data_3D6T # _model_server_result.job_id KRYJX-w98gIqRjDdApO9fQ _model_server_result.datetime_utc '2025-09-18 22:41:22' _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 3d6t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1}' # _entry.id 3D6T # _exptl.entry_id 3D6T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 112.76 _cell.angle_gamma 90 _cell.entry_id 3D6T _cell.length_a 69.919 _cell.length_b 53.167 _cell.length_c 42.736 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D6T _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 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 ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 software_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,C,D 1 1 A,B,C,D 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 53.385642 0 39.408296 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 covale ? covale1 A C MSE 1 B MSE 1335 1_555 A N LYS 2 B LYS 1336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale2 A C LEU 3 B LEU 1337 1_555 A N MSE 4 B MSE 1338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale3 A C MSE 4 B MSE 1338 1_555 A N ILE 5 B ILE 1339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.296 ? covale ? covale4 A C LEU 20 B LEU 1354 1_555 A N MSE 21 B MSE 1355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.313 ? covale ? covale5 A C PHE 74 B PHE 1408 1_555 A N MSE 75 B MSE 1409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale6 A C MSE 75 B MSE 1409 1_555 A N THR 76 B THR 1410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale7 A C ALA 96 B ALA 1430 1_555 A N MSE 97 B MSE 1431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 A C MSE 97 B MSE 1431 1_555 A N LYS 98 B LYS 1432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 C O2B GDP . B GDP 1 1_555 B MG MG . B MG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? # _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 3D6T _atom_sites.fract_transf_matrix[1][1] 0.014302 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018809 _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] 0.025375 _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 B 2 MG B 1 2 2 MG MG . C 3 GDP B 1 1 1 GDP GDP . D 4 HOH B 1 1506 1 HOH HOH . D 4 HOH B 2 1507 2 HOH HOH . D 4 HOH B 3 1508 3 HOH HOH . D 4 HOH B 4 1509 4 HOH HOH . D 4 HOH B 5 1510 5 HOH HOH . D 4 HOH B 6 1511 8 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 . . . C 3 12.007 -18.064 18.385 1 29.54 ? PB GDP 1 B 1 HETATM 2 O O1B GDP . . . C 3 12.007 -17.873 19.857 1 32.09 ? O1B GDP 1 B 1 HETATM 3 O O2B GDP . . . C 3 13.473 -18.326 18.07 1 36.72 ? O2B GDP 1 B 1 HETATM 4 O O3B GDP . . . C 3 11.476 -16.792 17.83 1 28.2 ? O3B GDP 1 B 1 HETATM 5 O O3A GDP . . . C 3 11.077 -19.285 17.898 1 33.49 ? O3A GDP 1 B 1 HETATM 6 P PA GDP . . . C 3 11.413 -20.746 17.418 1 30.63 ? PA GDP 1 B 1 HETATM 7 O O1A GDP . . . C 3 11.709 -21.075 15.986 1 32.74 ? O1A GDP 1 B 1 HETATM 8 O O2A GDP . . . C 3 12.456 -21.283 18.312 1 33.43 ? O2A GDP 1 B 1 HETATM 9 O O5' GDP . . . C 3 10.13 -21.499 17.882 1 35.24 ? O5' GDP 1 B 1 HETATM 10 C C5' GDP . . . C 3 8.804 -21.331 17.536 1 37.25 ? C5' GDP 1 B 1 HETATM 11 C C4' GDP . . . C 3 8.124 -22.719 17.621 1 38.34 ? C4' GDP 1 B 1 HETATM 12 O O4' GDP . . . C 3 7.075 -22.639 16.656 1 38.16 ? O4' GDP 1 B 1 HETATM 13 C C3' GDP . . . C 3 8.978 -23.92 17.201 1 41.14 ? C3' GDP 1 B 1 HETATM 14 O O3' GDP . . . C 3 8.59 -25.155 17.822 1 46.22 ? O3' GDP 1 B 1 HETATM 15 C C2' GDP . . . C 3 8.708 -24.163 15.735 1 41.68 ? C2' GDP 1 B 1 HETATM 16 O O2' GDP . . . C 3 8.739 -25.573 15.372 1 45.82 ? O2' GDP 1 B 1 HETATM 17 C C1' GDP . . . C 3 7.327 -23.552 15.596 1 38.76 ? C1' GDP 1 B 1 HETATM 18 N N9 GDP . . . C 3 7.258 -22.684 14.449 1 38.26 ? N9 GDP 1 B 1 HETATM 19 C C8 GDP . . . C 3 8.034 -21.639 14.124 1 37.29 ? C8 GDP 1 B 1 HETATM 20 N N7 GDP . . . C 3 7.625 -21.112 12.971 1 36.14 ? N7 GDP 1 B 1 HETATM 21 C C5 GDP . . . C 3 6.581 -21.848 12.552 1 37.66 ? C5 GDP 1 B 1 HETATM 22 C C6 GDP . . . C 3 5.645 -21.86 11.425 1 38.72 ? C6 GDP 1 B 1 HETATM 23 O O6 GDP . . . C 3 5.751 -20.982 10.519 1 38.64 ? O6 GDP 1 B 1 HETATM 24 N N1 GDP . . . C 3 4.679 -22.828 11.418 1 39.25 ? N1 GDP 1 B 1 HETATM 25 C C2 GDP . . . C 3 4.493 -23.772 12.357 1 37.38 ? C2 GDP 1 B 1 HETATM 26 N N2 GDP . . . C 3 3.491 -24.666 12.247 1 36.54 ? N2 GDP 1 B 1 HETATM 27 N N3 GDP . . . C 3 5.341 -23.815 13.396 1 38.37 ? N3 GDP 1 B 1 HETATM 28 C C4 GDP . . . C 3 6.344 -22.9 13.533 1 39.57 ? C4 GDP 1 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #