462 85 HOH HOH . H 6 HOH A 77 463 87 HOH HOH . H 6 HOH A 78 464 88 HOH HOH . H 6 HOH A 79 465 89 HOH HOH . H 6 HOH A 80 466 90 HOH HOH . H 6 HOH A 81 467 91 HOH HOH . H 6 HOH A 82 468 92 HOH HOH . H 6 HOH A 83 469 93 HOH HOH . H 6 HOH A 84 470 94 HOH HOH . H 6 HOH A 85 471 95 HOH HOH . H 6 HOH A 86 472 96 HOH HOH . H 6 HOH A 87 473 97 HOH HOH . H 6 HOH A 88 474 98 HOH HOH . H 6 HOH A 89 475 99 HOH HOH . H 6 HOH A 90 476 100 HOH HOH . H 6 HOH A 91 477 101 HOH HOH . H 6 HOH A 92 478 102 HOH HOH . H 6 HOH A 93 479 103 HOH HOH . H 6 HOH A 94 480 104 HOH HOH . H 6 HOH A 95 481 105 HOH HOH . H 6 HOH A 96 482 106 HOH HOH . H 6 HOH A 97 483 107 HOH HOH . H 6 HOH A 98 484 108 HOH HOH . H 6 HOH A 99 485 109 HOH HOH . H 6 HOH A 100 486 110 HOH HOH . H 6 HOH A 101 487 111 HOH HOH . H 6 HOH A 102 488 112 HOH HOH . H 6 HOH A 103 489 113 HOH HOH . H 6 HOH A 104 490 114 HOH HOH . H 6 HOH A 105 491 115 HOH HOH . H 6 HOH A 106 492 116 HOH HOH . H 6 HOH A 107 493 117 HOH HOH . H 6 HOH A 108 494 119 HOH HOH . H 6 HOH A 109 495 120 HOH HOH . H 6 HOH A 110 496 121 HOH HOH . H 6 HOH A 111 497 122 HOH HOH . H 6 HOH A 112 498 123 HOH HOH . H 6 HOH A 113 499 124 HOH HOH . H 6 HOH A 114 500 125 HOH HOH . H 6 HOH A 115 501 126 HOH HOH . H 6 HOH A 116 502 131 HOH HOH . H 6 HOH A 117 503 134 HOH HOH . H 6 HOH A 118 504 135 HOH HOH . H 6 HOH A 119 505 136 HOH HOH . H 6 HOH A 120 506 137 HOH HOH . H 6 HOH A 121 507 138 HOH HOH . H 6 HOH A 122 508 139 HOH HOH . H 6 HOH A 123 509 140 HOH HOH . H 6 HOH A 124 510 141 HOH HOH . H 6 HOH A 125 511 142 HOH HOH . H 6 HOH A 126 512 143 HOH HOH . H 6 HOH A 127 513 144 HOH HOH . H 6 HOH A 128 514 145 HOH HOH . H 6 HOH A 129 515 146 HOH HOH . H 6 HOH A 130 516 147 HOH HOH . H 6 HOH A 131 517 148 HOH HOH . H 6 HOH A 132 518 149 HOH HOH . H 6 HOH A 133 519 150 HOH HOH . H 6 HOH A 134 520 151 HOH HOH . H 6 HOH A 135 521 152 HOH HOH . H 6 HOH A 136 522 153 HOH HOH . H 6 HOH A 137 523 154 HOH HOH . H 6 HOH A 138 524 155 HOH HOH . H 6 HOH A 139 525 156 HOH HOH . H 6 HOH A 140 526 157 HOH HOH . H 6 HOH A 141 527 158 HOH HOH . H 6 HOH A 142 528 159 HOH HOH . H 6 HOH A 143 529 160 HOH HOH . H 6 HOH A 144 530 161 HOH HOH . H 6 HOH A 145 531 162 HOH HOH . H 6 HOH A 146 532 163 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 DMA . . . D 3 -55.977 13.194 2.443 1 79.35 ? C1 DMA 383 A 1 HETATM 2 O O1 DMA . . . D 3 -57.153 13.546 3.147 1 80.59 ? O1 DMA 383 A 1 HETATM 3 C C2 DMA . . . D 3 -55.298 14.449 2.028 1 72.86 ? C2 DMA 383 A 1 HETATM 4 C C3 DMA . . . D 3 -55.636 15.087 0.931 1 81.28 ? C3 DMA 383 A 1 HETATM 5 C C4 DMA . . . D 3 -56.713 14.583 0.059 1 88.65 ? C4 DMA 383 A 1 HETATM 6 C C5 DMA . . . D 3 -54.928 16.351 0.595 1 87.55 ? C5 DMA 383 A 1 HETATM 7 P PA DMA . . . D 3 -57.322 13.373 4.692 1 81.64 ? PA DMA 383 A 1 HETATM 8 O O1A DMA . . . D 3 -58.755 13.469 4.935 1 75.75 ? O1A DMA 383 A 1 HETATM 9 O O2A DMA . . . D 3 -56.426 14.391 5.227 1 82.92 ? O2A DMA 383 A 1 HETATM 10 O O3A DMA . . . D 3 -56.77 11.912 5.06 1 80.28 ? O3A DMA 383 A 1 HETATM 11 P PB DMA . . . D 3 -57.191 10.949 6.239 1 79.78 ? PB DMA 383 A 1 HETATM 12 O O1B DMA . . . D 3 -55.914 10.446 6.709 1 71 ? O1B DMA 383 A 1 HETATM 13 O O2B DMA . . . D 3 -58.023 9.905 5.63 1 72.83 ? O2B DMA 383 A 1 HETATM 14 O O3B DMA . . . D 3 -57.973 11.728 7.196 1 76.43 ? O3B DMA 383 A 1 # _model_server_stats.io_time_ms 45 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #