data_8PFH # _model_server_result.job_id JE2bA8kQCaXSjxBQJtyrWg _model_server_result.datetime_utc '2024-10-20 00:34:15' _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 8pfh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":401}' # _entry.id 8PFH # _exptl.entry_id 8PFH _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 109.68 _cell.angle_gamma 90 _cell.entry_id 8PFH _cell.length_a 258.178 _cell.length_b 69.373 _cell.length_c 92.533 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PFH _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall 'C 2y' _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_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 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 E N N ? 5 F N N ? 5 G N N ? 5 H 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 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 8PFH _atom_sites.fract_transf_matrix[1][1] 0.003873 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001385 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014415 _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] 0.011477 _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 5 GDP A 1 401 401 GDP GDP . F 5 GDP B 1 501 501 GDP GDP . G 5 GDP C 1 401 401 GDP GDP . H 5 GDP D 1 401 401 GDP GDP . # 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 5 0.593 0.46 73.064 1 39.28 ? PB GDP 401 C 1 HETATM 2 O O1B GDP . . . G 5 0.3 -0.12 71.694 1 37.71 -1 O1B GDP 401 C 1 HETATM 3 O O2B GDP . . . G 5 -0.256 1.669 73.385 1 39.3 ? O2B GDP 401 C 1 HETATM 4 O O3B GDP . . . G 5 0.567 -0.587 74.16 1 39.6 ? O3B GDP 401 C 1 HETATM 5 O O3A GDP . . . G 5 2.111 1.015 72.991 1 41.25 ? O3A GDP 401 C 1 HETATM 6 P PA GDP . . . G 5 2.927 2.384 72.876 1 43.16 ? PA GDP 401 C 1 HETATM 7 O O1A GDP . . . G 5 2.15 3.325 72.041 1 42.59 -1 O1A GDP 401 C 1 HETATM 8 O O2A GDP . . . G 5 3.363 2.807 74.228 1 44.49 ? O2A GDP 401 C 1 HETATM 9 O O5' GDP . . . G 5 4.207 1.964 72.026 1 43.91 ? O5' GDP 401 C 1 HETATM 10 C C5' GDP . . . G 5 5.139 3.017 71.716 1 45.69 ? C5' GDP 401 C 1 HETATM 11 C C4' GDP . . . G 5 6.45 2.457 71.222 1 46.58 ? C4' GDP 401 C 1 HETATM 12 O O4' GDP . . . G 5 6.224 1.676 70.031 1 44.79 ? O4' GDP 401 C 1 HETATM 13 C C3' GDP . . . G 5 7.482 3.522 70.86 1 47.61 ? C3' GDP 401 C 1 HETATM 14 O O3' GDP . . . G 5 8.385 3.71 71.947 1 47.66 ? O3' GDP 401 C 1 HETATM 15 C C2' GDP . . . G 5 8.197 2.92 69.649 1 46.54 ? C2' GDP 401 C 1 HETATM 16 O O2' GDP . . . G 5 9.276 2.073 70.03 1 46.04 ? O2' GDP 401 C 1 HETATM 17 C C1' GDP . . . G 5 7.08 2.109 68.992 1 44.86 ? C1' GDP 401 C 1 HETATM 18 N N9 GDP . . . G 5 6.278 2.855 68.007 1 43.9 ? N9 GDP 401 C 1 HETATM 19 C C8 GDP . . . G 5 5.452 3.927 68.228 1 44.43 ? C8 GDP 401 C 1 HETATM 20 N N7 GDP . . . G 5 4.843 4.341 67.139 1 43.23 ? N7 GDP 401 C 1 HETATM 21 C C5 GDP . . . G 5 5.297 3.49 66.145 1 42.02 ? C5 GDP 401 C 1 HETATM 22 C C6 GDP . . . G 5 4.992 3.426 64.749 1 40.95 ? C6 GDP 401 C 1 HETATM 23 O O6 GDP . . . G 5 4.223 4.152 64.12 1 40.76 ? O6 GDP 401 C 1 HETATM 24 N N1 GDP . . . G 5 5.673 2.404 64.114 1 40.38 ? N1 GDP 401 C 1 HETATM 25 C C2 GDP . . . G 5 6.54 1.536 64.721 1 40.54 ? C2 GDP 401 C 1 HETATM 26 N N2 GDP . . . G 5 7.112 0.588 63.951 1 40 ? N2 GDP 401 C 1 HETATM 27 N N3 GDP . . . G 5 6.833 1.583 66.021 1 41.51 ? N3 GDP 401 C 1 HETATM 28 C C4 GDP . . . G 5 6.181 2.57 66.666 1 42.33 ? C4 GDP 401 C 1 HETATM 29 H H5' GDP . . . G 5 4.747 3.524 70.976 1 32.63 ? H5' GDP 401 C 1 HETATM 30 H "H5''" GDP . . . G 5 5.239 3.683 72.426 1 32.63 ? "H5''" GDP 401 C 1 HETATM 31 H H4' GDP . . . G 5 6.812 1.845 71.895 1 32.86 ? H4' GDP 401 C 1 HETATM 32 H H3' GDP . . . G 5 7.095 4.408 70.709 1 33.57 ? H3' GDP 401 C 1 HETATM 33 H HO3' GDP . . . G 5 8.867 4.333 71.628 1 33.57 ? HO3' GDP 401 C 1 HETATM 34 H H2' GDP . . . G 5 8.544 3.598 69.035 1 33.81 ? H2' GDP 401 C 1 HETATM 35 H HO2' GDP . . . G 5 9.636 1.935 69.272 1 33.81 ? HO2' GDP 401 C 1 HETATM 36 H H1' GDP . . . G 5 7.432 1.308 68.553 1 33.25 ? H1' GDP 401 C 1 HETATM 37 H H8 GDP . . . G 5 5.35 4.321 69.118 1 33.55 ? H8 GDP 401 C 1 HETATM 38 H HN1 GDP . . . G 5 5.512 2.335 63.249 1 33.44 ? HN1 GDP 401 C 1 HETATM 39 H HN21 GDP . . . G 5 7.683 -0.017 64.247 1 33.13 ? HN21 GDP 401 C 1 HETATM 40 H HN22 GDP . . . G 5 6.886 0.592 63.097 1 33.13 ? HN22 GDP 401 C 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 40 #