data_8PML # _model_server_result.job_id mjfxFNhr-F9vZcGH8klCYg _model_server_result.datetime_utc '2024-12-03 08:54:11' _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 8pml # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":1001}' # _entry.id 8PML # _exptl.entry_id 8PML _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 8PML _cell.length_a 175.428 _cell.length_b 193.36 _cell.length_c 84.037 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PML _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 _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 I N N ? 2 K N N ? 2 M N N ? 2 O N N ? 2 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 metalc ? metalc1 A O ILE 76 A ILE 123 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc2 A OD1 ASP 121 A ASP 168 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc3 A OD2 ASP 121 A ASP 168 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.931 ? metalc ? metalc4 G O2G ATP . A ATP 1001 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc5 G O2B ATP . A ATP 1001 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc6 G O2A ATP . A ATP 1001 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc7 B O ILE 76 B ILE 123 1_555 J MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc8 B OD1 ASP 121 B ASP 168 1_555 J MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc9 B OD2 ASP 121 B ASP 168 1_555 J MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.768 ? metalc ? metalc10 I O2G ATP . B ATP 1001 1_555 J MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc11 I O2B ATP . B ATP 1001 1_555 J MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc12 I O2A ATP . B ATP 1001 1_555 J MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc13 C O ILE 76 C ILE 123 1_555 L MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc14 C OD1 ASP 121 C ASP 168 1_555 L MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc15 C OD2 ASP 121 C ASP 168 1_555 L MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.817 ? metalc ? metalc16 K O2G ATP . C ATP 1001 1_555 L MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc17 K O2B ATP . C ATP 1001 1_555 L MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc18 K O2A ATP . C ATP 1001 1_555 L MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc19 D O ILE 76 D ILE 123 1_555 N MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc20 D OD1 ASP 121 D ASP 168 1_555 N MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc21 M O2G ATP . D ATP 1001 1_555 N MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc22 M O2B ATP . D ATP 1001 1_555 N MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc23 M O2A ATP . D ATP 1001 1_555 N MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc24 E O ILE 76 E ILE 123 1_555 P MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc25 E OD1 ASP 121 E ASP 168 1_555 P MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? metalc ? metalc26 E OD2 ASP 121 E ASP 168 1_555 P MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? metalc ? metalc27 O O2G ATP . E ATP 1001 1_555 P MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc28 O O2B ATP . E ATP 1001 1_555 P MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc29 O O2A ATP . E ATP 1001 1_555 P MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc30 F O ILE 76 F ILE 123 1_555 R MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc31 F OD1 ASP 121 F ASP 168 1_555 R MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc32 F OD2 ASP 121 F ASP 168 1_555 R MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.757 ? metalc ? metalc33 Q O2G ATP . F ATP 1001 1_555 R MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc34 Q O2B ATP . F ATP 1001 1_555 R MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc35 Q O2A ATP . F ATP 1001 1_555 R MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? # _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 8PML _atom_sites.fract_transf_matrix[1][1] 0.0057 _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] 0.005172 _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] 0.0119 _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 2 ATP B 1 1001 1001 ATP ATP . J 3 MG B 1 1002 1002 MG MG . K 2 ATP C 1 1001 1001 ATP ATP . L 3 MG C 1 1002 1002 MG MG . M 2 ATP D 1 1001 1001 ATP ATP . N 3 MG D 1 1002 1002 MG MG . O 2 ATP E 1 1001 1001 ATP ATP . P 3 MG E 1 1002 1002 MG MG . Q 2 ATP F 1 1001 1001 ATP ATP . R 3 MG F 1 1002 1002 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 . . . Q 2 -37.802 50.51 -59.312 1 65.12 ? PG ATP 1001 F 1 HETATM 2 O O1G ATP . . . Q 2 -37.725 51.476 -58.156 1 44.63 ? O1G ATP 1001 F 1 HETATM 3 O O2G ATP . . . Q 2 -37.25 49.137 -59.041 1 56.15 ? O2G ATP 1001 F 1 HETATM 4 O O3G ATP . . . Q 2 -39.143 50.477 -59.995 1 47.81 ? O3G ATP 1001 F 1 HETATM 5 P PB ATP . . . Q 2 -35.217 50.956 -60.399 1 72.69 ? PB ATP 1001 F 1 HETATM 6 O O1B ATP . . . Q 2 -34.679 51.605 -61.654 1 62.82 ? O1B ATP 1001 F 1 HETATM 7 O O2B ATP . . . Q 2 -34.92 49.503 -60.15 1 53.35 ? O2B ATP 1001 F 1 HETATM 8 O O3B ATP . . . Q 2 -36.813 51.18 -60.393 1 64.36 ? O3B ATP 1001 F 1 HETATM 9 P PA ATP . . . Q 2 -33.94 51.24 -57.886 1 55.91 ? PA ATP 1001 F 1 HETATM 10 O O1A ATP . . . Q 2 -32.453 51.372 -58.117 1 46.62 ? O1A ATP 1001 F 1 HETATM 11 O O2A ATP . . . Q 2 -34.543 49.912 -57.496 1 52.38 ? O2A ATP 1001 F 1 HETATM 12 O O3A ATP . . . Q 2 -34.743 51.85 -59.146 1 52.26 ? O3A ATP 1001 F 1 HETATM 13 O O5' ATP . . . Q 2 -34.339 52.287 -56.736 1 53.07 ? O5' ATP 1001 F 1 HETATM 14 C C5' ATP . . . Q 2 -33.65 53.522 -56.59 1 56.75 ? C5' ATP 1001 F 1 HETATM 15 C C4' ATP . . . Q 2 -34.471 54.331 -55.599 1 50.16 ? C4' ATP 1001 F 1 HETATM 16 O O4' ATP . . . Q 2 -34.376 53.724 -54.313 1 45.54 ? O4' ATP 1001 F 1 HETATM 17 C C3' ATP . . . Q 2 -34.007 55.768 -55.434 1 65.79 ? C3' ATP 1001 F 1 HETATM 18 O O3' ATP . . . Q 2 -34.7 56.662 -56.312 1 63.98 ? O3' ATP 1001 F 1 HETATM 19 C C2' ATP . . . Q 2 -34.381 56.081 -54.005 1 60.01 ? C2' ATP 1001 F 1 HETATM 20 O O2' ATP . . . Q 2 -35.674 56.692 -54.022 1 58.97 ? O2' ATP 1001 F 1 HETATM 21 C C1' ATP . . . Q 2 -34.441 54.73 -53.306 1 48.33 ? C1' ATP 1001 F 1 HETATM 22 N N9 ATP . . . Q 2 -33.264 54.599 -52.407 1 51.88 ? N9 ATP 1001 F 1 HETATM 23 C C8 ATP . . . Q 2 -31.981 54.804 -52.761 1 53.84 ? C8 ATP 1001 F 1 HETATM 24 N N7 ATP . . . Q 2 -31.142 54.619 -51.708 1 62.64 ? N7 ATP 1001 F 1 HETATM 25 C C5 ATP . . . Q 2 -31.893 54.294 -50.641 1 45.09 ? C5 ATP 1001 F 1 HETATM 26 C C6 ATP . . . Q 2 -31.643 53.965 -49.216 1 47.63 ? C6 ATP 1001 F 1 HETATM 27 N N6 ATP . . . Q 2 -30.393 53.946 -48.695 1 53.89 ? N6 ATP 1001 F 1 HETATM 28 N N1 ATP . . . Q 2 -32.711 53.68 -48.443 1 53.53 ? N1 ATP 1001 F 1 HETATM 29 C C2 ATP . . . Q 2 -33.962 53.695 -48.943 1 57.73 ? C2 ATP 1001 F 1 HETATM 30 N N3 ATP . . . Q 2 -34.262 53.986 -50.223 1 60.24 ? N3 ATP 1001 F 1 HETATM 31 C C4 ATP . . . Q 2 -33.289 54.295 -51.108 1 50.1 ? C4 ATP 1001 F 1 # _model_server_stats.io_time_ms 86 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #