data_4AQV # _model_server_result.job_id Z4iRnusKT02_1bJmDvAMGg _model_server_result.datetime_utc '2024-10-22 03:21:13' _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 4aqv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":600}' # _entry.id 4AQV # _exptl.entry_id 4AQV _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _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 90 _cell.entry_id 4AQV _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4AQV _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 6 _struct_asym.id F _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 D MG MG . A MG 500 1_555 E O2G GTP . A GTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc2 H O2B ANP . C ANP 500 1_555 I MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc3 H O2G ANP . C ANP 500 1_555 I MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? # _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 133 n n PB O2B GDP sing 134 n n PB O3B GDP sing 135 n n PB O3A GDP sing 136 n n O2B HOB2 GDP sing 137 n n O3B HOB3 GDP sing 138 n n O3A PA GDP sing 139 n n PA O1A GDP doub 140 n n PA O2A GDP sing 141 n n PA O5' GDP sing 142 n n O2A HOA2 GDP sing 143 n n O5' C5' GDP sing 144 n n C5' C4' GDP sing 145 n n C5' H5' GDP sing 146 n n C5' "H5''" GDP sing 147 n n C4' O4' GDP sing 148 n n C4' C3' GDP sing 149 n n C4' H4' GDP sing 150 n n O4' C1' GDP sing 151 n n C3' O3' GDP sing 152 n n C3' C2' GDP sing 153 n n C3' H3' GDP sing 154 n n O3' HO3' GDP sing 155 n n C2' O2' GDP sing 156 n n C2' C1' GDP sing 157 n n C2' H2' GDP sing 158 n n O2' HO2' GDP sing 159 n n C1' N9 GDP sing 160 n n C1' H1' GDP sing 161 n n N9 C8 GDP sing 162 n y N9 C4 GDP sing 163 n y C8 N7 GDP doub 164 n y C8 H8 GDP sing 165 n n N7 C5 GDP sing 166 n y C5 C6 GDP sing 167 n n C5 C4 GDP doub 168 n y C6 O6 GDP doub 169 n n C6 N1 GDP sing 170 n n N1 C2 GDP sing 171 n n N1 HN1 GDP sing 172 n n C2 N2 GDP sing 173 n n C2 N3 GDP doub 174 n n N2 HN21 GDP sing 175 n n N2 HN22 GDP sing 176 n n N3 C4 GDP sing 177 n n # _atom_sites.entry_id 4AQV _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 D 4 MG A 1 500 500 MG MG . E 5 GTP A 1 501 501 GTP GTP . F 6 GDP B 1 600 600 GDP GDP . G 7 TA1 B 1 601 601 TA1 TA1 . H 8 ANP C 1 500 500 ANP ANP . I 4 MG C 1 501 501 MG MG . # 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 . . . F 6 55.438 50.589 94.18 1 22.28 ? PB GDP 600 B 1 HETATM 2 O O1B GDP . . . F 6 55.605 49.223 94.428 1 23.44 ? O1B GDP 600 B 1 HETATM 3 O O2B GDP . . . F 6 56.051 51.103 92.941 1 23.59 ? O2B GDP 600 B 1 HETATM 4 O O3B GDP . . . F 6 55.902 51.549 95.418 1 25.3 ? O3B GDP 600 B 1 HETATM 5 O O3A GDP . . . F 6 53.883 50.772 94.006 1 19.52 ? O3A GDP 600 B 1 HETATM 6 P PA GDP . . . F 6 52.654 49.641 94.069 1 20.51 ? PA GDP 600 B 1 HETATM 7 O O1A GDP . . . F 6 52.799 48.701 92.922 1 23.36 ? O1A GDP 600 B 1 HETATM 8 O O2A GDP . . . F 6 52.732 49.007 95.448 1 18 ? O2A GDP 600 B 1 HETATM 9 O O5' GDP . . . F 6 51.411 50.54 93.819 1 16.66 ? O5' GDP 600 B 1 HETATM 10 C C5' GDP . . . F 6 50.083 50.143 94.277 1 7.65 ? C5' GDP 600 B 1 HETATM 11 C C4' GDP . . . F 6 49.079 50.044 93.233 1 2.51 ? C4' GDP 600 B 1 HETATM 12 O O4' GDP . . . F 6 49.474 48.963 92.298 1 2 ? O4' GDP 600 B 1 HETATM 13 C C3' GDP . . . F 6 47.666 49.542 93.703 1 3.46 ? C3' GDP 600 B 1 HETATM 14 O O3' GDP . . . F 6 46.684 50.308 92.915 1 2.32 ? O3' GDP 600 B 1 HETATM 15 C C2' GDP . . . F 6 47.512 48.044 93.347 1 2.23 ? C2' GDP 600 B 1 HETATM 16 O O2' GDP . . . F 6 46.212 47.534 93.006 1 2 ? O2' GDP 600 B 1 HETATM 17 C C1' GDP . . . F 6 48.457 47.879 92.157 1 2 ? C1' GDP 600 B 1 HETATM 18 N N9 GDP . . . F 6 49.168 46.602 92.117 1 5.88 ? N9 GDP 600 B 1 HETATM 19 C C8 GDP . . . F 6 50.246 46.333 93.129 1 9.42 ? C8 GDP 600 B 1 HETATM 20 N N7 GDP . . . F 6 50.539 45.062 92.604 1 10.36 ? N7 GDP 600 B 1 HETATM 21 C C5 GDP . . . F 6 49.868 44.588 91.559 1 10.45 ? C5 GDP 600 B 1 HETATM 22 C C6 GDP . . . F 6 49.699 43.503 90.672 1 13.51 ? C6 GDP 600 B 1 HETATM 23 O O6 GDP . . . F 6 50.521 42.455 90.858 1 11.34 ? O6 GDP 600 B 1 HETATM 24 N N1 GDP . . . F 6 48.809 43.47 89.657 1 10.31 ? N1 GDP 600 B 1 HETATM 25 C C2 GDP . . . F 6 47.921 44.648 89.463 1 5.81 ? C2 GDP 600 B 1 HETATM 26 N N2 GDP . . . F 6 47.13 44.392 88.443 1 6.23 ? N2 GDP 600 B 1 HETATM 27 N N3 GDP . . . F 6 48.008 45.648 90.236 1 4.23 ? N3 GDP 600 B 1 HETATM 28 C C4 GDP . . . F 6 48.935 45.649 91.212 1 7.64 ? C4 GDP 600 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #