data_1ZVQ # _model_server_result.job_id a40MxJy8GqIEolTc0tGOyA _model_server_result.datetime_utc '2024-11-23 01:58:12' _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 1zvq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":180}' # _entry.id 1ZVQ # _exptl.entry_id 1ZVQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-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 1ZVQ _cell.length_a 92.992 _cell.length_b 92.992 _cell.length_c 121.015 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ZVQ _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 _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 D _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 OG SER 17 A SER 17 1_555 B MG MG . A MG 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc2 D O2B GDP . A GDP 180 1_555 B MG MG . A MG 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc3 B MG MG . A MG 181 1_555 E O HOH . A HOH 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc4 B MG MG . A MG 181 1_555 E O HOH . A HOH 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc5 B MG MG . A MG 181 1_555 E O HOH . A HOH 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc6 B MG MG . A MG 181 1_555 E O HOH . A HOH 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc7 C MG MG . A MG 182 1_555 E O HOH . A HOH 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc8 C MG MG . A MG 182 1_555 E O HOH . A HOH 220 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc9 C MG MG . A MG 182 1_555 E O HOH . A HOH 220 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.821 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 1ZVQ _atom_sites.fract_transf_matrix[1][1] 0.01075 _atom_sites.fract_transf_matrix[1][2] 0.00621 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01242 _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] 0.00826 _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 1 181 181 MG MG . C 2 MG A 1 182 182 MG MG . D 3 GDP A 1 180 180 GDP GDP . E 4 HOH A 1 183 1 HOH HOH . E 4 HOH A 2 184 2 HOH HOH . E 4 HOH A 3 185 3 HOH HOH . E 4 HOH A 4 186 4 HOH HOH . E 4 HOH A 5 187 5 HOH HOH . E 4 HOH A 6 188 6 HOH HOH . E 4 HOH A 7 189 7 HOH HOH . E 4 HOH A 8 190 8 HOH HOH . E 4 HOH A 9 191 9 HOH HOH . E 4 HOH A 10 192 10 HOH HOH . E 4 HOH A 11 193 11 HOH HOH . E 4 HOH A 12 194 12 HOH HOH . E 4 HOH A 13 195 13 HOH HOH . E 4 HOH A 14 196 14 HOH HOH . E 4 HOH A 15 197 15 HOH HOH . E 4 HOH A 16 198 16 HOH HOH . E 4 HOH A 17 199 17 HOH HOH . E 4 HOH A 18 200 18 HOH HOH . E 4 HOH A 19 201 19 HOH HOH . E 4 HOH A 20 202 20 HOH HOH . E 4 HOH A 21 203 21 HOH HOH . E 4 HOH A 22 204 22 HOH HOH . E 4 HOH A 23 205 23 HOH HOH . E 4 HOH A 24 206 24 HOH HOH . E 4 HOH A 25 207 25 HOH HOH . E 4 HOH A 26 208 26 HOH HOH . E 4 HOH A 27 209 27 HOH HOH . E 4 HOH A 28 210 28 HOH HOH . E 4 HOH A 29 211 29 HOH HOH . E 4 HOH A 30 212 30 HOH HOH . E 4 HOH A 31 213 31 HOH HOH . E 4 HOH A 32 214 32 HOH HOH . E 4 HOH A 33 215 33 HOH HOH . E 4 HOH A 34 216 34 HOH HOH . E 4 HOH A 35 217 35 HOH HOH . E 4 HOH A 36 218 36 HOH HOH . E 4 HOH A 37 219 37 HOH HOH . E 4 HOH A 38 220 38 HOH HOH . E 4 HOH A 39 221 39 HOH HOH . E 4 HOH A 40 222 40 HOH HOH . E 4 HOH A 41 223 41 HOH HOH . E 4 HOH A 42 224 42 HOH HOH . E 4 HOH A 43 225 43 HOH HOH . E 4 HOH A 44 226 44 HOH HOH . E 4 HOH A 45 227 45 HOH HOH . E 4 HOH A 46 228 46 HOH HOH . E 4 HOH A 47 229 47 HOH HOH . E 4 HOH A 48 230 48 HOH HOH . E 4 HOH A 49 231 49 HOH HOH . E 4 HOH A 50 232 50 HOH HOH . E 4 HOH A 51 233 51 HOH HOH . E 4 HOH A 52 234 52 HOH HOH . E 4 HOH A 53 235 53 HOH HOH . E 4 HOH A 54 236 54 HOH HOH . E 4 HOH A 55 237 55 HOH HOH . E 4 HOH A 56 238 56 HOH HOH . E 4 HOH A 57 239 57 HOH HOH . E 4 HOH A 58 240 58 HOH HOH . E 4 HOH A 59 241 59 HOH HOH . E 4 HOH A 60 242 60 HOH HOH . E 4 HOH A 61 243 61 HOH HOH . E 4 HOH A 62 244 62 HOH HOH . E 4 HOH A 63 245 63 HOH HOH . E 4 HOH A 64 246 64 HOH HOH . E 4 HOH A 65 247 65 HOH HOH . E 4 HOH A 66 248 66 HOH HOH . E 4 HOH A 67 249 67 HOH HOH . E 4 HOH A 68 250 68 HOH HOH . E 4 HOH A 69 251 69 HOH HOH . E 4 HOH A 70 252 70 HOH HOH . E 4 HOH A 71 253 71 HOH HOH . E 4 HOH A 72 254 72 HOH HOH . E 4 HOH A 73 255 73 HOH HOH . E 4 HOH A 74 256 74 HOH HOH . E 4 HOH A 75 257 75 HOH HOH . E 4 HOH A 76 258 76 HOH HOH . E 4 HOH A 77 259 77 HOH HOH . E 4 HOH A 78 260 78 HOH HOH . E 4 HOH A 79 261 79 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 GDP . . . D 3 -7.426 14.469 21.403 1 27.26 ? PB GDP 180 A 1 HETATM 2 O O1B GDP . . . D 3 -6.267 14.557 22.382 1 28.03 ? O1B GDP 180 A 1 HETATM 3 O O2B GDP . . . D 3 -7.677 15.848 20.851 1 25.38 ? O2B GDP 180 A 1 HETATM 4 O O3B GDP . . . D 3 -6.998 13.5 20.318 1 27.34 ? O3B GDP 180 A 1 HETATM 5 O O3A GDP . . . D 3 -8.71 13.912 22.199 1 26.72 ? O3A GDP 180 A 1 HETATM 6 P PA GDP . . . D 3 -10.265 14.307 22.01 1 27.83 ? PA GDP 180 A 1 HETATM 7 O O1A GDP . . . D 3 -10.578 15.65 22.575 1 25.1 ? O1A GDP 180 A 1 HETATM 8 O O2A GDP . . . D 3 -10.62 14.141 20.553 1 30.56 ? O2A GDP 180 A 1 HETATM 9 O O5' GDP . . . D 3 -10.993 13.169 22.855 1 27.86 ? O5' GDP 180 A 1 HETATM 10 C C5' GDP . . . D 3 -10.767 11.791 22.559 1 27.54 ? C5' GDP 180 A 1 HETATM 11 C C4' GDP . . . D 3 -11.908 10.995 23.139 1 27.59 ? C4' GDP 180 A 1 HETATM 12 O O4' GDP . . . D 3 -11.896 11.112 24.552 1 27.53 ? O4' GDP 180 A 1 HETATM 13 C C3' GDP . . . D 3 -13.241 11.588 22.692 1 29.28 ? C3' GDP 180 A 1 HETATM 14 O O3' GDP . . . D 3 -14.16 10.506 22.53 1 29.78 ? O3' GDP 180 A 1 HETATM 15 C C2' GDP . . . D 3 -13.699 12.463 23.845 1 28.65 ? C2' GDP 180 A 1 HETATM 16 O O2' GDP . . . D 3 -15.124 12.478 23.954 1 31.52 ? O2' GDP 180 A 1 HETATM 17 C C1' GDP . . . D 3 -13.098 11.724 25.023 1 26.35 ? C1' GDP 180 A 1 HETATM 18 N N9 GDP . . . D 3 -12.735 12.594 26.158 1 26.72 ? N9 GDP 180 A 1 HETATM 19 C C8 GDP . . . D 3 -11.909 13.657 26.141 1 24.78 ? C8 GDP 180 A 1 HETATM 20 N N7 GDP . . . D 3 -11.817 14.175 27.379 1 26.24 ? N7 GDP 180 A 1 HETATM 21 C C5 GDP . . . D 3 -12.558 13.421 28.204 1 25.63 ? C5 GDP 180 A 1 HETATM 22 C C6 GDP . . . D 3 -12.879 13.386 29.653 1 24.77 ? C6 GDP 180 A 1 HETATM 23 O O6 GDP . . . D 3 -12.416 14.24 30.433 1 26.88 ? O6 GDP 180 A 1 HETATM 24 N N1 GDP . . . D 3 -13.687 12.427 30.104 1 24.95 ? N1 GDP 180 A 1 HETATM 25 C C2 GDP . . . D 3 -14.232 11.496 29.285 1 25.28 ? C2 GDP 180 A 1 HETATM 26 N N2 GDP . . . D 3 -15.043 10.552 29.806 1 25.75 ? N2 GDP 180 A 1 HETATM 27 N N3 GDP . . . D 3 -13.966 11.443 27.967 1 25.51 ? N3 GDP 180 A 1 HETATM 28 C C4 GDP . . . D 3 -13.162 12.374 27.386 1 25.95 ? C4 GDP 180 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #