data_1SA0 # _model_server_result.job_id hWWevHAdCc5L22hNaXLmBQ _model_server_result.datetime_utc '2024-11-24 11:15:39' _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 1sa0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":602}' # _entry.id 1SA0 # _exptl.entry_id 1SA0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 120 _cell.entry_id 1SA0 _cell.length_a 328.69 _cell.length_b 328.691 _cell.length_c 54.679 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1SA0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,I,J,K,L,M,N _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 ? 6 I N N ? 6 M 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 metalc ? metalc1 A N GLY 144 A GLY 144 1_555 F MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.09 ? metalc ? metalc2 F MG MG . A MG 501 1_555 G O2G GTP . A GTP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.049 ? metalc ? metalc3 F MG MG . A MG 501 1_555 G O3G GTP . A GTP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc4 F MG MG . A MG 501 1_555 G O2B GTP . A GTP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.79 ? metalc ? metalc5 B ND2 ASN 99 B ASN 101 1_555 H MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.94 ? metalc ? metalc6 H MG MG . B MG 502 1_555 I O2A GDP . B GDP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.582 ? metalc ? metalc7 C N GLY 144 C GLY 144 1_555 K MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.116 ? metalc ? metalc8 K MG MG . C MG 503 1_555 L O2B GTP . C GTP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc9 K MG MG . C MG 503 1_555 L O3G GTP . C GTP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.848 ? metalc ? metalc10 K MG MG . C MG 503 1_555 L O2G GTP . C GTP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.89 ? # _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 140 n n PB O2B GDP sing 141 n n PB O3B GDP sing 142 n n PB O3A GDP sing 143 n n O2B HOB2 GDP sing 144 n n O3B HOB3 GDP sing 145 n n O3A PA GDP sing 146 n n PA O1A GDP doub 147 n n PA O2A GDP sing 148 n n PA O5' GDP sing 149 n n O2A HOA2 GDP sing 150 n n O5' C5' GDP sing 151 n n C5' C4' GDP sing 152 n n C5' H5' GDP sing 153 n n C5' "H5''" GDP sing 154 n n C4' O4' GDP sing 155 n n C4' C3' GDP sing 156 n n C4' H4' GDP sing 157 n n O4' C1' GDP sing 158 n n C3' O3' GDP sing 159 n n C3' C2' GDP sing 160 n n C3' H3' GDP sing 161 n n O3' HO3' GDP sing 162 n n C2' O2' GDP sing 163 n n C2' C1' GDP sing 164 n n C2' H2' GDP sing 165 n n O2' HO2' GDP sing 166 n n C1' N9 GDP sing 167 n n C1' H1' GDP sing 168 n n N9 C8 GDP sing 169 n y N9 C4 GDP sing 170 n y C8 N7 GDP doub 171 n y C8 H8 GDP sing 172 n n N7 C5 GDP sing 173 n y C5 C6 GDP sing 174 n n C5 C4 GDP doub 175 n y C6 O6 GDP doub 176 n n C6 N1 GDP sing 177 n n N1 C2 GDP sing 178 n n N1 HN1 GDP sing 179 n n C2 N2 GDP sing 180 n n C2 N3 GDP doub 181 n n N2 HN21 GDP sing 182 n n N2 HN22 GDP sing 183 n n N3 C4 GDP sing 184 n n # _atom_sites.entry_id 1SA0 _atom_sites.fract_transf_matrix[1][1] 0.003042 _atom_sites.fract_transf_matrix[1][2] 0.001757 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003513 _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] 0.018289 _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 F 4 MG A 1 501 601 MG MG . G 5 GTP A 1 600 600 GTP GTP . H 4 MG B 1 502 601 MG MG . I 6 GDP B 1 602 600 GDP GDP . J 7 CN2 B 1 700 700 CN2 COL . K 4 MG C 1 503 601 MG MG . L 5 GTP C 1 601 600 GTP GTP . M 6 GDP D 1 603 600 GDP GDP . N 7 CN2 D 1 701 700 CN2 COL . # 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 6 90.219 72.393 5.784 1 83.07 ? PB GDP 602 B 1 HETATM 2 O O1B GDP . . . I 6 90.122 73.715 6.442 1 83.07 ? O1B GDP 602 B 1 HETATM 3 O O2B GDP . . . I 6 91.576 71.744 6.068 1 83.07 ? O2B GDP 602 B 1 HETATM 4 O O3B GDP . . . I 6 89.127 71.379 6.18 1 83.07 ? O3B GDP 602 B 1 HETATM 5 O O3A GDP . . . I 6 90.063 72.787 4.238 1 83.07 ? O3A GDP 602 B 1 HETATM 6 P PA GDP . . . I 6 91.013 72.26 3.05 1 83.07 ? PA GDP 602 B 1 HETATM 7 O O1A GDP . . . I 6 92.225 71.68 3.667 1 83.07 ? O1A GDP 602 B 1 HETATM 8 O O2A GDP . . . I 6 90.259 71.247 2.14 1 83.07 ? O2A GDP 602 B 1 HETATM 9 O O5' GDP . . . I 6 91.428 73.613 2.26 1 83.07 ? O5' GDP 602 B 1 HETATM 10 C C5' GDP . . . I 6 90.524 74.225 1.367 1 83.07 ? C5' GDP 602 B 1 HETATM 11 C C4' GDP . . . I 6 91.266 74.901 0.227 1 83.07 ? C4' GDP 602 B 1 HETATM 12 O O4' GDP . . . I 6 92.638 74.665 0.368 1 83.07 ? O4' GDP 602 B 1 HETATM 13 C C3' GDP . . . I 6 90.863 74.319 -1.116 1 83.07 ? C3' GDP 602 B 1 HETATM 14 O O3' GDP . . . I 6 90.133 75.277 -1.834 1 83.07 ? O3' GDP 602 B 1 HETATM 15 C C2' GDP . . . I 6 92.143 73.968 -1.846 1 83.07 ? C2' GDP 602 B 1 HETATM 16 O O2' GDP . . . I 6 92.41 74.723 -3.006 1 83.07 ? O2' GDP 602 B 1 HETATM 17 C C1' GDP . . . I 6 93.224 74.246 -0.843 1 83.07 ? C1' GDP 602 B 1 HETATM 18 N N9 GDP . . . I 6 93.904 72.972 -0.657 1 83.07 ? N9 GDP 602 B 1 HETATM 19 C C8 GDP . . . I 6 93.34 71.798 -0.248 1 83.07 ? C8 GDP 602 B 1 HETATM 20 N N7 GDP . . . I 6 94.32 70.871 -0.216 1 83.07 ? N7 GDP 602 B 1 HETATM 21 C C5 GDP . . . I 6 95.485 71.441 -0.597 1 83.07 ? C5 GDP 602 B 1 HETATM 22 C C6 GDP . . . I 6 96.772 70.952 -0.743 1 83.07 ? C6 GDP 602 B 1 HETATM 23 O O6 GDP . . . I 6 96.953 69.743 -0.715 1 83.07 ? O6 GDP 602 B 1 HETATM 24 N N1 GDP . . . I 6 97.783 71.787 -1.164 1 83.07 ? N1 GDP 602 B 1 HETATM 25 C C2 GDP . . . I 6 97.508 73.106 -1.444 1 83.07 ? C2 GDP 602 B 1 HETATM 26 N N2 GDP . . . I 6 98.245 73.701 -2.358 1 83.07 ? N2 GDP 602 B 1 HETATM 27 N N3 GDP . . . I 6 96.23 73.583 -1.292 1 83.07 ? N3 GDP 602 B 1 HETATM 28 C C4 GDP . . . I 6 95.233 72.765 -0.884 1 83.07 ? C4 GDP 602 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #