data_2ZBD # _model_server_result.job_id 7FQD2STxrq0QNLXzT6I7dw _model_server_result.datetime_utc '2024-11-05 00:41:56' _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 2zbd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1002}' # _entry.id 2ZBD # _exptl.entry_id 2ZBD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _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 109.3 _cell.angle_gamma 90 _cell.entry_id 2ZBD _cell.length_a 162.9 _cell.length_b 75.1 _cell.length_c 152.1 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZBD _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 ? _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 _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 5 _struct_asym.id G _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 disulf ? disulf1 A SG CYS 877 A CYS 876 1_555 A SG CYS 889 A CYS 888 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 A C ACE 1 A ACE 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? metalc ? metalc1 A O VAL 305 A VAL 304 1_555 C CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? metalc ? metalc2 A O ALA 306 A ALA 305 1_555 C CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? metalc ? metalc3 A O ILE 308 A ILE 307 1_555 C CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc4 A OE1 GLU 310 A GLU 309 1_555 C CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? metalc ? metalc5 A OE2 GLU 310 A GLU 309 1_555 C CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? metalc ? metalc6 A OD2 ASP 352 A ASP 351 1_555 F MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc7 A O THR 354 A THR 353 1_555 F MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc8 A OD1 ASP 704 A ASP 703 1_555 F MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc9 A OD1 ASN 769 A ASN 768 1_555 B CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc10 A OE2 GLU 772 A GLU 771 1_555 B CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc11 A OD1 ASN 797 A ASN 796 1_555 C CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc12 A OG1 THR 800 A THR 799 1_555 B CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc13 A OD1 ASP 801 A ASP 800 1_555 B CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc14 A OD2 ASP 801 A ASP 800 1_555 C CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc15 A OE2 GLU 909 A GLU 908 1_555 B CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc16 B CA CA . A CA 995 1_555 J O HOH . A HOH 1014 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc17 B CA CA . A CA 995 1_555 J O HOH . A HOH 1015 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? metalc ? metalc18 D MG MG . A MG 997 1_555 G O1B ADP . A ADP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc19 F MG MG . A MG 1001 1_555 J O HOH . A HOH 1038 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc20 F MG MG . A MG 1001 1_555 J O HOH . A HOH 1041 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? # _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 7 n n PB O2B ADP sing 8 n n PB O3B ADP sing 9 n n PB O3A ADP sing 10 n n O2B HOB2 ADP sing 11 n n O3B HOB3 ADP sing 12 n n PA O1A ADP doub 13 n n PA O2A ADP sing 14 n n PA O3A ADP sing 15 n n PA O5' ADP sing 16 n n O2A HOA2 ADP sing 17 n n O5' C5' ADP sing 18 n n C5' C4' ADP sing 19 n n C5' "H5'1" ADP sing 20 n n C5' "H5'2" ADP sing 21 n n C4' O4' ADP sing 22 n n C4' C3' ADP sing 23 n n C4' H4' ADP sing 24 n n O4' C1' ADP sing 25 n n C3' O3' ADP sing 26 n n C3' C2' ADP sing 27 n n C3' H3' ADP sing 28 n n O3' HO3' ADP sing 29 n n C2' O2' ADP sing 30 n n C2' C1' ADP sing 31 n n C2' H2' ADP sing 32 n n O2' HO2' ADP sing 33 n n C1' N9 ADP sing 34 n n C1' H1' ADP sing 35 n n N9 C8 ADP sing 36 n y N9 C4 ADP sing 37 n y C8 N7 ADP doub 38 n y C8 H8 ADP sing 39 n n N7 C5 ADP sing 40 n y C5 C6 ADP sing 41 n y C5 C4 ADP doub 42 n y C6 N6 ADP sing 43 n n C6 N1 ADP doub 44 n y N6 HN61 ADP sing 45 n n N6 HN62 ADP sing 46 n n N1 C2 ADP sing 47 n y C2 N3 ADP doub 48 n y C2 H2 ADP sing 49 n n N3 C4 ADP sing 50 n y # _atom_sites.entry_id 2ZBD _atom_sites.fract_transf_matrix[1][1] 0.006139 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00215 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013316 _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] 0.006966 _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 CA A 1 995 995 CA CA . C 2 CA A 1 996 996 CA CA . D 3 MG A 1 997 997 MG MG . E 4 ALF A 1 998 998 ALF ALF . F 3 MG A 1 1001 1001 MG MG . G 5 ADP A 1 1002 1002 ADP ADP . H 6 PC1 A 1 1011 1011 PC1 PC1 . I 6 PC1 A 1 1012 1012 PC1 PC1 . J 7 HOH A 1 1013 1013 HOH HOH . J 7 HOH A 2 1014 1014 HOH HOH . J 7 HOH A 3 1015 1015 HOH HOH . J 7 HOH A 4 1016 1016 HOH HOH . J 7 HOH A 5 1017 1017 HOH HOH . J 7 HOH A 6 1018 1018 HOH HOH . J 7 HOH A 7 1019 1019 HOH HOH . J 7 HOH A 8 1020 1020 HOH HOH . J 7 HOH A 9 1021 1021 HOH HOH . J 7 HOH A 10 1022 1022 HOH HOH . J 7 HOH A 11 1023 1023 HOH HOH . J 7 HOH A 12 1024 1024 HOH HOH . J 7 HOH A 13 1025 1025 HOH HOH . J 7 HOH A 14 1026 1026 HOH HOH . J 7 HOH A 15 1027 1027 HOH HOH . J 7 HOH A 16 1028 1028 HOH HOH . J 7 HOH A 17 1029 1029 HOH HOH . J 7 HOH A 18 1030 1030 HOH HOH . J 7 HOH A 19 1031 1031 HOH HOH . J 7 HOH A 20 1032 1032 HOH HOH . J 7 HOH A 21 1033 1033 HOH HOH . J 7 HOH A 22 1034 1034 HOH HOH . J 7 HOH A 23 1035 1035 HOH HOH . J 7 HOH A 24 1036 1036 HOH HOH . J 7 HOH A 25 1037 1037 HOH HOH . J 7 HOH A 26 1038 1038 HOH HOH . J 7 HOH A 27 1039 1039 HOH HOH . J 7 HOH A 28 1040 1040 HOH HOH . J 7 HOH A 29 1041 1041 HOH HOH . J 7 HOH A 30 1042 1042 HOH HOH . J 7 HOH A 31 1043 1043 HOH HOH . J 7 HOH A 32 1044 1044 HOH HOH . J 7 HOH A 33 1045 1045 HOH HOH . J 7 HOH A 34 1046 1046 HOH HOH . J 7 HOH A 35 1047 1047 HOH HOH . J 7 HOH A 36 1048 1048 HOH HOH . J 7 HOH A 37 1049 1049 HOH HOH . J 7 HOH A 38 1050 1050 HOH HOH . J 7 HOH A 39 1051 1051 HOH HOH . J 7 HOH A 40 1052 1052 HOH HOH . J 7 HOH A 41 1053 1053 HOH HOH . J 7 HOH A 42 1054 1054 HOH HOH . J 7 HOH A 43 1055 1055 HOH HOH . J 7 HOH A 44 1056 1056 HOH HOH . J 7 HOH A 45 1057 1057 HOH HOH . J 7 HOH A 46 1058 1058 HOH HOH . J 7 HOH A 47 1059 1059 HOH HOH . J 7 HOH A 48 1060 1060 HOH HOH . J 7 HOH A 49 1061 1061 HOH HOH . J 7 HOH A 50 1062 1062 HOH HOH . J 7 HOH A 51 1063 1063 HOH HOH . J 7 HOH A 52 1064 1064 HOH HOH . J 7 HOH A 53 1065 1065 HOH HOH . J 7 HOH A 54 1066 1066 HOH HOH . J 7 HOH A 55 1067 1067 HOH HOH . J 7 HOH A 56 1068 1068 HOH HOH . J 7 HOH A 57 1069 1069 HOH HOH . J 7 HOH A 58 1070 1070 HOH HOH . J 7 HOH A 59 1071 1071 HOH HOH . J 7 HOH A 60 1072 1072 HOH HOH . J 7 HOH A 61 1073 1073 HOH HOH . J 7 HOH A 62 1074 1074 HOH HOH . J 7 HOH A 63 1075 1075 HOH HOH . J 7 HOH A 64 1076 1076 HOH HOH . J 7 HOH A 65 1077 1077 HOH HOH . J 7 HOH A 66 1078 1078 HOH HOH . J 7 HOH A 67 1079 1079 HOH HOH . J 7 HOH A 68 1080 1080 HOH HOH . J 7 HOH A 69 1081 1081 HOH HOH . J 7 HOH A 70 1082 1082 HOH HOH . J 7 HOH A 71 1083 1083 HOH HOH . J 7 HOH A 72 1084 1084 HOH HOH . J 7 HOH A 73 1085 1085 HOH HOH . J 7 HOH A 74 1086 1086 HOH HOH . J 7 HOH A 75 1087 1087 HOH HOH . J 7 HOH A 76 1088 1088 HOH HOH . J 7 HOH A 77 1089 1089 HOH HOH . J 7 HOH A 78 1090 1090 HOH HOH . J 7 HOH A 79 1091 1091 HOH HOH . J 7 HOH A 80 1092 1092 HOH HOH . J 7 HOH A 81 1093 1093 HOH HOH . J 7 HOH A 82 1094 1094 HOH HOH . J 7 HOH A 83 1095 1095 HOH HOH . J 7 HOH A 84 1096 1096 HOH HOH . J 7 HOH A 85 1097 1097 HOH HOH . J 7 HOH A 86 1098 1098 HOH HOH . J 7 HOH A 87 1099 1099 HOH HOH . J 7 HOH A 88 1100 1100 HOH HOH . J 7 HOH A 89 1101 1101 HOH HOH . J 7 HOH A 90 1102 1102 HOH HOH . J 7 HOH A 91 1103 1103 HOH HOH . J 7 HOH A 92 1104 1104 HOH HOH . J 7 HOH A 93 1105 1105 HOH HOH . J 7 HOH A 94 1106 1106 HOH HOH . J 7 HOH A 95 1107 1107 HOH HOH . J 7 HOH A 96 1108 1108 HOH HOH . J 7 HOH A 97 1109 1109 HOH HOH . J 7 HOH A 98 1110 1110 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 . . . G 5 72.934 30.271 58.791 1 52.38 ? PB ADP 1002 A 1 HETATM 2 O O1B ADP . . . G 5 74.1 29.315 58.925 1 49.98 ? O1B ADP 1002 A 1 HETATM 3 O O2B ADP . . . G 5 72.935 31.34 59.858 1 51.47 ? O2B ADP 1002 A 1 HETATM 4 O O3B ADP . . . G 5 72.679 30.705 57.375 1 48.94 ? O3B ADP 1002 A 1 HETATM 5 P PA ADP . . . G 5 71.433 27.975 59.682 1 53.26 ? PA ADP 1002 A 1 HETATM 6 O O1A ADP . . . G 5 72.414 27.123 58.92 1 52.84 ? O1A ADP 1002 A 1 HETATM 7 O O2A ADP . . . G 5 69.96 27.634 59.698 1 52.65 ? O2A ADP 1002 A 1 HETATM 8 O O3A ADP . . . G 5 71.551 29.503 59.148 1 53.14 ? O3A ADP 1002 A 1 HETATM 9 O O5' ADP . . . G 5 71.907 28.083 61.208 1 52.52 ? O5' ADP 1002 A 1 HETATM 10 C C5' ADP . . . G 5 71.09 28.765 62.16 1 53.18 ? C5' ADP 1002 A 1 HETATM 11 C C4' ADP . . . G 5 71.922 29.391 63.276 1 53.64 ? C4' ADP 1002 A 1 HETATM 12 O O4' ADP . . . G 5 72.462 28.364 64.099 1 53.77 ? O4' ADP 1002 A 1 HETATM 13 C C3' ADP . . . G 5 73.126 30.206 62.814 1 54.04 ? C3' ADP 1002 A 1 HETATM 14 O O3' ADP . . . G 5 72.795 31.576 62.6 1 55.28 ? O3' ADP 1002 A 1 HETATM 15 C C2' ADP . . . G 5 74.102 30.082 63.953 1 54.35 ? C2' ADP 1002 A 1 HETATM 16 O O2' ADP . . . G 5 73.851 31.117 64.904 1 53.01 ? O2' ADP 1002 A 1 HETATM 17 C C1' ADP . . . G 5 73.755 28.733 64.575 1 54.23 ? C1' ADP 1002 A 1 HETATM 18 N N9 ADP . . . G 5 74.696 27.677 64.14 1 54.5 ? N9 ADP 1002 A 1 HETATM 19 C C8 ADP . . . G 5 75.146 27.475 62.882 1 54.36 ? C8 ADP 1002 A 1 HETATM 20 N N7 ADP . . . G 5 75.99 26.415 62.83 1 54.82 ? N7 ADP 1002 A 1 HETATM 21 C C5 ADP . . . G 5 76.073 25.918 64.082 1 54.35 ? C5 ADP 1002 A 1 HETATM 22 C C6 ADP . . . G 5 76.779 24.798 64.733 1 53.71 ? C6 ADP 1002 A 1 HETATM 23 N N6 ADP . . . G 5 77.582 23.991 64.008 1 54.49 ? N6 ADP 1002 A 1 HETATM 24 N N1 ADP . . . G 5 76.598 24.618 66.059 1 54.3 ? N1 ADP 1002 A 1 HETATM 25 C C2 ADP . . . G 5 75.796 25.419 66.79 1 54.2 ? C2 ADP 1002 A 1 HETATM 26 N N3 ADP . . . G 5 75.125 26.456 66.259 1 54.34 ? N3 ADP 1002 A 1 HETATM 27 C C4 ADP . . . G 5 75.222 26.752 64.941 1 54.04 ? C4 ADP 1002 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #