data_4U40 # _model_server_result.job_id Y9dbQJ2kIyFaHdh7CcNtFQ _model_server_result.datetime_utc '2024-12-23 02:05:24' _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 4u40 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 4U40 # _exptl.entry_id 4U40 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 2 _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 4U40 _cell.length_a 80.339 _cell.length_b 87.595 _cell.length_c 91.45 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4U40 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H 1 1 A,C,D,E,F,G 2 1 B,H 3 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 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 A O SER 78 A SER 77 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc2 A O HIS 80 A HIS 79 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc3 A O ILE 83 A ILE 82 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc4 A OG1 THR 85 A THR 84 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc5 A O GLN 158 A GLN 157 1_555 F MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.877 ? metalc ? metalc6 A OD1 ASN 159 A ASN 158 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc7 A OD2 ASP 172 A ASP 171 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc8 C O1G ANP . A ANP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc9 C O1B ANP . A ANP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc10 C O1A ANP . A ANP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc11 E MG MG . A MG 403 1_555 G O HOH . A HOH 573 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc12 E MG MG . A MG 403 1_555 G O HOH . A HOH 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? # _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 4U40 _atom_sites.fract_transf_matrix[1][1] 0.012447 _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] 0.011416 _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] 0.010935 _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 C 2 ANP A 1 401 1 ANP DRG . D 3 MG A 1 402 1 MG MG . E 3 MG A 1 403 1 MG MG . F 3 MG A 1 404 1 MG MG . G 4 HOH A 1 501 84 HOH HOH . G 4 HOH A 2 502 130 HOH HOH . G 4 HOH A 3 503 148 HOH HOH . G 4 HOH A 4 504 67 HOH HOH . G 4 HOH A 5 505 34 HOH HOH . G 4 HOH A 6 506 80 HOH HOH . G 4 HOH A 7 507 37 HOH HOH . G 4 HOH A 8 508 32 HOH HOH . G 4 HOH A 9 509 40 HOH HOH . G 4 HOH A 10 510 144 HOH HOH . G 4 HOH A 11 511 1 HOH HOH . G 4 HOH A 12 512 96 HOH HOH . G 4 HOH A 13 513 87 HOH HOH . G 4 HOH A 14 514 23 HOH HOH . G 4 HOH A 15 515 122 HOH HOH . G 4 HOH A 16 516 172 HOH HOH . G 4 HOH A 17 517 4 HOH HOH . G 4 HOH A 18 518 5 HOH HOH . G 4 HOH A 19 519 6 HOH HOH . G 4 HOH A 20 520 7 HOH HOH . G 4 HOH A 21 521 10 HOH HOH . G 4 HOH A 22 522 12 HOH HOH . G 4 HOH A 23 523 13 HOH HOH . G 4 HOH A 24 524 14 HOH HOH . G 4 HOH A 25 525 18 HOH HOH . G 4 HOH A 26 526 25 HOH HOH . G 4 HOH A 27 527 26 HOH HOH . G 4 HOH A 28 528 28 HOH HOH . G 4 HOH A 29 529 30 HOH HOH . G 4 HOH A 30 530 31 HOH HOH . G 4 HOH A 31 531 33 HOH HOH . G 4 HOH A 32 532 36 HOH HOH . G 4 HOH A 33 533 41 HOH HOH . G 4 HOH A 34 534 45 HOH HOH . G 4 HOH A 35 535 49 HOH HOH . G 4 HOH A 36 536 50 HOH HOH . G 4 HOH A 37 537 55 HOH HOH . G 4 HOH A 38 538 60 HOH HOH . G 4 HOH A 39 539 63 HOH HOH . G 4 HOH A 40 540 64 HOH HOH . G 4 HOH A 41 541 65 HOH HOH . G 4 HOH A 42 542 72 HOH HOH . G 4 HOH A 43 543 73 HOH HOH . G 4 HOH A 44 544 75 HOH HOH . G 4 HOH A 45 545 77 HOH HOH . G 4 HOH A 46 546 79 HOH HOH . G 4 HOH A 47 547 83 HOH HOH . G 4 HOH A 48 548 86 HOH HOH . G 4 HOH A 49 549 90 HOH HOH . G 4 HOH A 50 550 92 HOH HOH . G 4 HOH A 51 551 93 HOH HOH . G 4 HOH A 52 552 94 HOH HOH . G 4 HOH A 53 553 97 HOH HOH . G 4 HOH A 54 554 98 HOH HOH . G 4 HOH A 55 555 99 HOH HOH . G 4 HOH A 56 556 100 HOH HOH . G 4 HOH A 57 557 101 HOH HOH . G 4 HOH A 58 558 103 HOH HOH . G 4 HOH A 59 559 106 HOH HOH . G 4 HOH A 60 560 109 HOH HOH . G 4 HOH A 61 561 111 HOH HOH . G 4 HOH A 62 562 112 HOH HOH . G 4 HOH A 63 563 118 HOH HOH . G 4 HOH A 64 564 126 HOH HOH . G 4 HOH A 65 565 132 HOH HOH . G 4 HOH A 66 566 133 HOH HOH . G 4 HOH A 67 567 141 HOH HOH . G 4 HOH A 68 568 142 HOH HOH . G 4 HOH A 69 569 147 HOH HOH . G 4 HOH A 70 570 150 HOH HOH . G 4 HOH A 71 571 151 HOH HOH . G 4 HOH A 72 572 152 HOH HOH . G 4 HOH A 73 573 156 HOH HOH . G 4 HOH A 74 574 157 HOH HOH . G 4 HOH A 75 575 159 HOH HOH . G 4 HOH A 76 576 161 HOH HOH . G 4 HOH A 77 577 166 HOH HOH . G 4 HOH A 78 578 170 HOH HOH . G 4 HOH A 79 579 171 HOH HOH . G 4 HOH A 80 580 173 HOH HOH . G 4 HOH A 81 581 174 HOH HOH . G 4 HOH A 82 582 175 HOH HOH . H 4 HOH B 1 401 66 HOH HOH . H 4 HOH B 2 402 56 HOH HOH . H 4 HOH B 3 403 104 HOH HOH . H 4 HOH B 4 404 125 HOH HOH . H 4 HOH B 5 405 81 HOH HOH . H 4 HOH B 6 406 117 HOH HOH . H 4 HOH B 7 407 143 HOH HOH . H 4 HOH B 8 408 91 HOH HOH . H 4 HOH B 9 409 22 HOH HOH . H 4 HOH B 10 410 102 HOH HOH . H 4 HOH B 11 411 129 HOH HOH . H 4 HOH B 12 412 110 HOH HOH . H 4 HOH B 13 413 145 HOH HOH . H 4 HOH B 14 414 127 HOH HOH . H 4 HOH B 15 415 2 HOH HOH . H 4 HOH B 16 416 3 HOH HOH . H 4 HOH B 17 417 8 HOH HOH . H 4 HOH B 18 418 9 HOH HOH . H 4 HOH B 19 419 11 HOH HOH . H 4 HOH B 20 420 15 HOH HOH . H 4 HOH B 21 421 17 HOH HOH . H 4 HOH B 22 422 19 HOH HOH . H 4 HOH B 23 423 20 HOH HOH . H 4 HOH B 24 424 21 HOH HOH . H 4 HOH B 25 425 24 HOH HOH . H 4 HOH B 26 426 29 HOH HOH . H 4 HOH B 27 427 35 HOH HOH . H 4 HOH B 28 428 38 HOH HOH . H 4 HOH B 29 429 39 HOH HOH . H 4 HOH B 30 430 42 HOH HOH . H 4 HOH B 31 431 43 HOH HOH . H 4 HOH B 32 432 44 HOH HOH . H 4 HOH B 33 433 46 HOH HOH . H 4 HOH B 34 434 47 HOH HOH . H 4 HOH B 35 435 48 HOH HOH . H 4 HOH B 36 436 51 HOH HOH . H 4 HOH B 37 437 52 HOH HOH . H 4 HOH B 38 438 53 HOH HOH . H 4 HOH B 39 439 58 HOH HOH . H 4 HOH B 40 440 59 HOH HOH . H 4 HOH B 41 441 61 HOH HOH . H 4 HOH B 42 442 62 HOH HOH . H 4 HOH B 43 443 68 HOH HOH . H 4 HOH B 44 444 69 HOH HOH . H 4 HOH B 45 445 70 HOH HOH . H 4 HOH B 46 446 71 HOH HOH . H 4 HOH B 47 447 74 HOH HOH . H 4 HOH B 48 448 76 HOH HOH . H 4 HOH B 49 449 78 HOH HOH . H 4 HOH B 50 450 85 HOH HOH . H 4 HOH B 51 451 88 HOH HOH . H 4 HOH B 52 452 89 HOH HOH . H 4 HOH B 53 453 95 HOH HOH . H 4 HOH B 54 454 105 HOH HOH . H 4 HOH B 55 455 107 HOH HOH . H 4 HOH B 56 456 116 HOH HOH . H 4 HOH B 57 457 120 HOH HOH . H 4 HOH B 58 458 123 HOH HOH . H 4 HOH B 59 459 131 HOH HOH . H 4 HOH B 60 460 134 HOH HOH . H 4 HOH B 61 461 135 HOH HOH . H 4 HOH B 62 462 136 HOH HOH . H 4 HOH B 63 463 137 HOH HOH . H 4 HOH B 64 464 138 HOH HOH . H 4 HOH B 65 465 139 HOH HOH . H 4 HOH B 66 466 140 HOH HOH . H 4 HOH B 67 467 146 HOH HOH . H 4 HOH B 68 468 149 HOH HOH . H 4 HOH B 69 469 154 HOH HOH . H 4 HOH B 70 470 158 HOH HOH . H 4 HOH B 71 471 160 HOH HOH . H 4 HOH B 72 472 165 HOH HOH . H 4 HOH B 73 473 168 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 2 -19.808 -35 -21.365 1 46.69 ? PG ANP 401 A 1 HETATM 2 O O1G ANP . . . C 2 -18.821 -34.57 -22.547 1 40.11 ? O1G ANP 401 A 1 HETATM 3 O O2G ANP . . . C 2 -21.131 -35.338 -21.924 1 52.66 ? O2G ANP 401 A 1 HETATM 4 O O3G ANP . . . C 2 -19.948 -33.704 -20.417 1 59.14 ? O3G ANP 401 A 1 HETATM 5 P PB ANP . . . C 2 -18.269 -37.389 -21.039 1 49.21 ? PB ANP 401 A 1 HETATM 6 O O1B ANP . . . C 2 -17.209 -36.794 -21.864 1 44.04 ? O1B ANP 401 A 1 HETATM 7 O O2B ANP . . . C 2 -17.615 -38.313 -19.909 1 51.14 ? O2B ANP 401 A 1 HETATM 8 N N3B ANP . . . C 2 -19.259 -36.222 -20.36 1 42.19 ? N3B ANP 401 A 1 HETATM 9 P PA ANP . . . C 2 -19.184 -38.626 -23.495 1 46.73 ? PA ANP 401 A 1 HETATM 10 O O1A ANP . . . C 2 -18.917 -37.408 -24.239 1 44.27 ? O1A ANP 401 A 1 HETATM 11 O O2A ANP . . . C 2 -20.632 -39.224 -23.893 1 53.7 ? O2A ANP 401 A 1 HETATM 12 O O3A ANP . . . C 2 -19.214 -38.304 -21.943 1 53.94 ? O3A ANP 401 A 1 HETATM 13 O O5' ANP . . . C 2 -18.004 -39.67 -23.811 1 55.64 ? O5' ANP 401 A 1 HETATM 14 C C5' ANP . . . C 2 -18.19 -41.085 -23.691 1 60.83 ? C5' ANP 401 A 1 HETATM 15 C C4' ANP . . . C 2 -16.865 -41.767 -24.037 1 59.92 ? C4' ANP 401 A 1 HETATM 16 O O4' ANP . . . C 2 -16.618 -41.748 -25.455 1 55.11 ? O4' ANP 401 A 1 HETATM 17 C C3' ANP . . . C 2 -15.767 -40.958 -23.325 1 56.9 ? C3' ANP 401 A 1 HETATM 18 O O3' ANP . . . C 2 -14.815 -41.811 -22.698 1 69.36 ? O3' ANP 401 A 1 HETATM 19 C C2' ANP . . . C 2 -15.122 -40.208 -24.511 1 55.14 ? C2' ANP 401 A 1 HETATM 20 O O2' ANP . . . C 2 -13.745 -39.967 -24.256 1 55.99 ? O2' ANP 401 A 1 HETATM 21 C C1' ANP . . . C 2 -15.355 -41.154 -25.724 1 50.76 ? C1' ANP 401 A 1 HETATM 22 N N9 ANP . . . C 2 -15.341 -40.277 -26.903 1 52.8 ? N9 ANP 401 A 1 HETATM 23 C C8 ANP . . . C 2 -16.049 -39.124 -27.062 1 45.79 ? C8 ANP 401 A 1 HETATM 24 N N7 ANP . . . C 2 -15.754 -38.56 -28.2 1 48.38 ? N7 ANP 401 A 1 HETATM 25 C C5 ANP . . . C 2 -14.827 -39.299 -28.853 1 42.72 ? C5 ANP 401 A 1 HETATM 26 C C6 ANP . . . C 2 -14.14 -39.189 -30.079 1 44.93 ? C6 ANP 401 A 1 HETATM 27 N N6 ANP . . . C 2 -14.315 -38.115 -30.94 1 40.06 ? N6 ANP 401 A 1 HETATM 28 N N1 ANP . . . C 2 -13.247 -40.13 -30.383 1 51.95 ? N1 ANP 401 A 1 HETATM 29 C C2 ANP . . . C 2 -13.025 -41.156 -29.573 1 51.51 ? C2 ANP 401 A 1 HETATM 30 N N3 ANP . . . C 2 -13.654 -41.299 -28.423 1 53.51 ? N3 ANP 401 A 1 HETATM 31 C C4 ANP . . . C 2 -14.546 -40.404 -28.02 1 51.38 ? C4 ANP 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 31 #