data_3C7K # _model_server_result.job_id S5wosnWgLjZ1pQiIjP5Byw _model_server_result.datetime_utc '2025-02-27 11:39:30' _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 3c7k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":361}' # _entry.id 3C7K # _exptl.entry_id 3C7K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _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 120 _cell.entry_id 3C7K _cell.length_a 96.357 _cell.length_b 96.357 _cell.length_c 235.61 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3C7K _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,K 1 1 C,D,H,I,J,L 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 G N N ? 5 J 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 A OG SER 26 A SER 47 1_555 E MG MG . A MG 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc2 A OG1 THR 161 A THR 182 1_555 E MG MG . A MG 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc3 G O2B GDP . A GDP 361 1_555 E MG MG . A MG 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc4 E MG MG . A MG 362 1_555 K O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? metalc ? metalc5 E MG MG . A MG 362 1_555 K O HOH . A HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? metalc ? metalc6 C OG SER 26 C SER 47 1_555 H MG MG . C MG 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc7 C OG1 THR 161 C THR 182 1_555 H MG MG . C MG 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc8 J O2B GDP . C GDP 361 1_555 H MG MG . C MG 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc9 H MG MG . C MG 362 1_555 L O HOH . C HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc10 H MG MG . C MG 362 1_555 L O HOH . C HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? # _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 87 n n PB O2B GDP sing 88 n n PB O3B GDP sing 89 n n PB O3A GDP sing 90 n n O2B HOB2 GDP sing 91 n n O3B HOB3 GDP sing 92 n n O3A PA GDP sing 93 n n PA O1A GDP doub 94 n n PA O2A GDP sing 95 n n PA O5' GDP sing 96 n n O2A HOA2 GDP sing 97 n n O5' C5' GDP sing 98 n n C5' C4' GDP sing 99 n n C5' H5' GDP sing 100 n n C5' "H5''" GDP sing 101 n n C4' O4' GDP sing 102 n n C4' C3' GDP sing 103 n n C4' H4' GDP sing 104 n n O4' C1' GDP sing 105 n n C3' O3' GDP sing 106 n n C3' C2' GDP sing 107 n n C3' H3' GDP sing 108 n n O3' HO3' GDP sing 109 n n C2' O2' GDP sing 110 n n C2' C1' GDP sing 111 n n C2' H2' GDP sing 112 n n O2' HO2' GDP sing 113 n n C1' N9 GDP sing 114 n n C1' H1' GDP sing 115 n n N9 C8 GDP sing 116 n y N9 C4 GDP sing 117 n y C8 N7 GDP doub 118 n y C8 H8 GDP sing 119 n n N7 C5 GDP sing 120 n y C5 C6 GDP sing 121 n n C5 C4 GDP doub 122 n y C6 O6 GDP doub 123 n n C6 N1 GDP sing 124 n n N1 C2 GDP sing 125 n n N1 HN1 GDP sing 126 n n C2 N2 GDP sing 127 n n C2 N3 GDP doub 128 n n N2 HN21 GDP sing 129 n n N2 HN22 GDP sing 130 n n N3 C4 GDP sing 131 n n # _atom_sites.entry_id 3C7K _atom_sites.fract_transf_matrix[1][1] 0.010378 _atom_sites.fract_transf_matrix[1][2] 0.005992 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011984 _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] 0.004244 _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 E 3 MG A 1 362 362 MG MG . F 4 ALF A 1 365 365 ALF ALF . G 5 GDP A 1 361 361 GDP GDP . H 3 MG C 1 362 362 MG MG . I 4 ALF C 1 365 365 ALF ALF . J 5 GDP C 1 361 361 GDP GDP . K 6 HOH A 1 401 401 HOH HOH . K 6 HOH A 2 402 402 HOH HOH . K 6 HOH A 3 403 403 HOH HOH . L 6 HOH C 1 401 401 HOH HOH . L 6 HOH C 2 402 402 HOH HOH . L 6 HOH C 3 403 403 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 . . . J 5 78.007 38.551 -73.376 1 15.14 ? PB GDP 361 C 1 HETATM 2 O O1B GDP . . . J 5 78.863 37.465 -74.108 1 15.26 ? O1B GDP 361 C 1 HETATM 3 O O2B GDP . . . J 5 77.292 38.299 -72.118 1 13.96 ? O2B GDP 361 C 1 HETATM 4 O O3B GDP . . . J 5 78.873 39.913 -73.157 1 14.47 ? O3B GDP 361 C 1 HETATM 5 O O3A GDP . . . J 5 77.075 39.282 -74.455 1 16.95 ? O3A GDP 361 C 1 HETATM 6 P PA GDP . . . J 5 75.545 39.712 -74.062 1 14.85 ? PA GDP 361 C 1 HETATM 7 O O1A GDP . . . J 5 74.785 38.345 -73.932 1 13.21 ? O1A GDP 361 C 1 HETATM 8 O O2A GDP . . . J 5 75.661 40.527 -72.671 1 13.43 ? O2A GDP 361 C 1 HETATM 9 O O5' GDP . . . J 5 75.193 40.475 -75.408 1 72.14 ? O5' GDP 361 C 1 HETATM 10 C C5' GDP . . . J 5 75.501 41.899 -75.477 1 71.58 ? C5' GDP 361 C 1 HETATM 11 C C4' GDP . . . J 5 74.437 42.694 -76.014 1 71.03 ? C4' GDP 361 C 1 HETATM 12 O O4' GDP . . . J 5 74.226 42.18 -77.394 1 70.58 ? O4' GDP 361 C 1 HETATM 13 C C3' GDP . . . J 5 73.043 42.439 -75.346 1 71.12 ? C3' GDP 361 C 1 HETATM 14 O O3' GDP . . . J 5 72.339 43.739 -75.412 1 69.29 ? O3' GDP 361 C 1 HETATM 15 C C2' GDP . . . J 5 72.274 41.402 -76.21 1 70.83 ? C2' GDP 361 C 1 HETATM 16 O O2' GDP . . . J 5 70.839 41.489 -76.263 1 73.17 ? O2' GDP 361 C 1 HETATM 17 C C1' GDP . . . J 5 72.879 41.617 -77.626 1 69.21 ? C1' GDP 361 C 1 HETATM 18 N N9 GDP . . . J 5 73.071 40.391 -78.448 1 66.55 ? N9 GDP 361 C 1 HETATM 19 C C8 GDP . . . J 5 73.844 39.222 -77.902 1 64.37 ? C8 GDP 361 C 1 HETATM 20 N N7 GDP . . . J 5 73.678 38.472 -79.086 1 62.66 ? N7 GDP 361 C 1 HETATM 21 C C5 GDP . . . J 5 73.004 38.967 -80.118 1 62.33 ? C5 GDP 361 C 1 HETATM 22 C C6 GDP . . . J 5 72.557 38.749 -81.418 1 62.21 ? C6 GDP 361 C 1 HETATM 23 O O6 GDP . . . J 5 72.883 37.584 -81.95 1 63.81 ? O6 GDP 361 C 1 HETATM 24 N N1 GDP . . . J 5 71.836 39.618 -82.149 1 63.08 ? N1 GDP 361 C 1 HETATM 25 C C2 GDP . . . J 5 71.489 40.921 -81.542 1 63.32 ? C2 GDP 361 C 1 HETATM 26 N N2 GDP . . . J 5 70.792 41.605 -82.415 1 63.9 ? N2 GDP 361 C 1 HETATM 27 N N3 GDP . . . J 5 71.866 41.181 -80.383 1 64.81 ? N3 GDP 361 C 1 HETATM 28 C C4 GDP . . . J 5 72.587 40.276 -79.693 1 64.8 ? C4 GDP 361 C 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #