data_7OTJ # _model_server_result.job_id ZTMyqtFDu6uOI5AKpl1xrA _model_server_result.datetime_utc '2024-10-10 12:21:18' _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 7otj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1001}' # _entry.id 7OTJ # _exptl.entry_id 7OTJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 117.279 _cell.angle_gamma 90 _cell.entry_id 7OTJ _cell.length_a 198.973 _cell.length_b 79.96 _cell.length_c 94.11 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7OTJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,Z,BA 1 1 B,D,S,T,U,V,W,X,Y,AA,CA 2 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 ? 3 E N N ? 3 S 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 OG SER 32 A SER 397 1_555 G MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc2 A OE1 GLU 242 A GLU 607 1_555 I K K . A K 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.103 ? metalc ? metalc3 A OE2 GLU 242 A GLU 607 1_555 I K K . A K 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.863 ? metalc ? metalc4 A O ASP 466 A ASP 831 1_555 I K K . A K 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.977 ? metalc ? metalc5 E O2B ADP . A ADP 1001 1_555 G MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc6 G MG MG . A MG 1003 1_555 Z O HOH . A HOH 1123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc7 G MG MG . A MG 1003 1_555 Z O HOH . A HOH 1125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc8 G MG MG . A MG 1003 1_555 Z O HOH . A HOH 1134 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc9 K K K . A K 1007 1_555 Z O HOH . A HOH 1115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.5 ? metalc ? metalc10 N K K . A K 1010 1_555 Z O HOH . A HOH 1151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.238 ? metalc ? metalc11 B OG SER 32 B SER 397 1_555 U MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc12 B O LYS 40 B LYS 405 1_555 X K K . B K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.13 ? metalc ? metalc13 B OD1 ASP 44 B ASP 409 1_555 X K K . B K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.969 ? metalc ? metalc14 B OE1 GLU 229 B GLU 594 1_555 V K K . B K 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.372 ? metalc ? metalc15 B OE2 GLU 229 B GLU 594 1_555 V K K . B K 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.441 ? metalc ? metalc16 S O1B ADP . B ADP 1001 1_555 U MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc17 U MG MG . B MG 1003 1_555 AA O HOH . B HOH 1110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc18 U MG MG . B MG 1003 1_555 AA O HOH . B HOH 1115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.96 ? metalc ? metalc19 U MG MG . B MG 1003 1_555 AA O HOH . B HOH 1132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc20 W K K . B K 1005 1_555 AA O HOH . B HOH 1135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 7OTJ _atom_sites.fract_transf_matrix[1][1] 0.005026 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002592 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012506 _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] 0.011955 _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 E 3 ADP A 1 1001 1001 ADP ADP . F 4 ALF A 1 1002 1002 ALF ALF . G 5 MG A 1 1003 1003 MG MG . H 6 K A 1 1004 2 K K . I 6 K A 1 1005 3 K K . J 6 K A 1 1006 4 K K . K 6 K A 1 1007 6 K K . L 6 K A 1 1008 7 K K . M 6 K A 1 1009 9 K K . N 6 K A 1 1010 10 K K . O 7 PO4 A 1 1011 1 PO4 PO4 . P 7 PO4 A 1 1012 3 PO4 PO4 . Q 7 PO4 A 1 1013 7 PO4 PO4 . R 7 PO4 A 1 1014 8 PO4 PO4 . S 3 ADP B 1 1001 1001 ADP ADP . T 4 ALF B 1 1002 1002 ALF ALF . U 5 MG B 1 1003 1003 MG MG . V 6 K B 1 1004 1 K K . W 6 K B 1 1005 5 K K . X 6 K B 1 1006 8 K K . Y 7 PO4 B 1 1007 9 PO4 PO4 . Z 8 HOH A 1 1101 62 HOH HOH . Z 8 HOH A 2 1102 72 HOH HOH . Z 8 HOH A 3 1103 64 HOH HOH . Z 8 HOH A 4 1104 67 HOH HOH . Z 8 HOH A 5 1105 86 HOH HOH . Z 8 HOH A 6 1106 117 HOH HOH . Z 8 HOH A 7 1107 61 HOH HOH . Z 8 HOH A 8 1108 13 HOH HOH . Z 8 HOH A 9 1109 59 HOH HOH . Z 8 HOH A 10 1110 105 HOH HOH . Z 8 HOH A 11 1111 83 HOH HOH . Z 8 HOH A 12 1112 52 HOH HOH . Z 8 HOH A 13 1113 18 HOH HOH . Z 8 HOH A 14 1114 35 HOH HOH . Z 8 HOH A 15 1115 80 HOH HOH . Z 8 HOH A 16 1116 33 HOH HOH . Z 8 HOH A 17 1117 107 HOH HOH . Z 8 HOH A 18 1118 98 HOH HOH . Z 8 HOH A 19 1119 10 HOH HOH . Z 8 HOH A 20 1120 3 HOH HOH . Z 8 HOH A 21 1121 55 HOH HOH . Z 8 HOH A 22 1122 54 HOH HOH . Z 8 HOH A 23 1123 1 HOH HOH . Z 8 HOH A 24 1124 51 HOH HOH . Z 8 HOH A 25 1125 16 HOH HOH . Z 8 HOH A 26 1126 40 HOH HOH . Z 8 HOH A 27 1127 111 HOH HOH . Z 8 HOH A 28 1128 103 HOH HOH . Z 8 HOH A 29 1129 23 HOH HOH . Z 8 HOH A 30 1130 50 HOH HOH . Z 8 HOH A 31 1131 7 HOH HOH . Z 8 HOH A 32 1132 25 HOH HOH . Z 8 HOH A 33 1133 79 HOH HOH . Z 8 HOH A 34 1134 15 HOH HOH . Z 8 HOH A 35 1135 20 HOH HOH . Z 8 HOH A 36 1136 37 HOH HOH . Z 8 HOH A 37 1137 34 HOH HOH . Z 8 HOH A 38 1138 30 HOH HOH . Z 8 HOH A 39 1139 29 HOH HOH . Z 8 HOH A 40 1140 56 HOH HOH . Z 8 HOH A 41 1141 11 HOH HOH . Z 8 HOH A 42 1142 19 HOH HOH . Z 8 HOH A 43 1143 8 HOH HOH . Z 8 HOH A 44 1144 75 HOH HOH . Z 8 HOH A 45 1145 88 HOH HOH . Z 8 HOH A 46 1146 114 HOH HOH . Z 8 HOH A 47 1147 102 HOH HOH . Z 8 HOH A 48 1148 82 HOH HOH . Z 8 HOH A 49 1149 85 HOH HOH . Z 8 HOH A 50 1150 90 HOH HOH . Z 8 HOH A 51 1151 45 HOH HOH . Z 8 HOH A 52 1152 96 HOH HOH . Z 8 HOH A 53 1153 36 HOH HOH . Z 8 HOH A 54 1154 87 HOH HOH . Z 8 HOH A 55 1155 42 HOH HOH . Z 8 HOH A 56 1156 60 HOH HOH . Z 8 HOH A 57 1157 32 HOH HOH . Z 8 HOH A 58 1158 65 HOH HOH . Z 8 HOH A 59 1159 73 HOH HOH . AA 8 HOH B 1 1101 71 HOH HOH . AA 8 HOH B 2 1102 21 HOH HOH . AA 8 HOH B 3 1103 4 HOH HOH . AA 8 HOH B 4 1104 68 HOH HOH . AA 8 HOH B 5 1105 24 HOH HOH . AA 8 HOH B 6 1106 5 HOH HOH . AA 8 HOH B 7 1107 99 HOH HOH . AA 8 HOH B 8 1108 38 HOH HOH . AA 8 HOH B 9 1109 77 HOH HOH . AA 8 HOH B 10 1110 2 HOH HOH . AA 8 HOH B 11 1111 58 HOH HOH . AA 8 HOH B 12 1112 104 HOH HOH . AA 8 HOH B 13 1113 63 HOH HOH . AA 8 HOH B 14 1114 46 HOH HOH . AA 8 HOH B 15 1115 28 HOH HOH . AA 8 HOH B 16 1116 70 HOH HOH . AA 8 HOH B 17 1117 76 HOH HOH . AA 8 HOH B 18 1118 57 HOH HOH . AA 8 HOH B 19 1119 110 HOH HOH . AA 8 HOH B 20 1120 26 HOH HOH . AA 8 HOH B 21 1121 14 HOH HOH . AA 8 HOH B 22 1122 6 HOH HOH . AA 8 HOH B 23 1123 109 HOH HOH . AA 8 HOH B 24 1124 48 HOH HOH . AA 8 HOH B 25 1125 27 HOH HOH . AA 8 HOH B 26 1126 95 HOH HOH . AA 8 HOH B 27 1127 41 HOH HOH . AA 8 HOH B 28 1128 89 HOH HOH . AA 8 HOH B 29 1129 53 HOH HOH . AA 8 HOH B 30 1130 101 HOH HOH . AA 8 HOH B 31 1131 43 HOH HOH . AA 8 HOH B 32 1132 17 HOH HOH . AA 8 HOH B 33 1133 12 HOH HOH . AA 8 HOH B 34 1134 74 HOH HOH . AA 8 HOH B 35 1135 81 HOH HOH . AA 8 HOH B 36 1136 84 HOH HOH . AA 8 HOH B 37 1137 97 HOH HOH . AA 8 HOH B 38 1138 31 HOH HOH . AA 8 HOH B 39 1139 115 HOH HOH . AA 8 HOH B 40 1140 44 HOH HOH . AA 8 HOH B 41 1141 66 HOH HOH . AA 8 HOH B 42 1142 47 HOH HOH . AA 8 HOH B 43 1143 112 HOH HOH . AA 8 HOH B 44 1144 106 HOH HOH . AA 8 HOH B 45 1145 113 HOH HOH . AA 8 HOH B 46 1146 91 HOH HOH . AA 8 HOH B 47 1147 49 HOH HOH . AA 8 HOH B 48 1148 93 HOH HOH . AA 8 HOH B 49 1149 100 HOH HOH . AA 8 HOH B 50 1150 94 HOH HOH . BA 8 HOH C 1 101 22 HOH HOH . BA 8 HOH C 2 102 108 HOH HOH . BA 8 HOH C 3 103 39 HOH HOH . CA 8 HOH D 1 101 9 HOH HOH . CA 8 HOH D 2 102 69 HOH HOH . CA 8 HOH D 3 103 92 HOH HOH . CA 8 HOH D 4 104 78 HOH HOH . CA 8 HOH D 5 105 116 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 ADP . . . E 3 8.002 2.885 77.647 1 50.8 ? PB ADP 1001 A 1 HETATM 2 O O1B ADP . . . E 3 6.813 3.432 76.879 1 37.19 ? O1B ADP 1001 A 1 HETATM 3 O O2B ADP . . . E 3 9.309 2.871 76.888 1 48.97 ? O2B ADP 1001 A 1 HETATM 4 O O3B ADP . . . E 3 8.107 3.394 79.061 1 46.82 ? O3B ADP 1001 A 1 HETATM 5 P PA ADP . . . E 3 8.768 0.178 78.12 1 47.13 ? PA ADP 1001 A 1 HETATM 6 O O1A ADP . . . E 3 9.154 -0.361 76.766 1 53.74 ? O1A ADP 1001 A 1 HETATM 7 O O2A ADP . . . E 3 9.833 0.626 79.088 1 40.19 ? O2A ADP 1001 A 1 HETATM 8 O O3A ADP . . . E 3 7.657 1.327 77.88 1 41.14 ? O3A ADP 1001 A 1 HETATM 9 O O5' ADP . . . E 3 7.862 -0.908 78.88 1 51.02 ? O5' ADP 1001 A 1 HETATM 10 C C5' ADP . . . E 3 7.754 -0.882 80.297 1 47.75 ? C5' ADP 1001 A 1 HETATM 11 C C4' ADP . . . E 3 7.384 -2.271 80.779 1 48.38 ? C4' ADP 1001 A 1 HETATM 12 O O4' ADP . . . E 3 6.241 -2.737 80.061 1 46.29 ? O4' ADP 1001 A 1 HETATM 13 C C3' ADP . . . E 3 8.518 -3.242 80.505 1 52.03 ? C3' ADP 1001 A 1 HETATM 14 O O3' ADP . . . E 3 8.882 -3.876 81.732 1 62.86 ? O3' ADP 1001 A 1 HETATM 15 C C2' ADP . . . E 3 7.959 -4.275 79.55 1 51.97 ? C2' ADP 1001 A 1 HETATM 16 O O2' ADP . . . E 3 8.346 -5.594 79.946 1 66.94 ? O2' ADP 1001 A 1 HETATM 17 C C1' ADP . . . E 3 6.454 -4.084 79.638 1 50.08 ? C1' ADP 1001 A 1 HETATM 18 N N9 ADP . . . E 3 5.827 -4.275 78.313 1 56.31 ? N9 ADP 1001 A 1 HETATM 19 C C8 ADP . . . E 3 6.03 -3.499 77.234 1 54.86 ? C8 ADP 1001 A 1 HETATM 20 N N7 ADP . . . E 3 5.301 -3.939 76.178 1 53.65 ? N7 ADP 1001 A 1 HETATM 21 C C5 ADP . . . E 3 4.617 -5.024 76.583 1 57.63 ? C5 ADP 1001 A 1 HETATM 22 C C6 ADP . . . E 3 3.659 -5.974 75.971 1 65.27 ? C6 ADP 1001 A 1 HETATM 23 N N6 ADP . . . E 3 3.283 -5.852 74.674 1 59.05 ? N6 ADP 1001 A 1 HETATM 24 N N1 ADP . . . E 3 3.18 -6.973 76.75 1 64.03 ? N1 ADP 1001 A 1 HETATM 25 C C2 ADP . . . E 3 3.548 -7.104 78.039 1 48.71 ? C2 ADP 1001 A 1 HETATM 26 N N3 ADP . . . E 3 4.409 -6.278 78.656 1 49.66 ? N3 ADP 1001 A 1 HETATM 27 C C4 ADP . . . E 3 4.968 -5.241 77.994 1 58.98 ? C4 ADP 1001 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #