data_1RFT # _model_server_result.job_id 5jzPhAY3ay0mfJK4RU4D5A _model_server_result.datetime_utc '2024-10-16 10:36:00' _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 1rft # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 1RFT # _exptl.entry_id 1RFT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 4 _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 120 _cell.entry_id 1RFT _cell.length_a 103.687 _cell.length_b 103.687 _cell.length_c 58.604 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RFT _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 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 OD2 ASP 113 A ASP 113 1_555 C K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.394 ? metalc ? metalc2 A O THR 148 A THR 148 1_555 C K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc3 A OG1 THR 186 A THR 186 1_555 C K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.453 ? metalc ? metalc4 D O2G ACP . A ACP 401 1_555 B ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? metalc ? metalc5 D O1B ACP . A ACP 401 1_555 B ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? metalc ? metalc6 D O1B ACP . A ACP 401 1_555 C K K . A K 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.919 ? metalc ? metalc7 C K K . A K 404 1_555 F O HOH . A HOH 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.045 ? # _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 1RFT _atom_sites.fract_transf_matrix[1][1] 0.009644 _atom_sites.fract_transf_matrix[1][2] 0.005568 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011136 _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] 0.017064 _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 ZN A 1 403 403 ZN ZN2 . C 3 K A 1 404 404 K K1 . D 4 ACP A 1 401 401 ACP ACP . E 5 PXM A 1 402 402 PXM PYM . F 6 HOH A 1 405 1 HOH WAT . F 6 HOH A 2 406 2 HOH WAT . F 6 HOH A 3 407 3 HOH WAT . F 6 HOH A 4 408 4 HOH WAT . F 6 HOH A 5 409 5 HOH WAT . F 6 HOH A 6 410 6 HOH WAT . F 6 HOH A 7 411 7 HOH WAT . F 6 HOH A 8 412 8 HOH WAT . F 6 HOH A 9 413 9 HOH WAT . F 6 HOH A 10 414 10 HOH WAT . F 6 HOH A 11 415 11 HOH WAT . F 6 HOH A 12 416 12 HOH WAT . F 6 HOH A 13 417 13 HOH WAT . F 6 HOH A 14 418 14 HOH WAT . F 6 HOH A 15 419 15 HOH WAT . F 6 HOH A 16 420 16 HOH WAT . F 6 HOH A 17 421 17 HOH WAT . F 6 HOH A 18 422 18 HOH WAT . F 6 HOH A 19 423 19 HOH WAT . F 6 HOH A 20 424 20 HOH WAT . F 6 HOH A 21 425 21 HOH WAT . F 6 HOH A 22 426 22 HOH WAT . F 6 HOH A 23 427 23 HOH WAT . F 6 HOH A 24 428 24 HOH WAT . F 6 HOH A 25 429 25 HOH WAT . F 6 HOH A 26 430 26 HOH WAT . F 6 HOH A 27 431 27 HOH WAT . F 6 HOH A 28 432 28 HOH WAT . F 6 HOH A 29 433 29 HOH WAT . F 6 HOH A 30 434 30 HOH WAT . F 6 HOH A 31 435 31 HOH WAT . F 6 HOH A 32 436 32 HOH WAT . F 6 HOH A 33 437 33 HOH WAT . F 6 HOH A 34 438 34 HOH WAT . F 6 HOH A 35 439 35 HOH WAT . F 6 HOH A 36 440 36 HOH WAT . F 6 HOH A 37 441 37 HOH WAT . F 6 HOH A 38 442 38 HOH WAT . F 6 HOH A 39 443 39 HOH WAT . F 6 HOH A 40 444 40 HOH WAT . F 6 HOH A 41 445 41 HOH WAT . F 6 HOH A 42 446 42 HOH WAT . F 6 HOH A 43 447 43 HOH WAT . F 6 HOH A 44 448 44 HOH WAT . F 6 HOH A 45 449 45 HOH WAT . F 6 HOH A 46 450 46 HOH WAT . F 6 HOH A 47 451 47 HOH WAT . F 6 HOH A 48 452 48 HOH WAT . F 6 HOH A 49 453 49 HOH WAT . F 6 HOH A 50 454 50 HOH WAT . F 6 HOH A 51 455 51 HOH WAT . F 6 HOH A 52 456 52 HOH WAT . F 6 HOH A 53 457 53 HOH WAT . F 6 HOH A 54 458 54 HOH WAT . F 6 HOH A 55 459 55 HOH WAT . F 6 HOH A 56 460 56 HOH WAT . F 6 HOH A 57 461 57 HOH WAT . F 6 HOH A 58 462 58 HOH WAT . F 6 HOH A 59 463 59 HOH WAT . F 6 HOH A 60 464 60 HOH WAT . F 6 HOH A 61 465 61 HOH WAT . F 6 HOH A 62 466 62 HOH WAT . F 6 HOH A 63 467 63 HOH WAT . F 6 HOH A 64 468 64 HOH WAT . F 6 HOH A 65 469 65 HOH WAT . F 6 HOH A 66 470 66 HOH WAT . F 6 HOH A 67 471 67 HOH WAT . F 6 HOH A 68 472 68 HOH WAT . F 6 HOH A 69 473 69 HOH WAT . F 6 HOH A 70 474 70 HOH WAT . F 6 HOH A 71 475 71 HOH WAT . F 6 HOH A 72 476 72 HOH WAT . F 6 HOH A 73 477 73 HOH WAT . F 6 HOH A 74 478 74 HOH WAT . F 6 HOH A 75 479 75 HOH WAT . F 6 HOH A 76 480 76 HOH WAT . F 6 HOH A 77 481 77 HOH WAT . F 6 HOH A 78 482 78 HOH WAT . F 6 HOH A 79 483 79 HOH WAT . F 6 HOH A 80 484 80 HOH WAT . F 6 HOH A 81 485 81 HOH WAT . F 6 HOH A 82 486 82 HOH WAT . F 6 HOH A 83 487 83 HOH WAT . F 6 HOH A 84 488 84 HOH WAT . F 6 HOH A 85 489 85 HOH WAT . F 6 HOH A 86 490 86 HOH WAT . F 6 HOH A 87 491 87 HOH WAT . F 6 HOH A 88 492 88 HOH WAT . F 6 HOH A 89 493 89 HOH WAT . F 6 HOH A 90 494 90 HOH WAT . F 6 HOH A 91 495 91 HOH WAT . F 6 HOH A 92 496 92 HOH WAT . F 6 HOH A 93 497 93 HOH WAT . F 6 HOH A 94 498 94 HOH WAT . F 6 HOH A 95 499 95 HOH WAT . F 6 HOH A 96 500 96 HOH WAT . F 6 HOH A 97 501 97 HOH WAT . F 6 HOH A 98 502 98 HOH WAT . F 6 HOH A 99 503 99 HOH WAT . F 6 HOH A 100 504 100 HOH WAT . F 6 HOH A 101 505 101 HOH WAT . F 6 HOH A 102 506 102 HOH WAT . F 6 HOH A 103 507 103 HOH WAT . F 6 HOH A 104 508 104 HOH WAT . F 6 HOH A 105 509 105 HOH WAT . F 6 HOH A 106 510 106 HOH WAT . F 6 HOH A 107 511 107 HOH WAT . F 6 HOH A 108 512 108 HOH WAT . F 6 HOH A 109 513 109 HOH WAT . F 6 HOH A 110 514 110 HOH WAT . F 6 HOH A 111 515 111 HOH WAT . F 6 HOH A 112 516 112 HOH WAT . F 6 HOH A 113 517 113 HOH WAT . F 6 HOH A 114 518 114 HOH WAT . F 6 HOH A 115 519 115 HOH WAT . F 6 HOH A 116 520 116 HOH WAT . F 6 HOH A 117 521 117 HOH WAT . F 6 HOH A 118 522 118 HOH WAT . F 6 HOH A 119 523 119 HOH WAT . F 6 HOH A 120 524 120 HOH WAT . F 6 HOH A 121 525 121 HOH WAT . F 6 HOH A 122 526 122 HOH WAT . F 6 HOH A 123 527 123 HOH WAT . F 6 HOH A 124 528 124 HOH WAT . F 6 HOH A 125 529 125 HOH WAT . F 6 HOH A 126 530 126 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 ACP . . . D 4 49.436 46.865 -5.555 1 30.65 ? PG ACP 401 A 1 HETATM 2 O O1G ACP . . . D 4 50.392 45.74 -5.338 1 31.67 ? O1G ACP 401 A 1 HETATM 3 O O2G ACP . . . D 4 48.079 46.478 -5.967 1 31.26 ? O2G ACP 401 A 1 HETATM 4 O O3G ACP . . . D 4 49.438 47.782 -4.343 1 29.6 ? O3G ACP 401 A 1 HETATM 5 P PB ACP . . . D 4 51.128 47.515 -7.93 1 19.85 ? PB ACP 401 A 1 HETATM 6 O O1B ACP . . . D 4 50.493 47.645 -9.254 1 20.41 ? O1B ACP 401 A 1 HETATM 7 O O2B ACP . . . D 4 51.937 46.337 -7.631 1 21.31 ? O2B ACP 401 A 1 HETATM 8 C C3B ACP . . . D 4 49.948 47.727 -6.809 1 25.83 ? C3B ACP 401 A 1 HETATM 9 P PA ACP . . . D 4 53.297 49.344 -7.71 1 24.41 ? PA ACP 401 A 1 HETATM 10 O O1A ACP . . . D 4 54.083 48.6 -6.701 1 24.67 ? O1A ACP 401 A 1 HETATM 11 O O2A ACP . . . D 4 53.761 49.392 -9.115 1 21.73 ? O2A ACP 401 A 1 HETATM 12 O O3A ACP . . . D 4 51.84 48.811 -7.631 1 23.98 ? O3A ACP 401 A 1 HETATM 13 O O5' ACP . . . D 4 53.064 50.787 -7.176 1 24.07 ? O5' ACP 401 A 1 HETATM 14 C C5' ACP . . . D 4 52.451 51.836 -7.918 1 24.69 ? C5' ACP 401 A 1 HETATM 15 C C4' ACP . . . D 4 52.934 53.162 -7.385 1 26.15 ? C4' ACP 401 A 1 HETATM 16 O O4' ACP . . . D 4 53.07 53.06 -5.953 1 26.18 ? O4' ACP 401 A 1 HETATM 17 C C3' ACP . . . D 4 54.269 53.638 -7.931 1 27.35 ? C3' ACP 401 A 1 HETATM 18 O O3' ACP . . . D 4 54.069 54.966 -8.401 1 27.52 ? O3' ACP 401 A 1 HETATM 19 C C2' ACP . . . D 4 55.19 53.561 -6.776 1 26.11 ? C2' ACP 401 A 1 HETATM 20 O O2' ACP . . . D 4 56.007 54.712 -6.699 1 29.58 ? O2' ACP 401 A 1 HETATM 21 C C1' ACP . . . D 4 54.355 53.497 -5.519 1 25.11 ? C1' ACP 401 A 1 HETATM 22 N N9 ACP . . . D 4 54.892 52.563 -4.484 1 24.87 ? N9 ACP 401 A 1 HETATM 23 C C8 ACP . . . D 4 54.281 51.491 -3.874 1 25.76 ? C8 ACP 401 A 1 HETATM 24 N N7 ACP . . . D 4 54.993 50.869 -2.98 1 25.07 ? N7 ACP 401 A 1 HETATM 25 C C5 ACP . . . D 4 56.163 51.585 -2.998 1 25.67 ? C5 ACP 401 A 1 HETATM 26 C C6 ACP . . . D 4 57.385 51.463 -2.269 1 25.67 ? C6 ACP 401 A 1 HETATM 27 N N6 ACP . . . D 4 57.549 50.511 -1.368 1 27.84 ? N6 ACP 401 A 1 HETATM 28 N N1 ACP . . . D 4 58.4 52.355 -2.516 1 25.43 ? N1 ACP 401 A 1 HETATM 29 C C2 ACP . . . D 4 58.231 53.321 -3.43 1 24.64 ? C2 ACP 401 A 1 HETATM 30 N N3 ACP . . . D 4 57.132 53.551 -4.188 1 25.18 ? N3 ACP 401 A 1 HETATM 31 C C4 ACP . . . D 4 56.121 52.631 -3.913 1 25.69 ? C4 ACP 401 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #