data_3RU3 # _model_server_result.job_id MVuop8EkQu_-WxOyzwEUrw _model_server_result.datetime_utc '2024-11-14 23:54:45' _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 3ru3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":494}' # _entry.id 3RU3 # _exptl.entry_id 3RU3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 3RU3 _cell.length_a 120.943 _cell.length_b 120.943 _cell.length_c 154.802 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RU3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexadecameric _pdbx_struct_assembly.oligomeric_count 16 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 5 'crystal symmetry operation' 5_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 6 'crystal symmetry operation' 6_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 7 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 8 'crystal symmetry operation' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 OD1 ASN 64 A ASN 52 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? metalc ? metalc2 A O ASP 126 A ASP 114 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? metalc ? metalc3 A OD1 ASP 126 A ASP 114 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.498 ? metalc ? metalc4 A O PHE 129 A PHE 117 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.964 ? metalc ? metalc5 A O VAL 158 A VAL 146 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.246 ? metalc ? metalc6 A O VAL 160 A VAL 148 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.935 ? metalc ? metalc7 A OG SER 162 A SER 150 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.928 ? metalc ? metalc8 D MG MG . A MG 492 1_555 F O1B ATP . A ATP 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc9 D MG MG . A MG 492 1_555 H O HOH . A HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.953 ? # _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 3RU3 _atom_sites.fract_transf_matrix[1][1] 0.008268 _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] 0.008268 _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] 0.00646 _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 C 3 K A 1 491 1 K K . D 4 MG A 1 492 2 MG MG . E 5 NDP A 1 493 3 NDP NDP . F 6 ATP A 1 494 4 ATP ATP . G 7 NPW A 1 495 5 NPW NPW . H 8 HOH A 1 496 1 HOH HOH . H 8 HOH A 2 497 2 HOH HOH . H 8 HOH A 3 498 3 HOH HOH . H 8 HOH A 4 499 4 HOH HOH . H 8 HOH A 5 500 5 HOH HOH . H 8 HOH A 6 501 7 HOH HOH . H 8 HOH A 7 502 8 HOH HOH . H 8 HOH A 8 503 9 HOH HOH . H 8 HOH A 9 504 10 HOH HOH . H 8 HOH A 10 505 11 HOH HOH . H 8 HOH A 11 506 12 HOH HOH . H 8 HOH A 12 507 13 HOH HOH . H 8 HOH A 13 508 14 HOH HOH . H 8 HOH A 14 509 15 HOH HOH . H 8 HOH A 15 510 16 HOH HOH . H 8 HOH A 16 511 17 HOH HOH . H 8 HOH A 17 512 18 HOH HOH . H 8 HOH A 18 513 19 HOH HOH . H 8 HOH A 19 514 20 HOH HOH . H 8 HOH A 20 515 21 HOH HOH . H 8 HOH A 21 516 22 HOH HOH . H 8 HOH A 22 517 23 HOH HOH . H 8 HOH A 23 518 24 HOH HOH . H 8 HOH A 24 519 25 HOH HOH . H 8 HOH A 25 520 26 HOH HOH . H 8 HOH A 26 521 27 HOH HOH . I 8 HOH B 1 8 6 HOH HOH . # 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 PB ATP . . . F 6 -21.134 5.334 -41.377 1 72.43 ? PB ATP 494 A 1 HETATM 2 O O1B ATP . . . F 6 -21.441 4.246 -42.432 1 70.43 ? O1B ATP 494 A 1 HETATM 3 O O2B ATP . . . F 6 -20.954 6.765 -41.836 1 73.77 ? O2B ATP 494 A 1 HETATM 4 O O3B ATP . . . F 6 -19.918 4.744 -40.53 1 68.38 ? O3B ATP 494 A 1 HETATM 5 P PA ATP . . . F 6 -23.674 5.033 -40.044 1 72.78 ? PA ATP 494 A 1 HETATM 6 O O1A ATP . . . F 6 -24.014 4.108 -41.216 1 67.32 ? O1A ATP 494 A 1 HETATM 7 O O2A ATP . . . F 6 -24.347 6.351 -39.632 1 71.47 ? O2A ATP 494 A 1 HETATM 8 O O3A ATP . . . F 6 -22.129 5.546 -40.125 1 72.67 ? O3A ATP 494 A 1 HETATM 9 O O5' ATP . . . F 6 -23.603 4.059 -38.744 1 76.79 ? O5' ATP 494 A 1 HETATM 10 C C5' ATP . . . F 6 -23.242 4.684 -37.494 1 82.45 ? C5' ATP 494 A 1 HETATM 11 C C4' ATP . . . F 6 -23.26 3.8 -36.232 1 84.71 ? C4' ATP 494 A 1 HETATM 12 O O4' ATP . . . F 6 -22.838 4.623 -35.132 1 86.94 ? O4' ATP 494 A 1 HETATM 13 C C3' ATP . . . F 6 -24.664 3.313 -35.86 1 85.87 ? C3' ATP 494 A 1 HETATM 14 O O3' ATP . . . F 6 -24.685 2.004 -35.296 1 85.62 ? O3' ATP 494 A 1 HETATM 15 C C2' ATP . . . F 6 -25.207 4.276 -34.823 1 87.8 ? C2' ATP 494 A 1 HETATM 16 O O2' ATP . . . F 6 -25.992 3.658 -33.794 1 88.99 ? O2' ATP 494 A 1 HETATM 17 C C1' ATP . . . F 6 -23.944 4.844 -34.206 1 89.29 ? C1' ATP 494 A 1 HETATM 18 N N9 ATP . . . F 6 -24.157 6.273 -33.779 1 90.95 ? N9 ATP 494 A 1 HETATM 19 C C8 ATP . . . F 6 -24.286 7.389 -34.543 1 91.43 ? C8 ATP 494 A 1 HETATM 20 N N7 ATP . . . F 6 -24.447 8.476 -33.747 1 91.48 ? N7 ATP 494 A 1 HETATM 21 C C5 ATP . . . F 6 -24.424 8.063 -32.46 1 91.54 ? C5 ATP 494 A 1 HETATM 22 C C6 ATP . . . F 6 -24.549 8.674 -31.107 1 93.31 ? C6 ATP 494 A 1 HETATM 23 N N6 ATP . . . F 6 -24.734 10.013 -30.964 1 95.38 ? N6 ATP 494 A 1 HETATM 24 N N1 ATP . . . F 6 -24.488 7.863 -30.015 1 91.55 ? N1 ATP 494 A 1 HETATM 25 C C2 ATP . . . F 6 -24.326 6.526 -30.129 1 90.7 ? C2 ATP 494 A 1 HETATM 26 N N3 ATP . . . F 6 -24.214 5.905 -31.319 1 89.74 ? N3 ATP 494 A 1 HETATM 27 C C4 ATP . . . F 6 -24.248 6.607 -32.487 1 90.99 ? C4 ATP 494 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #