data_5O74 # _model_server_result.job_id J8Ctkw8Q8kjmJ9g9BbI_zg _model_server_result.datetime_utc '2025-02-05 16:03:55' _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 5o74 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":500}' # _entry.id 5O74 # _exptl.entry_id 5O74 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 114.61 _cell.angle_beta 97.69 _cell.angle_gamma 100.74 _cell.entry_id 5O74 _cell.length_a 77.91 _cell.length_b 87.45 _cell.length_c 93.17 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5O74 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 PISA dimeric 2 author_and_software_defined_assembly 5 PISA dimeric 2 author_and_software_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,M 1 1 C,D,N 2 1 E,F,O 3 1 G,H,P 4 1 I,J,Q 5 1 K,L,R 6 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 M N N ? 3 N N N ? 3 O N N ? 3 P N N ? 3 Q N N ? 3 R 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 covale ? covale1 A SG CYS 176 A CYS 512 1_555 B C16 9MN 79 B 9MN 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.83 ? covale ? covale2 B C TYR 78 B TYR 78 1_555 B N 9MN 79 B 9MN 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale3 B C 9MN 79 B 9MN 79 1_555 B N GLY 80 B GLY 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale4 C SG CYS 176 C CYS 512 1_555 D C16 9MN 79 D 9MN 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.803 ? covale ? covale5 D C TYR 78 D TYR 78 1_555 D N 9MN 79 D 9MN 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 D C 9MN 79 D 9MN 79 1_555 D N GLY 80 D GLY 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale7 E SG CYS 176 E CYS 512 1_555 F C16 9MN 79 F 9MN 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.848 ? covale ? covale8 F C TYR 78 F TYR 78 1_555 F N 9MN 79 F 9MN 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale9 F C 9MN 79 F 9MN 79 1_555 F N GLY 80 F GLY 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale10 G SG CYS 176 G CYS 512 1_555 H C16 9MN 79 H 9MN 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.792 ? covale ? covale11 H C TYR 78 H TYR 78 1_555 H N 9MN 79 H 9MN 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale12 H C 9MN 79 H 9MN 79 1_555 H N GLY 80 H GLY 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale13 I SG CYS 176 I CYS 512 1_555 J C16 9MN 79 J 9MN 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.811 ? covale ? covale14 J C TYR 78 J TYR 78 1_555 J N 9MN 79 J 9MN 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale15 J C 9MN 79 J 9MN 79 1_555 J N GLY 80 J GLY 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale16 K SG CYS 176 K CYS 512 1_555 L C16 9MN 79 L 9MN 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.804 ? covale ? covale17 L C TYR 78 L TYR 78 1_555 L N 9MN 79 L 9MN 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale18 L C 9MN 79 L 9MN 79 1_555 L N GLY 80 L GLY 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? # _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 123 n n PB O2B GDP sing 124 n n PB O3B GDP sing 125 n n PB O3A GDP sing 126 n n O2B HOB2 GDP sing 127 n n O3B HOB3 GDP sing 128 n n O3A PA GDP sing 129 n n PA O1A GDP doub 130 n n PA O2A GDP sing 131 n n PA O5' GDP sing 132 n n O2A HOA2 GDP sing 133 n n O5' C5' GDP sing 134 n n C5' C4' GDP sing 135 n n C5' H5' GDP sing 136 n n C5' "H5''" GDP sing 137 n n C4' O4' GDP sing 138 n n C4' C3' GDP sing 139 n n C4' H4' GDP sing 140 n n O4' C1' GDP sing 141 n n C3' O3' GDP sing 142 n n C3' C2' GDP sing 143 n n C3' H3' GDP sing 144 n n O3' HO3' GDP sing 145 n n C2' O2' GDP sing 146 n n C2' C1' GDP sing 147 n n C2' H2' GDP sing 148 n n O2' HO2' GDP sing 149 n n C1' N9 GDP sing 150 n n C1' H1' GDP sing 151 n n N9 C8 GDP sing 152 n y N9 C4 GDP sing 153 n y C8 N7 GDP doub 154 n y C8 H8 GDP sing 155 n n N7 C5 GDP sing 156 n y C5 C6 GDP sing 157 n n C5 C4 GDP doub 158 n y C6 O6 GDP doub 159 n n C6 N1 GDP sing 160 n n N1 C2 GDP sing 161 n n N1 HN1 GDP sing 162 n n C2 N2 GDP sing 163 n n C2 N3 GDP doub 164 n n N2 HN21 GDP sing 165 n n N2 HN22 GDP sing 166 n n N3 C4 GDP sing 167 n n # _atom_sites.entry_id 5O74 _atom_sites.fract_transf_matrix[1][1] 0.012835 _atom_sites.fract_transf_matrix[1][2] 0.002435 _atom_sites.fract_transf_matrix[1][3] 0.003183 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011639 _atom_sites.fract_transf_matrix[2][3] 0.005919 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.012151 _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 M 3 GDP B 1 500 500 GDP GDP . N 3 GDP D 1 500 500 GDP GDP . O 3 GDP F 1 500 500 GDP GDP . P 3 GDP H 1 500 500 GDP GDP . Q 3 GDP J 1 500 500 GDP GDP . R 3 GDP L 1 500 500 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 . . . M 3 -2.988 2.969 -69.334 1 62.8 ? PB GDP 500 B 1 HETATM 2 O O1B GDP . . . M 3 -2.08 2.614 -70.485 1 60.56 ? O1B GDP 500 B 1 HETATM 3 O O2B GDP . . . M 3 -3.277 1.683 -68.602 1 72.63 ? O2B GDP 500 B 1 HETATM 4 O O3B GDP . . . M 3 -2.331 4.007 -68.458 1 80.63 ? O3B GDP 500 B 1 HETATM 5 O O3A GDP . . . M 3 -4.351 3.507 -69.975 1 63.55 ? O3A GDP 500 B 1 HETATM 6 P PA GDP . . . M 3 -4.33 4.638 -71.109 1 54.16 ? PA GDP 500 B 1 HETATM 7 O O1A GDP . . . M 3 -3.038 4.61 -71.898 1 68.23 ? O1A GDP 500 B 1 HETATM 8 O O2A GDP . . . M 3 -4.61 6.008 -70.554 1 70.64 ? O2A GDP 500 B 1 HETATM 9 O O5' GDP . . . M 3 -5.574 4.176 -71.998 1 66.88 ? O5' GDP 500 B 1 HETATM 10 C C5' GDP . . . M 3 -5.164 3.362 -73.081 1 69.83 ? C5' GDP 500 B 1 HETATM 11 C C4' GDP . . . M 3 -6.216 3.305 -74.164 1 65.79 ? C4' GDP 500 B 1 HETATM 12 O O4' GDP . . . M 3 -7.553 3.24 -73.664 1 70.94 ? O4' GDP 500 B 1 HETATM 13 C C3' GDP . . . M 3 -6.121 4.613 -74.925 1 64.05 ? C3' GDP 500 B 1 HETATM 14 O O3' GDP . . . M 3 -6.211 4.393 -76.338 1 64.17 ? O3' GDP 500 B 1 HETATM 15 C C2' GDP . . . M 3 -7.291 5.436 -74.429 1 76.21 ? C2' GDP 500 B 1 HETATM 16 O O2' GDP . . . M 3 -7.765 6.362 -75.416 1 67.62 ? O2' GDP 500 B 1 HETATM 17 C C1' GDP . . . M 3 -8.317 4.383 -74.043 1 86.49 ? C1' GDP 500 B 1 HETATM 18 N N9 GDP . . . M 3 -9.134 4.847 -72.906 1 91.3 ? N9 GDP 500 B 1 HETATM 19 C C8 GDP . . . M 3 -8.8 5.085 -71.627 1 92.34 ? C8 GDP 500 B 1 HETATM 20 N N7 GDP . . . M 3 -9.892 5.471 -70.91 1 88.57 ? N7 GDP 500 B 1 HETATM 21 C C5 GDP . . . M 3 -10.948 5.442 -71.742 1 89.34 ? C5 GDP 500 B 1 HETATM 22 C C6 GDP . . . M 3 -12.4 5.717 -71.67 1 104.59 ? C6 GDP 500 B 1 HETATM 23 O O6 GDP . . . M 3 -12.939 6.087 -70.602 1 95.2 ? O6 GDP 500 B 1 HETATM 24 N N1 GDP . . . M 3 -13.114 5.557 -72.792 1 90.42 ? N1 GDP 500 B 1 HETATM 25 C C2 GDP . . . M 3 -12.581 5.162 -73.959 1 107.38 ? C2 GDP 500 B 1 HETATM 26 N N2 GDP . . . M 3 -13.367 5.023 -75.051 1 124.15 ? N2 GDP 500 B 1 HETATM 27 N N3 GDP . . . M 3 -11.267 4.898 -74.094 1 93.34 ? N3 GDP 500 B 1 HETATM 28 C C4 GDP . . . M 3 -10.433 5.02 -73.045 1 90.07 ? C4 GDP 500 B 1 HETATM 29 H H4' GDP . . . M 3 -6.009 2.466 -74.843 1 78.94 ? H4' GDP 500 B 1 HETATM 30 H H3' GDP . . . M 3 -5.18 5.12 -74.669 1 76.86 ? H3' GDP 500 B 1 HETATM 31 H HO3' GDP . . . M 3 -6.125 5.237 -76.802 1 77.01 ? HO3' GDP 500 B 1 HETATM 32 H H2' GDP . . . M 3 -6.983 5.978 -73.524 1 91.45 ? H2' GDP 500 B 1 HETATM 33 H HO2' GDP . . . M 3 -7.05 6.965 -75.662 1 81.15 ? HO2' GDP 500 B 1 HETATM 34 H H1' GDP . . . M 3 -8.952 4.154 -74.91 1 103.79 ? H1' GDP 500 B 1 HETATM 35 H H8 GDP . . . M 3 -7.794 5.019 -71.231 1 110.81 ? H8 GDP 500 B 1 HETATM 36 H HN1 GDP . . . M 3 -14.136 5.746 -72.756 1 108.51 ? HN1 GDP 500 B 1 HETATM 37 H HN21 GDP . . . M 3 -14.356 5.214 -74.989 1 148.98 ? HN21 GDP 500 B 1 HETATM 38 H HN22 GDP . . . M 3 -12.964 4.728 -75.929 1 148.98 ? HN22 GDP 500 B 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 38 #