data_8PMI # _model_server_result.job_id rvgbMFAeCEAIasV4nChZZw _model_server_result.datetime_utc '2025-03-01 03:39:55' _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":"Z","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 . . . Z 2 34.976 50.206 59.786 1 111.72 ? PG ATP 1001 E 1 HETATM 2 O O1G ATP . . . Z 2 34.852 50.234 58.3 1 108.24 ? O1G ATP 1001 E 1 HETATM 3 O O2G ATP . . . Z 2 35.476 48.863 60.336 1 104.06 ? O2G ATP 1001 E 1 HETATM 4 O O3G ATP . . . Z 2 35.838 51.342 60.358 1 102.1 ? O3G ATP 1001 E 1 HETATM 5 P PB ATP . . . Z 2 32.379 49.546 61.12 1 98.1 ? PB ATP 1001 E 1 HETATM 6 O O1B ATP . . . Z 2 32.216 49.857 62.553 1 107.37 ? O1B ATP 1001 E 1 HETATM 7 O O2B ATP . . . Z 2 32.646 48.078 60.791 1 89.49 ? O2B ATP 1001 E 1 HETATM 8 O O3B ATP . . . Z 2 33.546 50.406 60.465 1 98.68 ? O3B ATP 1001 E 1 HETATM 9 P PA ATP . . . Z 2 30.831 50.381 58.744 1 85.3 ? PA ATP 1001 E 1 HETATM 10 O O1A ATP . . . Z 2 29.434 50.079 58.368 1 84.69 ? O1A ATP 1001 E 1 HETATM 11 O O2A ATP . . . Z 2 31.917 49.698 57.912 1 100.81 ? O2A ATP 1001 E 1 HETATM 12 O O3A ATP . . . Z 2 31.12 50.005 60.259 1 96.87 ? O3A ATP 1001 E 1 HETATM 13 O O5' ATP . . . Z 2 31.091 51.937 58.701 1 88.75 ? O5' ATP 1001 E 1 HETATM 14 C C5' ATP . . . Z 2 30.23 52.818 57.95 1 85.33 ? C5' ATP 1001 E 1 HETATM 15 C C4' ATP . . . Z 2 31.031 53.413 56.822 1 76.33 ? C4' ATP 1001 E 1 HETATM 16 O O4' ATP . . . Z 2 30.753 52.697 55.604 1 85.19 ? O4' ATP 1001 E 1 HETATM 17 C C3' ATP . . . Z 2 30.709 54.863 56.49 1 89.46 ? C3' ATP 1001 E 1 HETATM 18 O O3' ATP . . . Z 2 31.421 55.754 57.34 1 106.81 ? O3' ATP 1001 E 1 HETATM 19 C C2' ATP . . . Z 2 31.177 54.978 55.037 1 95.93 ? C2' ATP 1001 E 1 HETATM 20 O O2' ATP . . . Z 2 32.555 55.324 54.95 1 105.1 ? O2' ATP 1001 E 1 HETATM 21 C C1' ATP . . . Z 2 30.928 53.562 54.494 1 102.25 ? C1' ATP 1001 E 1 HETATM 22 N N9 ATP . . . Z 2 29.756 53.454 53.631 1 112.19 ? N9 ATP 1001 E 1 HETATM 23 C C8 ATP . . . Z 2 28.453 53.726 53.96 1 112.55 ? C8 ATP 1001 E 1 HETATM 24 N N7 ATP . . . Z 2 27.603 53.545 52.979 1 120.85 ? N7 ATP 1001 E 1 HETATM 25 C C5 ATP . . . Z 2 28.402 53.123 51.927 1 120.65 ? C5 ATP 1001 E 1 HETATM 26 C C6 ATP . . . Z 2 28.111 52.763 50.596 1 117.44 ? C6 ATP 1001 E 1 HETATM 27 N N6 ATP . . . Z 2 26.88 52.769 50.075 1 121.84 ? N6 ATP 1001 E 1 HETATM 28 N N1 ATP . . . Z 2 29.142 52.391 49.806 1 110.71 ? N1 ATP 1001 E 1 HETATM 29 C C2 ATP . . . Z 2 30.375 52.382 50.319 1 111.92 ? C2 ATP 1001 E 1 HETATM 30 N N3 ATP . . . Z 2 30.77 52.7 51.554 1 115.49 ? N3 ATP 1001 E 1 HETATM 31 C C4 ATP . . . Z 2 29.732 53.064 52.314 1 117.7 ? C4 ATP 1001 E 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #