data_8F8L # _model_server_result.job_id BSJrYdahrxvG1x3IZ3na9A _model_server_result.datetime_utc '2024-10-10 10:28:36' _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 8f8l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8F8L # _exptl.entry_id 8F8L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 246.092 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIMETHYLALLYL DIPHOSPHATE' _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 8F8L _cell.length_a 66.841 _cell.length_b 83.844 _cell.length_c 188.122 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8F8L _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _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 _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' 2_455 -x-1,-y,z -1 0 0 0 -1 0 0 0 1 -66.841 0 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 metalc ? metalc1 A OD1 ASP 119 A ASP 84 1_555 D CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc2 A OD2 ASP 119 A ASP 84 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc3 A OD1 ASP 123 A ASP 88 1_555 D CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.94 ? metalc ? metalc4 A OD2 ASP 123 A ASP 88 1_555 D CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc5 A OD2 ASP 123 A ASP 88 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc6 B O1A DMA . A DMA 401 1_555 D CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc7 B O1A DMA . A DMA 401 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? metalc ? metalc8 B O2B DMA . A DMA 401 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc9 D CA CA . A CA 403 1_555 F O HOH . A HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc10 D CA CA . A CA 403 1_555 F O HOH . A HOH 621 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc11 E CA CA . A CA 404 1_555 F O HOH . A HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc12 E CA CA . A CA 404 1_555 F O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? # _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 8F8L _atom_sites.fract_transf_matrix[1][1] 0.014961 _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] 0.011927 _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] 0.005316 _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 DMA A 1 401 401 DMA DMA . C 3 GOL A 1 402 402 GOL GOL . D 4 CA A 1 403 1 CA CA . E 4 CA A 1 404 2 CA CA . F 5 HOH A 1 501 9 HOH HOH . F 5 HOH A 2 502 138 HOH HOH . F 5 HOH A 3 503 103 HOH HOH . F 5 HOH A 4 504 4 HOH HOH . F 5 HOH A 5 505 14 HOH HOH . F 5 HOH A 6 506 3 HOH HOH . F 5 HOH A 7 507 100 HOH HOH . F 5 HOH A 8 508 8 HOH HOH . F 5 HOH A 9 509 23 HOH HOH . F 5 HOH A 10 510 50 HOH HOH . F 5 HOH A 11 511 7 HOH HOH . F 5 HOH A 12 512 10 HOH HOH . F 5 HOH A 13 513 31 HOH HOH . F 5 HOH A 14 514 129 HOH HOH . F 5 HOH A 15 515 12 HOH HOH . F 5 HOH A 16 516 6 HOH HOH . F 5 HOH A 17 517 22 HOH HOH . F 5 HOH A 18 518 25 HOH HOH . F 5 HOH A 19 519 2 HOH HOH . F 5 HOH A 20 520 81 HOH HOH . F 5 HOH A 21 521 67 HOH HOH . F 5 HOH A 22 522 39 HOH HOH . F 5 HOH A 23 523 45 HOH HOH . F 5 HOH A 24 524 63 HOH HOH . F 5 HOH A 25 525 105 HOH HOH . F 5 HOH A 26 526 30 HOH HOH . F 5 HOH A 27 527 55 HOH HOH . F 5 HOH A 28 528 84 HOH HOH . F 5 HOH A 29 529 48 HOH HOH . F 5 HOH A 30 530 108 HOH HOH . F 5 HOH A 31 531 18 HOH HOH . F 5 HOH A 32 532 36 HOH HOH . F 5 HOH A 33 533 127 HOH HOH . F 5 HOH A 34 534 44 HOH HOH . F 5 HOH A 35 535 47 HOH HOH . F 5 HOH A 36 536 13 HOH HOH . F 5 HOH A 37 537 85 HOH HOH . F 5 HOH A 38 538 19 HOH HOH . F 5 HOH A 39 539 16 HOH HOH . F 5 HOH A 40 540 11 HOH HOH . F 5 HOH A 41 541 27 HOH HOH . F 5 HOH A 42 542 125 HOH HOH . F 5 HOH A 43 543 133 HOH HOH . F 5 HOH A 44 544 43 HOH HOH . F 5 HOH A 45 545 5 HOH HOH . F 5 HOH A 46 546 41 HOH HOH . F 5 HOH A 47 547 24 HOH HOH . F 5 HOH A 48 548 80 HOH HOH . F 5 HOH A 49 549 76 HOH HOH . F 5 HOH A 50 550 96 HOH HOH . F 5 HOH A 51 551 49 HOH HOH . F 5 HOH A 52 552 101 HOH HOH . F 5 HOH A 53 553 54 HOH HOH . F 5 HOH A 54 554 26 HOH HOH . F 5 HOH A 55 555 70 HOH HOH . F 5 HOH A 56 556 40 HOH HOH . F 5 HOH A 57 557 82 HOH HOH . F 5 HOH A 58 558 20 HOH HOH . F 5 HOH A 59 559 115 HOH HOH . F 5 HOH A 60 560 83 HOH HOH . F 5 HOH A 61 561 52 HOH HOH . F 5 HOH A 62 562 64 HOH HOH . F 5 HOH A 63 563 53 HOH HOH . F 5 HOH A 64 564 98 HOH HOH . F 5 HOH A 65 565 87 HOH HOH . F 5 HOH A 66 566 72 HOH HOH . F 5 HOH A 67 567 91 HOH HOH . F 5 HOH A 68 568 94 HOH HOH . F 5 HOH A 69 569 79 HOH HOH . F 5 HOH A 70 570 35 HOH HOH . F 5 HOH A 71 571 102 HOH HOH . F 5 HOH A 72 572 65 HOH HOH . F 5 HOH A 73 573 118 HOH HOH . F 5 HOH A 74 574 106 HOH HOH . F 5 HOH A 75 575 92 HOH HOH . F 5 HOH A 76 576 60 HOH HOH . F 5 HOH A 77 577 59 HOH HOH . F 5 HOH A 78 578 28 HOH HOH . F 5 HOH A 79 579 21 HOH HOH . F 5 HOH A 80 580 37 HOH HOH . F 5 HOH A 81 581 17 HOH HOH . F 5 HOH A 82 582 107 HOH HOH . F 5 HOH A 83 583 62 HOH HOH . F 5 HOH A 84 584 38 HOH HOH . F 5 HOH A 85 585 74 HOH HOH . F 5 HOH A 86 586 32 HOH HOH . F 5 HOH A 87 587 130 HOH HOH . F 5 HOH A 88 588 89 HOH HOH . F 5 HOH A 89 589 58 HOH HOH . F 5 HOH A 90 590 75 HOH HOH . F 5 HOH A 91 591 66 HOH HOH . F 5 HOH A 92 592 131 HOH HOH . F 5 HOH A 93 593 15 HOH HOH . F 5 HOH A 94 594 78 HOH HOH . F 5 HOH A 95 595 117 HOH HOH . F 5 HOH A 96 596 46 HOH HOH . F 5 HOH A 97 597 77 HOH HOH . F 5 HOH A 98 598 61 HOH HOH . F 5 HOH A 99 599 113 HOH HOH . F 5 HOH A 100 600 137 HOH HOH . F 5 HOH A 101 601 86 HOH HOH . F 5 HOH A 102 602 97 HOH HOH . F 5 HOH A 103 603 99 HOH HOH . F 5 HOH A 104 604 29 HOH HOH . F 5 HOH A 105 605 1 HOH HOH . F 5 HOH A 106 606 119 HOH HOH . F 5 HOH A 107 607 33 HOH HOH . F 5 HOH A 108 608 120 HOH HOH . F 5 HOH A 109 609 114 HOH HOH . F 5 HOH A 110 610 112 HOH HOH . F 5 HOH A 111 611 90 HOH HOH . F 5 HOH A 112 612 68 HOH HOH . F 5 HOH A 113 613 51 HOH HOH . F 5 HOH A 114 614 110 HOH HOH . F 5 HOH A 115 615 126 HOH HOH . F 5 HOH A 116 616 57 HOH HOH . F 5 HOH A 117 617 111 HOH HOH . F 5 HOH A 118 618 132 HOH HOH . F 5 HOH A 119 619 69 HOH HOH . F 5 HOH A 120 620 109 HOH HOH . F 5 HOH A 121 621 121 HOH HOH . F 5 HOH A 122 622 34 HOH HOH . F 5 HOH A 123 623 122 HOH HOH . F 5 HOH A 124 624 123 HOH HOH . F 5 HOH A 125 625 135 HOH HOH . F 5 HOH A 126 626 116 HOH HOH . F 5 HOH A 127 627 88 HOH HOH . F 5 HOH A 128 628 104 HOH HOH . F 5 HOH A 129 629 95 HOH HOH . F 5 HOH A 130 630 42 HOH HOH . F 5 HOH A 131 631 134 HOH HOH . F 5 HOH A 132 632 128 HOH HOH . F 5 HOH A 133 633 136 HOH HOH . F 5 HOH A 134 634 56 HOH HOH . F 5 HOH A 135 635 71 HOH HOH . F 5 HOH A 136 636 73 HOH HOH . F 5 HOH A 137 637 93 HOH HOH . F 5 HOH A 138 638 124 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 . . . B 2 -25.736 -12.312 -33.573 1 47.49 ? C1 DMA 401 A 1 HETATM 2 O O1 DMA . . . B 2 -24.511 -12.767 -34.131 1 53.48 ? O1 DMA 401 A 1 HETATM 3 C C2 DMA . . . B 2 -25.545 -11.043 -32.804 1 51.56 ? C2 DMA 401 A 1 HETATM 4 C C3 DMA . . . B 2 -25.724 -10.901 -31.505 1 37.83 ? C3 DMA 401 A 1 HETATM 5 C C4 DMA . . . B 2 -25.557 -9.59 -30.8 1 39.85 ? C4 DMA 401 A 1 HETATM 6 C C5 DMA . . . B 2 -26.099 -12.043 -30.613 1 45.58 ? C5 DMA 401 A 1 HETATM 7 P PA DMA . . . B 2 -24.396 -13.013 -35.711 1 48.6 ? PA DMA 401 A 1 HETATM 8 O O1A DMA . . . B 2 -25.058 -11.862 -36.395 1 53.04 ? O1A DMA 401 A 1 HETATM 9 O O2A DMA . . . B 2 -22.976 -13.348 -36.027 1 65.64 ? O2A DMA 401 A 1 HETATM 10 O O3A DMA . . . B 2 -25.266 -14.345 -35.946 1 61.88 ? O3A DMA 401 A 1 HETATM 11 P PB DMA . . . B 2 -26.843 -14.756 -35.911 1 66.52 ? PB DMA 401 A 1 HETATM 12 O O1B DMA . . . B 2 -26.916 -16.057 -36.707 1 72.32 ? O1B DMA 401 A 1 HETATM 13 O O2B DMA . . . B 2 -27.601 -13.636 -36.582 1 58.56 ? O2B DMA 401 A 1 HETATM 14 O O3B DMA . . . B 2 -27.236 -14.912 -34.462 1 49.83 ? O3B DMA 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #