data_5F8M # _model_server_result.job_id NM-PrpYGitzigiR8RmnxBg _model_server_result.datetime_utc '2024-10-20 03:33:01' _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 5f8m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1005}' # _entry.id 5F8M # _exptl.entry_id 5F8M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 175.959 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PYROPHOSPHATE 2-' _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 5F8M _cell.length_a 63.64 _cell.length_b 76.71 _cell.length_c 150.104 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5F8M _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id H _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 OD2 ASP 233 A ASP 233 1_555 D MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.677 ? metalc ? metalc2 A OD1 ASP 233 A ASP 233 1_555 E MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc3 A O TYR 234 A TYR 234 1_555 D MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc4 A NE2 HIS 271 A HIS 271 1_555 F ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.914 ? metalc ? metalc5 A NE2 HIS 273 A HIS 273 1_555 F ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc6 A SG CYS 282 A CYS 282 1_555 F ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc7 A OD2 ASP 329 A ASP 329 1_555 D MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? metalc ? metalc8 A OD1 ASP 330 A ASP 330 1_555 E MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc9 A OE1 GLU 343 A GLU 343 1_555 F ZN ZN . A ZN 1003 4_545 ? ? ? ? ? ? ? ? ? ? ? ? 1.816 ? metalc ? metalc10 D MG MG . A MG 1001 1_555 H O2 POP . A POP 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc11 D MG MG . A MG 1001 1_555 C OP1 U 19 C U 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc12 E MG MG . A MG 1002 1_555 C O3' C 18 C C 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.84 ? metalc ? metalc13 E MG MG . A MG 1002 1_555 C OP1 U 19 C U 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? hydrog WATSON-CRICK hydrog1 B N1 A 18 B A 600 1_555 C N3 U 19 C U 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N6 A 18 B A 600 1_555 C O4 U 19 C U 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N1 G 19 B G 601 1_555 C N3 C 18 C C 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N2 G 19 B G 601 1_555 C O2 C 18 C C 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O6 G 19 B G 601 1_555 C N4 C 18 C C 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 G 20 B G 602 1_555 C N3 C 17 C C 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N2 G 20 B G 602 1_555 C O2 C 17 C C 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O6 G 20 B G 602 1_555 C N4 C 17 C C 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 U 21 B U 603 1_555 C N1 A 16 C A 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O4 U 21 B U 603 1_555 C N6 A 16 C A 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N3 C 22 B C 604 1_555 C N1 G 15 C G 698 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N4 C 22 B C 604 1_555 C O6 G 15 C G 698 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O2 C 22 B C 604 1_555 C N2 G 15 C G 698 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N3 U 23 B U 605 1_555 C N1 A 14 C A 697 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O4 U 23 B U 605 1_555 C N6 A 14 C A 697 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N3 C 24 B C 606 1_555 C N1 G 13 C G 696 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N4 C 24 B C 606 1_555 C O6 G 13 C G 696 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O2 C 24 B C 606 1_555 C N2 G 13 C G 696 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 U 25 B U 607 1_555 C N1 A 12 C A 695 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O4 U 25 B U 607 1_555 C N6 A 12 C A 695 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N3 C 26 B C 608 1_555 C N1 G 11 C G 694 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N4 C 26 B C 608 1_555 C O6 G 11 C G 694 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O2 C 26 B C 608 1_555 C N2 G 11 C G 694 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N3 U 27 B U 609 1_555 C N1 A 10 C A 693 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B O4 U 27 B U 609 1_555 C N6 A 10 C A 693 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'H2 O7 P2 -2' _chem_comp.formula_weight 175.959 _chem_comp.id POP _chem_comp.mon_nstd_flag . _chem_comp.name 'PYROPHOSPHATE 2-' _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 P1 O1 POP doub 388 n n P1 O2 POP sing 389 n n P1 O3 POP sing 390 n n P1 O POP sing 391 n n O2 HO2 POP sing 392 n n O P2 POP sing 393 n n P2 O4 POP doub 394 n n P2 O5 POP sing 395 n n P2 O6 POP sing 396 n n O5 HO5 POP sing 397 n n # _atom_sites.entry_id 5F8M _atom_sites.fract_transf_matrix[1][1] 0.015713 _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] 0.013036 _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] 0.006662 _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 D 4 MG A 1 1001 1001 MG MG . E 4 MG A 1 1002 1002 MG MG . F 5 ZN A 1 1003 2001 ZN ZN . G 6 SO4 A 1 1004 2 SO4 SO4 . H 7 POP A 1 1005 1 POP POP . I 8 GOL B 1 701 125 GOL GOL . J 9 HOH A 1 1101 31 HOH HOH . J 9 HOH A 2 1102 39 HOH HOH . J 9 HOH A 3 1103 60 HOH HOH . J 9 HOH A 4 1104 7 HOH HOH . J 9 HOH A 5 1105 21 HOH HOH . J 9 HOH A 6 1106 29 HOH HOH . J 9 HOH A 7 1107 46 HOH HOH . J 9 HOH A 8 1108 27 HOH HOH . J 9 HOH A 9 1109 59 HOH HOH . J 9 HOH A 10 1110 78 HOH HOH . J 9 HOH A 11 1111 43 HOH HOH . J 9 HOH A 12 1112 32 HOH HOH . J 9 HOH A 13 1113 11 HOH HOH . J 9 HOH A 14 1114 70 HOH HOH . J 9 HOH A 15 1115 71 HOH HOH . J 9 HOH A 16 1116 12 HOH HOH . J 9 HOH A 17 1117 19 HOH HOH . J 9 HOH A 18 1118 24 HOH HOH . J 9 HOH A 19 1119 44 HOH HOH . J 9 HOH A 20 1120 2 HOH HOH . J 9 HOH A 21 1121 9 HOH HOH . J 9 HOH A 22 1122 65 HOH HOH . J 9 HOH A 23 1123 23 HOH HOH . J 9 HOH A 24 1124 56 HOH HOH . J 9 HOH A 25 1125 42 HOH HOH . J 9 HOH A 26 1126 36 HOH HOH . J 9 HOH A 27 1127 15 HOH HOH . J 9 HOH A 28 1128 4 HOH HOH . J 9 HOH A 29 1129 8 HOH HOH . J 9 HOH A 30 1130 48 HOH HOH . J 9 HOH A 31 1131 30 HOH HOH . J 9 HOH A 32 1132 14 HOH HOH . J 9 HOH A 33 1133 45 HOH HOH . J 9 HOH A 34 1134 26 HOH HOH . J 9 HOH A 35 1135 13 HOH HOH . J 9 HOH A 36 1136 57 HOH HOH . J 9 HOH A 37 1137 3 HOH HOH . J 9 HOH A 38 1138 28 HOH HOH . J 9 HOH A 39 1139 20 HOH HOH . J 9 HOH A 40 1140 22 HOH HOH . J 9 HOH A 41 1141 54 HOH HOH . J 9 HOH A 42 1142 5 HOH HOH . J 9 HOH A 43 1143 66 HOH HOH . J 9 HOH A 44 1144 63 HOH HOH . J 9 HOH A 45 1145 33 HOH HOH . J 9 HOH A 46 1146 50 HOH HOH . J 9 HOH A 47 1147 51 HOH HOH . J 9 HOH A 48 1148 40 HOH HOH . J 9 HOH A 49 1149 73 HOH HOH . J 9 HOH A 50 1150 38 HOH HOH . J 9 HOH A 51 1151 25 HOH HOH . J 9 HOH A 52 1152 10 HOH HOH . J 9 HOH A 53 1153 16 HOH HOH . J 9 HOH A 54 1154 1 HOH HOH . J 9 HOH A 55 1155 37 HOH HOH . J 9 HOH A 56 1156 41 HOH HOH . J 9 HOH A 57 1157 74 HOH HOH . J 9 HOH A 58 1158 47 HOH HOH . J 9 HOH A 59 1159 49 HOH HOH . J 9 HOH A 60 1160 6 HOH HOH . J 9 HOH A 61 1161 34 HOH HOH . J 9 HOH A 62 1162 53 HOH HOH . J 9 HOH A 63 1163 79 HOH HOH . J 9 HOH A 64 1164 52 HOH HOH . J 9 HOH A 65 1165 35 HOH HOH . J 9 HOH A 66 1166 76 HOH HOH . J 9 HOH A 67 1167 75 HOH HOH . J 9 HOH A 68 1168 72 HOH HOH . J 9 HOH A 69 1169 64 HOH HOH . J 9 HOH A 70 1170 58 HOH HOH . K 9 HOH B 1 801 68 HOH HOH . K 9 HOH B 2 802 55 HOH HOH . K 9 HOH B 3 803 17 HOH HOH . K 9 HOH B 4 804 67 HOH HOH . K 9 HOH B 5 805 62 HOH HOH . K 9 HOH B 6 806 61 HOH HOH . L 9 HOH C 1 801 69 HOH HOH . L 9 HOH C 2 802 77 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 P1 POP . . . H 7 -7.923 -9.627 9.758 0.65 42.71 ? P1 POP 1005 A 1 HETATM 2 O O1 POP . . . H 7 -9.294 -9.296 9.268 0.65 51.26 ? O1 POP 1005 A 1 HETATM 3 O O2 POP . . . H 7 -7.845 -11.127 9.68 0.65 46.01 ? O2 POP 1005 A 1 HETATM 4 O O3 POP . . . H 7 -7.795 -9.24 11.201 0.65 52.75 ? O3 POP 1005 A 1 HETATM 5 O O POP . . . H 7 -6.794 -8.862 8.911 0.65 59.19 ? O POP 1005 A 1 HETATM 6 P P2 POP . . . H 7 -6.477 -7.278 8.627 0.65 70.8 ? P2 POP 1005 A 1 HETATM 7 O O4 POP . . . H 7 -5.101 -6.931 9.188 0.65 67.87 ? O4 POP 1005 A 1 HETATM 8 O O5 POP . . . H 7 -6.38 -6.996 7.125 0.65 64.11 ? O5 POP 1005 A 1 HETATM 9 O O6 POP . . . H 7 -7.508 -6.279 9.145 0.65 59.2 ? O6 POP 1005 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 9 #