data_7RKF # _model_server_result.job_id Nj5VFTL7gDGVi70oxepTgw _model_server_result.datetime_utc '2025-04-22 23:46:43' _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 7rkf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":401}' # _entry.id 7RKF # _exptl.entry_id 7RKF _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 7 _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 7RKF _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7RKF _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 ? _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 7 _struct_asym.id G _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 disulf ? disulf1 D SG CYS 22 D CYS 22 1_555 D SG CYS 96 D CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf2 D SG CYS 159 D CYS 147 1_555 D SG CYS 229 D CYS 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 E SG CYS 8 L CYS 8 1_555 E SG CYS 34 L CYS 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 E SG CYS 12 L CYS 12 1_555 E SG CYS 50 L CYS 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 F SG CYS 31 R CYS 23 1_555 F SG CYS 271 R CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 F SG CYS 112 R CYS 104 1_555 F SG CYS 181 R CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 E C PCA 1 L PCA 1 1_555 E N HIS 2 L HIS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 E ND2 ASN 9 L ASN 9 1_555 H C1 NAG . L NAG 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _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 7RKF _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 G 7 GDP A 1 401 401 GDP GDP . H 8 NAG L 1 101 101 NAG NAG . # 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 . . . G 7 133.41 114.044 82.275 1 45.85 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . G 7 133.308 112.599 81.869 1 45.85 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . G 7 134.16 114.141 83.578 1 45.85 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . G 7 132.032 114.634 82.416 1 45.85 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . G 7 134.229 114.833 81.15 1 45.85 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . G 7 135.822 114.799 81.276 1 45.85 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . G 7 136.252 113.464 81.824 1 45.85 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . G 7 136.3 115.927 82.152 1 45.85 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . G 7 136.315 115.001 79.763 1 45.85 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . G 7 135.634 115.901 78.897 1 45.85 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . G 7 136.447 116.03 77.622 1 45.85 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . G 7 135.927 117.08 76.809 1 45.85 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . G 7 137.881 116.363 77.964 1 45.85 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . G 7 138.717 115.269 77.592 1 45.85 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . G 7 138.228 117.572 77.133 1 45.85 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . G 7 139.32 117.247 76.273 1 45.85 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . G 7 136.995 117.882 76.308 1 45.85 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . G 7 136.651 119.314 76.451 1 45.85 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . G 7 135.869 119.832 77.407 1 45.85 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . G 7 135.755 121.174 77.269 1 45.85 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . G 7 136.487 121.533 76.206 1 45.85 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . G 7 136.8 122.795 75.51 1 45.85 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . G 7 136.331 123.877 75.913 1 45.85 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . G 7 137.598 122.745 74.442 1 45.85 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . G 7 138.113 121.591 73.991 1 45.85 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . G 7 138.916 121.621 72.902 1 45.85 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . G 7 137.868 120.396 74.582 1 45.85 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . G 7 137.077 120.306 75.672 1 45.85 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #