data_9IK1 # _model_server_result.job_id x9uu4vTd_eJT4LU6Bfj2JQ _model_server_result.datetime_utc '2024-10-19 02:18:12' _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 9ik1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":402}' # _entry.id 9IK1 # _exptl.entry_id 9IK1 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 9IK1 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9IK1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U _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 ? 3 E N N ? 3 K N N ? 3 Q 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 102 A CYS 107 1_555 A SG CYS 148 A CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 111 A CYS 116 1_555 A SG CYS 132 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 117 A CYS 122 1_555 A SG CYS 142 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf4 A SG CYS 198 A CYS 203 1_555 A SG CYS 208 A CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf5 A SG CYS 242 A CYS 247 1_555 A SG CYS 251 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 B SG CYS 102 B CYS 107 1_555 B SG CYS 148 B CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 B SG CYS 111 B CYS 116 1_555 B SG CYS 132 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 B SG CYS 117 B CYS 122 1_555 B SG CYS 142 B CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 B SG CYS 198 B CYS 203 1_555 B SG CYS 208 B CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf10 B SG CYS 242 B CYS 247 1_555 B SG CYS 251 B CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf11 C SG CYS 102 C CYS 107 1_555 C SG CYS 148 C CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf12 C SG CYS 111 C CYS 116 1_555 C SG CYS 132 C CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf13 C SG CYS 117 C CYS 122 1_555 C SG CYS 142 C CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf14 C SG CYS 198 C CYS 203 1_555 C SG CYS 208 C CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf15 C SG CYS 242 C CYS 247 1_555 C SG CYS 251 C CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? covale ? covale1 A ND2 ASN 165 A ASN 170 1_555 F C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale2 A ND2 ASN 189 A ASN 194 1_555 G C1 NAG . A NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale3 A ND2 ASN 285 A ASN 290 1_555 H C1 NAG . A NAG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale4 B ND2 ASN 165 B ASN 170 1_555 L C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale5 B ND2 ASN 189 B ASN 194 1_555 M C1 NAG . B NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale6 B ND2 ASN 285 B ASN 290 1_555 N C1 NAG . B NAG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale7 C ND2 ASN 165 C ASN 170 1_555 R C1 NAG . C NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale8 C ND2 ASN 189 C ASN 194 1_555 S C1 NAG . C NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale9 C ND2 ASN 285 C ASN 290 1_555 T C1 NAG . C NAG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? metalc ? metalc1 A OD2 ASP 153 A ASP 158 1_555 I MG MG . A MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc2 E O1G ATP . A ATP 402 1_555 O MG MG . B MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc3 I MG MG . A MG 406 1_555 Q O1G ATP . C ATP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc4 B OD2 ASP 153 B ASP 158 1_555 O MG MG . B MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc5 K O2G ATP . B ATP 402 1_555 U MG MG . C MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc6 C OD2 ASP 153 C ASP 158 1_555 U MG MG . C MG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? # _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 137 n n PG O2G ATP sing 138 n n PG O3G ATP sing 139 n n PG O3B ATP sing 140 n n O2G HOG2 ATP sing 141 n n O3G HOG3 ATP sing 142 n n PB O1B ATP doub 143 n n PB O2B ATP sing 144 n n PB O3B ATP sing 145 n n PB O3A ATP sing 146 n n O2B HOB2 ATP sing 147 n n PA O1A ATP doub 148 n n PA O2A ATP sing 149 n n PA O3A ATP sing 150 n n PA O5' ATP sing 151 n n O2A HOA2 ATP sing 152 n n O5' C5' ATP sing 153 n n C5' C4' ATP sing 154 n n C5' "H5'1" ATP sing 155 n n C5' "H5'2" ATP sing 156 n n C4' O4' ATP sing 157 n n C4' C3' ATP sing 158 n n C4' H4' ATP sing 159 n n O4' C1' ATP sing 160 n n C3' O3' ATP sing 161 n n C3' C2' ATP sing 162 n n C3' H3' ATP sing 163 n n O3' HO3' ATP sing 164 n n C2' O2' ATP sing 165 n n C2' C1' ATP sing 166 n n C2' H2' ATP sing 167 n n O2' HO2' ATP sing 168 n n C1' N9 ATP sing 169 n n C1' H1' ATP sing 170 n n N9 C8 ATP sing 171 n y N9 C4 ATP sing 172 n y C8 N7 ATP doub 173 n y C8 H8 ATP sing 174 n n N7 C5 ATP sing 175 n y C5 C6 ATP sing 176 n y C5 C4 ATP doub 177 n y C6 N6 ATP sing 178 n n C6 N1 ATP doub 179 n y N6 HN61 ATP sing 180 n n N6 HN62 ATP sing 181 n n N1 C2 ATP sing 182 n y C2 N3 ATP doub 183 n y C2 H2 ATP sing 184 n n N3 C4 ATP sing 185 n y # _atom_sites.entry_id 9IK1 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 D 2 A1L2M A 1 401 1 A1L2M KGR . E 3 ATP A 1 402 1 ATP ATP . F 4 NAG A 1 403 1 NAG NAG . G 4 NAG A 1 404 2 NAG NAG . H 4 NAG A 1 405 7 NAG NAG . I 5 MG A 1 406 3 MG MG . J 2 A1L2M B 1 401 2 A1L2M KGR . K 3 ATP B 1 402 2 ATP ATP . L 4 NAG B 1 403 3 NAG NAG . M 4 NAG B 1 404 4 NAG NAG . N 4 NAG B 1 405 8 NAG NAG . O 5 MG B 1 406 1 MG MG . P 2 A1L2M C 1 401 3 A1L2M KGR . Q 3 ATP C 1 402 3 ATP ATP . R 4 NAG C 1 403 5 NAG NAG . S 4 NAG C 1 404 6 NAG NAG . T 4 NAG C 1 405 9 NAG NAG . U 5 MG C 1 406 2 MG MG . # 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 . . . K 3 105.174 106.076 86.167 1 87.23 ? PG ATP 402 B 1 HETATM 2 O O1G ATP . . . K 3 105.728 107.461 86.334 1 87.23 ? O1G ATP 402 B 1 HETATM 3 O O2G ATP . . . K 3 104.837 105.69 84.754 1 87.23 ? O2G ATP 402 B 1 HETATM 4 O O3G ATP . . . K 3 104.111 105.731 87.161 1 87.23 ? O3G ATP 402 B 1 HETATM 5 P PB ATP . . . K 3 106.495 104.352 87.964 1 87.23 ? PB ATP 402 B 1 HETATM 6 O O1B ATP . . . K 3 105.323 103.421 88.085 1 87.23 ? O1B ATP 402 B 1 HETATM 7 O O2B ATP . . . K 3 107.88 103.79 88.096 1 87.23 ? O2B ATP 402 B 1 HETATM 8 O O3B ATP . . . K 3 106.402 105.12 86.558 1 87.23 ? O3B ATP 402 B 1 HETATM 9 P PA ATP . . . K 3 106.415 105.16 90.606 1 87.23 ? PA ATP 402 B 1 HETATM 10 O O1A ATP . . . K 3 107.437 106.026 91.282 1 87.23 ? O1A ATP 402 B 1 HETATM 11 O O2A ATP . . . K 3 106.485 103.665 90.693 1 87.23 ? O2A ATP 402 B 1 HETATM 12 O O3A ATP . . . K 3 106.346 105.522 89.046 1 87.23 ? O3A ATP 402 B 1 HETATM 13 O O5' ATP . . . K 3 104.957 105.618 91.084 1 87.23 ? O5' ATP 402 B 1 HETATM 14 C C5' ATP . . . K 3 104.123 104.747 91.837 1 87.23 ? C5' ATP 402 B 1 HETATM 15 C C4' ATP . . . K 3 102.681 105.016 91.441 1 87.23 ? C4' ATP 402 B 1 HETATM 16 O O4' ATP . . . K 3 102.308 106.322 91.861 1 87.23 ? O4' ATP 402 B 1 HETATM 17 C C3' ATP . . . K 3 102.514 104.975 89.938 1 87.23 ? C3' ATP 402 B 1 HETATM 18 O O3' ATP . . . K 3 101.498 104.035 89.606 1 87.23 ? O3' ATP 402 B 1 HETATM 19 C C2' ATP . . . K 3 102.045 106.346 89.522 1 87.23 ? C2' ATP 402 B 1 HETATM 20 O O2' ATP . . . K 3 100.907 106.21 88.676 1 87.23 ? O2' ATP 402 B 1 HETATM 21 C C1' ATP . . . K 3 101.666 107.037 90.81 1 87.23 ? C1' ATP 402 B 1 HETATM 22 N N9 ATP . . . K 3 102.145 108.435 90.824 1 87.23 ? N9 ATP 402 B 1 HETATM 23 C C8 ATP . . . K 3 103.422 108.812 90.965 1 87.23 ? C8 ATP 402 B 1 HETATM 24 N N7 ATP . . . K 3 103.536 110.158 90.949 1 87.23 ? N7 ATP 402 B 1 HETATM 25 C C5 ATP . . . K 3 102.306 110.662 90.795 1 87.23 ? C5 ATP 402 B 1 HETATM 26 C C6 ATP . . . K 3 101.717 112.008 90.695 1 87.23 ? C6 ATP 402 B 1 HETATM 27 N N6 ATP . . . K 3 102.493 113.107 90.76 1 87.23 ? N6 ATP 402 B 1 HETATM 28 N N1 ATP . . . K 3 100.386 112.103 90.538 1 87.23 ? N1 ATP 402 B 1 HETATM 29 C C2 ATP . . . K 3 99.608 111.015 90.472 1 87.23 ? C2 ATP 402 B 1 HETATM 30 N N3 ATP . . . K 3 100.074 109.762 90.555 1 87.23 ? N3 ATP 402 B 1 HETATM 31 C C4 ATP . . . K 3 101.392 109.523 90.713 1 87.23 ? C4 ATP 402 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #