data_8PEX # _model_server_result.job_id yzKNS6Fs7oKoq601yEjP6Q _model_server_result.datetime_utc '2024-10-11 10:21:33' _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 8pex # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":501}' # _entry.id 8PEX # _exptl.entry_id 8PEX _exptl.method 'ELECTRON MICROSCOPY' # _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 12 _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 8PEX _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PEX _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 22-meric _pdbx_struct_assembly.oligomeric_count 22 _pdbx_struct_assembly.details author_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,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA _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 ? _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 ? 3 W N N ? 3 Y N N ? 3 AA N N ? 3 CA N N ? 3 EA N N ? 3 GA N N ? 3 IA N N ? 3 KA N N ? 3 MA N N ? 3 OA N N ? 3 QA N N ? 3 SA 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 OG1 THR 185 A THR 185 1_555 X MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc2 W O2G AGS . A AGS 501 1_555 X MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc3 W O1B AGS . A AGS 501 1_555 X MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc4 B OG1 THR 185 B THR 185 1_555 Z MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc5 Y O2G AGS . B AGS 501 1_555 Z MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc6 Y O1B AGS . B AGS 501 1_555 Z MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc7 C OG1 THR 185 C THR 185 1_555 BA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc8 AA O2G AGS . C AGS 501 1_555 BA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc9 AA O1B AGS . C AGS 501 1_555 BA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc10 D OG1 THR 185 D THR 185 1_555 DA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc11 CA O2G AGS . D AGS 501 1_555 DA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc12 CA O1B AGS . D AGS 501 1_555 DA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc13 E OG1 THR 185 E THR 185 1_555 FA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc14 EA O2G AGS . E AGS 501 1_555 FA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc15 EA O1B AGS . E AGS 501 1_555 FA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc16 F OG1 THR 185 F THR 185 1_555 HA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc17 GA O2G AGS . F AGS 501 1_555 HA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc18 GA O3G AGS . F AGS 501 1_555 HA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.825 ? metalc ? metalc19 GA O1B AGS . F AGS 501 1_555 HA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc20 G OG1 THR 185 I THR 185 1_555 JA MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc21 IA O2G AGS . I AGS 501 1_555 JA MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc22 IA O1B AGS . I AGS 501 1_555 JA MG MG . I MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc23 H OG1 THR 185 J THR 185 1_555 LA MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc24 KA O2G AGS . J AGS 501 1_555 LA MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc25 KA O1B AGS . J AGS 501 1_555 LA MG MG . J MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc26 I OG1 THR 185 K THR 185 1_555 NA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc27 MA O2G AGS . K AGS 501 1_555 NA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc28 MA O1B AGS . K AGS 501 1_555 NA MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc29 J OG1 THR 185 L THR 185 1_555 PA MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc30 OA O2G AGS . L AGS 501 1_555 PA MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc31 OA O1B AGS . L AGS 501 1_555 PA MG MG . L MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc32 K OG1 THR 185 M THR 185 1_555 RA MG MG . M MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc33 QA O2G AGS . M AGS 501 1_555 RA MG MG . M MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc34 QA O1B AGS . M AGS 501 1_555 RA MG MG . M MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc35 L OG1 THR 185 N THR 185 1_555 TA MG MG . N MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc36 SA O2G AGS . N AGS 501 1_555 TA MG MG . N MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc37 SA O1B AGS . N AGS 501 1_555 TA MG MG . N MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? # _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 8PEX _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 W 3 AGS A 1 501 501 AGS AGS . X 4 MG A 1 502 502 MG MG . Y 3 AGS B 1 501 501 AGS AGS . Z 4 MG B 1 502 502 MG MG . AA 3 AGS C 1 501 501 AGS AGS . BA 4 MG C 1 502 502 MG MG . CA 3 AGS D 1 501 501 AGS AGS . DA 4 MG D 1 502 502 MG MG . EA 3 AGS E 1 501 501 AGS AGS . FA 4 MG E 1 502 502 MG MG . GA 3 AGS F 1 501 501 AGS AGS . HA 4 MG F 1 502 502 MG MG . IA 3 AGS I 1 501 501 AGS AGS . JA 4 MG I 1 502 502 MG MG . KA 3 AGS J 1 501 501 AGS AGS . LA 4 MG J 1 502 502 MG MG . MA 3 AGS K 1 501 501 AGS AGS . NA 4 MG K 1 502 502 MG MG . OA 3 AGS L 1 501 501 AGS AGS . PA 4 MG L 1 502 502 MG MG . QA 3 AGS M 1 501 501 AGS AGS . RA 4 MG M 1 502 502 MG MG . SA 3 AGS N 1 501 501 AGS AGS . TA 4 MG N 1 502 502 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 AGS . . . W 3 160.916 155.66 181.907 1 110.34 ? PG AGS 501 A 1 HETATM 2 S S1G AGS . . . W 3 162.013 156.399 180.476 1 112.1 ? S1G AGS 501 A 1 HETATM 3 O O2G AGS . . . W 3 159.798 154.765 181.296 1 109.98 ? O2G AGS 501 A 1 HETATM 4 O O3G AGS . . . W 3 161.808 154.799 182.851 1 111.43 ? O3G AGS 501 A 1 HETATM 5 P PB AGS . . . W 3 158.888 156.582 183.469 1 112.46 ? PB AGS 501 A 1 HETATM 6 O O1B AGS . . . W 3 157.947 155.838 182.602 1 112.25 ? O1B AGS 501 A 1 HETATM 7 O O2B AGS . . . W 3 158.376 157.974 183.847 1 111.77 ? O2B AGS 501 A 1 HETATM 8 O O3B AGS . . . W 3 160.266 156.816 182.723 1 110.45 ? O3B AGS 501 A 1 HETATM 9 P PA AGS . . . W 3 158.376 154.432 185.089 1 111.76 ? PA AGS 501 A 1 HETATM 10 O O1A AGS . . . W 3 159.126 153.304 184.49 1 111.26 ? O1A AGS 501 A 1 HETATM 11 O O2A AGS . . . W 3 156.955 154.594 184.543 1 109.87 ? O2A AGS 501 A 1 HETATM 12 O O3A AGS . . . W 3 159.119 155.81 184.835 1 111.75 ? O3A AGS 501 A 1 HETATM 13 O O5' AGS . . . W 3 158.377 154.241 186.661 1 111.92 ? O5' AGS 501 A 1 HETATM 14 C C5' AGS . . . W 3 159.225 155.037 187.514 1 111.47 ? C5' AGS 501 A 1 HETATM 15 C C4' AGS . . . W 3 159.029 154.603 188.946 1 111.19 ? C4' AGS 501 A 1 HETATM 16 O O4' AGS . . . W 3 157.999 155.407 189.563 1 111.07 ? O4' AGS 501 A 1 HETATM 17 C C3' AGS . . . W 3 158.62 153.14 189.137 1 111.12 ? C3' AGS 501 A 1 HETATM 18 O O3' AGS . . . W 3 159.37 152.537 190.185 1 111.12 ? O3' AGS 501 A 1 HETATM 19 C C2' AGS . . . W 3 157.131 153.232 189.486 1 111.34 ? C2' AGS 501 A 1 HETATM 20 O O2' AGS . . . W 3 156.722 152.172 190.343 1 111.57 ? O2' AGS 501 A 1 HETATM 21 C C1' AGS . . . W 3 157.075 154.567 190.221 1 111.59 ? C1' AGS 501 A 1 HETATM 22 N N9 AGS . . . W 3 155.765 155.209 190.197 1 111.25 ? N9 AGS 501 A 1 HETATM 23 C C8 AGS . . . W 3 155.414 156.351 189.526 1 111.35 ? C8 AGS 501 A 1 HETATM 24 N N7 AGS . . . W 3 154.16 156.7 189.685 1 110.38 ? N7 AGS 501 A 1 HETATM 25 C C5 AGS . . . W 3 153.649 155.717 190.518 1 110.33 ? C5 AGS 501 A 1 HETATM 26 C C6 AGS . . . W 3 152.367 155.51 191.065 1 111.2 ? C6 AGS 501 A 1 HETATM 27 N N6 AGS . . . W 3 151.326 156.315 190.844 1 112.43 ? N6 AGS 501 A 1 HETATM 28 N N1 AGS . . . W 3 152.192 154.429 191.859 1 111.17 ? N1 AGS 501 A 1 HETATM 29 C C2 AGS . . . W 3 153.231 153.62 192.084 1 111.1 ? C2 AGS 501 A 1 HETATM 30 N N3 AGS . . . W 3 154.481 153.714 191.624 1 111 ? N3 AGS 501 A 1 HETATM 31 C C4 AGS . . . W 3 154.626 154.791 190.842 1 110.77 ? C4 AGS 501 A 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 123 _model_server_stats.query_time_ms 524 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #