data_5DT3 # _model_server_result.job_id 76H28Zuuf_f7a8DUIqcEnQ _model_server_result.datetime_utc '2024-11-24 05:43:06' _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 5dt3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 5DT3 # _exptl.entry_id 5DT3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 5DT3 _cell.length_a 82.469 _cell.length_b 82.469 _cell.length_c 172.984 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DT3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _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 _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 covale ? covale1 A C ARG 163 A ARG 286 1_555 A N TPO 164 A TPO 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale2 A C TPO 164 A TPO 287 1_555 A N THR 165 A THR 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 A OD1 ASN 138 A ASN 261 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc2 A OD2 ASP 151 A ASP 274 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc3 B MG MG . A MG 401 1_555 D O2A ATP . A ATP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc4 B MG MG . A MG 401 1_555 D O2B ATP . A ATP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 5DT3 _atom_sites.fract_transf_matrix[1][1] 0.012126 _atom_sites.fract_transf_matrix[1][2] 0.007001 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014002 _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] 0.005781 _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 MG A 1 401 1 MG MG . C 3 SO4 A 1 402 1 SO4 SO4 . D 4 ATP A 1 403 1 ATP ATP . E 5 HOH A 1 501 15 HOH HOH . E 5 HOH A 2 502 16 HOH HOH . E 5 HOH A 3 503 59 HOH HOH . E 5 HOH A 4 504 12 HOH HOH . E 5 HOH A 5 505 43 HOH HOH . E 5 HOH A 6 506 21 HOH HOH . E 5 HOH A 7 507 22 HOH HOH . E 5 HOH A 8 508 9 HOH HOH . E 5 HOH A 9 509 46 HOH HOH . E 5 HOH A 10 510 47 HOH HOH . E 5 HOH A 11 511 17 HOH HOH . E 5 HOH A 12 512 61 HOH HOH . E 5 HOH A 13 513 5 HOH HOH . E 5 HOH A 14 514 24 HOH HOH . E 5 HOH A 15 515 11 HOH HOH . E 5 HOH A 16 516 44 HOH HOH . E 5 HOH A 17 517 51 HOH HOH . E 5 HOH A 18 518 56 HOH HOH . E 5 HOH A 19 519 45 HOH HOH . E 5 HOH A 20 520 10 HOH HOH . E 5 HOH A 21 521 79 HOH HOH . E 5 HOH A 22 522 6 HOH HOH . E 5 HOH A 23 523 18 HOH HOH . E 5 HOH A 24 524 81 HOH HOH . E 5 HOH A 25 525 64 HOH HOH . E 5 HOH A 26 526 3 HOH HOH . E 5 HOH A 27 527 4 HOH HOH . E 5 HOH A 28 528 1 HOH HOH . E 5 HOH A 29 529 85 HOH HOH . E 5 HOH A 30 530 29 HOH HOH . E 5 HOH A 31 531 28 HOH HOH . E 5 HOH A 32 532 20 HOH HOH . E 5 HOH A 33 533 54 HOH HOH . E 5 HOH A 34 534 63 HOH HOH . E 5 HOH A 35 535 8 HOH HOH . E 5 HOH A 36 536 7 HOH HOH . E 5 HOH A 37 537 35 HOH HOH . E 5 HOH A 38 538 33 HOH HOH . E 5 HOH A 39 539 40 HOH HOH . E 5 HOH A 40 540 37 HOH HOH . E 5 HOH A 41 541 25 HOH HOH . E 5 HOH A 42 542 48 HOH HOH . E 5 HOH A 43 543 2 HOH HOH . E 5 HOH A 44 544 27 HOH HOH . E 5 HOH A 45 545 42 HOH HOH . E 5 HOH A 46 546 71 HOH HOH . E 5 HOH A 47 547 84 HOH HOH . E 5 HOH A 48 548 31 HOH HOH . E 5 HOH A 49 549 19 HOH HOH . E 5 HOH A 50 550 32 HOH HOH . E 5 HOH A 51 551 41 HOH HOH . E 5 HOH A 52 552 14 HOH HOH . E 5 HOH A 53 553 83 HOH HOH . E 5 HOH A 54 554 36 HOH HOH . E 5 HOH A 55 555 70 HOH HOH . E 5 HOH A 56 556 34 HOH HOH . E 5 HOH A 57 557 38 HOH HOH . E 5 HOH A 58 558 52 HOH HOH . E 5 HOH A 59 559 53 HOH HOH . E 5 HOH A 60 560 75 HOH HOH . E 5 HOH A 61 561 30 HOH HOH . E 5 HOH A 62 562 62 HOH HOH . E 5 HOH A 63 563 76 HOH HOH . E 5 HOH A 64 564 60 HOH HOH . E 5 HOH A 65 565 57 HOH HOH . E 5 HOH A 66 566 26 HOH HOH . E 5 HOH A 67 567 69 HOH HOH . E 5 HOH A 68 568 13 HOH HOH . E 5 HOH A 69 569 39 HOH HOH . E 5 HOH A 70 570 78 HOH HOH . E 5 HOH A 71 571 49 HOH HOH . E 5 HOH A 72 572 82 HOH HOH . E 5 HOH A 73 573 65 HOH HOH . E 5 HOH A 74 574 73 HOH HOH . E 5 HOH A 75 575 67 HOH HOH . E 5 HOH A 76 576 66 HOH HOH . E 5 HOH A 77 577 74 HOH HOH . E 5 HOH A 78 578 77 HOH HOH . E 5 HOH A 79 579 80 HOH HOH . E 5 HOH A 80 580 68 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 ATP . . . D 4 12.63 -22.311 -6.403 1 90.96 ? PG ATP 403 A 1 HETATM 2 O O1G ATP . . . D 4 12.63 -22.176 -7.972 1 90.93 ? O1G ATP 403 A 1 HETATM 3 O O2G ATP . . . D 4 13.739 -23.344 -5.987 1 89.11 ? O2G ATP 403 A 1 HETATM 4 O O3G ATP . . . D 4 12.858 -20.901 -5.76 1 94.03 ? O3G ATP 403 A 1 HETATM 5 P PB ATP . . . D 4 10.412 -23.65 -4.831 1 60.97 ? PB ATP 403 A 1 HETATM 6 O O1B ATP . . . D 4 9.697 -22.585 -4.005 1 64.24 ? O1B ATP 403 A 1 HETATM 7 O O2B ATP . . . D 4 11.255 -24.507 -3.985 1 56.32 ? O2B ATP 403 A 1 HETATM 8 O O3B ATP . . . D 4 11.215 -22.969 -6.034 1 74.22 ? O3B ATP 403 A 1 HETATM 9 P PA ATP . . . D 4 9.025 -26.029 -5.961 1 55.7 ? PA ATP 403 A 1 HETATM 10 O O1A ATP . . . D 4 8.835 -25.916 -7.478 1 59.14 ? O1A ATP 403 A 1 HETATM 11 O O2A ATP . . . D 4 10.221 -26.872 -5.649 1 53.18 ? O2A ATP 403 A 1 HETATM 12 O O3A ATP . . . D 4 9.214 -24.545 -5.398 1 61.03 ? O3A ATP 403 A 1 HETATM 13 O O5' ATP . . . D 4 7.632 -26.534 -5.302 1 58 ? O5' ATP 403 A 1 HETATM 14 C C5' ATP . . . D 4 7.399 -26.483 -3.868 1 53.84 ? C5' ATP 403 A 1 HETATM 15 C C4' ATP . . . D 4 6.72 -27.752 -3.424 1 52.35 ? C4' ATP 403 A 1 HETATM 16 O O4' ATP . . . D 4 5.42 -27.855 -4.054 1 55.34 ? O4' ATP 403 A 1 HETATM 17 C C3' ATP . . . D 4 7.432 -29.047 -3.804 1 52.58 ? C3' ATP 403 A 1 HETATM 18 O O3' ATP . . . D 4 8.513 -29.409 -2.954 1 54.19 ? O3' ATP 403 A 1 HETATM 19 C C2' ATP . . . D 4 6.282 -30.047 -3.784 1 55.18 ? C2' ATP 403 A 1 HETATM 20 O O2' ATP . . . D 4 5.967 -30.393 -2.44 1 56.12 ? O2' ATP 403 A 1 HETATM 21 C C1' ATP . . . D 4 5.163 -29.209 -4.411 1 57.13 ? C1' ATP 403 A 1 HETATM 22 N N9 ATP . . . D 4 5.095 -29.313 -5.873 1 55.43 ? N9 ATP 403 A 1 HETATM 23 C C8 ATP . . . D 4 5.777 -28.534 -6.769 1 52.93 ? C8 ATP 403 A 1 HETATM 24 N N7 ATP . . . D 4 5.469 -28.763 -8.022 1 52.5 ? N7 ATP 403 A 1 HETATM 25 C C5 ATP . . . D 4 4.52 -29.769 -7.948 1 51.65 ? C5 ATP 403 A 1 HETATM 26 C C6 ATP . . . D 4 3.835 -30.496 -8.942 1 52.59 ? C6 ATP 403 A 1 HETATM 27 N N6 ATP . . . D 4 3.92 -30.216 -10.244 1 52.33 ? N6 ATP 403 A 1 HETATM 28 N N1 ATP . . . D 4 3.046 -31.524 -8.542 1 52.64 ? N1 ATP 403 A 1 HETATM 29 C C2 ATP . . . D 4 2.939 -31.78 -7.234 1 53.97 ? C2 ATP 403 A 1 HETATM 30 N N3 ATP . . . D 4 3.518 -31.146 -6.207 1 54.94 ? N3 ATP 403 A 1 HETATM 31 C C4 ATP . . . D 4 4.297 -30.138 -6.632 1 53.79 ? C4 ATP 403 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 437 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #