data_2GMK # _model_server_result.job_id FKM2zKCJHn_VBYHyMBQUEA _model_server_result.datetime_utc '2025-03-06 02:16:22' _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 2gmk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":942}' # _entry.id 2GMK # _exptl.entry_id 2GMK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _entity.pdbx_number_of_molecules 4 _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 2GMK _cell.length_a 28.994 _cell.length_b 52.112 _cell.length_c 66.142 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GMK _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 ? _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 _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 B N N ? 2 C N N ? 2 D N N ? 2 E 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 disulf ? disulf1 A SG CYS 19 A CYS 19 1_555 A SG CYS 68 A CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf2 A SG CYS 30 A CYS 30 1_555 A SG CYS 75 A CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf3 A SG CYS 48 A CYS 48 1_555 A SG CYS 90 A CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf4 A SG CYS 87 A CYS 87 1_555 A SG CYS 104 A CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? covale ? covale1 A C PCA 1 A PCA 1 1_555 A N ASP 2 A ASP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE MONOPHOSPHATE' _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 P O1P AMP doub 13 n n P O2P AMP sing 14 n n P O3P AMP sing 15 n n P O5' AMP sing 16 n n O2P HOP2 AMP sing 17 n n O3P HOP3 AMP sing 18 n n O5' C5' AMP sing 19 n n C5' C4' AMP sing 20 n n C5' "H5'1" AMP sing 21 n n C5' "H5'2" AMP sing 22 n n C4' O4' AMP sing 23 n n C4' C3' AMP sing 24 n n C4' H4' AMP sing 25 n n O4' C1' AMP sing 26 n n C3' O3' AMP sing 27 n n C3' C2' AMP sing 28 n n C3' H3' AMP sing 29 n n O3' HO3' AMP sing 30 n n C2' O2' AMP sing 31 n n C2' C1' AMP sing 32 n n C2' H2' AMP sing 33 n n O2' HO2' AMP sing 34 n n C1' N9 AMP sing 35 n n C1' H1' AMP sing 36 n n N9 C8 AMP sing 37 n y N9 C4 AMP sing 38 n y C8 N7 AMP doub 39 n y C8 H8 AMP sing 40 n n N7 C5 AMP sing 41 n y C5 C6 AMP sing 42 n y C5 C4 AMP doub 43 n y C6 N6 AMP sing 44 n n C6 N1 AMP doub 45 n y N6 HN61 AMP sing 46 n n N6 HN62 AMP sing 47 n n N1 C2 AMP sing 48 n y C2 N3 AMP doub 49 n y C2 H2 AMP sing 50 n n N3 C4 AMP sing 51 n y # _atom_sites.entry_id 2GMK _atom_sites.fract_transf_matrix[1][1] 0.03449 _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] 0.01919 _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] 0.01512 _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 AMP A 1 940 941 AMP AMP . C 2 AMP A 1 941 941 AMP AMP . D 2 AMP A 1 942 941 AMP AMP . E 2 AMP A 1 943 941 AMP AMP . F 3 HOH A 1 944 1 HOH HOH . F 3 HOH A 2 945 2 HOH HOH . F 3 HOH A 3 946 3 HOH HOH . F 3 HOH A 4 947 4 HOH HOH . F 3 HOH A 5 948 5 HOH HOH . F 3 HOH A 6 949 6 HOH HOH . F 3 HOH A 7 950 7 HOH HOH . F 3 HOH A 8 951 8 HOH HOH . F 3 HOH A 9 952 9 HOH HOH . F 3 HOH A 10 953 10 HOH HOH . F 3 HOH A 11 954 11 HOH HOH . F 3 HOH A 12 955 12 HOH HOH . F 3 HOH A 13 956 13 HOH HOH . F 3 HOH A 14 957 14 HOH HOH . F 3 HOH A 15 958 15 HOH HOH . F 3 HOH A 16 959 16 HOH HOH . F 3 HOH A 17 960 17 HOH HOH . F 3 HOH A 18 961 18 HOH HOH . F 3 HOH A 19 962 19 HOH HOH . F 3 HOH A 20 963 20 HOH HOH . F 3 HOH A 21 964 21 HOH HOH . F 3 HOH A 22 965 22 HOH HOH . F 3 HOH A 23 966 23 HOH HOH . F 3 HOH A 24 967 24 HOH HOH . F 3 HOH A 25 968 25 HOH HOH . F 3 HOH A 26 969 26 HOH HOH . F 3 HOH A 27 970 27 HOH HOH . F 3 HOH A 28 971 28 HOH HOH . F 3 HOH A 29 972 29 HOH HOH . F 3 HOH A 30 973 30 HOH HOH . F 3 HOH A 31 974 31 HOH HOH . F 3 HOH A 32 975 32 HOH HOH . F 3 HOH A 33 976 33 HOH HOH . F 3 HOH A 34 977 34 HOH HOH . F 3 HOH A 35 978 35 HOH HOH . F 3 HOH A 36 979 36 HOH HOH . F 3 HOH A 37 980 37 HOH HOH . F 3 HOH A 38 981 38 HOH HOH . F 3 HOH A 39 982 39 HOH HOH . F 3 HOH A 40 983 40 HOH HOH . F 3 HOH A 41 984 41 HOH HOH . F 3 HOH A 42 985 42 HOH HOH . F 3 HOH A 43 986 43 HOH HOH . F 3 HOH A 44 987 44 HOH HOH . F 3 HOH A 45 988 45 HOH HOH . F 3 HOH A 46 989 46 HOH HOH . F 3 HOH A 47 990 47 HOH HOH . F 3 HOH A 48 991 48 HOH HOH . F 3 HOH A 49 992 49 HOH HOH . F 3 HOH A 50 993 50 HOH HOH . F 3 HOH A 51 994 51 HOH HOH . F 3 HOH A 52 995 52 HOH HOH . F 3 HOH A 53 996 53 HOH HOH . F 3 HOH A 54 997 54 HOH HOH . F 3 HOH A 55 998 55 HOH HOH . F 3 HOH A 56 999 56 HOH HOH . F 3 HOH A 57 1000 57 HOH HOH . F 3 HOH A 58 1001 58 HOH HOH . F 3 HOH A 59 1002 59 HOH HOH . F 3 HOH A 60 1003 60 HOH HOH . F 3 HOH A 61 1004 61 HOH HOH . F 3 HOH A 62 1005 62 HOH HOH . F 3 HOH A 63 1006 63 HOH HOH . F 3 HOH A 64 1007 64 HOH HOH . F 3 HOH A 65 1008 65 HOH HOH . F 3 HOH A 66 1009 66 HOH HOH . F 3 HOH A 67 1010 67 HOH HOH . F 3 HOH A 68 1011 68 HOH HOH . F 3 HOH A 69 1012 69 HOH HOH . F 3 HOH A 70 1013 70 HOH HOH . F 3 HOH A 71 1014 71 HOH HOH . F 3 HOH A 72 1015 72 HOH HOH . F 3 HOH A 73 1016 73 HOH HOH . F 3 HOH A 74 1017 74 HOH HOH . F 3 HOH A 75 1018 75 HOH HOH . F 3 HOH A 76 1019 76 HOH HOH . F 3 HOH A 77 1020 77 HOH HOH . F 3 HOH A 78 1021 78 HOH HOH . F 3 HOH A 79 1022 79 HOH HOH . F 3 HOH A 80 1023 80 HOH HOH . F 3 HOH A 81 1024 81 HOH HOH . F 3 HOH A 82 1025 82 HOH HOH . F 3 HOH A 83 1026 83 HOH HOH . F 3 HOH A 84 1027 84 HOH HOH . F 3 HOH A 85 1028 85 HOH HOH . F 3 HOH A 86 1029 86 HOH HOH . F 3 HOH A 87 1030 87 HOH HOH . F 3 HOH A 88 1031 88 HOH HOH . F 3 HOH A 89 1032 89 HOH HOH . F 3 HOH A 90 1033 90 HOH HOH . F 3 HOH A 91 1034 91 HOH HOH . F 3 HOH A 92 1035 92 HOH HOH . F 3 HOH A 93 1036 93 HOH HOH . F 3 HOH A 94 1037 94 HOH HOH . F 3 HOH A 95 1038 95 HOH HOH . F 3 HOH A 96 1039 96 HOH HOH . F 3 HOH A 97 1040 97 HOH HOH . F 3 HOH A 98 1041 98 HOH HOH . F 3 HOH A 99 1042 99 HOH HOH . F 3 HOH A 100 1043 100 HOH HOH . F 3 HOH A 101 1044 101 HOH HOH . F 3 HOH A 102 1045 102 HOH HOH . F 3 HOH A 103 1046 103 HOH HOH . F 3 HOH A 104 1047 104 HOH HOH . F 3 HOH A 105 1048 105 HOH HOH . F 3 HOH A 106 1049 106 HOH HOH . F 3 HOH A 107 1050 107 HOH HOH . F 3 HOH A 108 1051 108 HOH HOH . F 3 HOH A 109 1052 109 HOH HOH . F 3 HOH A 110 1053 110 HOH HOH . F 3 HOH A 111 1054 111 HOH HOH . F 3 HOH A 112 1055 112 HOH HOH . F 3 HOH A 113 1056 113 HOH HOH . F 3 HOH A 114 1057 114 HOH HOH . F 3 HOH A 115 1058 115 HOH HOH . F 3 HOH A 116 1059 116 HOH HOH . F 3 HOH A 117 1060 117 HOH HOH . F 3 HOH A 118 1061 118 HOH HOH . F 3 HOH A 119 1062 119 HOH HOH . F 3 HOH A 120 1063 120 HOH HOH . F 3 HOH A 121 1064 121 HOH HOH . F 3 HOH A 122 1065 122 HOH HOH . F 3 HOH A 123 1066 123 HOH HOH . F 3 HOH A 124 1067 124 HOH HOH . F 3 HOH A 125 1068 125 HOH HOH . F 3 HOH A 126 1069 126 HOH HOH . F 3 HOH A 127 1070 127 HOH HOH . F 3 HOH A 128 1071 128 HOH HOH . F 3 HOH A 129 1072 129 HOH HOH . F 3 HOH A 130 1073 130 HOH HOH . F 3 HOH A 131 1074 131 HOH HOH . F 3 HOH A 132 1075 132 HOH HOH . F 3 HOH A 133 1076 133 HOH HOH . F 3 HOH A 134 1077 134 HOH HOH . F 3 HOH A 135 1078 135 HOH HOH . F 3 HOH A 136 1079 136 HOH HOH . F 3 HOH A 137 1080 137 HOH HOH . F 3 HOH A 138 1081 138 HOH HOH . F 3 HOH A 139 1082 139 HOH HOH . F 3 HOH A 140 1083 140 HOH HOH . F 3 HOH A 141 1084 141 HOH HOH . F 3 HOH A 142 1085 142 HOH HOH . F 3 HOH A 143 1086 143 HOH HOH . F 3 HOH A 144 1087 144 HOH HOH . F 3 HOH A 145 1088 145 HOH HOH . F 3 HOH A 146 1089 146 HOH HOH . F 3 HOH A 147 1090 147 HOH HOH . F 3 HOH A 148 1091 148 HOH HOH . F 3 HOH A 149 1092 149 HOH HOH . F 3 HOH A 150 1093 150 HOH HOH . F 3 HOH A 151 1094 151 HOH HOH . F 3 HOH A 152 1095 152 HOH HOH . F 3 HOH A 153 1096 153 HOH HOH . F 3 HOH A 154 1097 154 HOH HOH . F 3 HOH A 155 1098 155 HOH HOH . F 3 HOH A 156 1099 156 HOH HOH . F 3 HOH A 157 1100 157 HOH HOH . F 3 HOH A 158 1101 158 HOH HOH . F 3 HOH A 159 1102 159 HOH HOH . F 3 HOH A 160 1103 160 HOH HOH . F 3 HOH A 161 1104 161 HOH HOH . F 3 HOH A 162 1105 162 HOH HOH . F 3 HOH A 163 1106 163 HOH HOH . F 3 HOH A 164 1107 164 HOH HOH . F 3 HOH A 165 1108 165 HOH HOH . F 3 HOH A 166 1109 166 HOH HOH . F 3 HOH A 167 1110 167 HOH HOH . F 3 HOH A 168 1111 168 HOH HOH . F 3 HOH A 169 1112 169 HOH HOH . F 3 HOH A 170 1113 170 HOH HOH . F 3 HOH A 171 1114 171 HOH HOH . F 3 HOH A 172 1115 172 HOH HOH . F 3 HOH A 173 1116 173 HOH HOH . F 3 HOH A 174 1117 175 HOH HOH . F 3 HOH A 175 1118 176 HOH HOH . F 3 HOH A 176 1119 177 HOH HOH . F 3 HOH A 177 1120 178 HOH HOH . F 3 HOH A 178 1121 179 HOH HOH . F 3 HOH A 179 1122 180 HOH HOH . F 3 HOH A 180 1123 181 HOH HOH . F 3 HOH A 181 1124 182 HOH HOH . F 3 HOH A 182 1125 183 HOH HOH . F 3 HOH A 183 1126 184 HOH HOH . F 3 HOH A 184 1127 185 HOH HOH . F 3 HOH A 185 1128 186 HOH HOH . F 3 HOH A 186 1129 187 HOH HOH . F 3 HOH A 187 1130 188 HOH HOH . F 3 HOH A 188 1131 189 HOH HOH . F 3 HOH A 189 1132 190 HOH HOH . F 3 HOH A 190 1133 191 HOH HOH . F 3 HOH A 191 1134 192 HOH HOH . F 3 HOH A 192 1135 193 HOH HOH . F 3 HOH A 193 1136 194 HOH HOH . F 3 HOH A 194 1137 195 HOH HOH . F 3 HOH A 195 1138 196 HOH HOH . F 3 HOH A 196 1139 198 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 P AMP . . . D 2 -20.121 1.574 11.708 1 40.42 ? P AMP 942 A 1 HETATM 2 O O1P AMP . . . D 2 -19.959 1.096 13.133 1 45.39 ? O1P AMP 942 A 1 HETATM 3 O O2P AMP . . . D 2 -19.803 3.045 11.519 1 42.01 ? O2P AMP 942 A 1 HETATM 4 O O3P AMP . . . D 2 -21.414 1.151 11.043 1 42.52 ? O3P AMP 942 A 1 HETATM 5 O O5' AMP . . . D 2 -18.976 0.81 10.875 1 40.94 ? O5' AMP 942 A 1 HETATM 6 C C5' AMP . . . D 2 -18.601 -0.542 11.16 1 38 ? C5' AMP 942 A 1 HETATM 7 C C4' AMP . . . D 2 -17.288 -0.842 10.442 1 35.62 ? C4' AMP 942 A 1 HETATM 8 O O4' AMP . . . D 2 -17.452 -0.622 9.035 1 31.94 ? O4' AMP 942 A 1 HETATM 9 C C3' AMP . . . D 2 -16.16 0.079 10.883 1 34.74 ? C3' AMP 942 A 1 HETATM 10 O O3' AMP . . . D 2 -14.94 -0.668 10.908 1 39.8 ? O3' AMP 942 A 1 HETATM 11 C C2' AMP . . . D 2 -16.082 1.147 9.808 1 31.65 ? C2' AMP 942 A 1 HETATM 12 O O2' AMP . . . D 2 -14.756 1.665 9.649 1 30.05 ? O2' AMP 942 A 1 HETATM 13 C C1' AMP . . . D 2 -16.529 0.371 8.579 1 28.28 ? C1' AMP 942 A 1 HETATM 14 N N9 AMP . . . D 2 -17.232 1.216 7.583 1 24.82 ? N9 AMP 942 A 1 HETATM 15 C C8 AMP . . . D 2 -18.403 1.862 7.75 1 25.79 ? C8 AMP 942 A 1 HETATM 16 N N7 AMP . . . D 2 -18.764 2.533 6.619 1 24.48 ? N7 AMP 942 A 1 HETATM 17 C C5 AMP . . . D 2 -17.801 2.295 5.717 1 21.99 ? C5 AMP 942 A 1 HETATM 18 C C6 AMP . . . D 2 -17.54 2.678 4.312 1 22.35 ? C6 AMP 942 A 1 HETATM 19 N N6 AMP . . . D 2 -18.413 3.469 3.651 1 23.58 ? N6 AMP 942 A 1 HETATM 20 N N1 AMP . . . D 2 -16.408 2.205 3.73 1 25.91 ? N1 AMP 942 A 1 HETATM 21 C C2 AMP . . . D 2 -15.532 1.402 4.374 1 26.87 ? C2 AMP 942 A 1 HETATM 22 N N3 AMP . . . D 2 -15.702 1.013 5.647 1 25.34 ? N3 AMP 942 A 1 HETATM 23 C C4 AMP . . . D 2 -16.798 1.422 6.351 1 24.41 ? C4 AMP 942 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 408 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 23 #