data_2GCP # _model_server_result.job_id ay9Iruw5rj8TYRAO4CsCLA _model_server_result.datetime_utc '2024-10-20 00:38:57' _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 2gcp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1001}' # _entry.id 2GCP # _exptl.entry_id 2GCP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _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 2GCP _cell.length_a 59.435 _cell.length_b 59.435 _cell.length_c 138.09 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GCP _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 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 _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 3 _struct_asym.id E _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 39 A THR 19 1_555 B MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc2 A OG1 THR 57 A THR 37 1_555 B MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc3 A NE2 HIS 125 A HIS 105 1_555 C MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.991 ? metalc ? metalc4 E O3G GSP . A GSP 1001 1_555 B MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc5 E O2B GSP . A GSP 1001 1_555 B MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc6 B MG MG . A MG 2001 1_555 H O HOH . A HOH 3025 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc7 B MG MG . A MG 2001 1_555 H O HOH . A HOH 3036 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc8 C MG MG . A MG 2002 1_555 H O HOH . A HOH 3089 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.075 ? metalc ? metalc9 C MG MG . A MG 2002 1_555 H O HOH . A HOH 3090 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.988 ? metalc ? metalc10 C MG MG . A MG 2002 1_555 H O HOH . A HOH 3091 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.067 ? # _chem_comp.formula 'C10 H16 N5 O13 P3 S' _chem_comp.formula_weight 539.246 _chem_comp.id GSP _chem_comp.mon_nstd_flag . _chem_comp.name "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _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 PG O3B GSP sing 138 n n PG S1G GSP doub 139 n n PG O2G GSP sing 140 n n PG O3G GSP sing 141 n n O3B PB GSP sing 142 n n O2G HOG2 GSP sing 143 n n O3G HOG3 GSP sing 144 n n PB O1B GSP doub 145 n n PB O2B GSP sing 146 n n PB O3A GSP sing 147 n n O2B HOB2 GSP sing 148 n n PA O1A GSP doub 149 n n PA O2A GSP sing 150 n n PA O3A GSP sing 151 n n PA O5' GSP sing 152 n n O2A HOA2 GSP sing 153 n n O5' C5' GSP sing 154 n n C5' C4' GSP sing 155 n n C5' "H5'1" GSP sing 156 n n C5' "H5'2" GSP sing 157 n n C4' O4' GSP sing 158 n n C4' C3' GSP sing 159 n n C4' H4' GSP sing 160 n n O4' C1' GSP sing 161 n n C3' O3' GSP sing 162 n n C3' C2' GSP sing 163 n n C3' H3' GSP sing 164 n n O3' HO3' GSP sing 165 n n C2' O2' GSP sing 166 n n C2' C1' GSP sing 167 n n C2' H2' GSP sing 168 n n O2' HO2' GSP sing 169 n n C1' N9 GSP sing 170 n n C1' H1' GSP sing 171 n n N9 C8 GSP sing 172 n y N9 C4 GSP sing 173 n y C8 N7 GSP doub 174 n y C8 H8 GSP sing 175 n n N7 C5 GSP sing 176 n y C5 C6 GSP sing 177 n n C5 C4 GSP doub 178 n y C6 O6 GSP doub 179 n n C6 N1 GSP sing 180 n n N1 C2 GSP sing 181 n n N1 HN1 GSP sing 182 n n C2 N2 GSP sing 183 n n C2 N3 GSP doub 184 n n N2 HN21 GSP sing 185 n n N2 HN22 GSP sing 186 n n N3 C4 GSP sing 187 n n # _atom_sites.entry_id 2GCP _atom_sites.fract_transf_matrix[1][1] 0.01682 _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] 0.01682 _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] 0.00724 _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 MG A 1 2001 2001 MG MG . C 2 MG A 1 2002 2002 MG MG . D 2 MG A 1 2003 2003 MG MG . E 3 GSP A 1 1001 1001 GSP GSP . F 4 EDO A 1 3001 3001 EDO EDO . G 4 EDO A 1 3002 3002 EDO EDO . H 5 HOH A 1 3003 1 HOH HOH . H 5 HOH A 2 3004 2 HOH HOH . H 5 HOH A 3 3005 3 HOH HOH . H 5 HOH A 4 3006 4 HOH HOH . H 5 HOH A 5 3007 5 HOH HOH . H 5 HOH A 6 3008 6 HOH HOH . H 5 HOH A 7 3009 7 HOH HOH . H 5 HOH A 8 3010 8 HOH HOH . H 5 HOH A 9 3011 9 HOH HOH . H 5 HOH A 10 3012 10 HOH HOH . H 5 HOH A 11 3013 11 HOH HOH . H 5 HOH A 12 3014 12 HOH HOH . H 5 HOH A 13 3015 13 HOH HOH . H 5 HOH A 14 3016 14 HOH HOH . H 5 HOH A 15 3017 15 HOH HOH . H 5 HOH A 16 3018 16 HOH HOH . H 5 HOH A 17 3019 17 HOH HOH . H 5 HOH A 18 3020 18 HOH HOH . H 5 HOH A 19 3021 19 HOH HOH . H 5 HOH A 20 3022 20 HOH HOH . H 5 HOH A 21 3023 21 HOH HOH . H 5 HOH A 22 3024 22 HOH HOH . H 5 HOH A 23 3025 23 HOH HOH . H 5 HOH A 24 3026 24 HOH HOH . H 5 HOH A 25 3027 25 HOH HOH . H 5 HOH A 26 3028 26 HOH HOH . H 5 HOH A 27 3029 27 HOH HOH . H 5 HOH A 28 3030 28 HOH HOH . H 5 HOH A 29 3031 29 HOH HOH . H 5 HOH A 30 3032 30 HOH HOH . H 5 HOH A 31 3033 31 HOH HOH . H 5 HOH A 32 3034 32 HOH HOH . H 5 HOH A 33 3035 33 HOH HOH . H 5 HOH A 34 3036 34 HOH HOH . H 5 HOH A 35 3037 35 HOH HOH . H 5 HOH A 36 3038 36 HOH HOH . H 5 HOH A 37 3039 37 HOH HOH . H 5 HOH A 38 3040 38 HOH HOH . H 5 HOH A 39 3041 39 HOH HOH . H 5 HOH A 40 3042 40 HOH HOH . H 5 HOH A 41 3043 41 HOH HOH . H 5 HOH A 42 3044 43 HOH HOH . H 5 HOH A 43 3045 44 HOH HOH . H 5 HOH A 44 3046 45 HOH HOH . H 5 HOH A 45 3047 46 HOH HOH . H 5 HOH A 46 3048 47 HOH HOH . H 5 HOH A 47 3049 48 HOH HOH . H 5 HOH A 48 3050 49 HOH HOH . H 5 HOH A 49 3051 50 HOH HOH . H 5 HOH A 50 3052 51 HOH HOH . H 5 HOH A 51 3053 52 HOH HOH . H 5 HOH A 52 3054 53 HOH HOH . H 5 HOH A 53 3055 54 HOH HOH . H 5 HOH A 54 3056 55 HOH HOH . H 5 HOH A 55 3057 56 HOH HOH . H 5 HOH A 56 3058 57 HOH HOH . H 5 HOH A 57 3059 58 HOH HOH . H 5 HOH A 58 3060 59 HOH HOH . H 5 HOH A 59 3061 60 HOH HOH . H 5 HOH A 60 3062 61 HOH HOH . H 5 HOH A 61 3063 62 HOH HOH . H 5 HOH A 62 3064 63 HOH HOH . H 5 HOH A 63 3065 64 HOH HOH . H 5 HOH A 64 3066 65 HOH HOH . H 5 HOH A 65 3067 66 HOH HOH . H 5 HOH A 66 3068 67 HOH HOH . H 5 HOH A 67 3069 68 HOH HOH . H 5 HOH A 68 3070 69 HOH HOH . H 5 HOH A 69 3071 70 HOH HOH . H 5 HOH A 70 3072 71 HOH HOH . H 5 HOH A 71 3073 72 HOH HOH . H 5 HOH A 72 3074 73 HOH HOH . H 5 HOH A 73 3075 74 HOH HOH . H 5 HOH A 74 3076 75 HOH HOH . H 5 HOH A 75 3077 76 HOH HOH . H 5 HOH A 76 3078 77 HOH HOH . H 5 HOH A 77 3079 78 HOH HOH . H 5 HOH A 78 3080 79 HOH HOH . H 5 HOH A 79 3081 80 HOH HOH . H 5 HOH A 80 3082 81 HOH HOH . H 5 HOH A 81 3083 82 HOH HOH . H 5 HOH A 82 3084 83 HOH HOH . H 5 HOH A 83 3085 84 HOH HOH . H 5 HOH A 84 3086 85 HOH HOH . H 5 HOH A 85 3087 86 HOH HOH . H 5 HOH A 86 3088 87 HOH HOH . H 5 HOH A 87 3089 88 HOH HOH . H 5 HOH A 88 3090 89 HOH HOH . H 5 HOH A 89 3091 90 HOH HOH . H 5 HOH A 90 3092 91 HOH HOH . H 5 HOH A 91 3093 92 HOH HOH . H 5 HOH A 92 3094 93 HOH HOH . H 5 HOH A 93 3095 94 HOH HOH . H 5 HOH A 94 3096 95 HOH HOH . H 5 HOH A 95 3097 96 HOH HOH . H 5 HOH A 96 3098 97 HOH HOH . H 5 HOH A 97 3099 98 HOH HOH . H 5 HOH A 98 3100 99 HOH HOH . H 5 HOH A 99 3101 100 HOH HOH . H 5 HOH A 100 3102 101 HOH HOH . H 5 HOH A 101 3103 102 HOH HOH . H 5 HOH A 102 3104 103 HOH HOH . H 5 HOH A 103 3105 104 HOH HOH . H 5 HOH A 104 3106 105 HOH HOH . H 5 HOH A 105 3107 106 HOH HOH . H 5 HOH A 106 3108 107 HOH HOH . H 5 HOH A 107 3109 108 HOH HOH . H 5 HOH A 108 3110 109 HOH HOH . H 5 HOH A 109 3111 110 HOH HOH . H 5 HOH A 110 3112 111 HOH HOH . H 5 HOH A 111 3113 112 HOH HOH . H 5 HOH A 112 3114 114 HOH HOH . H 5 HOH A 113 3115 115 HOH HOH . H 5 HOH A 114 3116 116 HOH HOH . H 5 HOH A 115 3117 117 HOH HOH . H 5 HOH A 116 3118 118 HOH HOH . H 5 HOH A 117 3119 119 HOH HOH . H 5 HOH A 118 3120 120 HOH HOH . H 5 HOH A 119 3121 121 HOH HOH . H 5 HOH A 120 3122 122 HOH HOH . H 5 HOH A 121 3123 123 HOH HOH . H 5 HOH A 122 3124 125 HOH HOH . H 5 HOH A 123 3125 126 HOH HOH . H 5 HOH A 124 3126 127 HOH HOH . H 5 HOH A 125 3127 128 HOH HOH . H 5 HOH A 126 3128 129 HOH HOH . H 5 HOH A 127 3129 130 HOH HOH . H 5 HOH A 128 3130 131 HOH HOH . H 5 HOH A 129 3131 132 HOH HOH . H 5 HOH A 130 3132 133 HOH HOH . H 5 HOH A 131 3133 134 HOH HOH . H 5 HOH A 132 3134 135 HOH HOH . H 5 HOH A 133 3135 137 HOH HOH . H 5 HOH A 134 3136 138 HOH HOH . H 5 HOH A 135 3137 139 HOH HOH . H 5 HOH A 136 3138 140 HOH HOH . H 5 HOH A 137 3139 142 HOH HOH . H 5 HOH A 138 3140 143 HOH HOH . H 5 HOH A 139 3141 144 HOH HOH . H 5 HOH A 140 3142 145 HOH HOH . H 5 HOH A 141 3143 146 HOH HOH . H 5 HOH A 142 3144 147 HOH HOH . H 5 HOH A 143 3145 148 HOH HOH . H 5 HOH A 144 3146 149 HOH HOH . H 5 HOH A 145 3147 150 HOH HOH . H 5 HOH A 146 3148 151 HOH HOH . H 5 HOH A 147 3149 153 HOH HOH . H 5 HOH A 148 3150 154 HOH HOH . H 5 HOH A 149 3151 155 HOH HOH . H 5 HOH A 150 3152 157 HOH HOH . H 5 HOH A 151 3153 158 HOH HOH . H 5 HOH A 152 3154 160 HOH HOH . H 5 HOH A 153 3155 161 HOH HOH . H 5 HOH A 154 3156 162 HOH HOH . H 5 HOH A 155 3157 164 HOH HOH . H 5 HOH A 156 3158 167 HOH HOH . H 5 HOH A 157 3159 169 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 PG GSP . . . E 3 17.658 17.098 14.081 1 10.5 ? PG GSP 1001 A 1 HETATM 2 O O3B GSP . . . E 3 17.019 16.35 15.417 1 9.28 ? O3B GSP 1001 A 1 HETATM 3 S S1G GSP . . . E 3 19.329 17.638 14.551 1 11.84 ? S1G GSP 1001 A 1 HETATM 4 O O2G GSP . . . E 3 16.706 18.24 13.708 1 10.36 ? O2G GSP 1001 A 1 HETATM 5 O O3G GSP . . . E 3 17.679 15.958 13.043 1 10.86 ? O3G GSP 1001 A 1 HETATM 6 P PB GSP . . . E 3 15.665 15.483 15.601 1 9.1 ? PB GSP 1001 A 1 HETATM 7 O O1B GSP . . . E 3 14.576 16.433 15.95 1 7.79 ? O1B GSP 1001 A 1 HETATM 8 O O2B GSP . . . E 3 15.301 14.595 14.481 1 9.33 ? O2B GSP 1001 A 1 HETATM 9 P PA GSP . . . E 3 16.053 12.919 16.959 1 12.07 ? PA GSP 1001 A 1 HETATM 10 O O1A GSP . . . E 3 14.758 12.269 16.705 1 7.99 ? O1A GSP 1001 A 1 HETATM 11 O O2A GSP . . . E 3 17.171 12.337 16.176 1 13.7 ? O2A GSP 1001 A 1 HETATM 12 O O3A GSP . . . E 3 15.995 14.535 16.865 1 9.1 ? O3A GSP 1001 A 1 HETATM 13 O O5' GSP . . . E 3 16.33 12.803 18.543 1 11.8 ? O5' GSP 1001 A 1 HETATM 14 C C5' GSP . . . E 3 17.303 13.609 19.214 1 11.55 ? C5' GSP 1001 A 1 HETATM 15 C C4' GSP . . . E 3 17.787 12.862 20.461 1 10.99 ? C4' GSP 1001 A 1 HETATM 16 O O4' GSP . . . E 3 16.655 12.722 21.308 1 12.31 ? O4' GSP 1001 A 1 HETATM 17 C C3' GSP . . . E 3 18.255 11.439 20.204 1 12.26 ? C3' GSP 1001 A 1 HETATM 18 O O3' GSP . . . E 3 19.297 11.127 21.112 1 13.58 ? O3' GSP 1001 A 1 HETATM 19 C C2' GSP . . . E 3 17.036 10.567 20.499 1 10.48 ? C2' GSP 1001 A 1 HETATM 20 O O2' GSP . . . E 3 17.35 9.224 20.844 1 9.66 ? O2' GSP 1001 A 1 HETATM 21 C C1' GSP . . . E 3 16.31 11.376 21.562 1 11.3 ? C1' GSP 1001 A 1 HETATM 22 N N9 GSP . . . E 3 14.838 11.18 21.521 1 12.82 ? N9 GSP 1001 A 1 HETATM 23 C C8 GSP . . . E 3 13.996 11.164 20.427 1 12.47 ? C8 GSP 1001 A 1 HETATM 24 N N7 GSP . . . E 3 12.735 10.89 20.811 1 13.11 ? N7 GSP 1001 A 1 HETATM 25 C C5 GSP . . . E 3 12.753 10.721 22.17 1 15.4 ? C5 GSP 1001 A 1 HETATM 26 C C6 GSP . . . E 3 11.75 10.463 23.119 1 13.58 ? C6 GSP 1001 A 1 HETATM 27 O O6 GSP . . . E 3 10.559 10.301 22.781 1 12.93 ? O6 GSP 1001 A 1 HETATM 28 N N1 GSP . . . E 3 12.119 10.373 24.453 1 12.94 ? N1 GSP 1001 A 1 HETATM 29 C C2 GSP . . . E 3 13.428 10.527 24.84 1 12.49 ? C2 GSP 1001 A 1 HETATM 30 N N2 GSP . . . E 3 13.774 10.443 26.103 1 12.88 ? N2 GSP 1001 A 1 HETATM 31 N N3 GSP . . . E 3 14.402 10.802 23.921 1 13.73 ? N3 GSP 1001 A 1 HETATM 32 C C4 GSP . . . E 3 14.072 10.898 22.611 1 14.36 ? C4 GSP 1001 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #