data_6MLQ # _model_server_result.job_id DgHKqyhfqYUxTz_fwIDEBw _model_server_result.datetime_utc '2024-11-17 11:45:54' _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 6mlq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":600}' # _entry.id 6MLQ # _exptl.entry_id 6MLQ _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 6MLQ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6MLQ _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 ? _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 501 1_555 E O1G GTP . A GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc2 D MG MG . A MG 501 1_555 E O3A GTP . A GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc3 D MG MG . A MG 501 1_555 E O1A GTP . A GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc4 H O1B ADP . C ADP 401 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc5 H O3B ADP . C ADP 401 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc6 H O1A ADP . C ADP 401 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc7 H O3A ADP . C ADP 401 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.898 ? # _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 127 n n PB O2B GDP sing 128 n n PB O3B GDP sing 129 n n PB O3A GDP sing 130 n n O2B HOB2 GDP sing 131 n n O3B HOB3 GDP sing 132 n n O3A PA GDP sing 133 n n PA O1A GDP doub 134 n n PA O2A GDP sing 135 n n PA O5' GDP sing 136 n n O2A HOA2 GDP sing 137 n n O5' C5' GDP sing 138 n n C5' C4' GDP sing 139 n n C5' H5' GDP sing 140 n n C5' "H5''" GDP sing 141 n n C4' O4' GDP sing 142 n n C4' C3' GDP sing 143 n n C4' H4' GDP sing 144 n n O4' C1' GDP sing 145 n n C3' O3' GDP sing 146 n n C3' C2' GDP sing 147 n n C3' H3' GDP sing 148 n n O3' HO3' GDP sing 149 n n C2' O2' GDP sing 150 n n C2' C1' GDP sing 151 n n C2' H2' GDP sing 152 n n O2' HO2' GDP sing 153 n n C1' N9 GDP sing 154 n n C1' H1' GDP sing 155 n n N9 C8 GDP sing 156 n y N9 C4 GDP sing 157 n y C8 N7 GDP doub 158 n y C8 H8 GDP sing 159 n n N7 C5 GDP sing 160 n y C5 C6 GDP sing 161 n n C5 C4 GDP doub 162 n y C6 O6 GDP doub 163 n n C6 N1 GDP sing 164 n n N1 C2 GDP sing 165 n n N1 HN1 GDP sing 166 n n C2 N2 GDP sing 167 n n C2 N3 GDP doub 168 n n N2 HN21 GDP sing 169 n n N2 HN22 GDP sing 170 n n N3 C4 GDP sing 171 n n # _atom_sites.entry_id 6MLQ _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 1 501 501 MG MG . E 5 GTP A 1 502 502 GTP GTP . F 6 GDP B 1 600 600 GDP GDP . G 7 TA1 B 1 601 601 TA1 TA1 . H 8 ADP C 1 401 401 ADP ADP . I 4 MG C 1 402 402 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 34.944 81.311 141.729 1 148.83 ? PB GDP 600 B 1 HETATM 2 O O1B GDP . . . F 6 36.027 81.205 140.686 1 148.83 ? O1B GDP 600 B 1 HETATM 3 O O2B GDP . . . F 6 35.261 80.432 142.908 1 148.83 ? O2B GDP 600 B 1 HETATM 4 O O3B GDP . . . F 6 34.815 82.74 142.192 1 148.83 ? O3B GDP 600 B 1 HETATM 5 O O3A GDP . . . F 6 33.559 80.847 141.072 1 148.83 ? O3A GDP 600 B 1 HETATM 6 P PA GDP . . . F 6 33.125 81.514 139.683 1 148.83 ? PA GDP 600 B 1 HETATM 7 O O1A GDP . . . F 6 33.717 80.739 138.536 1 148.83 ? O1A GDP 600 B 1 HETATM 8 O O2A GDP . . . F 6 33.544 82.959 139.618 1 148.83 ? O2A GDP 600 B 1 HETATM 9 O O5' GDP . . . F 6 31.524 81.407 139.699 1 148.83 ? O5' GDP 600 B 1 HETATM 10 C C5' GDP . . . F 6 30.786 82.611 139.54 1 148.83 ? C5' GDP 600 B 1 HETATM 11 C C4' GDP . . . F 6 29.349 82.308 139.164 1 148.83 ? C4' GDP 600 B 1 HETATM 12 O O4' GDP . . . F 6 29.32 81.214 138.256 1 148.83 ? O4' GDP 600 B 1 HETATM 13 C C3' GDP . . . F 6 28.52 81.904 140.365 1 148.83 ? C3' GDP 600 B 1 HETATM 14 O O3' GDP . . . F 6 27.671 82.985 140.75 1 148.83 ? O3' GDP 600 B 1 HETATM 15 C C2' GDP . . . F 6 27.678 80.745 139.888 1 148.83 ? C2' GDP 600 B 1 HETATM 16 O O2' GDP . . . F 6 26.316 81.16 139.825 1 148.83 ? O2' GDP 600 B 1 HETATM 17 C C1' GDP . . . F 6 28.17 80.412 138.493 1 148.83 ? C1' GDP 600 B 1 HETATM 18 N N9 GDP . . . F 6 28.539 78.983 138.459 1 148.83 ? N9 GDP 600 B 1 HETATM 19 C C8 GDP . . . F 6 29.445 78.389 139.248 1 148.83 ? C8 GDP 600 B 1 HETATM 20 N N7 GDP . . . F 6 29.547 77.068 138.962 1 148.83 ? N7 GDP 600 B 1 HETATM 21 C C5 GDP . . . F 6 28.691 76.812 137.965 1 148.83 ? C5 GDP 600 B 1 HETATM 22 C C6 GDP . . . F 6 28.296 75.628 137.187 1 148.83 ? C6 GDP 600 B 1 HETATM 23 O O6 GDP . . . F 6 28.818 74.522 137.409 1 148.83 ? O6 GDP 600 B 1 HETATM 24 N N1 GDP . . . F 6 27.373 75.78 136.239 1 148.83 ? N1 GDP 600 B 1 HETATM 25 C C2 GDP . . . F 6 26.805 76.967 135.983 1 148.83 ? C2 GDP 600 B 1 HETATM 26 N N2 GDP . . . F 6 25.876 77.037 135.004 1 148.83 ? N2 GDP 600 B 1 HETATM 27 N N3 GDP . . . F 6 27.116 78.096 136.655 1 148.83 ? N3 GDP 600 B 1 HETATM 28 C C4 GDP . . . F 6 28.028 78.074 137.641 1 148.83 ? C4 GDP 600 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 28 #