data_6H5B # _model_server_result.job_id '_fcPt-dhVtUnq8MBWavjbQ' _model_server_result.datetime_utc '2024-11-16 06:55:18' _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 6h5b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 6H5B # _exptl.entry_id 6H5B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 539.246 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 6H5B _cell.length_a 135.101 _cell.length_b 135.101 _cell.length_c 60.382 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6H5B _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall 'P 64' _symmetry.space_group_name_H-M 'P 64' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 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,D,E,F,G,H,M 1 1 B,I,J,N 2 1 C,K,L,O 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 NZ LYS 25 A LYS 25 1_555 D O2B GSP . A GSP 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.299 ? metalc ? metalc1 A OG1 THR 26 A THR 26 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc2 A OG1 THR 54 A THR 54 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc3 D O2G GSP . A GSP 301 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc4 D O1B GSP . A GSP 301 1_555 E MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.919 ? # _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 ? # _atom_sites.entry_id 6H5B _atom_sites.fract_transf_matrix[1][1] 0.007402 _atom_sites.fract_transf_matrix[1][2] 0.004273 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008547 _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] 0.016561 _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 D 3 GSP A 1 301 301 GSP GSP . E 4 MG A 1 302 302 MG MG . F 5 EPE A 1 303 303 EPE EPE . G 5 EPE A 1 304 304 EPE EPE . H 6 1PE A 1 305 305 1PE 1PE . I 7 PEG B 1 201 201 PEG PEG . J 7 PEG B 1 202 201 PEG PEG . K 6 1PE C 1 201 306 1PE 1PE . L 7 PEG C 1 202 202 PEG PEG . M 8 HOH A 1 401 415 HOH HOH . M 8 HOH A 2 402 416 HOH HOH . M 8 HOH A 3 403 401 HOH HOH . M 8 HOH A 4 404 405 HOH HOH . M 8 HOH A 5 405 409 HOH HOH . M 8 HOH A 6 406 404 HOH HOH . M 8 HOH A 7 407 414 HOH HOH . M 8 HOH A 8 408 407 HOH HOH . M 8 HOH A 9 409 406 HOH HOH . N 8 HOH B 1 301 412 HOH HOH . N 8 HOH B 2 302 411 HOH HOH . N 8 HOH B 3 303 408 HOH HOH . O 8 HOH C 1 301 413 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 PG GSP . . . D 3 -63.279 -14.437 16.215 1 35.15 ? PG GSP 301 A 1 HETATM 2 O O3B GSP . . . D 3 -63.906 -13.172 16.983 1 31.35 ? O3B GSP 301 A 1 HETATM 3 S S1G GSP . . . D 3 -64.505 -15.23 15.333 1 54.51 ? S1G GSP 301 A 1 HETATM 4 O O2G GSP . . . D 3 -62.163 -13.95 15.258 1 31.27 ? O2G GSP 301 A 1 HETATM 5 O O3G GSP . . . D 3 -62.689 -15.41 17.258 1 50.07 ? O3G GSP 301 A 1 HETATM 6 P PB GSP . . . D 3 -62.926 -12.034 17.565 1 32.67 ? PB GSP 301 A 1 HETATM 7 O O1B GSP . . . D 3 -62.058 -11.474 16.498 1 34.74 ? O1B GSP 301 A 1 HETATM 8 O O2B GSP . . . D 3 -62.111 -12.579 18.682 1 41.01 ? O2B GSP 301 A 1 HETATM 9 P PA GSP . . . D 3 -64.587 -9.813 17.142 1 39.19 ? PA GSP 301 A 1 HETATM 10 O O1A GSP . . . D 3 -65.003 -10.332 15.808 1 30.55 ? O1A GSP 301 A 1 HETATM 11 O O2A GSP . . . D 3 -63.574 -8.739 16.99 1 47.77 ? O2A GSP 301 A 1 HETATM 12 O O3A GSP . . . D 3 -63.98 -10.949 18.118 1 32.93 ? O3A GSP 301 A 1 HETATM 13 O O5' GSP . . . D 3 -65.805 -9.262 18.037 1 33.46 ? O5' GSP 301 A 1 HETATM 14 C C5' GSP . . . D 3 -66.878 -10.091 18.417 1 34.75 ? C5' GSP 301 A 1 HETATM 15 C C4' GSP . . . D 3 -68.071 -9.192 18.717 1 37.32 ? C4' GSP 301 A 1 HETATM 16 O O4' GSP . . . D 3 -68.036 -8.76 20.065 1 42.54 ? O4' GSP 301 A 1 HETATM 17 C C3' GSP . . . D 3 -68.013 -7.942 17.858 1 28.92 ? C3' GSP 301 A 1 HETATM 18 O O3' GSP . . . D 3 -69.295 -7.702 17.329 1 31.97 ? O3' GSP 301 A 1 HETATM 19 C C2' GSP . . . D 3 -67.633 -6.828 18.805 1 29.47 ? C2' GSP 301 A 1 HETATM 20 O O2' GSP . . . D 3 -68.344 -5.648 18.53 1 40.61 ? O2' GSP 301 A 1 HETATM 21 C C1' GSP . . . D 3 -68.072 -7.349 20.147 1 31.5 ? C1' GSP 301 A 1 HETATM 22 N N9 GSP . . . D 3 -67.151 -6.81 21.154 1 33.67 ? N9 GSP 301 A 1 HETATM 23 C C8 GSP . . . D 3 -65.795 -6.64 21.038 1 30.67 ? C8 GSP 301 A 1 HETATM 24 N N7 GSP . . . D 3 -65.343 -6.103 22.198 1 31.55 ? N7 GSP 301 A 1 HETATM 25 C C5 GSP . . . D 3 -66.388 -5.929 23.041 1 32.24 ? C5 GSP 301 A 1 HETATM 26 C C6 GSP . . . D 3 -66.485 -5.424 24.331 1 37.13 ? C6 GSP 301 A 1 HETATM 27 O O6 GSP . . . D 3 -65.481 -5.028 24.922 1 46.03 ? O6 GSP 301 A 1 HETATM 28 N N1 GSP . . . D 3 -67.719 -5.369 24.945 1 33.11 ? N1 GSP 301 A 1 HETATM 29 C C2 GSP . . . D 3 -68.844 -5.816 24.277 1 34.34 ? C2 GSP 301 A 1 HETATM 30 N N2 GSP . . . D 3 -70.036 -5.77 24.865 1 42.32 ? N2 GSP 301 A 1 HETATM 31 N N3 GSP . . . D 3 -68.743 -6.317 22.998 1 30.99 ? N3 GSP 301 A 1 HETATM 32 C C4 GSP . . . D 3 -67.532 -6.369 22.393 1 35.29 ? C4 GSP 301 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 32 #