data_5KPR # _model_server_result.job_id Kh3JAKO2W9eHOmn9oe6amQ _model_server_result.datetime_utc '2024-10-11 19:24:55' _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 5kpr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 5KPR # _exptl.entry_id 5KPR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC 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 120 _cell.entry_id 5KPR _cell.length_a 98.965 _cell.length_b 98.965 _cell.length_c 68.783 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KPR _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 _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' 6_554 -x,-x+y,-z-2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -45.855333 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 B MG MG . A MG 401 1_555 C O3G ANP . A ANP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc2 B MG MG . A MG 401 1_555 C O2B ANP . A ANP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc3 B MG MG . A MG 401 1_555 F O HOH . A HOH 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc4 B MG MG . A MG 401 1_555 F O HOH . A HOH 553 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc5 B MG MG . A MG 401 1_555 F O HOH . A HOH 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc6 B MG MG . A MG 401 1_555 F O HOH . A HOH 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? # _chem_comp.formula 'C10 H17 N6 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id ANP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _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 PG O1G ANP doub 13 n n PG O2G ANP sing 14 n n PG O3G ANP sing 15 n n PG N3B ANP sing 16 n n O2G HOG2 ANP sing 17 n n O3G HOG3 ANP sing 18 n n PB O1B ANP doub 19 n n PB O2B ANP sing 20 n n PB N3B ANP sing 21 n n PB O3A ANP sing 22 n n O2B HOB2 ANP sing 23 n n N3B HNB1 ANP sing 24 n n PA O1A ANP doub 25 n n PA O2A ANP sing 26 n n PA O3A ANP sing 27 n n PA O5' ANP sing 28 n n O2A HOA2 ANP sing 29 n n O5' C5' ANP sing 30 n n C5' C4' ANP sing 31 n n C5' "H5'1" ANP sing 32 n n C5' "H5'2" ANP sing 33 n n C4' O4' ANP sing 34 n n C4' C3' ANP sing 35 n n C4' H4' ANP sing 36 n n O4' C1' ANP sing 37 n n C3' O3' ANP sing 38 n n C3' C2' ANP sing 39 n n C3' H3' ANP sing 40 n n O3' HO3' ANP sing 41 n n C2' O2' ANP sing 42 n n C2' C1' ANP sing 43 n n C2' H2' ANP sing 44 n n O2' HO2' ANP sing 45 n n C1' N9 ANP sing 46 n n C1' H1' ANP sing 47 n n N9 C8 ANP sing 48 n y N9 C4 ANP sing 49 n y C8 N7 ANP doub 50 n y C8 H8 ANP sing 51 n n N7 C5 ANP sing 52 n y C5 C6 ANP sing 53 n y C5 C4 ANP doub 54 n y C6 N6 ANP sing 55 n n C6 N1 ANP doub 56 n y N6 HN61 ANP sing 57 n n N6 HN62 ANP sing 58 n n N1 C2 ANP sing 59 n y C2 N3 ANP doub 60 n y C2 H2 ANP sing 61 n n N3 C4 ANP sing 62 n y # _atom_sites.entry_id 5KPR _atom_sites.fract_transf_matrix[1][1] 0.010105 _atom_sites.fract_transf_matrix[1][2] 0.005834 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011668 _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] 0.014538 _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 1 401 1 MG MG . C 3 ANP A 1 402 501 ANP ANP . D 4 EDO A 1 403 3 EDO EDO . E 5 PAU A 1 404 1 PAU PAU . F 6 HOH A 1 501 18 HOH HOH . F 6 HOH A 2 502 70 HOH HOH . F 6 HOH A 3 503 106 HOH HOH . F 6 HOH A 4 504 121 HOH HOH . F 6 HOH A 5 505 138 HOH HOH . F 6 HOH A 6 506 99 HOH HOH . F 6 HOH A 7 507 50 HOH HOH . F 6 HOH A 8 508 81 HOH HOH . F 6 HOH A 9 509 33 HOH HOH . F 6 HOH A 10 510 104 HOH HOH . F 6 HOH A 11 511 57 HOH HOH . F 6 HOH A 12 512 78 HOH HOH . F 6 HOH A 13 513 14 HOH HOH . F 6 HOH A 14 514 124 HOH HOH . F 6 HOH A 15 515 69 HOH HOH . F 6 HOH A 16 516 55 HOH HOH . F 6 HOH A 17 517 125 HOH HOH . F 6 HOH A 18 518 103 HOH HOH . F 6 HOH A 19 519 36 HOH HOH . F 6 HOH A 20 520 79 HOH HOH . F 6 HOH A 21 521 2 HOH HOH . F 6 HOH A 22 522 116 HOH HOH . F 6 HOH A 23 523 38 HOH HOH . F 6 HOH A 24 524 91 HOH HOH . F 6 HOH A 25 525 126 HOH HOH . F 6 HOH A 26 526 86 HOH HOH . F 6 HOH A 27 527 107 HOH HOH . F 6 HOH A 28 528 117 HOH HOH . F 6 HOH A 29 529 7 HOH HOH . F 6 HOH A 30 530 23 HOH HOH . F 6 HOH A 31 531 34 HOH HOH . F 6 HOH A 32 532 31 HOH HOH . F 6 HOH A 33 533 35 HOH HOH . F 6 HOH A 34 534 46 HOH HOH . F 6 HOH A 35 535 9 HOH HOH . F 6 HOH A 36 536 123 HOH HOH . F 6 HOH A 37 537 72 HOH HOH . F 6 HOH A 38 538 45 HOH HOH . F 6 HOH A 39 539 114 HOH HOH . F 6 HOH A 40 540 142 HOH HOH . F 6 HOH A 41 541 157 HOH HOH . F 6 HOH A 42 542 90 HOH HOH . F 6 HOH A 43 543 5 HOH HOH . F 6 HOH A 44 544 12 HOH HOH . F 6 HOH A 45 545 49 HOH HOH . F 6 HOH A 46 546 65 HOH HOH . F 6 HOH A 47 547 101 HOH HOH . F 6 HOH A 48 548 83 HOH HOH . F 6 HOH A 49 549 88 HOH HOH . F 6 HOH A 50 550 118 HOH HOH . F 6 HOH A 51 551 87 HOH HOH . F 6 HOH A 52 552 110 HOH HOH . F 6 HOH A 53 553 1 HOH HOH . F 6 HOH A 54 554 61 HOH HOH . F 6 HOH A 55 555 112 HOH HOH . F 6 HOH A 56 556 54 HOH HOH . F 6 HOH A 57 557 109 HOH HOH . F 6 HOH A 58 558 13 HOH HOH . F 6 HOH A 59 559 4 HOH HOH . F 6 HOH A 60 560 149 HOH HOH . F 6 HOH A 61 561 158 HOH HOH . F 6 HOH A 62 562 73 HOH HOH . F 6 HOH A 63 563 52 HOH HOH . F 6 HOH A 64 564 97 HOH HOH . F 6 HOH A 65 565 6 HOH HOH . F 6 HOH A 66 566 44 HOH HOH . F 6 HOH A 67 567 27 HOH HOH . F 6 HOH A 68 568 128 HOH HOH . F 6 HOH A 69 569 144 HOH HOH . F 6 HOH A 70 570 17 HOH HOH . F 6 HOH A 71 571 10 HOH HOH . F 6 HOH A 72 572 130 HOH HOH . F 6 HOH A 73 573 66 HOH HOH . F 6 HOH A 74 574 71 HOH HOH . F 6 HOH A 75 575 141 HOH HOH . F 6 HOH A 76 576 28 HOH HOH . F 6 HOH A 77 577 21 HOH HOH . F 6 HOH A 78 578 42 HOH HOH . F 6 HOH A 79 579 132 HOH HOH . F 6 HOH A 80 580 80 HOH HOH . F 6 HOH A 81 581 3 HOH HOH . F 6 HOH A 82 582 25 HOH HOH . F 6 HOH A 83 583 95 HOH HOH . F 6 HOH A 84 584 40 HOH HOH . F 6 HOH A 85 585 122 HOH HOH . F 6 HOH A 86 586 19 HOH HOH . F 6 HOH A 87 587 74 HOH HOH . F 6 HOH A 88 588 108 HOH HOH . F 6 HOH A 89 589 56 HOH HOH . F 6 HOH A 90 590 20 HOH HOH . F 6 HOH A 91 591 105 HOH HOH . F 6 HOH A 92 592 98 HOH HOH . F 6 HOH A 93 593 100 HOH HOH . F 6 HOH A 94 594 11 HOH HOH . F 6 HOH A 95 595 77 HOH HOH . F 6 HOH A 96 596 137 HOH HOH . F 6 HOH A 97 597 29 HOH HOH . F 6 HOH A 98 598 76 HOH HOH . F 6 HOH A 99 599 153 HOH HOH . F 6 HOH A 100 600 41 HOH HOH . F 6 HOH A 101 601 59 HOH HOH . F 6 HOH A 102 602 62 HOH HOH . F 6 HOH A 103 603 8 HOH HOH . F 6 HOH A 104 604 134 HOH HOH . F 6 HOH A 105 605 156 HOH HOH . F 6 HOH A 106 606 53 HOH HOH . F 6 HOH A 107 607 94 HOH HOH . F 6 HOH A 108 608 60 HOH HOH . F 6 HOH A 109 609 16 HOH HOH . F 6 HOH A 110 610 39 HOH HOH . F 6 HOH A 111 611 30 HOH HOH . F 6 HOH A 112 612 51 HOH HOH . F 6 HOH A 113 613 139 HOH HOH . F 6 HOH A 114 614 32 HOH HOH . F 6 HOH A 115 615 15 HOH HOH . F 6 HOH A 116 616 133 HOH HOH . F 6 HOH A 117 617 115 HOH HOH . F 6 HOH A 118 618 119 HOH HOH . F 6 HOH A 119 619 154 HOH HOH . F 6 HOH A 120 620 85 HOH HOH . F 6 HOH A 121 621 84 HOH HOH . F 6 HOH A 122 622 37 HOH HOH . F 6 HOH A 123 623 58 HOH HOH . F 6 HOH A 124 624 43 HOH HOH . F 6 HOH A 125 625 159 HOH HOH . F 6 HOH A 126 626 120 HOH HOH . F 6 HOH A 127 627 22 HOH HOH . F 6 HOH A 128 628 67 HOH HOH . F 6 HOH A 129 629 75 HOH HOH . F 6 HOH A 130 630 63 HOH HOH . F 6 HOH A 131 631 145 HOH HOH . F 6 HOH A 132 632 64 HOH HOH . F 6 HOH A 133 633 89 HOH HOH . F 6 HOH A 134 634 136 HOH HOH . F 6 HOH A 135 635 131 HOH HOH . F 6 HOH A 136 636 68 HOH HOH . F 6 HOH A 137 637 147 HOH HOH . F 6 HOH A 138 638 162 HOH HOH . F 6 HOH A 139 639 151 HOH HOH . F 6 HOH A 140 640 24 HOH HOH . F 6 HOH A 141 641 143 HOH HOH . F 6 HOH A 142 642 92 HOH HOH . F 6 HOH A 143 643 129 HOH HOH . F 6 HOH A 144 644 93 HOH HOH . F 6 HOH A 145 645 148 HOH HOH . F 6 HOH A 146 646 102 HOH HOH . F 6 HOH A 147 647 150 HOH HOH . F 6 HOH A 148 648 127 HOH HOH . F 6 HOH A 149 649 155 HOH HOH . F 6 HOH A 150 650 48 HOH HOH . F 6 HOH A 151 651 160 HOH HOH . F 6 HOH A 152 652 152 HOH HOH . F 6 HOH A 153 653 26 HOH HOH . F 6 HOH A 154 654 135 HOH HOH . F 6 HOH A 155 655 113 HOH HOH . F 6 HOH A 156 656 146 HOH HOH . F 6 HOH A 157 657 161 HOH HOH . F 6 HOH A 158 658 82 HOH HOH . F 6 HOH A 159 659 111 HOH HOH . F 6 HOH A 160 660 140 HOH HOH . F 6 HOH A 161 661 47 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 ANP . . . C 3 26.614 -17.693 -13.307 1 16.11 ? PG ANP 402 A 1 HETATM 2 O O1G ANP . . . C 3 25.897 -18.259 -14.507 1 16.9 ? O1G ANP 402 A 1 HETATM 3 O O2G ANP . . . C 3 27.736 -16.742 -13.773 1 17.53 ? O2G ANP 402 A 1 HETATM 4 O O3G ANP . . . C 3 27.181 -18.858 -12.451 1 15.87 ? O3G ANP 402 A 1 HETATM 5 P PB ANP . . . C 3 25.447 -16.617 -10.844 1 14.96 ? PB ANP 402 A 1 HETATM 6 O O1B ANP . . . C 3 25.273 -15.141 -10.47 1 14.2 ? O1B ANP 402 A 1 HETATM 7 O O2B ANP . . . C 3 26.674 -17.299 -10.186 1 14.11 ? O2B ANP 402 A 1 HETATM 8 N N3B ANP . . . C 3 25.475 -16.798 -12.487 1 16.76 ? N3B ANP 402 A 1 HETATM 9 P PA ANP . . . C 3 23.545 -17.768 -9.026 1 12.7 ? PA ANP 402 A 1 HETATM 10 O O1A ANP . . . C 3 23.905 -19.209 -8.612 1 12.76 ? O1A ANP 402 A 1 HETATM 11 O O2A ANP . . . C 3 23.966 -16.769 -7.931 1 13.62 ? O2A ANP 402 A 1 HETATM 12 O O3A ANP . . . C 3 24.167 -17.418 -10.424 1 11.56 ? O3A ANP 402 A 1 HETATM 13 O O5' ANP . . . C 3 21.988 -17.752 -9.311 1 12.15 ? O5' ANP 402 A 1 HETATM 14 C C5' ANP . . . C 3 21.361 -16.675 -9.95 1 13.11 ? C5' ANP 402 A 1 HETATM 15 C C4' ANP . . . C 3 19.871 -16.895 -10.025 1 13.6 ? C4' ANP 402 A 1 HETATM 16 O O4' ANP . . . C 3 19.333 -16.916 -8.736 1 14.26 ? O4' ANP 402 A 1 HETATM 17 C C3' ANP . . . C 3 19.104 -15.867 -10.787 1 12.11 ? C3' ANP 402 A 1 HETATM 18 O O3' ANP . . . C 3 19.107 -16.151 -12.155 1 13.85 ? O3' ANP 402 A 1 HETATM 19 C C2' ANP . . . C 3 17.749 -15.986 -10.193 1 14.37 ? C2' ANP 402 A 1 HETATM 20 O O2' ANP . . . C 3 16.955 -16.925 -10.869 1 13.53 ? O2' ANP 402 A 1 HETATM 21 C C1' ANP . . . C 3 18.006 -16.478 -8.801 1 12.14 ? C1' ANP 402 A 1 HETATM 22 N N9 ANP . . . C 3 17.892 -15.521 -7.724 1 14.04 ? N9 ANP 402 A 1 HETATM 23 C C8 ANP . . . C 3 17.604 -15.836 -6.449 1 14.8 ? C8 ANP 402 A 1 HETATM 24 N N7 ANP . . . C 3 17.627 -14.76 -5.682 1 18.2 ? N7 ANP 402 A 1 HETATM 25 C C5 ANP . . . C 3 17.951 -13.711 -6.43 1 15 ? C5 ANP 402 A 1 HETATM 26 C C6 ANP . . . C 3 18.099 -12.355 -6.177 1 18.79 ? C6 ANP 402 A 1 HETATM 27 N N6 ANP . . . C 3 17.915 -11.831 -4.865 1 23.73 ? N6 ANP 402 A 1 HETATM 28 N N1 ANP . . . C 3 18.422 -11.526 -7.178 1 21.21 ? N1 ANP 402 A 1 HETATM 29 C C2 ANP . . . C 3 18.616 -11.988 -8.424 1 19.22 ? C2 ANP 402 A 1 HETATM 30 N N3 ANP . . . C 3 18.465 -13.299 -8.713 1 17.14 ? N3 ANP 402 A 1 HETATM 31 C C4 ANP . . . C 3 18.131 -14.179 -7.747 1 15.36 ? C4 ANP 402 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 31 #