data_8PMI # _model_server_result.job_id 4YDCtsRBnUlRKyDVZbIHKA _model_server_result.datetime_utc '2025-03-01 03:20:05' _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 8pmi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":1001}' # _entry.id 8PMI # _exptl.entry_id 8PMI _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 6 _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 8PMI _cell.length_a 174.276 _cell.length_b 189.186 _cell.length_c 89.922 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PMI _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall 'P 2 2ab' _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA _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 G N N ? 2 K N N ? 2 R N N ? 2 V N N ? 2 Z N N ? 2 CA 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 metalc ? metalc1 A O ILE 86 A ILE 121 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc2 A OD1 ASP 131 A ASP 166 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc3 G O2G ATP . A ATP 1001 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc4 G O2B ATP . A ATP 1001 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.835 ? metalc ? metalc5 G O2A ATP . A ATP 1001 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc6 B O ILE 86 B ILE 121 1_555 L MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc7 B OD1 ASP 131 B ASP 166 1_555 L MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc8 K O2G ATP . B ATP 1001 1_555 L MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc9 K O2B ATP . B ATP 1001 1_555 L MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? metalc ? metalc10 K O2A ATP . B ATP 1001 1_555 L MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.905 ? metalc ? metalc11 C O ILE 86 C ILE 121 1_555 S MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc12 C OD1 ASP 131 C ASP 166 1_555 S MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? metalc ? metalc13 R O2G ATP . C ATP 1001 1_555 S MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.878 ? metalc ? metalc14 R O2B ATP . C ATP 1001 1_555 S MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.857 ? metalc ? metalc15 R O2A ATP . C ATP 1001 1_555 S MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc16 D O ILE 86 D ILE 121 1_555 W MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc17 D OD2 ASP 131 D ASP 166 1_555 W MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.941 ? metalc ? metalc18 V O2G ATP . D ATP 1001 1_555 W MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc19 V O2A ATP . D ATP 1001 1_555 W MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? metalc ? metalc20 E O ILE 86 E ILE 121 1_555 AA MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? metalc ? metalc21 E OD1 ASP 131 E ASP 166 1_555 AA MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc22 E OD2 ASP 131 E ASP 166 1_555 AA MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.743 ? metalc ? metalc23 Z O2B ATP . E ATP 1001 1_555 AA MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.863 ? metalc ? metalc24 Z O2A ATP . E ATP 1001 1_555 AA MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.93 ? metalc ? metalc25 F O ILE 86 F ILE 121 1_555 DA MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc26 F OD1 ASP 131 F ASP 166 1_555 DA MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc27 CA O2G ATP . F ATP 1001 1_555 DA MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.859 ? metalc ? metalc28 CA O2B ATP . F ATP 1001 1_555 DA MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc29 CA O2A ATP . F ATP 1001 1_555 DA MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? # _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 8PMI _atom_sites.fract_transf_matrix[1][1] 0.005738 _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] 0.005286 _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] 0.011121 _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 G 2 ATP A 1 1001 1001 ATP ATP . H 3 MG A 1 1002 1002 MG MG . I 4 SO4 A 1 1003 6 SO4 SO4 . J 4 SO4 A 1 1004 7 SO4 SO4 . K 2 ATP B 1 1001 1001 ATP ATP . L 3 MG B 1 1002 1002 MG MG . M 3 MG B 1 1003 1 MG MG . N 4 SO4 B 1 1004 2 SO4 SO4 . O 4 SO4 B 1 1005 8 SO4 SO4 . P 4 SO4 B 1 1006 10 SO4 SO4 . Q 4 SO4 B 1 1007 12 SO4 SO4 . R 2 ATP C 1 1001 1001 ATP ATP . S 3 MG C 1 1002 1002 MG MG . T 4 SO4 C 1 1003 1 SO4 SO4 . U 4 SO4 C 1 1004 3 SO4 SO4 . V 2 ATP D 1 1001 1001 ATP ATP . W 3 MG D 1 1002 1002 MG MG . X 4 SO4 D 1 1003 4 SO4 SO4 . Y 4 SO4 D 1 1004 5 SO4 SO4 . Z 2 ATP E 1 1001 1001 ATP ATP . AA 3 MG E 1 1002 1002 MG MG . BA 5 NH4 E 1 1003 1003 NH4 NH4 . CA 2 ATP F 1 1001 1001 ATP ATP . DA 3 MG F 1 1002 1002 MG MG . EA 4 SO4 F 1 1003 9 SO4 SO4 . FA 4 SO4 F 1 1004 11 SO4 SO4 . # 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 2 25.21 4.725 -3.442 1 59.95 ? PG ATP 1001 B 1 HETATM 2 O O1G ATP . . . K 2 25.08 5.142 -4.87 1 49.11 ? O1G ATP 1001 B 1 HETATM 3 O O2G ATP . . . K 2 24.102 5.289 -2.525 1 55.48 ? O2G ATP 1001 B 1 HETATM 4 O O3G ATP . . . K 2 26.562 5.026 -2.808 1 51.17 ? O3G ATP 1001 B 1 HETATM 5 P PB ATP . . . K 2 24.078 2.105 -2.722 1 57.13 ? PB ATP 1001 B 1 HETATM 6 O O1B ATP . . . K 2 23.742 1.037 -3.677 1 57.75 ? O1B ATP 1001 B 1 HETATM 7 O O2B ATP . . . K 2 22.923 2.909 -2.125 1 44.83 ? O2B ATP 1001 B 1 HETATM 8 O O3B ATP . . . K 2 25.06 3.16 -3.322 1 48.92 ? O3B ATP 1001 B 1 HETATM 9 P PA ATP . . . K 2 25.585 2.152 -0.222 1 53.08 ? PA ATP 1001 B 1 HETATM 10 O O1A ATP . . . K 2 25.233 1.357 0.973 1 49.27 ? O1A ATP 1001 B 1 HETATM 11 O O2A ATP . . . K 2 25.175 3.629 -0.195 1 51.84 ? O2A ATP 1001 B 1 HETATM 12 O O3A ATP . . . K 2 24.932 1.553 -1.502 1 34.31 ? O3A ATP 1001 B 1 HETATM 13 O O5' ATP . . . K 2 27.121 2.04 -0.56 1 46.44 ? O5' ATP 1001 B 1 HETATM 14 C C5' ATP . . . K 2 27.956 1.053 0.079 1 42.45 ? C5' ATP 1001 B 1 HETATM 15 C C4' ATP . . . K 2 29.402 1.385 -0.188 1 37.48 ? C4' ATP 1001 B 1 HETATM 16 O O4' ATP . . . K 2 29.933 2.173 0.899 1 43.9 ? O4' ATP 1001 B 1 HETATM 17 C C3' ATP . . . K 2 30.339 0.19 -0.296 1 35.82 ? C3' ATP 1001 B 1 HETATM 18 O O3' ATP . . . K 2 30.322 -0.331 -1.62 1 54.35 ? O3' ATP 1001 B 1 HETATM 19 C C2' ATP . . . K 2 31.692 0.812 0.056 1 41.51 ? C2' ATP 1001 B 1 HETATM 20 O O2' ATP . . . K 2 32.298 1.443 -1.066 1 44.34 ? O2' ATP 1001 B 1 HETATM 21 C C1' ATP . . . K 2 31.297 1.847 1.116 1 38.37 ? C1' ATP 1001 B 1 HETATM 22 N N9 ATP . . . K 2 31.449 1.374 2.488 1 35.09 ? N9 ATP 1001 B 1 HETATM 23 C C8 ATP . . . K 2 31.025 0.175 3 1 43.59 ? C8 ATP 1001 B 1 HETATM 24 N N7 ATP . . . K 2 31.304 0.006 4.269 1 49.69 ? N7 ATP 1001 B 1 HETATM 25 C C5 ATP . . . K 2 31.962 1.176 4.62 1 42.93 ? C5 ATP 1001 B 1 HETATM 26 C C6 ATP . . . K 2 32.52 1.626 5.832 1 42.77 ? C6 ATP 1001 B 1 HETATM 27 N N6 ATP . . . K 2 32.503 0.918 6.967 1 54.42 ? N6 ATP 1001 B 1 HETATM 28 N N1 ATP . . . K 2 33.105 2.844 5.841 1 36.96 ? N1 ATP 1001 B 1 HETATM 29 C C2 ATP . . . K 2 33.126 3.555 4.71 1 47.52 ? C2 ATP 1001 B 1 HETATM 30 N N3 ATP . . . K 2 32.633 3.234 3.511 1 49.79 ? N3 ATP 1001 B 1 HETATM 31 C C4 ATP . . . K 2 32.06 2.028 3.531 1 40.29 ? C4 ATP 1001 B 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 88 _model_server_stats.create_model_time_ms 150 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #