data_8GZY # _model_server_result.job_id OVV-AJaYd50fFf25l9BoVw _model_server_result.datetime_utc '2024-10-19 13:21:55' _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 8gzy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 8GZY # _exptl.entry_id 8GZY _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 92.674 _cell.angle_gamma 90 _cell.entry_id 8GZY _cell.length_a 89.335 _cell.length_b 66.233 _cell.length_c 102.79 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GZY _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 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 ? dimeric 2 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,J 1 1 C,D,H,K,L 2 1 E,F,I,M,N 3 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 ? 3 G N N ? 3 H N N ? 3 I N 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 70 n n PB O2B GDP sing 71 n n PB O3B GDP sing 72 n n PB O3A GDP sing 73 n n O2B HOB2 GDP sing 74 n n O3B HOB3 GDP sing 75 n n O3A PA GDP sing 76 n n PA O1A GDP doub 77 n n PA O2A GDP sing 78 n n PA O5' GDP sing 79 n n O2A HOA2 GDP sing 80 n n O5' C5' GDP sing 81 n n C5' C4' GDP sing 82 n n C5' H5' GDP sing 83 n n C5' "H5''" GDP sing 84 n n C4' O4' GDP sing 85 n n C4' C3' GDP sing 86 n n C4' H4' GDP sing 87 n n O4' C1' GDP sing 88 n n C3' O3' GDP sing 89 n n C3' C2' GDP sing 90 n n C3' H3' GDP sing 91 n n O3' HO3' GDP sing 92 n n C2' O2' GDP sing 93 n n C2' C1' GDP sing 94 n n C2' H2' GDP sing 95 n n O2' HO2' GDP sing 96 n n C1' N9 GDP sing 97 n n C1' H1' GDP sing 98 n n N9 C8 GDP sing 99 n y N9 C4 GDP sing 100 n y C8 N7 GDP doub 101 n y C8 H8 GDP sing 102 n n N7 C5 GDP sing 103 n y C5 C6 GDP sing 104 n n C5 C4 GDP doub 105 n y C6 O6 GDP doub 106 n n C6 N1 GDP sing 107 n n N1 C2 GDP sing 108 n n N1 HN1 GDP sing 109 n n C2 N2 GDP sing 110 n n C2 N3 GDP doub 111 n n N2 HN21 GDP sing 112 n n N2 HN22 GDP sing 113 n n N3 C4 GDP sing 114 n n # _atom_sites.entry_id 8GZY _atom_sites.fract_transf_matrix[1][1] 0.011194 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000523 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015098 _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] 0.009739 _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 3 GDP A 1 401 401 GDP GDP . H 3 GDP C 1 401 401 GDP GDP . I 3 GDP E 1 401 401 GDP GDP . J 4 HOH A 1 501 5 HOH HOH . J 4 HOH A 2 502 2 HOH HOH . K 4 HOH C 1 501 8 HOH HOH . K 4 HOH C 2 502 9 HOH HOH . K 4 HOH C 3 503 7 HOH HOH . L 4 HOH D 1 101 1 HOH HOH . L 4 HOH D 2 102 3 HOH HOH . M 4 HOH E 1 501 6 HOH HOH . N 4 HOH F 1 101 4 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 . . . I 3 46.094 -43.691 74.155 1 81.09 ? PB GDP 401 E 1 HETATM 2 O O1B GDP . . . I 3 45.739 -44.863 73.259 1 76.42 ? O1B GDP 401 E 1 HETATM 3 O O2B GDP . . . I 3 46.903 -42.637 73.432 1 65.23 ? O2B GDP 401 E 1 HETATM 4 O O3B GDP . . . I 3 46.771 -44.231 75.404 1 75.15 ? O3B GDP 401 E 1 HETATM 5 O O3A GDP . . . I 3 44.716 -43.037 74.61 1 73.71 ? O3A GDP 401 E 1 HETATM 6 P PA GDP . . . I 3 44.65 -41.637 75.378 1 76.02 ? PA GDP 401 E 1 HETATM 7 O O1A GDP . . . I 3 44.096 -40.565 74.458 1 81.49 ? O1A GDP 401 E 1 HETATM 8 O O2A GDP . . . I 3 45.977 -41.157 75.913 1 74.95 ? O2A GDP 401 E 1 HETATM 9 O O5' GDP . . . I 3 43.561 -42.021 76.506 1 72.29 ? O5' GDP 401 E 1 HETATM 10 C C5' GDP . . . I 3 43.907 -42.793 77.657 1 73.54 ? C5' GDP 401 E 1 HETATM 11 C C4' GDP . . . I 3 43.303 -42.189 78.935 1 75.88 ? C4' GDP 401 E 1 HETATM 12 O O4' GDP . . . I 3 44.023 -40.996 79.244 1 77.52 ? O4' GDP 401 E 1 HETATM 13 C C3' GDP . . . I 3 41.84 -41.726 78.878 1 73.8 ? C3' GDP 401 E 1 HETATM 14 O O3' GDP . . . I 3 40.897 -42.744 79.234 1 67.21 ? O3' GDP 401 E 1 HETATM 15 C C2' GDP . . . I 3 41.763 -40.5 79.793 1 69.87 ? C2' GDP 401 E 1 HETATM 16 O O2' GDP . . . I 3 41.312 -40.75 81.126 1 66.94 ? O2' GDP 401 E 1 HETATM 17 C C1' GDP . . . I 3 43.193 -40.033 79.908 1 73.97 ? C1' GDP 401 E 1 HETATM 18 N N9 GDP . . . I 3 43.297 -38.747 79.193 1 76.45 ? N9 GDP 401 E 1 HETATM 19 C C8 GDP . . . I 3 42.666 -38.44 78.043 1 73.34 ? C8 GDP 401 E 1 HETATM 20 N N7 GDP . . . I 3 42.998 -37.185 77.647 1 74.02 ? N7 GDP 401 E 1 HETATM 21 C C5 GDP . . . I 3 43.857 -36.679 78.545 1 69.61 ? C5 GDP 401 E 1 HETATM 22 C C6 GDP . . . I 3 44.597 -35.423 78.725 1 70 ? C6 GDP 401 E 1 HETATM 23 O O6 GDP . . . I 3 44.466 -34.491 77.9 1 73.56 ? O6 GDP 401 E 1 HETATM 24 N N1 GDP . . . I 3 45.396 -35.317 79.802 1 70.84 ? N1 GDP 401 E 1 HETATM 25 C C2 GDP . . . I 3 45.542 -36.299 80.702 1 66.46 ? C2 GDP 401 E 1 HETATM 26 N N2 GDP . . . I 3 46.366 -36.128 81.769 1 71.43 ? N2 GDP 401 E 1 HETATM 27 N N3 GDP . . . I 3 44.894 -37.472 80.59 1 68.96 ? N3 GDP 401 E 1 HETATM 28 C C4 GDP . . . I 3 44.055 -37.713 79.563 1 73.36 ? C4 GDP 401 E 1 # _model_server_stats.io_time_ms 109 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #