data_5Y0N # _model_server_result.job_id sAyEdafcvQQ-fsjwOnF6vQ _model_server_result.datetime_utc '2024-11-29 06:53:03' _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 5y0n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1001}' # _entry.id 5Y0N # _exptl.entry_id 5Y0N _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 5Y0N _cell.length_a 68.037 _cell.length_b 68.021 _cell.length_c 209.952 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Y0N _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,F _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 # 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 D 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 covale ? covale1 A C MSE 21 A MSE 1 1_555 A N LYS 22 A LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C VAL 56 A VAL 36 1_555 A N MSE 57 A MSE 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale3 A C MSE 57 A MSE 37 1_555 A N SER 58 A SER 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale4 A C LYS 77 A LYS 57 1_555 A N MSE 78 A MSE 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 A C MSE 78 A MSE 58 1_555 A N ALA 79 A ALA 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale6 A C PRO 199 A PRO 179 1_555 A N MSE 200 A MSE 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.313 ? covale ? covale7 A C MSE 200 A MSE 180 1_555 A N LYS 201 A LYS 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale8 A C ALA 233 A ALA 213 1_555 A N MSE 234 A MSE 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale9 A C MSE 234 A MSE 214 1_555 A N ILE 235 A ILE 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale10 A C PHE 313 A PHE 293 1_555 A N MSE 314 A MSE 294 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale11 A C MSE 314 A MSE 294 1_555 A N GLU 315 A GLU 295 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale12 A C ARG 329 A ARG 309 1_555 A N MSE 330 A MSE 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale13 A C MSE 330 A MSE 310 1_555 A N ASN 331 A ASN 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale14 A C ASP 342 A ASP 322 1_555 A N MSE 343 A MSE 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale15 A C MSE 343 A MSE 323 1_555 A N GLN 344 A GLN 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale16 A C GLY 359 A GLY 339 1_555 A N MSE 360 A MSE 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale17 A C MSE 360 A MSE 340 1_555 A N THR 361 A THR 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale18 B C MSE 21 B MSE 1 1_555 B N LYS 22 B LYS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale19 B C VAL 56 B VAL 36 1_555 B N MSE 57 B MSE 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale20 B C MSE 57 B MSE 37 1_555 B N SER 58 B SER 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale21 B C LYS 77 B LYS 57 1_555 B N MSE 78 B MSE 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale22 B C MSE 78 B MSE 58 1_555 B N ALA 79 B ALA 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale23 B C PRO 199 B PRO 179 1_555 B N MSE 200 B MSE 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale24 B C MSE 200 B MSE 180 1_555 B N LYS 201 B LYS 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale25 B C ALA 233 B ALA 213 1_555 B N MSE 234 B MSE 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale26 B C MSE 234 B MSE 214 1_555 B N ILE 235 B ILE 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale27 B C PHE 313 B PHE 293 1_555 B N MSE 314 B MSE 294 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale28 B C MSE 314 B MSE 294 1_555 B N GLU 315 B GLU 295 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale29 B C ARG 329 B ARG 309 1_555 B N MSE 330 B MSE 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale30 B C MSE 330 B MSE 310 1_555 B N ASN 331 B ASN 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale31 B C ASP 342 B ASP 322 1_555 B N MSE 343 B MSE 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale32 B C MSE 343 B MSE 323 1_555 B N GLN 344 B GLN 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale33 B C GLY 359 B GLY 339 1_555 B N MSE 360 B MSE 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale34 B C MSE 360 B MSE 340 1_555 B N THR 361 B THR 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? # _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 5Y0N _atom_sites.fract_transf_matrix[1][1] 0.014698 _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] 0.014701 _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] 0.004763 _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 ATP A 1 1001 1001 ATP ATP . D 2 ATP B 1 1001 1001 ATP ATP . E 3 HOH A 1 1101 38 HOH HOH . E 3 HOH A 2 1102 116 HOH HOH . E 3 HOH A 3 1103 21 HOH HOH . E 3 HOH A 4 1104 58 HOH HOH . E 3 HOH A 5 1105 2 HOH HOH . E 3 HOH A 6 1106 72 HOH HOH . E 3 HOH A 7 1107 9 HOH HOH . E 3 HOH A 8 1108 32 HOH HOH . E 3 HOH A 9 1109 88 HOH HOH . E 3 HOH A 10 1110 28 HOH HOH . E 3 HOH A 11 1111 17 HOH HOH . E 3 HOH A 12 1112 146 HOH HOH . E 3 HOH A 13 1113 73 HOH HOH . E 3 HOH A 14 1114 27 HOH HOH . E 3 HOH A 15 1115 5 HOH HOH . E 3 HOH A 16 1116 44 HOH HOH . E 3 HOH A 17 1117 12 HOH HOH . E 3 HOH A 18 1118 41 HOH HOH . E 3 HOH A 19 1119 24 HOH HOH . E 3 HOH A 20 1120 20 HOH HOH . E 3 HOH A 21 1121 143 HOH HOH . E 3 HOH A 22 1122 92 HOH HOH . E 3 HOH A 23 1123 40 HOH HOH . E 3 HOH A 24 1124 29 HOH HOH . E 3 HOH A 25 1125 134 HOH HOH . E 3 HOH A 26 1126 52 HOH HOH . E 3 HOH A 27 1127 97 HOH HOH . E 3 HOH A 28 1128 99 HOH HOH . E 3 HOH A 29 1129 37 HOH HOH . E 3 HOH A 30 1130 117 HOH HOH . E 3 HOH A 31 1131 55 HOH HOH . E 3 HOH A 32 1132 108 HOH HOH . E 3 HOH A 33 1133 15 HOH HOH . E 3 HOH A 34 1134 14 HOH HOH . E 3 HOH A 35 1135 129 HOH HOH . E 3 HOH A 36 1136 64 HOH HOH . E 3 HOH A 37 1137 110 HOH HOH . E 3 HOH A 38 1138 80 HOH HOH . E 3 HOH A 39 1139 109 HOH HOH . F 3 HOH B 1 1101 23 HOH HOH . F 3 HOH B 2 1102 4 HOH HOH . F 3 HOH B 3 1103 43 HOH HOH . F 3 HOH B 4 1104 90 HOH HOH . F 3 HOH B 5 1105 33 HOH HOH . F 3 HOH B 6 1106 16 HOH HOH . F 3 HOH B 7 1107 78 HOH HOH . F 3 HOH B 8 1108 6 HOH HOH . F 3 HOH B 9 1109 82 HOH HOH . F 3 HOH B 10 1110 8 HOH HOH . F 3 HOH B 11 1111 128 HOH HOH . F 3 HOH B 12 1112 1 HOH HOH . F 3 HOH B 13 1113 34 HOH HOH . F 3 HOH B 14 1114 105 HOH HOH . F 3 HOH B 15 1115 19 HOH HOH . F 3 HOH B 16 1116 74 HOH HOH . F 3 HOH B 17 1117 65 HOH HOH . F 3 HOH B 18 1118 69 HOH HOH . F 3 HOH B 19 1119 130 HOH HOH . F 3 HOH B 20 1120 118 HOH HOH . F 3 HOH B 21 1121 3 HOH HOH . F 3 HOH B 22 1122 138 HOH HOH . F 3 HOH B 23 1123 67 HOH HOH . F 3 HOH B 24 1124 81 HOH HOH . F 3 HOH B 25 1125 76 HOH HOH . F 3 HOH B 26 1126 131 HOH HOH . F 3 HOH B 27 1127 46 HOH HOH . F 3 HOH B 28 1128 93 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 . . . C 2 20.495 4.899 -56.112 1 175.81 ? PG ATP 1001 A 1 HETATM 2 O O1G ATP . . . C 2 19.931 5.247 -57.476 1 174.23 ? O1G ATP 1001 A 1 HETATM 3 O O2G ATP . . . C 2 19.985 5.821 -55.017 1 172.2 ? O2G ATP 1001 A 1 HETATM 4 O O3G ATP . . . C 2 22.004 4.746 -56.095 1 178.7 ? O3G ATP 1001 A 1 HETATM 5 P PB ATP . . . C 2 20.265 1.958 -56.366 1 216.91 ? PB ATP 1001 A 1 HETATM 6 O O1B ATP . . . C 2 20.173 2.08 -57.876 1 215.92 ? O1B ATP 1001 A 1 HETATM 7 O O2B ATP . . . C 2 21.577 1.485 -55.769 1 215.98 ? O2B ATP 1001 A 1 HETATM 8 O O3B ATP . . . C 2 19.896 3.424 -55.738 1 242.17 ? O3B ATP 1001 A 1 HETATM 9 P PA ATP . . . C 2 18.929 -0.681 -55.787 1 75.27 ? PA ATP 1001 A 1 HETATM 10 O O1A ATP . . . C 2 20.317 -1.25 -55.605 1 67.84 ? O1A ATP 1001 A 1 HETATM 11 O O2A ATP . . . C 2 17.798 -1.09 -54.874 1 74.02 ? O2A ATP 1001 A 1 HETATM 12 O O3A ATP . . . C 2 19.041 0.968 -55.836 1 242.65 ? O3A ATP 1001 A 1 HETATM 13 O O5' ATP . . . C 2 18.4 -1.02 -57.277 1 86.24 ? O5' ATP 1001 A 1 HETATM 14 C C5' ATP . . . C 2 18.246 -2.341 -57.798 1 83.05 ? C5' ATP 1001 A 1 HETATM 15 C C4' ATP . . . C 2 18.443 -2.302 -59.317 1 77.92 ? C4' ATP 1001 A 1 HETATM 16 O O4' ATP . . . C 2 17.529 -1.378 -59.918 1 79.83 ? O4' ATP 1001 A 1 HETATM 17 C C3' ATP . . . C 2 19.833 -1.815 -59.681 1 70.17 ? C3' ATP 1001 A 1 HETATM 18 O O3' ATP . . . C 2 20.302 -2.619 -60.766 1 69.23 ? O3' ATP 1001 A 1 HETATM 19 C C2' ATP . . . C 2 19.61 -0.375 -60.092 1 64.42 ? C2' ATP 1001 A 1 HETATM 20 O O2' ATP . . . C 2 20.611 0.111 -60.979 1 65.56 ? O2' ATP 1001 A 1 HETATM 21 C C1' ATP . . . C 2 18.237 -0.439 -60.724 1 75.5 ? C1' ATP 1001 A 1 HETATM 22 N N9 ATP . . . C 2 17.552 0.876 -60.744 1 85.87 ? N9 ATP 1001 A 1 HETATM 23 C C8 ATP . . . C 2 16.865 1.434 -59.734 1 90.92 ? C8 ATP 1001 A 1 HETATM 24 N N7 ATP . . . C 2 16.361 2.649 -60.092 1 95.03 ? N7 ATP 1001 A 1 HETATM 25 C C5 ATP . . . C 2 16.724 2.888 -61.368 1 95.38 ? C5 ATP 1001 A 1 HETATM 26 C C6 ATP . . . C 2 16.531 3.98 -62.362 1 91.53 ? C6 ATP 1001 A 1 HETATM 27 N N6 ATP . . . C 2 15.83 5.102 -62.075 1 90.72 ? N6 ATP 1001 A 1 HETATM 28 N N1 ATP . . . C 2 17.083 3.821 -63.581 1 86.06 ? N1 ATP 1001 A 1 HETATM 29 C C2 ATP . . . C 2 17.779 2.713 -63.89 1 85.94 ? C2 ATP 1001 A 1 HETATM 30 N N3 ATP . . . C 2 17.998 1.696 -63.044 1 89.78 ? N3 ATP 1001 A 1 HETATM 31 C C4 ATP . . . C 2 17.505 1.713 -61.787 1 91.71 ? C4 ATP 1001 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 35 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #