data_2PMI # _model_server_result.job_id 2QeKOTudRUWCx0W5RhB71g _model_server_result.datetime_utc '2025-07-30 16:27:23' _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 2pmi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":3001}' # _entry.id 2PMI # _exptl.entry_id 2PMI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _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 2PMI _cell.length_a 146.592 _cell.length_b 146.592 _cell.length_c 212.848 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2PMI _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 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 ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F 1 1 C,D,G 2 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 E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H16 N5 O12 P3 S' _chem_comp.formula_weight 523.247 _chem_comp.id AGS _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ATP-GAMMA-S;ADENOSINE 5'-(3-THIOTRIPHOSPHATE);ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" # 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 S1G AGS doub 1 n n PG O2G AGS sing 2 n n PG O3G AGS sing 3 n n PG O3B AGS sing 4 n n PB O1B AGS doub 5 n n PB O2B AGS sing 6 n n PB O3B AGS sing 7 n n PB O3A AGS sing 8 n n PA O1A AGS doub 9 n n PA O2A AGS sing 10 n n PA O3A AGS sing 11 n n PA O5' AGS sing 12 n n O5' C5' AGS sing 13 n n C5' C4' AGS sing 14 n n C4' O4' AGS sing 15 n n C4' C3' AGS sing 16 n n O4' C1' AGS sing 17 n n C3' O3' AGS sing 18 n n C3' C2' AGS sing 19 n n C2' O2' AGS sing 20 n n C2' C1' AGS sing 21 n n C1' N9 AGS sing 22 n n N9 C8 AGS sing 23 n y N9 C4 AGS sing 24 n y C8 N7 AGS doub 25 n y N7 C5 AGS sing 26 n y C5 C6 AGS sing 27 n y C5 C4 AGS doub 28 n y C6 N6 AGS sing 29 n n C6 N1 AGS doub 30 n y N1 C2 AGS sing 31 n y C2 N3 AGS doub 32 n y N3 C4 AGS sing 33 n y O2G HOG2 AGS sing 34 n n O3G H21 AGS sing 35 n n O2B HOB2 AGS sing 36 n n O2A HOA2 AGS sing 37 n n C5' "H5'1" AGS sing 38 n n C5' "H5'2" AGS sing 39 n n C4' H4' AGS sing 40 n n C3' H3' AGS sing 41 n n O3' HO3' AGS sing 42 n n C2' H2' AGS sing 43 n n O2' HO2' AGS sing 44 n n C1' H1' AGS sing 45 n n C8 H8 AGS sing 46 n n N6 HN61 AGS sing 47 n n N6 HN62 AGS sing 48 n n C2 H2 AGS sing 49 n n # _atom_sites.entry_id 2PMI _atom_sites.fract_transf_matrix[1][1] 0.006822 _atom_sites.fract_transf_matrix[1][2] 0.003938 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007877 _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] 0.004698 _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 E 3 AGS A 1 3001 3001 AGS AGS . F 4 MES B 1 1001 1001 MES MES . G 4 MES D 1 2001 2001 MES MES . # 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 AGS . . . E 3 -77.195 22.327 -3.506 1 114.72 ? PG AGS 3001 A 1 HETATM 2 S S1G AGS . . . E 3 -78.961 22.71 -3.026 1 112.77 ? S1G AGS 3001 A 1 HETATM 3 O O2G AGS . . . E 3 -77.013 20.727 -3.435 1 102.86 ? O2G AGS 3001 A 1 HETATM 4 O O3G AGS . . . E 3 -76.189 23.02 -2.452 1 113.19 ? O3G AGS 3001 A 1 HETATM 5 P PB AGS . . . E 3 -77.6 23.926 -5.788 1 118.86 ? PB AGS 3001 A 1 HETATM 6 O O1B AGS . . . E 3 -78.127 24.941 -4.848 1 118.08 ? O1B AGS 3001 A 1 HETATM 7 O O2B AGS . . . E 3 -76.534 24.729 -6.702 1 109.9 ? O2B AGS 3001 A 1 HETATM 8 O O3B AGS . . . E 3 -76.779 22.763 -5.013 1 115.59 ? O3B AGS 3001 A 1 HETATM 9 P PA AGS . . . E 3 -79.56 21.934 -6.526 1 106.68 ? PA AGS 3001 A 1 HETATM 10 O O1A AGS . . . E 3 -79.343 21.258 -7.82 1 106.41 ? O1A AGS 3001 A 1 HETATM 11 O O2A AGS . . . E 3 -78.847 20.913 -5.497 1 106.47 ? O2A AGS 3001 A 1 HETATM 12 O O3A AGS . . . E 3 -78.861 23.399 -6.676 1 114.45 ? O3A AGS 3001 A 1 HETATM 13 O O5' AGS . . . E 3 -81.167 22.084 -6.366 1 99.78 ? O5' AGS 3001 A 1 HETATM 14 C C5' AGS . . . E 3 -81.69 21.075 -5.492 1 97.79 ? C5' AGS 3001 A 1 HETATM 15 C C4' AGS . . . E 3 -82.545 19.955 -6.119 1 98.48 ? C4' AGS 3001 A 1 HETATM 16 O O4' AGS . . . E 3 -82.823 19.967 -7.542 1 93.8 ? O4' AGS 3001 A 1 HETATM 17 C C3' AGS . . . E 3 -82.105 18.5 -5.814 1 100.4 ? C3' AGS 3001 A 1 HETATM 18 O O3' AGS . . . E 3 -80.707 18.218 -6.004 1 104.8 ? O3' AGS 3001 A 1 HETATM 19 C C2' AGS . . . E 3 -82.984 17.689 -6.799 1 92.91 ? C2' AGS 3001 A 1 HETATM 20 O O2' AGS . . . E 3 -84.28 17.377 -6.271 1 89.79 ? O2' AGS 3001 A 1 HETATM 21 C C1' AGS . . . E 3 -83.086 18.617 -8.032 1 86.4 ? C1' AGS 3001 A 1 HETATM 22 N N9 AGS . . . E 3 -82.114 18.212 -9.076 1 75.67 ? N9 AGS 3001 A 1 HETATM 23 C C8 AGS . . . E 3 -81.101 18.968 -9.595 1 74.32 ? C8 AGS 3001 A 1 HETATM 24 N N7 AGS . . . E 3 -80.405 18.331 -10.486 1 72.9 ? N7 AGS 3001 A 1 HETATM 25 C C5 AGS . . . E 3 -80.925 17.095 -10.623 1 73.25 ? C5 AGS 3001 A 1 HETATM 26 C C6 AGS . . . E 3 -80.638 15.941 -11.4 1 76.21 ? C6 AGS 3001 A 1 HETATM 27 N N6 AGS . . . E 3 -79.577 15.924 -12.293 1 76.51 ? N6 AGS 3001 A 1 HETATM 28 N N1 AGS . . . E 3 -81.413 14.853 -11.263 1 76.2 ? N1 AGS 3001 A 1 HETATM 29 C C2 AGS . . . E 3 -82.449 14.814 -10.422 1 77.95 ? C2 AGS 3001 A 1 HETATM 30 N N3 AGS . . . E 3 -82.734 15.877 -9.677 1 76.11 ? N3 AGS 3001 A 1 HETATM 31 C C4 AGS . . . E 3 -82.025 17.011 -9.735 1 71.89 ? C4 AGS 3001 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 480 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #