data_5WDE # _model_server_result.job_id 74exfmvdyTaNNLfoQuy-Lg _model_server_result.datetime_utc '2024-10-10 19:15:27' _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 5wde # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":901}' # _entry.id 5WDE # _exptl.entry_id 5WDE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 120 _cell.entry_id 5WDE _cell.length_a 187.608 _cell.length_b 187.608 _cell.length_c 151.363 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WDE _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA _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 2 _struct_asym.id B _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 OG1 THR 95 A THR 535 1_555 C MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc2 B O3B ADP . A ADP 901 1_555 C MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc3 C MG MG . A MG 902 1_555 XA O HOH . A HOH 1013 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc4 C MG MG . A MG 902 1_555 XA O HOH . A HOH 1017 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc5 C MG MG . A MG 902 1_555 XA O HOH . A HOH 1074 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc6 C MG MG . A MG 902 1_555 XA O HOH . A HOH 1088 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? # _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 5WDE _atom_sites.fract_transf_matrix[1][1] 0.00533 _atom_sites.fract_transf_matrix[1][2] 0.003077 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006155 _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] 0.006607 _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 B 2 ADP A 1 901 901 ADP ADP . C 3 MG A 1 902 902 MG MG . D 4 UNX A 1 903 401 UNX UNX . E 4 UNX A 1 904 402 UNX UNX . F 4 UNX A 1 905 403 UNX UNX . G 4 UNX A 1 906 404 UNX UNX . H 4 UNX A 1 907 405 UNX UNX . I 4 UNX A 1 908 408 UNX UNX . J 4 UNX A 1 909 410 UNX UNX . K 4 UNX A 1 910 411 UNX UNX . L 4 UNX A 1 911 412 UNX UNX . M 4 UNX A 1 912 413 UNX UNX . N 4 UNX A 1 913 414 UNX UNX . O 4 UNX A 1 914 416 UNX UNX . P 4 UNX A 1 915 421 UNX UNX . Q 4 UNX A 1 916 425 UNX UNX . R 4 UNX A 1 917 426 UNX UNX . S 4 UNX A 1 918 427 UNX UNX . T 4 UNX A 1 919 428 UNX UNX . U 4 UNX A 1 920 429 UNX UNX . V 4 UNX A 1 921 430 UNX UNX . W 4 UNX A 1 922 431 UNX UNX . X 4 UNX A 1 923 432 UNX UNX . Y 4 UNX A 1 924 433 UNX UNX . Z 4 UNX A 1 925 434 UNX UNX . AA 4 UNX A 1 926 435 UNX UNX . BA 4 UNX A 1 927 436 UNX UNX . CA 4 UNX A 1 928 437 UNX UNX . DA 4 UNX A 1 929 438 UNX UNX . EA 4 UNX A 1 930 439 UNX UNX . FA 4 UNX A 1 931 440 UNX UNX . GA 4 UNX A 1 932 441 UNX UNX . HA 4 UNX A 1 933 442 UNX UNX . IA 4 UNX A 1 934 443 UNX UNX . JA 4 UNX A 1 935 444 UNX UNX . KA 4 UNX A 1 936 445 UNX UNX . LA 4 UNX A 1 937 446 UNX UNX . MA 4 UNX A 1 938 447 UNX UNX . NA 4 UNX A 1 939 448 UNX UNX . OA 4 UNX A 1 940 449 UNX UNX . PA 4 UNX A 1 941 450 UNX UNX . QA 4 UNX A 1 942 451 UNX UNX . RA 4 UNX A 1 943 452 UNX UNX . SA 4 UNX A 1 944 453 UNX UNX . TA 4 UNX A 1 945 454 UNX UNX . UA 4 UNX A 1 946 455 UNX UNX . VA 4 UNX A 1 947 456 UNX UNX . WA 4 UNX A 1 948 457 UNX UNX . XA 5 HOH A 1 1001 183 HOH HOH . XA 5 HOH A 2 1002 146 HOH HOH . XA 5 HOH A 3 1003 198 HOH HOH . XA 5 HOH A 4 1004 197 HOH HOH . XA 5 HOH A 5 1005 49 HOH HOH . XA 5 HOH A 6 1006 101 HOH HOH . XA 5 HOH A 7 1007 12 HOH HOH . XA 5 HOH A 8 1008 50 HOH HOH . XA 5 HOH A 9 1009 113 HOH HOH . XA 5 HOH A 10 1010 62 HOH HOH . XA 5 HOH A 11 1011 43 HOH HOH . XA 5 HOH A 12 1012 179 HOH HOH . XA 5 HOH A 13 1013 153 HOH HOH . XA 5 HOH A 14 1014 202 HOH HOH . XA 5 HOH A 15 1015 175 HOH HOH . XA 5 HOH A 16 1016 24 HOH HOH . XA 5 HOH A 17 1017 168 HOH HOH . XA 5 HOH A 18 1018 44 HOH HOH . XA 5 HOH A 19 1019 135 HOH HOH . XA 5 HOH A 20 1020 23 HOH HOH . XA 5 HOH A 21 1021 45 HOH HOH . XA 5 HOH A 22 1022 193 HOH HOH . XA 5 HOH A 23 1023 4 HOH HOH . XA 5 HOH A 24 1024 33 HOH HOH . XA 5 HOH A 25 1025 3 HOH HOH . XA 5 HOH A 26 1026 6 HOH HOH . XA 5 HOH A 27 1027 13 HOH HOH . XA 5 HOH A 28 1028 90 HOH HOH . XA 5 HOH A 29 1029 35 HOH HOH . XA 5 HOH A 30 1030 2 HOH HOH . XA 5 HOH A 31 1031 73 HOH HOH . XA 5 HOH A 32 1032 34 HOH HOH . XA 5 HOH A 33 1033 10 HOH HOH . XA 5 HOH A 34 1034 83 HOH HOH . XA 5 HOH A 35 1035 14 HOH HOH . XA 5 HOH A 36 1036 21 HOH HOH . XA 5 HOH A 37 1037 80 HOH HOH . XA 5 HOH A 38 1038 199 HOH HOH . XA 5 HOH A 39 1039 28 HOH HOH . XA 5 HOH A 40 1040 207 HOH HOH . XA 5 HOH A 41 1041 100 HOH HOH . XA 5 HOH A 42 1042 74 HOH HOH . XA 5 HOH A 43 1043 177 HOH HOH . XA 5 HOH A 44 1044 8 HOH HOH . XA 5 HOH A 45 1045 16 HOH HOH . XA 5 HOH A 46 1046 61 HOH HOH . XA 5 HOH A 47 1047 75 HOH HOH . XA 5 HOH A 48 1048 56 HOH HOH . XA 5 HOH A 49 1049 37 HOH HOH . XA 5 HOH A 50 1050 103 HOH HOH . XA 5 HOH A 51 1051 25 HOH HOH . XA 5 HOH A 52 1052 51 HOH HOH . XA 5 HOH A 53 1053 69 HOH HOH . XA 5 HOH A 54 1054 129 HOH HOH . XA 5 HOH A 55 1055 29 HOH HOH . XA 5 HOH A 56 1056 205 HOH HOH . XA 5 HOH A 57 1057 27 HOH HOH . XA 5 HOH A 58 1058 98 HOH HOH . XA 5 HOH A 59 1059 106 HOH HOH . XA 5 HOH A 60 1060 102 HOH HOH . XA 5 HOH A 61 1061 59 HOH HOH . XA 5 HOH A 62 1062 154 HOH HOH . XA 5 HOH A 63 1063 84 HOH HOH . XA 5 HOH A 64 1064 7 HOH HOH . XA 5 HOH A 65 1065 139 HOH HOH . XA 5 HOH A 66 1066 204 HOH HOH . XA 5 HOH A 67 1067 192 HOH HOH . XA 5 HOH A 68 1068 40 HOH HOH . XA 5 HOH A 69 1069 64 HOH HOH . XA 5 HOH A 70 1070 41 HOH HOH . XA 5 HOH A 71 1071 86 HOH HOH . XA 5 HOH A 72 1072 66 HOH HOH . XA 5 HOH A 73 1073 52 HOH HOH . XA 5 HOH A 74 1074 169 HOH HOH . XA 5 HOH A 75 1075 91 HOH HOH . XA 5 HOH A 76 1076 63 HOH HOH . XA 5 HOH A 77 1077 125 HOH HOH . XA 5 HOH A 78 1078 67 HOH HOH . XA 5 HOH A 79 1079 26 HOH HOH . XA 5 HOH A 80 1080 5 HOH HOH . XA 5 HOH A 81 1081 109 HOH HOH . XA 5 HOH A 82 1082 55 HOH HOH . XA 5 HOH A 83 1083 78 HOH HOH . XA 5 HOH A 84 1084 46 HOH HOH . XA 5 HOH A 85 1085 81 HOH HOH . XA 5 HOH A 86 1086 42 HOH HOH . XA 5 HOH A 87 1087 18 HOH HOH . XA 5 HOH A 88 1088 172 HOH HOH . XA 5 HOH A 89 1089 178 HOH HOH . XA 5 HOH A 90 1090 117 HOH HOH . XA 5 HOH A 91 1091 123 HOH HOH . XA 5 HOH A 92 1092 70 HOH HOH . XA 5 HOH A 93 1093 60 HOH HOH . XA 5 HOH A 94 1094 87 HOH HOH . XA 5 HOH A 95 1095 88 HOH HOH . XA 5 HOH A 96 1096 95 HOH HOH . XA 5 HOH A 97 1097 107 HOH HOH . XA 5 HOH A 98 1098 31 HOH HOH . XA 5 HOH A 99 1099 188 HOH HOH . XA 5 HOH A 100 1100 15 HOH HOH . XA 5 HOH A 101 1101 166 HOH HOH . XA 5 HOH A 102 1102 195 HOH HOH . XA 5 HOH A 103 1103 65 HOH HOH . XA 5 HOH A 104 1104 112 HOH HOH . XA 5 HOH A 105 1105 203 HOH HOH . XA 5 HOH A 106 1106 47 HOH HOH . XA 5 HOH A 107 1107 132 HOH HOH . XA 5 HOH A 108 1108 38 HOH HOH . XA 5 HOH A 109 1109 184 HOH HOH . XA 5 HOH A 110 1110 68 HOH HOH . XA 5 HOH A 111 1111 126 HOH HOH . XA 5 HOH A 112 1112 92 HOH HOH . XA 5 HOH A 113 1113 200 HOH HOH . XA 5 HOH A 114 1114 173 HOH HOH . XA 5 HOH A 115 1115 118 HOH HOH . XA 5 HOH A 116 1116 94 HOH HOH . XA 5 HOH A 117 1117 190 HOH HOH . XA 5 HOH A 118 1118 89 HOH HOH . XA 5 HOH A 119 1119 194 HOH HOH . XA 5 HOH A 120 1120 206 HOH HOH . XA 5 HOH A 121 1121 191 HOH HOH . XA 5 HOH A 122 1122 138 HOH HOH . XA 5 HOH A 123 1123 110 HOH HOH . XA 5 HOH A 124 1124 111 HOH HOH . XA 5 HOH A 125 1125 114 HOH HOH . XA 5 HOH A 126 1126 189 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 . . . B 2 -10.115 29.752 49.411 1 31.12 ? PB ADP 901 A 1 HETATM 2 O O1B ADP . . . B 2 -11.461 29.177 49.057 1 30.93 ? O1B ADP 901 A 1 HETATM 3 O O2B ADP . . . B 2 -10.197 30.834 50.469 1 29.5 ? O2B ADP 901 A 1 HETATM 4 O O3B ADP . . . B 2 -9.009 28.748 49.657 1 28.67 ? O3B ADP 901 A 1 HETATM 5 P PA ADP . . . B 2 -8.737 30.061 46.877 1 32.79 ? PA ADP 901 A 1 HETATM 6 O O1A ADP . . . B 2 -9.39 28.843 46.285 1 35.03 ? O1A ADP 901 A 1 HETATM 7 O O2A ADP . . . B 2 -7.29 30.07 47.295 1 33.11 ? O2A ADP 901 A 1 HETATM 8 O O3A ADP . . . B 2 -9.666 30.568 48.091 1 31.53 ? O3A ADP 901 A 1 HETATM 9 O O5' ADP . . . B 2 -8.926 31.294 45.842 1 37.74 ? O5' ADP 901 A 1 HETATM 10 C C5' ADP . . . B 2 -10.122 31.474 45.069 1 36.49 ? C5' ADP 901 A 1 HETATM 11 C C4' ADP . . . B 2 -9.725 31.991 43.691 1 40.89 ? C4' ADP 901 A 1 HETATM 12 O O4' ADP . . . B 2 -9.113 33.285 43.799 1 40.13 ? O4' ADP 901 A 1 HETATM 13 C C3' ADP . . . B 2 -8.695 31.066 43.074 1 44.59 ? C3' ADP 901 A 1 HETATM 14 O O3' ADP . . . B 2 -9.016 30.892 41.695 1 50.71 ? O3' ADP 901 A 1 HETATM 15 C C2' ADP . . . B 2 -7.377 31.802 43.182 1 45.82 ? C2' ADP 901 A 1 HETATM 16 O O2' ADP . . . B 2 -6.555 31.543 42.043 1 49.9 ? O2' ADP 901 A 1 HETATM 17 C C1' ADP . . . B 2 -7.795 33.26 43.253 1 36.49 ? C1' ADP 901 A 1 HETATM 18 N N9 ADP . . . B 2 -6.934 34.058 44.155 1 38.99 ? N9 ADP 901 A 1 HETATM 19 C C8 ADP . . . B 2 -7.005 34.078 45.497 1 37.05 ? C8 ADP 901 A 1 HETATM 20 N N7 ADP . . . B 2 -6.092 34.934 46.022 1 34.82 ? N7 ADP 901 A 1 HETATM 21 C C5 ADP . . . B 2 -5.424 35.485 44.994 1 36.85 ? C5 ADP 901 A 1 HETATM 22 C C6 ADP . . . B 2 -4.332 36.468 44.842 1 34.13 ? C6 ADP 901 A 1 HETATM 23 N N6 ADP . . . B 2 -3.757 37.053 45.917 1 33.79 ? N6 ADP 901 A 1 HETATM 24 N N1 ADP . . . B 2 -3.928 36.758 43.59 1 39.06 ? N1 ADP 901 A 1 HETATM 25 C C2 ADP . . . B 2 -4.493 36.194 42.509 1 39.28 ? C2 ADP 901 A 1 HETATM 26 N N3 ADP . . . B 2 -5.488 35.296 42.57 1 41.69 ? N3 ADP 901 A 1 HETATM 27 C C4 ADP . . . B 2 -5.985 34.908 43.766 1 39.73 ? C4 ADP 901 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #