data_1XMS # _model_server_result.job_id mPyGiso7AOulwJsyVzetdA _model_server_result.datetime_utc '2025-03-06 03:42:14' _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 1xms # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":400}' # _entry.id 1XMS # _exptl.entry_id 1XMS _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 1XMS _cell.length_a 100.7 _cell.length_b 100.7 _cell.length_c 81.9 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XMS _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_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 1,2,3,4,5,6 # 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_555 -y,x-y,z+1/3 -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 27.3 3 'crystal symmetry operation' 3_555 -x+y,-x,z+2/3 -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 54.6 4 'crystal symmetry operation' 4_555 -x,-y,z+1/2 -1 0 0 0 -1 0 0 0 1 0 0 40.95 5 'crystal symmetry operation' 5_555 y,-x+y,z+5/6 0.5 0.866025 0 -0.866025 0.5 0 0 0 1 0 0 68.25 6 'crystal symmetry operation' 6_555 x-y,x,z+1/6 0.5 -0.866025 0 0.866025 0.5 0 0 0 1 0 0 13.65 # _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 A OG1 THR 77 A THR 73 1_555 B MN MN . A MN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc2 C N3B ANP . A ANP 400 1_555 B MN MN . A MN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? metalc ? metalc3 D O HOH . A HOH 449 1_555 B MN MN . A MN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? # _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 1XMS _atom_sites.fract_transf_matrix[1][1] 0.00993 _atom_sites.fract_transf_matrix[1][2] 0.005733 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011467 _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] 0.01221 _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 MN A 1 701 701 MN MN . C 3 ANP A 1 400 400 ANP ANP . D 4 HOH A 1 401 401 HOH WAT . D 4 HOH A 2 402 402 HOH WAT . D 4 HOH A 3 403 403 HOH WAT . D 4 HOH A 4 404 404 HOH WAT . D 4 HOH A 5 405 405 HOH WAT . D 4 HOH A 6 406 406 HOH WAT . D 4 HOH A 7 407 407 HOH WAT . D 4 HOH A 8 408 408 HOH WAT . D 4 HOH A 9 409 409 HOH WAT . D 4 HOH A 10 410 410 HOH WAT . D 4 HOH A 11 411 411 HOH WAT . D 4 HOH A 12 412 412 HOH WAT . D 4 HOH A 13 413 413 HOH WAT . D 4 HOH A 14 414 414 HOH WAT . D 4 HOH A 15 415 415 HOH WAT . D 4 HOH A 16 416 416 HOH WAT . D 4 HOH A 17 417 417 HOH WAT . D 4 HOH A 18 418 418 HOH WAT . D 4 HOH A 19 419 419 HOH WAT . D 4 HOH A 20 420 420 HOH WAT . D 4 HOH A 21 421 421 HOH WAT . D 4 HOH A 22 422 422 HOH WAT . D 4 HOH A 23 423 423 HOH WAT . D 4 HOH A 24 424 424 HOH WAT . D 4 HOH A 25 425 425 HOH WAT . D 4 HOH A 26 426 426 HOH WAT . D 4 HOH A 27 427 427 HOH WAT . D 4 HOH A 28 428 428 HOH WAT . D 4 HOH A 29 429 429 HOH WAT . D 4 HOH A 30 430 430 HOH WAT . D 4 HOH A 31 431 431 HOH WAT . D 4 HOH A 32 432 432 HOH WAT . D 4 HOH A 33 433 433 HOH WAT . D 4 HOH A 34 434 434 HOH WAT . D 4 HOH A 35 435 435 HOH WAT . D 4 HOH A 36 436 436 HOH WAT . D 4 HOH A 37 437 437 HOH WAT . D 4 HOH A 38 438 438 HOH WAT . D 4 HOH A 39 439 439 HOH WAT . D 4 HOH A 40 440 440 HOH WAT . D 4 HOH A 41 441 441 HOH WAT . D 4 HOH A 42 442 442 HOH WAT . D 4 HOH A 43 443 443 HOH WAT . D 4 HOH A 44 444 444 HOH WAT . D 4 HOH A 45 445 445 HOH WAT . D 4 HOH A 46 446 446 HOH WAT . D 4 HOH A 47 447 447 HOH WAT . D 4 HOH A 48 448 448 HOH WAT . D 4 HOH A 49 449 449 HOH WAT . D 4 HOH A 50 450 450 HOH WAT . D 4 HOH A 51 451 451 HOH WAT . D 4 HOH A 52 452 452 HOH WAT . D 4 HOH A 53 453 453 HOH WAT . D 4 HOH A 54 454 454 HOH WAT . D 4 HOH A 55 455 455 HOH WAT . D 4 HOH A 56 457 457 HOH WAT . D 4 HOH A 57 458 458 HOH WAT . D 4 HOH A 58 459 459 HOH WAT . D 4 HOH A 59 460 460 HOH WAT . D 4 HOH A 60 461 461 HOH WAT . D 4 HOH A 61 462 462 HOH WAT . D 4 HOH A 62 463 463 HOH WAT . D 4 HOH A 63 464 464 HOH WAT . D 4 HOH A 64 465 465 HOH WAT . D 4 HOH A 65 466 466 HOH WAT . D 4 HOH A 66 467 467 HOH WAT . D 4 HOH A 67 468 468 HOH WAT . D 4 HOH A 68 469 469 HOH WAT . D 4 HOH A 69 470 470 HOH WAT . D 4 HOH A 70 471 471 HOH WAT . D 4 HOH A 71 472 472 HOH WAT . D 4 HOH A 72 473 473 HOH WAT . D 4 HOH A 73 474 474 HOH WAT . D 4 HOH A 74 475 475 HOH WAT . D 4 HOH A 75 476 476 HOH WAT . D 4 HOH A 76 477 477 HOH WAT . D 4 HOH A 77 478 478 HOH WAT . D 4 HOH A 78 479 479 HOH WAT . D 4 HOH A 79 480 480 HOH WAT . D 4 HOH A 80 481 481 HOH WAT . D 4 HOH A 81 482 482 HOH WAT . D 4 HOH A 82 483 483 HOH WAT . D 4 HOH A 83 484 484 HOH WAT . D 4 HOH A 84 485 485 HOH WAT . D 4 HOH A 85 486 486 HOH WAT . D 4 HOH A 86 487 487 HOH WAT . D 4 HOH A 87 488 488 HOH WAT . D 4 HOH A 88 489 489 HOH WAT . D 4 HOH A 89 490 490 HOH WAT . D 4 HOH A 90 491 491 HOH WAT . D 4 HOH A 91 492 492 HOH WAT . D 4 HOH A 92 493 493 HOH WAT . D 4 HOH A 93 494 494 HOH WAT . D 4 HOH A 94 495 495 HOH WAT . D 4 HOH A 95 496 496 HOH WAT . D 4 HOH A 96 498 498 HOH WAT . D 4 HOH A 97 499 499 HOH WAT . D 4 HOH A 98 500 500 HOH WAT . D 4 HOH A 99 501 501 HOH WAT . D 4 HOH A 100 502 502 HOH WAT . D 4 HOH A 101 503 503 HOH WAT . D 4 HOH A 102 504 504 HOH WAT . D 4 HOH A 103 505 505 HOH WAT . D 4 HOH A 104 506 506 HOH WAT . D 4 HOH A 105 507 507 HOH WAT . D 4 HOH A 106 508 508 HOH WAT . D 4 HOH A 107 509 509 HOH WAT . D 4 HOH A 108 510 510 HOH WAT . D 4 HOH A 109 511 511 HOH WAT . D 4 HOH A 110 512 512 HOH WAT . D 4 HOH A 111 513 513 HOH WAT . D 4 HOH A 112 514 514 HOH WAT . D 4 HOH A 113 515 515 HOH WAT . D 4 HOH A 114 516 516 HOH WAT . D 4 HOH A 115 517 517 HOH WAT . D 4 HOH A 116 518 518 HOH WAT . D 4 HOH A 117 519 519 HOH WAT . D 4 HOH A 118 520 520 HOH WAT . D 4 HOH A 119 521 521 HOH WAT . D 4 HOH A 120 522 522 HOH WAT . D 4 HOH A 121 523 523 HOH WAT . D 4 HOH A 122 524 524 HOH WAT . D 4 HOH A 123 525 525 HOH WAT . D 4 HOH A 124 526 526 HOH WAT . D 4 HOH A 125 527 527 HOH WAT . # 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 20.834 7.859 7.931 1 54.5 ? PG ANP 400 A 1 HETATM 2 O O1G ANP . . . C 3 20.457 7.595 6.582 1 59.75 ? O1G ANP 400 A 1 HETATM 3 O O2G ANP . . . C 3 20.489 6.758 8.868 1 59.78 ? O2G ANP 400 A 1 HETATM 4 O O3G ANP . . . C 3 20.177 9.081 8.323 1 58.96 ? O3G ANP 400 A 1 HETATM 5 P PB ANP . . . C 3 23.668 6.871 8.13 1 49.11 ? PB ANP 400 A 1 HETATM 6 O O1B ANP . . . C 3 23.203 5.609 7.515 1 52.32 ? O1B ANP 400 A 1 HETATM 7 O O2B ANP . . . C 3 24.719 7.582 7.431 1 52.59 ? O2B ANP 400 A 1 HETATM 8 N N3B ANP . . . C 3 22.456 7.846 8.283 1 56.07 ? N3B ANP 400 A 1 HETATM 9 P PA ANP . . . C 3 25.381 7.563 10.357 1 53.92 ? PA ANP 400 A 1 HETATM 10 O O1A ANP . . . C 3 26.79 7.638 9.744 1 54.42 ? O1A ANP 400 A 1 HETATM 11 O O2A ANP . . . C 3 24.882 8.954 10.372 1 55.92 ? O2A ANP 400 A 1 HETATM 12 O O3A ANP . . . C 3 24.465 6.563 9.476 1 53.87 ? O3A ANP 400 A 1 HETATM 13 O O5' ANP . . . C 3 25.696 6.874 11.829 1 57.52 ? O5' ANP 400 A 1 HETATM 14 C C5' ANP . . . C 3 26.957 6.077 12.209 1 62.35 ? C5' ANP 400 A 1 HETATM 15 C C4' ANP . . . C 3 27.231 6.227 13.511 1 65.87 ? C4' ANP 400 A 1 HETATM 16 O O4' ANP . . . C 3 27.575 7.646 13.378 1 68.2 ? O4' ANP 400 A 1 HETATM 17 C C3' ANP . . . C 3 26.015 6.33 14.505 1 66.57 ? C3' ANP 400 A 1 HETATM 18 O O3' ANP . . . C 3 25.339 5.243 15.012 1 66.66 ? O3' ANP 400 A 1 HETATM 19 C C2' ANP . . . C 3 26.625 7.431 15.479 1 68.38 ? C2' ANP 400 A 1 HETATM 20 O O2' ANP . . . C 3 27.365 6.631 16.547 1 69.63 ? O2' ANP 400 A 1 HETATM 21 C C1' ANP . . . C 3 27.602 8.251 14.66 1 69.1 ? C1' ANP 400 A 1 HETATM 22 N N9 ANP . . . C 3 27.252 9.548 14.584 1 69.51 ? N9 ANP 400 A 1 HETATM 23 C C8 ANP . . . C 3 26.6 10.234 13.556 1 69.66 ? C8 ANP 400 A 1 HETATM 24 N N7 ANP . . . C 3 26.369 11.479 13.715 1 70.13 ? N7 ANP 400 A 1 HETATM 25 C C5 ANP . . . C 3 26.891 11.69 14.936 1 70.47 ? C5 ANP 400 A 1 HETATM 26 C C6 ANP . . . C 3 26.942 12.875 15.668 1 70.42 ? C6 ANP 400 A 1 HETATM 27 N N6 ANP . . . C 3 26.485 14.109 15.345 1 71.35 ? N6 ANP 400 A 1 HETATM 28 N N1 ANP . . . C 3 27.556 12.825 16.949 1 70.14 ? N1 ANP 400 A 1 HETATM 29 C C2 ANP . . . C 3 28.08 11.601 17.42 1 69.8 ? C2 ANP 400 A 1 HETATM 30 N N3 ANP . . . C 3 28.081 10.406 16.794 1 69.64 ? N3 ANP 400 A 1 HETATM 31 C C4 ANP . . . C 3 27.449 10.526 15.512 1 70.01 ? C4 ANP 400 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 241 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #