data_5TV8 # _model_server_result.job_id 9HtodEUW20TlV3ObUjzhaw _model_server_result.datetime_utc '2024-11-15 09:35:40' _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 5tv8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 5TV8 # _exptl.entry_id 5TV8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _entity.pdbx_number_of_molecules 2 _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 5TV8 _cell.length_a 68.576 _cell.length_b 106.381 _cell.length_c 113.553 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5TV8 _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 F N 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 disulf ? disulf1 A SG CYS 173 A CYS 173 1_555 A SG CYS 230 A CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf2 B SG CYS 173 B CYS 173 1_555 B SG CYS 230 B CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc1 C O2B APC . A APC 301 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc2 F O1B APC . B APC 301 1_555 G MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id APC _chem_comp.mon_nstd_flag . _chem_comp.name 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ALPHA,BETA-METHYLENEADENOSINE-5'-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 APC doub 13 n n PG O2G APC sing 14 n n PG O3G APC sing 15 n n PG O3B APC sing 16 n n O2G HOG2 APC sing 17 n n O3G HOG3 APC sing 18 n n PB O1B APC doub 19 n n PB O2B APC sing 20 n n PB O3B APC sing 21 n n PB C3A APC sing 22 n n O2B HOB2 APC sing 23 n n PA O1A APC doub 24 n n PA O2A APC sing 25 n n PA C3A APC sing 26 n n PA O5' APC sing 27 n n O2A HOA2 APC sing 28 n n C3A H3A1 APC sing 29 n n C3A H3A2 APC sing 30 n n O5' C5' APC sing 31 n n C5' C4' APC sing 32 n n C5' "H5'1" APC sing 33 n n C5' "H5'2" APC sing 34 n n C4' O4' APC sing 35 n n C4' C3' APC sing 36 n n C4' H4' APC sing 37 n n O4' C1' APC sing 38 n n C3' O3' APC sing 39 n n C3' C2' APC sing 40 n n C3' H3' APC sing 41 n n O3' HO3' APC sing 42 n n C2' O2' APC sing 43 n n C2' C1' APC sing 44 n n C2' H2' APC sing 45 n n O2' HO2' APC sing 46 n n C1' N9 APC sing 47 n n C1' H1' APC sing 48 n n N9 C8 APC sing 49 n y N9 C4 APC sing 50 n y C8 N7 APC doub 51 n y C8 H8 APC sing 52 n n N7 C5 APC sing 53 n y C5 C6 APC sing 54 n y C5 C4 APC doub 55 n y C6 N6 APC sing 56 n n C6 N1 APC doub 57 n y N6 HN61 APC sing 58 n n N6 HN62 APC sing 59 n n N1 C2 APC sing 60 n y C2 N3 APC doub 61 n y C2 H2 APC sing 62 n n N3 C4 APC sing 63 n y # _atom_sites.entry_id 5TV8 _atom_sites.fract_transf_matrix[1][1] 0.014582 _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] 0.0094 _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] 0.008806 _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 APC A 1 301 400 APC APC . D 3 MG A 1 302 401 MG MG . E 4 PML A 1 303 500 PML PML . F 2 APC B 1 301 400 APC APC . G 3 MG B 1 302 401 MG MG . H 4 PML B 1 303 500 PML PML . I 5 HOH A 1 401 123 HOH HOH . I 5 HOH A 2 402 53 HOH HOH . I 5 HOH A 3 403 41 HOH HOH . I 5 HOH A 4 404 105 HOH HOH . I 5 HOH A 5 405 43 HOH HOH . I 5 HOH A 6 406 94 HOH HOH . I 5 HOH A 7 407 11 HOH HOH . I 5 HOH A 8 408 32 HOH HOH . I 5 HOH A 9 409 24 HOH HOH . I 5 HOH A 10 410 71 HOH HOH . I 5 HOH A 11 411 18 HOH HOH . I 5 HOH A 12 412 86 HOH HOH . I 5 HOH A 13 413 64 HOH HOH . I 5 HOH A 14 414 3 HOH HOH . I 5 HOH A 15 415 69 HOH HOH . I 5 HOH A 16 416 4 HOH HOH . I 5 HOH A 17 417 151 HOH HOH . I 5 HOH A 18 418 14 HOH HOH . I 5 HOH A 19 419 90 HOH HOH . I 5 HOH A 20 420 23 HOH HOH . I 5 HOH A 21 421 12 HOH HOH . I 5 HOH A 22 422 38 HOH HOH . I 5 HOH A 23 423 46 HOH HOH . I 5 HOH A 24 424 107 HOH HOH . I 5 HOH A 25 425 44 HOH HOH . I 5 HOH A 26 426 33 HOH HOH . I 5 HOH A 27 427 10 HOH HOH . I 5 HOH A 28 428 77 HOH HOH . I 5 HOH A 29 429 52 HOH HOH . I 5 HOH A 30 430 89 HOH HOH . I 5 HOH A 31 431 134 HOH HOH . I 5 HOH A 32 432 63 HOH HOH . I 5 HOH A 33 433 87 HOH HOH . I 5 HOH A 34 434 70 HOH HOH . I 5 HOH A 35 435 15 HOH HOH . I 5 HOH A 36 436 116 HOH HOH . I 5 HOH A 37 437 162 HOH HOH . I 5 HOH A 38 438 106 HOH HOH . I 5 HOH A 39 439 97 HOH HOH . I 5 HOH A 40 440 83 HOH HOH . I 5 HOH A 41 441 35 HOH HOH . I 5 HOH A 42 442 74 HOH HOH . I 5 HOH A 43 443 100 HOH HOH . I 5 HOH A 44 444 72 HOH HOH . I 5 HOH A 45 445 96 HOH HOH . I 5 HOH A 46 446 6 HOH HOH . I 5 HOH A 47 447 16 HOH HOH . I 5 HOH A 48 448 62 HOH HOH . I 5 HOH A 49 449 104 HOH HOH . I 5 HOH A 50 450 141 HOH HOH . I 5 HOH A 51 451 110 HOH HOH . I 5 HOH A 52 452 59 HOH HOH . I 5 HOH A 53 453 143 HOH HOH . I 5 HOH A 54 454 75 HOH HOH . I 5 HOH A 55 455 20 HOH HOH . I 5 HOH A 56 456 56 HOH HOH . I 5 HOH A 57 457 88 HOH HOH . I 5 HOH A 58 458 126 HOH HOH . I 5 HOH A 59 459 48 HOH HOH . I 5 HOH A 60 460 54 HOH HOH . I 5 HOH A 61 461 66 HOH HOH . I 5 HOH A 62 462 9 HOH HOH . I 5 HOH A 63 463 34 HOH HOH . I 5 HOH A 64 464 81 HOH HOH . I 5 HOH A 65 465 109 HOH HOH . I 5 HOH A 66 466 65 HOH HOH . I 5 HOH A 67 467 78 HOH HOH . I 5 HOH A 68 468 91 HOH HOH . I 5 HOH A 69 469 42 HOH HOH . I 5 HOH A 70 470 30 HOH HOH . I 5 HOH A 71 471 129 HOH HOH . I 5 HOH A 72 472 103 HOH HOH . I 5 HOH A 73 473 111 HOH HOH . I 5 HOH A 74 474 115 HOH HOH . I 5 HOH A 75 475 144 HOH HOH . I 5 HOH A 76 476 168 HOH HOH . I 5 HOH A 77 477 138 HOH HOH . I 5 HOH A 78 478 121 HOH HOH . I 5 HOH A 79 479 57 HOH HOH . I 5 HOH A 80 480 165 HOH HOH . I 5 HOH A 81 481 102 HOH HOH . I 5 HOH A 82 482 45 HOH HOH . I 5 HOH A 83 483 8 HOH HOH . I 5 HOH A 84 484 114 HOH HOH . I 5 HOH A 85 485 131 HOH HOH . I 5 HOH A 86 486 26 HOH HOH . I 5 HOH A 87 487 150 HOH HOH . I 5 HOH A 88 488 25 HOH HOH . I 5 HOH A 89 489 80 HOH HOH . I 5 HOH A 90 490 152 HOH HOH . I 5 HOH A 91 491 140 HOH HOH . I 5 HOH A 92 492 95 HOH HOH . J 5 HOH B 1 401 112 HOH HOH . J 5 HOH B 2 402 157 HOH HOH . J 5 HOH B 3 403 47 HOH HOH . J 5 HOH B 4 404 133 HOH HOH . J 5 HOH B 5 405 108 HOH HOH . J 5 HOH B 6 406 28 HOH HOH . J 5 HOH B 7 407 31 HOH HOH . J 5 HOH B 8 408 50 HOH HOH . J 5 HOH B 9 409 153 HOH HOH . J 5 HOH B 10 410 147 HOH HOH . J 5 HOH B 11 411 61 HOH HOH . J 5 HOH B 12 412 55 HOH HOH . J 5 HOH B 13 413 160 HOH HOH . J 5 HOH B 14 414 164 HOH HOH . J 5 HOH B 15 415 119 HOH HOH . J 5 HOH B 16 416 122 HOH HOH . J 5 HOH B 17 417 132 HOH HOH . J 5 HOH B 18 418 40 HOH HOH . J 5 HOH B 19 419 85 HOH HOH . J 5 HOH B 20 420 170 HOH HOH . J 5 HOH B 21 421 82 HOH HOH . J 5 HOH B 22 422 27 HOH HOH . J 5 HOH B 23 423 49 HOH HOH . J 5 HOH B 24 424 92 HOH HOH . J 5 HOH B 25 425 7 HOH HOH . J 5 HOH B 26 426 60 HOH HOH . J 5 HOH B 27 427 127 HOH HOH . J 5 HOH B 28 428 125 HOH HOH . J 5 HOH B 29 429 113 HOH HOH . J 5 HOH B 30 430 29 HOH HOH . J 5 HOH B 31 431 117 HOH HOH . J 5 HOH B 32 432 76 HOH HOH . J 5 HOH B 33 433 21 HOH HOH . J 5 HOH B 34 434 139 HOH HOH . J 5 HOH B 35 435 149 HOH HOH . J 5 HOH B 36 436 145 HOH HOH . J 5 HOH B 37 437 148 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 APC . . . C 2 -2.145 20.478 7.569 1 101.92 ? PG APC 301 A 1 HETATM 2 O O1G APC . . . C 2 -2.961 21.102 6.46 1 96.31 ? O1G APC 301 A 1 HETATM 3 O O2G APC . . . C 2 -2.963 20.141 8.798 1 100.88 ? O2G APC 301 A 1 HETATM 4 O O3G APC . . . C 2 -0.838 21.197 7.843 1 99.3 ? O3G APC 301 A 1 HETATM 5 P PB APC . . . C 2 -2.692 18.156 6.094 1 89.19 ? PB APC 301 A 1 HETATM 6 O O1B APC . . . C 2 -2.287 16.597 6.118 1 97.55 ? O1B APC 301 A 1 HETATM 7 O O2B APC . . . C 2 -4.1 18.314 6.541 1 82.77 ? O2B APC 301 A 1 HETATM 8 O O3B APC . . . C 2 -1.691 19.031 7.003 1 94.59 ? O3B APC 301 A 1 HETATM 9 P PA APC . . . C 2 -2.509 17.418 3.245 1 70.81 ? PA APC 301 A 1 HETATM 10 O O1A APC . . . C 2 -2.51 18.097 1.938 1 66.56 ? O1A APC 301 A 1 HETATM 11 O O2A APC . . . C 2 -3.761 16.42 3.435 1 70.2 ? O2A APC 301 A 1 HETATM 12 C C3A APC . . . C 2 -2.532 18.786 4.416 1 80.46 ? C3A APC 301 A 1 HETATM 13 O O5' APC . . . C 2 -1.172 16.547 3.403 1 71.12 ? O5' APC 301 A 1 HETATM 14 C C5' APC . . . C 2 -1.043 15.386 2.59 1 67.77 ? C5' APC 301 A 1 HETATM 15 C C4' APC . . . C 2 0.425 15.079 2.358 1 64.84 ? C4' APC 301 A 1 HETATM 16 O O4' APC . . . C 2 1.079 16.176 1.719 1 62.91 ? O4' APC 301 A 1 HETATM 17 C C3' APC . . . C 2 1.159 14.833 3.664 1 64 ? C3' APC 301 A 1 HETATM 18 O O3' APC . . . C 2 1.168 13.433 3.959 1 63.4 ? O3' APC 301 A 1 HETATM 19 C C2' APC . . . C 2 2.542 15.372 3.404 1 62.09 ? C2' APC 301 A 1 HETATM 20 O O2' APC . . . C 2 3.332 14.313 2.868 1 65.44 ? O2' APC 301 A 1 HETATM 21 C C1' APC . . . C 2 2.381 16.367 2.278 1 61.19 ? C1' APC 301 A 1 HETATM 22 N N9 APC . . . C 2 2.464 17.782 2.719 1 58.68 ? N9 APC 301 A 1 HETATM 23 C C8 APC . . . C 2 1.573 18.435 3.509 1 57.7 ? C8 APC 301 A 1 HETATM 24 N N7 APC . . . C 2 1.933 19.73 3.696 1 53.26 ? N7 APC 301 A 1 HETATM 25 C C5 APC . . . C 2 3.077 19.926 2.993 1 53.66 ? C5 APC 301 A 1 HETATM 26 C C6 APC . . . C 2 4 21.066 2.743 1 50.25 ? C6 APC 301 A 1 HETATM 27 N N6 APC . . . C 2 3.772 22.289 3.29 1 52.7 ? N6 APC 301 A 1 HETATM 28 N N1 APC . . . C 2 5.078 20.844 1.953 1 49.89 ? N1 APC 301 A 1 HETATM 29 C C2 APC . . . C 2 5.325 19.63 1.406 1 53.29 ? C2 APC 301 A 1 HETATM 30 N N3 APC . . . C 2 4.536 18.55 1.592 1 52.15 ? N3 APC 301 A 1 HETATM 31 C C4 APC . . . C 2 3.42 18.637 2.356 1 53.22 ? C4 APC 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 31 #