data_4YXW # _model_server_result.job_id 44hgQxN_pA7bLdDcf11BKA _model_server_result.datetime_utc '2024-11-21 18:33:20' _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 4yxw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":603}' # _entry.id 4YXW # _exptl.entry_id 4YXW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 114.061 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 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 90 _cell.entry_id 4YXW _cell.length_a 105.353 _cell.length_b 123.052 _cell.length_c 261.276 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YXW _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details nonameric _pdbx_struct_assembly.oligomeric_count 9 _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,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA _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 # _struct_asym.details ? _struct_asym.entity_id 9 _struct_asym.id S _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 metalc ? metalc1 A OG1 THR 176 A THR 176 1_555 K MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc2 J O1G ANP . A ANP 600 1_555 K MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc3 J O1B ANP . A ANP 600 1_555 K MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc4 K MG MG . A MG 601 1_555 W O HOH . A HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc5 K MG MG . A MG 601 1_555 W O HOH . A HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc6 K MG MG . A MG 601 1_555 W O HOH . A HOH 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc7 B OG1 THR 176 B THR 176 1_555 M MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc8 L O1G ANP . B ANP 600 1_555 M MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc9 L O1B ANP . B ANP 600 1_555 M MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc10 M MG MG . B MG 601 1_555 X O HOH . B HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc11 M MG MG . B MG 601 1_555 X O HOH . B HOH 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc12 M MG MG . B MG 601 1_555 X O HOH . B HOH 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc13 C OG1 THR 176 C THR 176 1_555 O MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc14 N O1G ANP . C ANP 600 1_555 O MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc15 N O1B ANP . C ANP 600 1_555 O MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc16 O MG MG . C MG 601 1_555 Y O HOH . C HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc17 O MG MG . C MG 601 1_555 Y O HOH . C HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc18 O MG MG . C MG 601 1_555 Y O HOH . C HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc19 D OG1 THR 167 D THR 163 1_555 Q MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc20 P O1G ANP . D ANP 600 1_555 Q MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc21 P O1B ANP . D ANP 600 1_555 Q MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc22 Q MG MG . D MG 601 1_555 Z O HOH . D HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc23 Q MG MG . D MG 601 1_555 Z O HOH . D HOH 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc24 Q MG MG . D MG 601 1_555 Z O HOH . D HOH 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc25 F OG1 THR 167 F THR 163 1_555 U MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc26 F O LEU 418 F LEU 414 1_555 V NA NA . F NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc27 T O1G ANP . F ANP 600 1_555 U MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc28 T O1B ANP . F ANP 600 1_555 U MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc29 U MG MG . F MG 601 1_555 BA O HOH . F HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc30 U MG MG . F MG 601 1_555 BA O HOH . F HOH 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc31 U MG MG . F MG 601 1_555 BA O HOH . F HOH 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? # _chem_comp.formula 'H3 O3 P S' _chem_comp.formula_weight 114.061 _chem_comp.id TS6 _chem_comp.mon_nstd_flag . _chem_comp.name Monothiophosphate _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'phosphorothioic O,O,S-acid' # 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 O1P P TS6 doub 384 n n S2P P TS6 sing 385 n n P O3P TS6 sing 386 n n P O4P TS6 sing 387 n n S2P HS2P TS6 sing 388 n n O3P HO3P TS6 sing 389 n n O4P HO4P TS6 sing 390 n n # _atom_sites.entry_id 4YXW _atom_sites.fract_transf_matrix[1][1] 0.009492 _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] 0.008127 _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] 0.003827 _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 J 6 ANP A 1 600 600 ANP ANP . K 7 MG A 1 601 601 MG MG . L 6 ANP B 1 600 600 ANP ANP . M 7 MG B 1 601 601 MG MG . N 6 ANP C 1 600 600 ANP ANP . O 7 MG C 1 601 601 MG MG . P 6 ANP D 1 600 600 ANP ANP . Q 7 MG D 1 601 601 MG MG . R 8 CL D 1 503 1 CL CL . S 9 TS6 E 1 603 1 TS6 TS6 . T 6 ANP F 1 600 600 ANP ANP . U 7 MG F 1 601 601 MG MG . V 10 NA F 1 503 1 NA NA . W 11 HOH A 1 701 247 HOH HOH . W 11 HOH A 2 702 242 HOH HOH . W 11 HOH A 3 703 703 HOH HOH . W 11 HOH A 4 704 701 HOH HOH . W 11 HOH A 5 705 702 HOH HOH . W 11 HOH A 6 706 13 HOH HOH . X 11 HOH B 1 701 276 HOH HOH . X 11 HOH B 2 702 269 HOH HOH . X 11 HOH B 3 703 330 HOH HOH . X 11 HOH B 4 704 701 HOH HOH . X 11 HOH B 5 705 703 HOH HOH . X 11 HOH B 6 706 702 HOH HOH . X 11 HOH B 7 707 261 HOH HOH . Y 11 HOH C 1 701 425 HOH HOH . Y 11 HOH C 2 702 701 HOH HOH . Y 11 HOH C 3 703 702 HOH HOH . Y 11 HOH C 4 704 703 HOH HOH . Z 11 HOH D 1 701 346 HOH HOH . Z 11 HOH D 2 702 173 HOH HOH . Z 11 HOH D 3 703 63 HOH HOH . Z 11 HOH D 4 704 703 HOH HOH . Z 11 HOH D 5 705 701 HOH HOH . Z 11 HOH D 6 706 125 HOH HOH . Z 11 HOH D 7 707 702 HOH HOH . Z 11 HOH D 8 708 74 HOH HOH . AA 11 HOH E 1 701 139 HOH HOH . AA 11 HOH E 2 702 166 HOH HOH . AA 11 HOH E 3 703 13 HOH HOH . BA 11 HOH F 1 701 427 HOH HOH . BA 11 HOH F 2 702 703 HOH HOH . BA 11 HOH F 3 703 424 HOH HOH . BA 11 HOH F 4 704 69 HOH HOH . BA 11 HOH F 5 705 702 HOH HOH . BA 11 HOH F 6 706 423 HOH HOH . BA 11 HOH F 7 707 426 HOH HOH . BA 11 HOH F 8 708 701 HOH HOH . BA 11 HOH F 9 709 207 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 P TS6 . . . S 9 42.752 139.476 29.259 1 109.45 ? P TS6 603 E 1 HETATM 2 O O1P TS6 . . . S 9 43.112 138.632 27.936 1 107.49 ? O1P TS6 603 E 1 HETATM 3 S S2P TS6 . . . S 9 40.687 139.564 29.478 1 100.87 ? S2P TS6 603 E 1 HETATM 4 O O3P TS6 . . . S 9 43.308 140.843 29.135 1 108.77 ? O3P TS6 603 E 1 HETATM 5 O O4P TS6 . . . S 9 43.407 138.754 30.542 1 108.7 ? O4P TS6 603 E 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 50 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 5 #