data_5X1S # _model_server_result.job_id V_Cl9bT41iN9mHWEixtZhg _model_server_result.datetime_utc '2024-11-05 01:36:35' _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 5x1s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5X1S # _exptl.entry_id 5X1S _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _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 5X1S _cell.length_a 59.318 _cell.length_b 65.602 _cell.length_c 78.14 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5X1S _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 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 _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 # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # 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 PG O1G ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 5X1S _atom_sites.fract_transf_matrix[1][1] 0.016858 _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] 0.015243 _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] 0.012798 _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 ACP A 1 401 1 ACP ACP . C 3 GOL A 1 402 1 GOL GOL . D 4 HOH A 1 501 48 HOH HOH . D 4 HOH A 2 502 167 HOH HOH . D 4 HOH A 3 503 43 HOH HOH . D 4 HOH A 4 504 113 HOH HOH . D 4 HOH A 5 505 166 HOH HOH . D 4 HOH A 6 506 153 HOH HOH . D 4 HOH A 7 507 16 HOH HOH . D 4 HOH A 8 508 92 HOH HOH . D 4 HOH A 9 509 114 HOH HOH . D 4 HOH A 10 510 20 HOH HOH . D 4 HOH A 11 511 80 HOH HOH . D 4 HOH A 12 512 107 HOH HOH . D 4 HOH A 13 513 162 HOH HOH . D 4 HOH A 14 514 62 HOH HOH . D 4 HOH A 15 515 63 HOH HOH . D 4 HOH A 16 516 79 HOH HOH . D 4 HOH A 17 517 25 HOH HOH . D 4 HOH A 18 518 54 HOH HOH . D 4 HOH A 19 519 119 HOH HOH . D 4 HOH A 20 520 101 HOH HOH . D 4 HOH A 21 521 75 HOH HOH . D 4 HOH A 22 522 44 HOH HOH . D 4 HOH A 23 523 52 HOH HOH . D 4 HOH A 24 524 156 HOH HOH . D 4 HOH A 25 525 127 HOH HOH . D 4 HOH A 26 526 34 HOH HOH . D 4 HOH A 27 527 104 HOH HOH . D 4 HOH A 28 528 47 HOH HOH . D 4 HOH A 29 529 1 HOH HOH . D 4 HOH A 30 530 38 HOH HOH . D 4 HOH A 31 531 105 HOH HOH . D 4 HOH A 32 532 78 HOH HOH . D 4 HOH A 33 533 69 HOH HOH . D 4 HOH A 34 534 55 HOH HOH . D 4 HOH A 35 535 133 HOH HOH . D 4 HOH A 36 536 128 HOH HOH . D 4 HOH A 37 537 3 HOH HOH . D 4 HOH A 38 538 11 HOH HOH . D 4 HOH A 39 539 118 HOH HOH . D 4 HOH A 40 540 31 HOH HOH . D 4 HOH A 41 541 108 HOH HOH . D 4 HOH A 42 542 57 HOH HOH . D 4 HOH A 43 543 125 HOH HOH . D 4 HOH A 44 544 40 HOH HOH . D 4 HOH A 45 545 21 HOH HOH . D 4 HOH A 46 546 89 HOH HOH . D 4 HOH A 47 547 66 HOH HOH . D 4 HOH A 48 548 15 HOH HOH . D 4 HOH A 49 549 87 HOH HOH . D 4 HOH A 50 550 134 HOH HOH . D 4 HOH A 51 551 17 HOH HOH . D 4 HOH A 52 552 4 HOH HOH . D 4 HOH A 53 553 141 HOH HOH . D 4 HOH A 54 554 117 HOH HOH . D 4 HOH A 55 555 56 HOH HOH . D 4 HOH A 56 556 45 HOH HOH . D 4 HOH A 57 557 22 HOH HOH . D 4 HOH A 58 558 95 HOH HOH . D 4 HOH A 59 559 72 HOH HOH . D 4 HOH A 60 560 83 HOH HOH . D 4 HOH A 61 561 59 HOH HOH . D 4 HOH A 62 562 60 HOH HOH . D 4 HOH A 63 563 19 HOH HOH . D 4 HOH A 64 564 58 HOH HOH . D 4 HOH A 65 565 97 HOH HOH . D 4 HOH A 66 566 103 HOH HOH . D 4 HOH A 67 567 68 HOH HOH . D 4 HOH A 68 568 93 HOH HOH . D 4 HOH A 69 569 81 HOH HOH . D 4 HOH A 70 570 64 HOH HOH . D 4 HOH A 71 571 30 HOH HOH . D 4 HOH A 72 572 85 HOH HOH . D 4 HOH A 73 573 131 HOH HOH . D 4 HOH A 74 574 142 HOH HOH . D 4 HOH A 75 575 24 HOH HOH . D 4 HOH A 76 576 102 HOH HOH . D 4 HOH A 77 577 106 HOH HOH . D 4 HOH A 78 578 33 HOH HOH . D 4 HOH A 79 579 130 HOH HOH . D 4 HOH A 80 580 70 HOH HOH . D 4 HOH A 81 581 37 HOH HOH . D 4 HOH A 82 582 112 HOH HOH . D 4 HOH A 83 583 35 HOH HOH . D 4 HOH A 84 584 126 HOH HOH . D 4 HOH A 85 585 99 HOH HOH . D 4 HOH A 86 586 148 HOH HOH . D 4 HOH A 87 587 140 HOH HOH . D 4 HOH A 88 588 42 HOH HOH . D 4 HOH A 89 589 94 HOH HOH . D 4 HOH A 90 590 36 HOH HOH . D 4 HOH A 91 591 71 HOH HOH . D 4 HOH A 92 592 124 HOH HOH . D 4 HOH A 93 593 23 HOH HOH . D 4 HOH A 94 594 50 HOH HOH . D 4 HOH A 95 595 53 HOH HOH . D 4 HOH A 96 596 67 HOH HOH . D 4 HOH A 97 597 2 HOH HOH . D 4 HOH A 98 598 26 HOH HOH . D 4 HOH A 99 599 96 HOH HOH . D 4 HOH A 100 600 73 HOH HOH . D 4 HOH A 101 601 77 HOH HOH . D 4 HOH A 102 602 86 HOH HOH . D 4 HOH A 103 603 7 HOH HOH . D 4 HOH A 104 604 6 HOH HOH . D 4 HOH A 105 605 51 HOH HOH . D 4 HOH A 106 606 138 HOH HOH . D 4 HOH A 107 607 9 HOH HOH . D 4 HOH A 108 608 5 HOH HOH . D 4 HOH A 109 609 143 HOH HOH . D 4 HOH A 110 610 88 HOH HOH . D 4 HOH A 111 611 27 HOH HOH . D 4 HOH A 112 612 115 HOH HOH . D 4 HOH A 113 613 65 HOH HOH . D 4 HOH A 114 614 144 HOH HOH . D 4 HOH A 115 615 10 HOH HOH . D 4 HOH A 116 616 136 HOH HOH . D 4 HOH A 117 617 14 HOH HOH . D 4 HOH A 118 618 28 HOH HOH . D 4 HOH A 119 619 39 HOH HOH . D 4 HOH A 120 620 151 HOH HOH . D 4 HOH A 121 621 61 HOH HOH . D 4 HOH A 122 622 32 HOH HOH . D 4 HOH A 123 623 100 HOH HOH . D 4 HOH A 124 624 111 HOH HOH . D 4 HOH A 125 625 18 HOH HOH . D 4 HOH A 126 626 90 HOH HOH . D 4 HOH A 127 627 110 HOH HOH . D 4 HOH A 128 628 12 HOH HOH . D 4 HOH A 129 629 49 HOH HOH . D 4 HOH A 130 630 152 HOH HOH . D 4 HOH A 131 631 165 HOH HOH . D 4 HOH A 132 632 46 HOH HOH . D 4 HOH A 133 633 8 HOH HOH . D 4 HOH A 134 634 135 HOH HOH . D 4 HOH A 135 635 159 HOH HOH . D 4 HOH A 136 636 139 HOH HOH . D 4 HOH A 137 637 122 HOH HOH . D 4 HOH A 138 638 121 HOH HOH . D 4 HOH A 139 639 98 HOH HOH . D 4 HOH A 140 640 109 HOH HOH . D 4 HOH A 141 641 150 HOH HOH . D 4 HOH A 142 642 91 HOH HOH . D 4 HOH A 143 643 82 HOH HOH . D 4 HOH A 144 644 29 HOH HOH . D 4 HOH A 145 645 137 HOH HOH . D 4 HOH A 146 646 41 HOH HOH . D 4 HOH A 147 647 13 HOH HOH . D 4 HOH A 148 648 147 HOH HOH . D 4 HOH A 149 649 120 HOH HOH . D 4 HOH A 150 650 76 HOH HOH . D 4 HOH A 151 651 74 HOH HOH . D 4 HOH A 152 652 157 HOH HOH . D 4 HOH A 153 653 154 HOH HOH . D 4 HOH A 154 654 149 HOH HOH . D 4 HOH A 155 655 84 HOH HOH . D 4 HOH A 156 656 163 HOH HOH . D 4 HOH A 157 657 155 HOH HOH . D 4 HOH A 158 658 145 HOH HOH . D 4 HOH A 159 659 123 HOH HOH . D 4 HOH A 160 660 129 HOH HOH . D 4 HOH A 161 661 146 HOH HOH . D 4 HOH A 162 662 116 HOH HOH . D 4 HOH A 163 663 161 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 P PG ACP . . . B 2 5.741 21.138 28.636 1 53.08 ? PG ACP 401 A 1 HETATM 2 O O1G ACP . . . B 2 5.892 20.413 27.205 1 51.26 ? O1G ACP 401 A 1 HETATM 3 O O2G ACP . . . B 2 6.533 20.398 29.64 1 49.86 ? O2G ACP 401 A 1 HETATM 4 O O3G ACP . . . B 2 6.269 22.656 28.56 1 51.9 ? O3G ACP 401 A 1 HETATM 5 P PB ACP . . . B 2 2.996 21.055 27.592 1 31.07 ? PB ACP 401 A 1 HETATM 6 O O1B ACP . . . B 2 3.752 21.721 26.337 1 35.74 ? O1B ACP 401 A 1 HETATM 7 O O2B ACP . . . B 2 1.678 21.683 27.837 1 28.53 ? O2B ACP 401 A 1 HETATM 8 C C3B ACP . . . B 2 3.992 21.18 29.1 1 33.89 ? C3B ACP 401 A 1 HETATM 9 P PA ACP . . . B 2 3.36 18.401 26.434 1 24.3 ? PA ACP 401 A 1 HETATM 10 O O1A ACP . . . B 2 4.131 19.003 25.282 1 25.34 ? O1A ACP 401 A 1 HETATM 11 O O2A ACP . . . B 2 2.195 17.566 25.983 1 25.75 ? O2A ACP 401 A 1 HETATM 12 O O3A ACP . . . B 2 2.662 19.498 27.373 1 34.26 ? O3A ACP 401 A 1 HETATM 13 O O5' ACP . . . B 2 4.385 17.493 27.276 1 24.97 ? O5' ACP 401 A 1 HETATM 14 C C5' ACP . . . B 2 3.936 16.586 28.283 1 22.92 ? C5' ACP 401 A 1 HETATM 15 C C4' ACP . . . B 2 4.331 17.121 29.652 1 16.87 ? C4' ACP 401 A 1 HETATM 16 O O4' ACP . . . B 2 3.937 16.142 30.621 1 18.03 ? O4' ACP 401 A 1 HETATM 17 C C3' ACP . . . B 2 5.832 17.327 29.815 1 18.65 ? C3' ACP 401 A 1 HETATM 18 O O3' ACP . . . B 2 6.085 18.52 30.562 1 20.9 ? O3' ACP 401 A 1 HETATM 19 C C2' ACP . . . B 2 6.273 16.156 30.663 1 15.28 ? C2' ACP 401 A 1 HETATM 20 O O2' ACP . . . B 2 7.336 16.511 31.552 1 16.94 ? O2' ACP 401 A 1 HETATM 21 C C1' ACP . . . B 2 5.035 15.849 31.471 1 17.09 ? C1' ACP 401 A 1 HETATM 22 N N9 ACP . . . B 2 4.902 14.428 31.838 1 14.18 ? N9 ACP 401 A 1 HETATM 23 C C8 ACP . . . B 2 4.496 13.449 31.016 1 14.06 ? C8 ACP 401 A 1 HETATM 24 N N7 ACP . . . B 2 4.446 12.269 31.683 1 14.28 ? N7 ACP 401 A 1 HETATM 25 C C5 ACP . . . B 2 4.811 12.525 32.958 1 13.5 ? C5 ACP 401 A 1 HETATM 26 C C6 ACP . . . B 2 4.945 11.724 34.186 1 13.16 ? C6 ACP 401 A 1 HETATM 27 N N6 ACP . . . B 2 4.699 10.396 34.144 1 11.99 ? N6 ACP 401 A 1 HETATM 28 N N1 ACP . . . B 2 5.354 12.342 35.318 1 13.13 ? N1 ACP 401 A 1 HETATM 29 C C2 ACP . . . B 2 5.61 13.672 35.345 1 16.07 ? C2 ACP 401 A 1 HETATM 30 N N3 ACP . . . B 2 5.493 14.472 34.255 1 13.77 ? N3 ACP 401 A 1 HETATM 31 C C4 ACP . . . B 2 5.107 13.95 33.065 1 14.37 ? C4 ACP 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #