data_6QVJ # _model_server_result.job_id cQWtlT3CYDYManvu4y4jYg _model_server_result.datetime_utc '2024-11-26 12:57:00' _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 6qvj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":501}' # _entry.id 6QVJ # _exptl.entry_id 6QVJ _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 2 _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 6QVJ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QVJ _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 PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 J N N ? 6 L 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 metalc ? metalc1 B OE2 GLU 71 O GLU 71 1_555 G MG MG . O MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.976 ? metalc ? metalc2 F O1G GTP . O GTP 501 1_555 G MG MG . O MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc3 F O2G GTP . O GTP 501 1_555 G MG MG . O MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? metalc ? metalc4 F O3B GTP . O GTP 501 1_555 G MG MG . O MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? metalc ? metalc5 F O1B GTP . O GTP 501 1_555 G MG MG . O MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc6 C OE2 GLU 71 X GLU 71 1_555 I MG MG . X MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc7 H O1G GTP . X GTP 501 1_555 I MG MG . X MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? metalc ? metalc8 H O3B GTP . X GTP 501 1_555 I MG MG . X MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.967 ? metalc ? metalc9 H O1B GTP . X GTP 501 1_555 I MG MG . X MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? # _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 6QVJ _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 F 4 GTP O 1 501 501 GTP GTP . G 5 MG O 1 502 502 MG MG . H 4 GTP X 1 501 501 GTP GTP . I 5 MG X 1 502 502 MG MG . J 6 GDP S 1 501 501 GDP GDP . K 7 TA1 S 1 502 601 TA1 TA1 . L 6 GDP U 1 501 501 GDP GDP . M 7 TA1 U 1 502 601 TA1 TA1 . # 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 . . . J 6 180.454 277.454 352.408 1 97.09 ? PB GDP 501 S 1 HETATM 2 O O1B GDP . . . J 6 180.074 277.484 350.936 1 97.09 ? O1B GDP 501 S 1 HETATM 3 O O2B GDP . . . J 6 181.661 278.348 352.604 1 97.09 ? O2B GDP 501 S 1 HETATM 4 O O3B GDP . . . J 6 179.328 277.773 353.299 1 97.09 ? O3B GDP 501 S 1 HETATM 5 O O3A GDP . . . J 6 180.981 275.982 352.686 1 97.09 ? O3A GDP 501 S 1 HETATM 6 P PA GDP . . . J 6 182.073 275.155 351.882 1 97.09 ? PA GDP 501 S 1 HETATM 7 O O1A GDP . . . J 6 182.252 275.856 350.56 1 97.09 ? O1A GDP 501 S 1 HETATM 8 O O2A GDP . . . J 6 183.344 275.182 352.624 1 97.09 ? O2A GDP 501 S 1 HETATM 9 O O5' GDP . . . J 6 181.451 273.722 351.627 1 97.09 ? O5' GDP 501 S 1 HETATM 10 C C5' GDP . . . J 6 181.959 272.48 352.152 1 97.09 ? C5' GDP 501 S 1 HETATM 11 C C4' GDP . . . J 6 182.191 271.536 351.003 1 97.09 ? C4' GDP 501 S 1 HETATM 12 O O4' GDP . . . J 6 183.198 272.088 350.127 1 97.09 ? O4' GDP 501 S 1 HETATM 13 C C3' GDP . . . J 6 182.674 270.14 351.388 1 97.09 ? C3' GDP 501 S 1 HETATM 14 O O3' GDP . . . J 6 182.045 269.159 350.575 1 97.09 ? O3' GDP 501 S 1 HETATM 15 C C2' GDP . . . J 6 184.177 270.212 351.125 1 97.09 ? C2' GDP 501 S 1 HETATM 16 O O2' GDP . . . J 6 184.705 268.952 350.735 1 97.09 ? O2' GDP 501 S 1 HETATM 17 C C1' GDP . . . J 6 184.225 271.142 349.927 1 97.09 ? C1' GDP 501 S 1 HETATM 18 N N9 GDP . . . J 6 185.496 271.858 349.812 1 97.09 ? N9 GDP 501 S 1 HETATM 19 C C8 GDP . . . J 6 185.985 272.807 350.66 1 97.09 ? C8 GDP 501 S 1 HETATM 20 N N7 GDP . . . J 6 187.156 273.265 350.3 1 97.09 ? N7 GDP 501 S 1 HETATM 21 C C5 GDP . . . J 6 187.45 272.573 349.14 1 97.09 ? C5 GDP 501 S 1 HETATM 22 C C6 GDP . . . J 6 188.555 272.658 348.282 1 97.09 ? C6 GDP 501 S 1 HETATM 23 O O6 GDP . . . J 6 189.541 273.371 348.422 1 97.09 ? O6 GDP 501 S 1 HETATM 24 N N1 GDP . . . J 6 188.439 271.825 347.194 1 97.09 ? N1 GDP 501 S 1 HETATM 25 C C2 GDP . . . J 6 187.384 270.997 346.952 1 97.09 ? C2 GDP 501 S 1 HETATM 26 N N2 GDP . . . J 6 187.413 270.29 345.824 1 97.09 ? N2 GDP 501 S 1 HETATM 27 N N3 GDP . . . J 6 186.341 270.893 347.768 1 97.09 ? N3 GDP 501 S 1 HETATM 28 C C4 GDP . . . J 6 186.438 271.707 348.83 1 97.09 ? C4 GDP 501 S 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #