data_3ID8 # _model_server_result.job_id 8-j0dPuFaMFg46KUt01xow _model_server_result.datetime_utc '2024-11-30 09:19:19' _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 3id8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":600}' # _entry.id 3ID8 # _exptl.entry_id 3ID8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 4 _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 90 _cell.entry_id 3ID8 _cell.length_a 67 _cell.length_b 82.6 _cell.length_c 86.8 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ID8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 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,E,F,G _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 4 _struct_asym.id D _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 210 A ASP 205 1_555 E MG MG . A MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc2 A O MET 243 A MET 238 1_555 F K K . A K 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc3 A O VAL 246 A VAL 241 1_555 F K K . A K 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.895 ? metalc ? metalc4 A O VAL 249 A VAL 244 1_555 F K K . A K 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? metalc ? metalc5 A O GLY 251 A GLY 246 1_555 F K K . A K 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? metalc ? metalc6 D O2G ANP . A ANP 600 1_555 E MG MG . A MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc7 D O1B ANP . A ANP 600 1_555 E MG MG . A MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.894 ? # _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 3ID8 _atom_sites.fract_transf_matrix[1][1] 0.014925 _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] 0.012107 _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] 0.011521 _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 GLC A 1 500 500 GLC GLC . C 3 MRK A 1 501 501 MRK MRK . D 4 ANP A 1 600 600 ANP UNK . E 5 MG A 1 700 700 MG MG . F 6 K A 1 800 800 K K . G 7 HOH A 1 466 1 HOH HOH . G 7 HOH A 2 467 2 HOH HOH . G 7 HOH A 3 468 3 HOH HOH . G 7 HOH A 4 469 4 HOH HOH . G 7 HOH A 5 470 6 HOH HOH . G 7 HOH A 6 471 7 HOH HOH . G 7 HOH A 7 472 8 HOH HOH . G 7 HOH A 8 473 9 HOH HOH . G 7 HOH A 9 474 10 HOH HOH . G 7 HOH A 10 475 11 HOH HOH . G 7 HOH A 11 476 12 HOH HOH . G 7 HOH A 12 477 13 HOH HOH . G 7 HOH A 13 478 14 HOH HOH . G 7 HOH A 14 479 15 HOH HOH . G 7 HOH A 15 480 16 HOH HOH . G 7 HOH A 16 481 18 HOH HOH . G 7 HOH A 17 482 20 HOH HOH . G 7 HOH A 18 483 21 HOH HOH . G 7 HOH A 19 484 22 HOH HOH . G 7 HOH A 20 485 23 HOH HOH . G 7 HOH A 21 486 24 HOH HOH . G 7 HOH A 22 487 25 HOH HOH . G 7 HOH A 23 488 26 HOH HOH . G 7 HOH A 24 489 28 HOH HOH . G 7 HOH A 25 490 29 HOH HOH . G 7 HOH A 26 491 31 HOH HOH . G 7 HOH A 27 492 32 HOH HOH . G 7 HOH A 28 493 33 HOH HOH . G 7 HOH A 29 494 34 HOH HOH . G 7 HOH A 30 495 35 HOH HOH . G 7 HOH A 31 496 36 HOH HOH . G 7 HOH A 32 497 37 HOH HOH . G 7 HOH A 33 498 38 HOH HOH . G 7 HOH A 34 499 40 HOH HOH . G 7 HOH A 35 502 41 HOH HOH . G 7 HOH A 36 503 42 HOH HOH . G 7 HOH A 37 504 43 HOH HOH . G 7 HOH A 38 505 44 HOH HOH . G 7 HOH A 39 506 45 HOH HOH . G 7 HOH A 40 507 46 HOH HOH . G 7 HOH A 41 508 47 HOH HOH . G 7 HOH A 42 509 48 HOH HOH . G 7 HOH A 43 510 49 HOH HOH . G 7 HOH A 44 511 50 HOH HOH . G 7 HOH A 45 512 51 HOH HOH . G 7 HOH A 46 513 52 HOH HOH . G 7 HOH A 47 514 53 HOH HOH . G 7 HOH A 48 515 54 HOH HOH . G 7 HOH A 49 516 56 HOH HOH . G 7 HOH A 50 517 58 HOH HOH . G 7 HOH A 51 518 59 HOH HOH . G 7 HOH A 52 519 61 HOH HOH . G 7 HOH A 53 520 62 HOH HOH . G 7 HOH A 54 521 63 HOH HOH . G 7 HOH A 55 522 64 HOH HOH . G 7 HOH A 56 523 65 HOH HOH . G 7 HOH A 57 524 66 HOH HOH . G 7 HOH A 58 525 68 HOH HOH . G 7 HOH A 59 526 69 HOH HOH . G 7 HOH A 60 527 70 HOH HOH . G 7 HOH A 61 528 72 HOH HOH . G 7 HOH A 62 529 74 HOH HOH . G 7 HOH A 63 530 75 HOH HOH . G 7 HOH A 64 531 76 HOH HOH . G 7 HOH A 65 532 77 HOH HOH . G 7 HOH A 66 533 78 HOH HOH . G 7 HOH A 67 534 79 HOH HOH . G 7 HOH A 68 535 80 HOH HOH . G 7 HOH A 69 536 81 HOH HOH . G 7 HOH A 70 537 82 HOH HOH . G 7 HOH A 71 538 83 HOH HOH . G 7 HOH A 72 539 84 HOH HOH . G 7 HOH A 73 540 85 HOH HOH . G 7 HOH A 74 541 86 HOH HOH . G 7 HOH A 75 542 87 HOH HOH . G 7 HOH A 76 543 88 HOH HOH . G 7 HOH A 77 544 89 HOH HOH . G 7 HOH A 78 545 90 HOH HOH . G 7 HOH A 79 546 91 HOH HOH . G 7 HOH A 80 547 92 HOH HOH . G 7 HOH A 81 548 94 HOH HOH . G 7 HOH A 82 549 95 HOH HOH . G 7 HOH A 83 550 96 HOH HOH . G 7 HOH A 84 551 97 HOH HOH . G 7 HOH A 85 552 98 HOH HOH . G 7 HOH A 86 553 99 HOH HOH . G 7 HOH A 87 554 101 HOH HOH . G 7 HOH A 88 555 102 HOH HOH . G 7 HOH A 89 556 103 HOH HOH . G 7 HOH A 90 557 104 HOH HOH . G 7 HOH A 91 558 105 HOH HOH . G 7 HOH A 92 559 108 HOH HOH . G 7 HOH A 93 560 109 HOH HOH . G 7 HOH A 94 561 110 HOH HOH . G 7 HOH A 95 562 111 HOH HOH . G 7 HOH A 96 563 113 HOH HOH . G 7 HOH A 97 564 116 HOH HOH . G 7 HOH A 98 565 117 HOH HOH . G 7 HOH A 99 566 118 HOH HOH . G 7 HOH A 100 567 119 HOH HOH . G 7 HOH A 101 568 120 HOH HOH . G 7 HOH A 102 569 121 HOH HOH . G 7 HOH A 103 570 122 HOH HOH . G 7 HOH A 104 571 125 HOH HOH . G 7 HOH A 105 572 126 HOH HOH . G 7 HOH A 106 573 127 HOH HOH . G 7 HOH A 107 574 129 HOH HOH . G 7 HOH A 108 575 130 HOH HOH . G 7 HOH A 109 576 131 HOH HOH . G 7 HOH A 110 577 132 HOH HOH . G 7 HOH A 111 578 134 HOH HOH . G 7 HOH A 112 579 136 HOH HOH . G 7 HOH A 113 580 137 HOH HOH . G 7 HOH A 114 581 138 HOH HOH . G 7 HOH A 115 582 140 HOH HOH . G 7 HOH A 116 583 141 HOH HOH . G 7 HOH A 117 584 142 HOH HOH . G 7 HOH A 118 585 153 HOH HOH . G 7 HOH A 119 586 154 HOH HOH . G 7 HOH A 120 587 156 HOH HOH . G 7 HOH A 121 588 163 HOH HOH . G 7 HOH A 122 589 171 HOH HOH . G 7 HOH A 123 590 176 HOH HOH . G 7 HOH A 124 591 177 HOH HOH . G 7 HOH A 125 592 178 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 . . . D 4 -25.491 -3.16 6.901 0.5 33.82 ? PG ANP 600 A 1 HETATM 2 O O1G ANP . . . D 4 -26.709 -2.451 7.389 0.5 33.78 ? O1G ANP 600 A 1 HETATM 3 O O2G ANP . . . D 4 -24.211 -2.61 7.476 0.5 35.14 ? O2G ANP 600 A 1 HETATM 4 O O3G ANP . . . D 4 -25.551 -4.667 6.988 0.5 35.89 ? O3G ANP 600 A 1 HETATM 5 P PB ANP . . . D 4 -23.976 -2.614 4.467 0.5 35.34 ? PB ANP 600 A 1 HETATM 6 O O1B ANP . . . D 4 -23.311 -1.409 5.124 0.5 35.16 ? O1B ANP 600 A 1 HETATM 7 O O2B ANP . . . D 4 -23.235 -3.93 4.427 0.5 33.66 ? O2B ANP 600 A 1 HETATM 8 N N3B ANP . . . D 4 -25.431 -2.81 5.258 0.5 35.25 ? N3B ANP 600 A 1 HETATM 9 P PA ANP . . . D 4 -24.706 -0.843 2.398 0.5 34.2 ? PA ANP 600 A 1 HETATM 10 O O1A ANP . . . D 4 -24.652 0.142 3.526 0.5 33.94 ? O1A ANP 600 A 1 HETATM 11 O O2A ANP . . . D 4 -23.948 -0.545 1.13 0.5 35.09 ? O2A ANP 600 A 1 HETATM 12 O O3A ANP . . . D 4 -24.252 -2.293 2.921 0.5 34.32 ? O3A ANP 600 A 1 HETATM 13 O O5' ANP . . . D 4 -26.264 -1.071 2.004 0.5 32.91 ? O5' ANP 600 A 1 HETATM 14 C C5' ANP . . . D 4 -26.748 -2.154 1.205 0.5 29.45 ? C5' ANP 600 A 1 HETATM 15 C C4' ANP . . . D 4 -28.271 -2.057 1.208 0.5 29 ? C4' ANP 600 A 1 HETATM 16 O O4' ANP . . . D 4 -28.652 -0.741 0.791 0.5 27.78 ? O4' ANP 600 A 1 HETATM 17 C C3' ANP . . . D 4 -28.962 -3.058 0.287 0.5 28.3 ? C3' ANP 600 A 1 HETATM 18 O O3' ANP . . . D 4 -29.962 -3.775 1.02 0.5 27.44 ? O3' ANP 600 A 1 HETATM 19 C C2' ANP . . . D 4 -29.615 -2.234 -0.808 0.5 27.87 ? C2' ANP 600 A 1 HETATM 20 O O2' ANP . . . D 4 -30.984 -2.626 -1.017 0.5 28.49 ? O2' ANP 600 A 1 HETATM 21 C C1' ANP . . . D 4 -29.527 -0.782 -0.337 0.5 26.1 ? C1' ANP 600 A 1 HETATM 22 N N9 ANP . . . D 4 -29.094 0.148 -1.429 0.5 24.49 ? N9 ANP 600 A 1 HETATM 23 C C8 ANP . . . D 4 -28.349 -0.142 -2.512 0.5 23.37 ? C8 ANP 600 A 1 HETATM 24 N N7 ANP . . . D 4 -28.201 0.982 -3.256 0.5 22.85 ? N7 ANP 600 A 1 HETATM 25 C C5 ANP . . . D 4 -28.87 1.988 -2.641 0.5 22.19 ? C5 ANP 600 A 1 HETATM 26 C C6 ANP . . . D 4 -29.088 3.346 -2.916 0.5 21.92 ? C6 ANP 600 A 1 HETATM 27 N N6 ANP . . . D 4 -28.577 3.945 -4.023 0.5 22.37 ? N6 ANP 600 A 1 HETATM 28 N N1 ANP . . . D 4 -29.82 4.088 -2.045 0.5 20.77 ? N1 ANP 600 A 1 HETATM 29 C C2 ANP . . . D 4 -30.343 3.536 -0.945 0.5 19.59 ? C2 ANP 600 A 1 HETATM 30 N N3 ANP . . . D 4 -30.147 2.241 -0.671 0.5 20.3 ? N3 ANP 600 A 1 HETATM 31 C C4 ANP . . . D 4 -29.422 1.448 -1.49 0.5 21.98 ? C4 ANP 600 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 418 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #