data_1GIT # _model_server_result.job_id 3_ll8fxxnTsmMlDJoMP3Dg _model_server_result.datetime_utc '2025-02-28 15:12:16' _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 1git # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":355}' # _entry.id 1GIT # _exptl.entry_id 1GIT _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 90 _cell.angle_gamma 90 _cell.entry_id 1GIT _cell.length_a 77.1 _cell.length_b 77.1 _cell.length_c 144.6 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1GIT _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 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 # _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 # _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 1GIT _atom_sites.fract_transf_matrix[1][1] 0.01297 _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] 0.01297 _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] 0.006916 _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 PO4 A 1 356 356 PO4 PO4 . C 3 GDP A 1 355 355 GDP GDP . D 4 HOH A 1 401 401 HOH HOH . D 4 HOH A 2 402 402 HOH HOH . D 4 HOH A 3 403 403 HOH HOH . D 4 HOH A 4 404 404 HOH HOH . D 4 HOH A 5 405 405 HOH HOH . D 4 HOH A 6 406 406 HOH HOH . D 4 HOH A 7 407 407 HOH HOH . D 4 HOH A 8 408 408 HOH HOH . D 4 HOH A 9 409 409 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 68.473 -9.209 53.995 1 7.93 ? PB GDP 355 A 1 HETATM 2 O O1B GDP . . . C 3 67.27 -9.601 53.281 1 9.28 ? O1B GDP 355 A 1 HETATM 3 O O2B GDP . . . C 3 68.748 -7.768 53.968 1 13.32 ? O2B GDP 355 A 1 HETATM 4 O O3B GDP . . . C 3 68.589 -9.926 55.288 1 10.82 ? O3B GDP 355 A 1 HETATM 5 O O3A GDP . . . C 3 69.612 -9.79 53.085 1 5.52 ? O3A GDP 355 A 1 HETATM 6 P PA GDP . . . C 3 71.059 -9.341 52.605 1 2.44 ? PA GDP 355 A 1 HETATM 7 O O1A GDP . . . C 3 70.934 -8.577 51.373 1 8.23 ? O1A GDP 355 A 1 HETATM 8 O O2A GDP . . . C 3 71.902 -8.849 53.667 1 3.34 ? O2A GDP 355 A 1 HETATM 9 O O5' GDP . . . C 3 71.666 -10.742 52.094 1 2 ? O5' GDP 355 A 1 HETATM 10 C C5' GDP . . . C 3 72.342 -11.599 53.027 1 2 ? C5' GDP 355 A 1 HETATM 11 C C4' GDP . . . C 3 73.526 -12.267 52.469 1 2.17 ? C4' GDP 355 A 1 HETATM 12 O O4' GDP . . . C 3 73.063 -12.599 51.135 1 5.34 ? O4' GDP 355 A 1 HETATM 13 C C3' GDP . . . C 3 74.616 -11.348 52.173 1 2.97 ? C3' GDP 355 A 1 HETATM 14 O O3' GDP . . . C 3 75.9 -11.952 52.375 1 3.72 ? O3' GDP 355 A 1 HETATM 15 C C2' GDP . . . C 3 74.354 -10.965 50.703 1 3.25 ? C2' GDP 355 A 1 HETATM 16 O O2' GDP . . . C 3 75.488 -10.44 50.061 1 6.89 ? O2' GDP 355 A 1 HETATM 17 C C1' GDP . . . C 3 73.952 -12.26 50.072 1 2 ? C1' GDP 355 A 1 HETATM 18 N N9 GDP . . . C 3 73.375 -12.125 48.746 1 2.87 ? N9 GDP 355 A 1 HETATM 19 C C8 GDP . . . C 3 72.319 -11.403 48.328 1 2 ? C8 GDP 355 A 1 HETATM 20 N N7 GDP . . . C 3 71.789 -11.725 47.213 1 2 ? N7 GDP 355 A 1 HETATM 21 C C5 GDP . . . C 3 72.686 -12.653 46.718 1 2 ? C5 GDP 355 A 1 HETATM 22 C C6 GDP . . . C 3 72.598 -13.456 45.556 1 4.78 ? C6 GDP 355 A 1 HETATM 23 O O6 GDP . . . C 3 71.761 -13.467 44.656 1 6.2 ? O6 GDP 355 A 1 HETATM 24 N N1 GDP . . . C 3 73.627 -14.337 45.435 1 10.18 ? N1 GDP 355 A 1 HETATM 25 C C2 GDP . . . C 3 74.708 -14.4 46.318 1 12.72 ? C2 GDP 355 A 1 HETATM 26 N N2 GDP . . . C 3 75.785 -14.986 45.821 1 8.71 ? N2 GDP 355 A 1 HETATM 27 N N3 GDP . . . C 3 74.767 -13.725 47.503 1 6.57 ? N3 GDP 355 A 1 HETATM 28 C C4 GDP . . . C 3 73.706 -12.857 47.62 1 5.09 ? C4 GDP 355 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #