data_5X9H # _model_server_result.job_id i2icA6dFZLqZ3IxEBQuNAg _model_server_result.datetime_utc '2024-10-15 11:27:57' _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 5x9h # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5X9H # _exptl.entry_id 5X9H _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.02 _cell.angle_gamma 90 _cell.entry_id 5X9H _cell.length_a 135.33 _cell.length_b 85.651 _cell.length_c 156.558 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5X9H _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 C N N ? 2 L 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 OD2 ASP 114 A ASP 91 1_555 G MG MG . A MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.727 ? metalc ? metalc2 A OD1 ASP 118 A ASP 95 1_555 I MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc3 A OD2 ASP 118 A ASP 95 1_555 I MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.67 ? metalc ? metalc4 A O GLY 159 A GLY 136 1_555 I MG MG . A MG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.815 ? metalc ? metalc5 A O ALA 246 A ALA 223 1_555 H MG MG . A MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc6 A OD1 ASP 249 A ASP 226 1_555 H MG MG . A MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc7 A OD2 ASP 249 A ASP 226 1_555 K MG MG . A MG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.95 ? metalc ? metalc8 A OD2 ASP 270 A ASP 247 1_555 G MG MG . A MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.666 ? metalc ? metalc9 A OD1 ASP 282 A ASP 259 1_555 F MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc10 B OD2 ASP 114 B ASP 91 1_555 P MG MG . B MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc11 B OD1 ASP 118 B ASP 95 1_555 Q MG MG . B MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc12 B OD2 ASP 118 B ASP 95 1_555 Q MG MG . B MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? metalc ? metalc13 B O GLY 159 B GLY 136 1_555 Q MG MG . B MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc14 B O ALA 246 B ALA 223 1_555 M MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc15 B OD1 ASP 249 B ASP 226 1_555 M MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc16 B OD2 ASP 270 B ASP 247 1_555 P MG MG . B MG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc17 B OD1 ASP 282 B ASP 259 1_555 O MG MG . B MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? # _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 5X9H _atom_sites.fract_transf_matrix[1][1] 0.007389 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001306 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011675 _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] 0.006486 _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 2 ATP A 1 501 2 ATP ATP . D 3 MG A 1 502 1001 MG MG . E 3 MG A 1 503 1002 MG MG . F 3 MG A 1 504 1003 MG MG . G 3 MG A 1 505 1004 MG MG . H 3 MG A 1 506 1005 MG MG . I 3 MG A 1 507 1006 MG MG . J 3 MG A 1 508 1008 MG MG . K 3 MG A 1 509 1013 MG MG . L 2 ATP B 1 501 1 ATP ATP . M 3 MG B 1 502 1007 MG MG . N 3 MG B 1 503 1009 MG MG . O 3 MG B 1 504 1010 MG MG . P 3 MG B 1 505 1011 MG MG . Q 3 MG B 1 506 1012 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 . . . C 2 10.143 10.17 157.874 1 214.36 ? PG ATP 501 A 1 HETATM 2 O O1G ATP . . . C 2 10.098 11.101 156.688 1 190.13 ? O1G ATP 501 A 1 HETATM 3 O O2G ATP . . . C 2 10.867 10.684 159.1 1 198.93 ? O2G ATP 501 A 1 HETATM 4 O O3G ATP . . . C 2 10.502 8.768 157.452 1 203.45 ? O3G ATP 501 A 1 HETATM 5 P PB ATP . . . C 2 8.121 9.082 159.58 1 213.26 ? PB ATP 501 A 1 HETATM 6 O O1B ATP . . . C 2 6.613 8.927 159.476 1 159.91 ? O1B ATP 501 A 1 HETATM 7 O O2B ATP . . . C 2 8.787 9.566 160.862 1 166.6 ? O2B ATP 501 A 1 HETATM 8 O O3B ATP . . . C 2 8.608 10.05 158.37 1 176.21 ? O3B ATP 501 A 1 HETATM 9 P PA ATP . . . C 2 7.92 6.62 158.248 1 138.61 ? PA ATP 501 A 1 HETATM 10 O O1A ATP . . . C 2 7.458 7.446 157.082 1 126.19 ? O1A ATP 501 A 1 HETATM 11 O O2A ATP . . . C 2 6.978 5.746 159.044 1 127.95 ? O2A ATP 501 A 1 HETATM 12 O O3A ATP . . . C 2 8.733 7.638 159.196 1 147.86 ? O3A ATP 501 A 1 HETATM 13 O O5' ATP . . . C 2 9.085 5.71 157.657 1 117.05 ? O5' ATP 501 A 1 HETATM 14 C C5' ATP . . . C 2 9.743 4.777 158.475 1 126.09 ? C5' ATP 501 A 1 HETATM 15 C C4' ATP . . . C 2 11.17 5.254 158.338 1 130.57 ? C4' ATP 501 A 1 HETATM 16 O O4' ATP . . . C 2 11.962 4.441 159.173 1 141.63 ? O4' ATP 501 A 1 HETATM 17 C C3' ATP . . . C 2 11.686 5.084 156.924 1 130.55 ? C3' ATP 501 A 1 HETATM 18 O O3' ATP . . . C 2 12.513 6.209 156.654 1 123.87 ? O3' ATP 501 A 1 HETATM 19 C C2' ATP . . . C 2 12.515 3.814 156.931 1 133.86 ? C2' ATP 501 A 1 HETATM 20 O O2' ATP . . . C 2 13.785 3.994 156.31 1 141.08 ? O2' ATP 501 A 1 HETATM 21 C C1' ATP . . . C 2 12.819 3.603 158.388 1 131.28 ? C1' ATP 501 A 1 HETATM 22 N N9 ATP . . . C 2 12.67 2.2 158.85 1 116.01 ? N9 ATP 501 A 1 HETATM 23 C C8 ATP . . . C 2 11.535 1.534 159.182 1 109.2 ? C8 ATP 501 A 1 HETATM 24 N N7 ATP . . . C 2 11.803 0.277 159.629 1 107.44 ? N7 ATP 501 A 1 HETATM 25 C C5 ATP . . . C 2 13.142 0.159 159.586 1 108.34 ? C5 ATP 501 A 1 HETATM 26 C C6 ATP . . . C 2 14.11 -0.892 159.895 1 109.66 ? C6 ATP 501 A 1 HETATM 27 N N6 ATP . . . C 2 13.643 -2.07 160.349 1 120.35 ? N6 ATP 501 A 1 HETATM 28 N N1 ATP . . . C 2 15.424 -0.637 159.706 1 110.93 ? N1 ATP 501 A 1 HETATM 29 C C2 ATP . . . C 2 15.86 0.553 159.261 1 111.84 ? C2 ATP 501 A 1 HETATM 30 N N3 ATP . . . C 2 15.042 1.567 158.957 1 111.31 ? N3 ATP 501 A 1 HETATM 31 C C4 ATP . . . C 2 13.707 1.418 159.089 1 109.83 ? C4 ATP 501 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #