data_2XKA # _model_server_result.job_id df7b61fUJBreO_rL97QHuQ _model_server_result.datetime_utc '2025-04-01 13:47:34' _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 2xka # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":900}' # _entry.id 2XKA # _exptl.entry_id 2XKA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _entity.pdbx_number_of_molecules 7 _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 2XKA _cell.length_a 51.06 _cell.length_b 85.15 _cell.length_c 632.23 _cell.Z_PDB 28 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2XKA _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 PISA monomeric 1 author_and_software_defined_assembly 5 PISA monomeric 1 author_and_software_defined_assembly 6 PISA monomeric 1 author_and_software_defined_assembly 7 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,H,I 1 1 B,J,K 2 1 C,L,M 3 1 D,N,O 4 1 E,P,Q 5 1 F,R,S 6 1 G,T,U 7 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 ? 2 H N N ? 2 J N N ? 2 L N N ? 2 N N N ? 2 P N N ? 2 R N N ? 2 T 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 OE1 GLN 32 A GLN 32 1_555 I MG MG . A MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc2 H O3G GSP . A GSP 900 1_555 I MG MG . A MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc3 H O1B GSP . A GSP 900 1_555 I MG MG . A MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc4 B OD2 ASP 64 B ASP 64 1_555 K MG MG . B MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc5 J O3G GSP . B GSP 900 1_555 K MG MG . B MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc6 J O1B GSP . B GSP 900 1_555 K MG MG . B MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc7 L O3G GSP . C GSP 900 1_555 M MG MG . C MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.9 ? metalc ? metalc8 L O1B GSP . C GSP 900 1_555 M MG MG . C MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc9 D OD2 ASP 64 D ASP 64 1_555 O MG MG . D MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc10 N O3G GSP . D GSP 900 1_555 O MG MG . D MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.805 ? metalc ? metalc11 N O1B GSP . D GSP 900 1_555 O MG MG . D MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.667 ? metalc ? metalc12 E OD2 ASP 64 E ASP 64 1_555 Q MG MG . E MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc13 P O3G GSP . E GSP 900 1_555 Q MG MG . E MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.869 ? metalc ? metalc14 P O1B GSP . E GSP 900 1_555 Q MG MG . E MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc15 F OD2 ASP 64 F ASP 64 1_555 S MG MG . F MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc16 R O3G GSP . F GSP 900 1_555 S MG MG . F MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.906 ? metalc ? metalc17 R O1B GSP . F GSP 900 1_555 S MG MG . F MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc18 G OE1 GLN 32 G GLN 32 1_555 U MG MG . G MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? metalc ? metalc19 T O1B GSP . G GSP 900 1_555 U MG MG . G MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? metalc ? metalc20 T O3G GSP . G GSP 900 1_555 U MG MG . G MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? # _chem_comp.formula 'C10 H16 N5 O13 P3 S' _chem_comp.formula_weight 539.246 _chem_comp.id GSP _chem_comp.mon_nstd_flag . _chem_comp.name "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _chem_comp.type non-polymer _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 PG O3B GSP sing 129 n n PG S1G GSP doub 130 n n PG O2G GSP sing 131 n n PG O3G GSP sing 132 n n O3B PB GSP sing 133 n n O2G HOG2 GSP sing 134 n n O3G HOG3 GSP sing 135 n n PB O1B GSP doub 136 n n PB O2B GSP sing 137 n n PB O3A GSP sing 138 n n O2B HOB2 GSP sing 139 n n PA O1A GSP doub 140 n n PA O2A GSP sing 141 n n PA O3A GSP sing 142 n n PA O5' GSP sing 143 n n O2A HOA2 GSP sing 144 n n O5' C5' GSP sing 145 n n C5' C4' GSP sing 146 n n C5' "H5'1" GSP sing 147 n n C5' "H5'2" GSP sing 148 n n C4' O4' GSP sing 149 n n C4' C3' GSP sing 150 n n C4' H4' GSP sing 151 n n O4' C1' GSP sing 152 n n C3' O3' GSP sing 153 n n C3' C2' GSP sing 154 n n C3' H3' GSP sing 155 n n O3' HO3' GSP sing 156 n n C2' O2' GSP sing 157 n n C2' C1' GSP sing 158 n n C2' H2' GSP sing 159 n n O2' HO2' GSP sing 160 n n C1' N9 GSP sing 161 n n C1' H1' GSP sing 162 n n N9 C8 GSP sing 163 n y N9 C4 GSP sing 164 n y C8 N7 GSP doub 165 n y C8 H8 GSP sing 166 n n N7 C5 GSP sing 167 n y C5 C6 GSP sing 168 n n C5 C4 GSP doub 169 n y C6 O6 GSP doub 170 n n C6 N1 GSP sing 171 n n N1 C2 GSP sing 172 n n N1 HN1 GSP sing 173 n n C2 N2 GSP sing 174 n n C2 N3 GSP doub 175 n n N2 HN21 GSP sing 176 n n N2 HN22 GSP sing 177 n n N3 C4 GSP sing 178 n n # _atom_sites.entry_id 2XKA _atom_sites.fract_transf_matrix[1][1] 0.019585 _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] 0.011744 _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] 0.001582 _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 H 2 GSP A 1 900 900 GSP GSP . I 3 MG A 1 999 999 MG MG . J 2 GSP B 1 900 900 GSP GSP . K 3 MG B 1 999 999 MG MG . L 2 GSP C 1 900 900 GSP GSP . M 3 MG C 1 999 999 MG MG . N 2 GSP D 1 900 900 GSP GSP . O 3 MG D 1 999 999 MG MG . P 2 GSP E 1 900 900 GSP GSP . Q 3 MG E 1 999 999 MG MG . R 2 GSP F 1 900 900 GSP GSP . S 3 MG F 1 999 999 MG MG . T 2 GSP G 1 900 900 GSP GSP . U 3 MG G 1 999 999 MG MG . # 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 PG GSP . . . L 2 38.253 -35.615 77.416 1 15.84 ? PG GSP 900 C 1 HETATM 2 O O3B GSP . . . L 2 38.707 -35.427 78.949 1 16.08 ? O3B GSP 900 C 1 HETATM 3 S S1G GSP . . . L 2 39.083 -34.484 76.426 1 18.05 ? S1G GSP 900 C 1 HETATM 4 O O2G GSP . . . L 2 38.714 -37.031 77.002 1 14.31 ? O2G GSP 900 C 1 HETATM 5 O O3G GSP . . . L 2 36.727 -35.398 77.319 1 14.69 ? O3G GSP 900 C 1 HETATM 6 P PB GSP . . . L 2 37.699 -35.738 80.164 1 16.2 ? PB GSP 900 C 1 HETATM 7 O O1B GSP . . . L 2 36.323 -35.381 79.7 1 16.51 ? O1B GSP 900 C 1 HETATM 8 O O2B GSP . . . L 2 38.11 -34.981 81.367 1 15.43 ? O2B GSP 900 C 1 HETATM 9 P PA GSP . . . L 2 36.553 -38.125 81.057 1 14.73 ? PA GSP 900 C 1 HETATM 10 O O1A GSP . . . L 2 35.521 -38.264 79.992 1 15.58 ? O1A GSP 900 C 1 HETATM 11 O O2A GSP . . . L 2 35.894 -37.486 82.235 1 14.67 ? O2A GSP 900 C 1 HETATM 12 O O3A GSP . . . L 2 37.826 -37.327 80.46 1 14.8 ? O3A GSP 900 C 1 HETATM 13 O O5' GSP . . . L 2 37.119 -39.58 81.429 1 14.04 ? O5' GSP 900 C 1 HETATM 14 C C5' GSP . . . L 2 38.199 -39.84 82.295 1 13.63 ? C5' GSP 900 C 1 HETATM 15 C C4' GSP . . . L 2 38.178 -41.31 82.721 1 13.3 ? C4' GSP 900 C 1 HETATM 16 O O4' GSP . . . L 2 37.145 -41.538 83.667 1 13.09 ? O4' GSP 900 C 1 HETATM 17 C C3' GSP . . . L 2 37.882 -42.236 81.556 1 13.12 ? C3' GSP 900 C 1 HETATM 18 O O3' GSP . . . L 2 38.659 -43.412 81.653 1 12.58 ? O3' GSP 900 C 1 HETATM 19 C C2' GSP . . . L 2 36.375 -42.479 81.676 1 13.1 ? C2' GSP 900 C 1 HETATM 20 O O2' GSP . . . L 2 35.947 -43.679 81.054 1 13.77 ? O2' GSP 900 C 1 HETATM 21 C C1' GSP . . . L 2 36.175 -42.452 83.18 1 12.79 ? C1' GSP 900 C 1 HETATM 22 N N9 GSP . . . L 2 34.882 -41.987 83.695 1 12.54 ? N9 GSP 900 C 1 HETATM 23 C C8 GSP . . . L 2 33.961 -41.179 83.084 1 12.78 ? C8 GSP 900 C 1 HETATM 24 N N7 GSP . . . L 2 32.932 -40.953 83.945 1 12.4 ? N7 GSP 900 C 1 HETATM 25 C C5 GSP . . . L 2 33.192 -41.607 85.087 1 11.78 ? C5 GSP 900 C 1 HETATM 26 C C6 GSP . . . L 2 32.475 -41.696 86.245 1 11.37 ? C6 GSP 900 C 1 HETATM 27 O O6 GSP . . . L 2 31.412 -41.107 86.319 1 11.38 ? O6 GSP 900 C 1 HETATM 28 N N1 GSP . . . L 2 32.966 -42.415 87.309 1 12.25 ? N1 GSP 900 C 1 HETATM 29 C C2 GSP . . . L 2 34.185 -43.066 87.208 1 12.93 ? C2 GSP 900 C 1 HETATM 30 N N2 GSP . . . L 2 34.613 -43.757 88.268 1 13.61 ? N2 GSP 900 C 1 HETATM 31 N N3 GSP . . . L 2 34.918 -42.992 86.027 1 12.34 ? N3 GSP 900 C 1 HETATM 32 C C4 GSP . . . L 2 34.418 -42.259 84.975 1 12.79 ? C4 GSP 900 C 1 # _model_server_stats.io_time_ms 37 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 106 _model_server_stats.query_time_ms 1007 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 32 #