data_8PMG # _model_server_result.job_id 1PstrienY-_NGFdpWEZcpw _model_server_result.datetime_utc '2025-03-01 03:19:09' _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 8pmg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":1001}' # _entry.id 8PMG # _exptl.entry_id 8PMG _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 8PMG _cell.length_a 173.41 _cell.length_b 191.031 _cell.length_c 90.253 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PMG _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 _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 N N N ? 2 P N N ? 2 T N N ? 2 W 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 D SG CYS 291 D CYS 326 1_555 D SG CYS 291 D CYS 326 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc1 A O ILE 86 A ILE 121 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc2 G O2G ATP . A ATP 1001 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc3 G O2B ATP . A ATP 1001 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc4 G O2A ATP . A ATP 1001 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc5 B O ILE 86 B ILE 121 1_555 L MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc6 K O2G ATP . B ATP 1001 1_555 L MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.651 ? metalc ? metalc7 K O2B ATP . B ATP 1001 1_555 L MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc8 K O2A ATP . B ATP 1001 1_555 L MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc9 C O ILE 86 C ILE 121 1_555 O MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc10 C OD1 ASP 131 C ASP 166 1_555 O MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? metalc ? metalc11 N O2G ATP . C ATP 1001 1_555 O MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc12 N O2B ATP . C ATP 1001 1_555 O MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc13 N O2A ATP . C ATP 1001 1_555 O MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc14 D O ILE 86 D ILE 121 1_555 Q MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc15 D OD1 ASP 131 D ASP 166 1_555 Q MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.862 ? metalc ? metalc16 D OD2 ASP 131 D ASP 166 1_555 Q MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? metalc ? metalc17 P O2G ATP . D ATP 1001 1_555 Q MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? metalc ? metalc18 P O2B ATP . D ATP 1001 1_555 Q MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc19 P O2A ATP . D ATP 1001 1_555 Q MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc20 E O ILE 86 E ILE 121 1_555 U MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc21 E OD2 ASP 131 E ASP 166 1_555 U MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.962 ? metalc ? metalc22 T O2G ATP . E ATP 1001 1_555 U MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc23 T O2B ATP . E ATP 1001 1_555 U MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc24 T O2A ATP . E ATP 1001 1_555 U MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc25 F O ILE 86 F ILE 121 1_555 X MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc26 W O2G ATP . F ATP 1001 1_555 X MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? metalc ? metalc27 W O2B ATP . F ATP 1001 1_555 X MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc28 W O2A ATP . F ATP 1001 1_555 X MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? # _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 8PMG _atom_sites.fract_transf_matrix[1][1] 0.005767 _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] 0.005235 _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] 0.01108 _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 PO4 A 1 1003 6 PO4 PO4 . J 5 NA A 1 1004 1 NA NA . K 2 ATP B 1 1001 1001 ATP ATP . L 3 MG B 1 1002 1002 MG MG . M 4 PO4 B 1 1003 4 PO4 PO4 . N 2 ATP C 1 1001 1001 ATP ATP . O 3 MG C 1 1002 1002 MG MG . P 2 ATP D 1 1001 1001 ATP ATP . Q 3 MG D 1 1002 1002 MG MG . R 4 PO4 D 1 1003 2 PO4 PO4 . S 4 PO4 D 1 1004 5 PO4 PO4 . T 2 ATP E 1 1001 1001 ATP ATP . U 3 MG E 1 1002 1002 MG MG . V 4 PO4 E 1 1003 1 PO4 PO4 . W 2 ATP F 1 1001 1001 ATP ATP . X 3 MG F 1 1002 1002 MG MG . Y 4 PO4 F 1 1003 3 PO4 PO4 . # 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 . . . N 2 81.499 48.123 -11.392 1 59.05 ? PG ATP 1001 C 1 HETATM 2 O O1G ATP . . . N 2 81.81 47.117 -10.337 1 65.15 ? O1G ATP 1001 C 1 HETATM 3 O O2G ATP . . . N 2 80.336 49.055 -11.032 1 61.82 ? O2G ATP 1001 C 1 HETATM 4 O O3G ATP . . . N 2 81.236 47.505 -12.77 1 70.82 ? O3G ATP 1001 C 1 HETATM 5 P PB ATP . . . N 2 83.072 50.508 -12.288 1 76.66 ? PB ATP 1001 C 1 HETATM 6 O O1B ATP . . . N 2 84.477 50.909 -12.064 1 76.25 ? O1B ATP 1001 C 1 HETATM 7 O O2B ATP . . . N 2 82.016 51.5 -11.799 1 72.27 ? O2B ATP 1001 C 1 HETATM 8 O O3B ATP . . . N 2 82.741 49.102 -11.624 1 71.89 ? O3B ATP 1001 C 1 HETATM 9 P PA ATP . . . N 2 81.553 50.42 -14.826 1 64.28 ? PA ATP 1001 C 1 HETATM 10 O O1A ATP . . . N 2 81.683 51.675 -15.593 1 55.12 ? O1A ATP 1001 C 1 HETATM 11 O O2A ATP . . . N 2 80.268 50.281 -14.008 1 65.84 ? O2A ATP 1001 C 1 HETATM 12 O O3A ATP . . . N 2 82.77 50.215 -13.823 1 53.84 ? O3A ATP 1001 C 1 HETATM 13 O O5' ATP . . . N 2 81.658 49.148 -15.754 1 81.81 ? O5' ATP 1001 C 1 HETATM 14 C C5' ATP . . . N 2 82.253 49.221 -17.066 1 64.72 ? C5' ATP 1001 C 1 HETATM 15 C C4' ATP . . . N 2 82.056 47.881 -17.728 1 52.4 ? C4' ATP 1001 C 1 HETATM 16 O O4' ATP . . . N 2 80.796 47.867 -18.425 1 50.08 ? O4' ATP 1001 C 1 HETATM 17 C C3' ATP . . . N 2 83.077 47.519 -18.796 1 57.69 ? C3' ATP 1001 C 1 HETATM 18 O O3' ATP . . . N 2 84.251 46.972 -18.207 1 64.99 ? O3' ATP 1001 C 1 HETATM 19 C C2' ATP . . . N 2 82.32 46.478 -19.629 1 59.92 ? C2' ATP 1001 C 1 HETATM 20 O O2' ATP . . . N 2 82.489 45.163 -19.113 1 59.74 ? O2' ATP 1001 C 1 HETATM 21 C C1' ATP . . . N 2 80.857 46.925 -19.483 1 52.95 ? C1' ATP 1001 C 1 HETATM 22 N N9 ATP . . . N 2 80.295 47.537 -20.682 1 57.64 ? N9 ATP 1001 C 1 HETATM 23 C C8 ATP . . . N 2 80.82 48.571 -21.414 1 67.68 ? C8 ATP 1001 C 1 HETATM 24 N N7 ATP . . . N 2 80.094 48.917 -22.449 1 68.11 ? N7 ATP 1001 C 1 HETATM 25 C C5 ATP . . . N 2 79.013 48.049 -22.396 1 61.7 ? C5 ATP 1001 C 1 HETATM 26 C C6 ATP . . . N 2 77.877 47.894 -23.214 1 61.97 ? C6 ATP 1001 C 1 HETATM 27 N N6 ATP . . . N 2 77.63 48.642 -24.294 1 70.25 ? N6 ATP 1001 C 1 HETATM 28 N N1 ATP . . . N 2 76.99 46.93 -22.882 1 67.86 ? N1 ATP 1001 C 1 HETATM 29 C C2 ATP . . . N 2 77.23 46.179 -21.804 1 64.73 ? C2 ATP 1001 C 1 HETATM 30 N N3 ATP . . . N 2 78.263 46.233 -20.961 1 63.19 ? N3 ATP 1001 C 1 HETATM 31 C C4 ATP . . . N 2 79.124 47.193 -21.312 1 60.11 ? C4 ATP 1001 C 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #