data_7VCX # _model_server_result.job_id sMWF26hauau2cKhJ6m6J-Q _model_server_result.datetime_utc '2024-10-18 15:24:51' _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 7vcx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":903}' # _entry.id 7VCX # _exptl.entry_id 7VCX _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.247 _entity.id 2 _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 7VCX _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7VCX _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 hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 ? 2 G N N ? 2 I N N ? 2 K N N ? 2 M N N ? 2 O N N ? 2 Q N N ? 2 S N N ? 2 U N N ? 2 W N N ? 2 Y N N ? 2 AA N N ? 2 CA 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 252 A THR 252 1_555 H MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc2 A OG1 THR 525 A THR 525 1_555 J MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc3 G O2G AGS . A AGS 901 1_555 H MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc4 G O2B AGS . A AGS 901 1_555 H MG MG . A MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc5 I O2G AGS . A AGS 903 1_555 J MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc6 I O1B AGS . A AGS 903 1_555 J MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc7 I O1A AGS . A AGS 903 1_555 J MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc8 B OG1 THR 252 B THR 252 1_555 L MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc9 B OG1 THR 525 B THR 525 1_555 N MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc10 K O2G AGS . B AGS 901 1_555 L MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc11 K O2B AGS . B AGS 901 1_555 L MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc12 M O2G AGS . B AGS 903 1_555 N MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc13 M O1B AGS . B AGS 903 1_555 N MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc14 M O1A AGS . B AGS 903 1_555 N MG MG . B MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc15 C OG1 THR 252 C THR 252 1_555 P MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc16 C OG1 THR 525 C THR 525 1_555 R MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc17 O O2G AGS . C AGS 901 1_555 P MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc18 O O2B AGS . C AGS 901 1_555 P MG MG . C MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc19 Q O2G AGS . C AGS 903 1_555 R MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc20 Q O1B AGS . C AGS 903 1_555 R MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc21 Q O1A AGS . C AGS 903 1_555 R MG MG . C MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc22 D OG1 THR 252 D THR 252 1_555 T MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc23 D OG1 THR 525 D THR 525 1_555 V MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc24 S O2G AGS . D AGS 901 1_555 T MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc25 S O2B AGS . D AGS 901 1_555 T MG MG . D MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc26 U O2G AGS . D AGS 903 1_555 V MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc27 U O1B AGS . D AGS 903 1_555 V MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc28 U O1A AGS . D AGS 903 1_555 V MG MG . D MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc29 E OG1 THR 252 E THR 252 1_555 X MG MG . E MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc30 E OG1 THR 525 E THR 525 1_555 Z MG MG . E MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc31 W O2G AGS . E AGS 901 1_555 X MG MG . E MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc32 W O2B AGS . E AGS 901 1_555 X MG MG . E MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc33 Y O2G AGS . E AGS 903 1_555 Z MG MG . E MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc34 Y O1B AGS . E AGS 903 1_555 Z MG MG . E MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc35 Y O1A AGS . E AGS 903 1_555 Z MG MG . E MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc36 F OG1 THR 252 F THR 252 1_555 BA MG MG . F MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc37 F OG1 THR 525 F THR 525 1_555 DA MG MG . F MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc38 AA O2G AGS . F AGS 901 1_555 BA MG MG . F MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc39 AA O2B AGS . F AGS 901 1_555 BA MG MG . F MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc40 CA O2G AGS . F AGS 903 1_555 DA MG MG . F MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc41 CA O1B AGS . F AGS 903 1_555 DA MG MG . F MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc42 CA O1A AGS . F AGS 903 1_555 DA MG MG . F MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? # _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 7VCX _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 G 2 AGS A 1 901 807 AGS AGS . H 3 MG A 1 902 808 MG MG . I 2 AGS A 1 903 809 AGS AGS . J 3 MG A 1 904 810 MG MG . K 2 AGS B 1 901 807 AGS AGS . L 3 MG B 1 902 808 MG MG . M 2 AGS B 1 903 809 AGS AGS . N 3 MG B 1 904 810 MG MG . O 2 AGS C 1 901 807 AGS AGS . P 3 MG C 1 902 808 MG MG . Q 2 AGS C 1 903 809 AGS AGS . R 3 MG C 1 904 810 MG MG . S 2 AGS D 1 901 807 AGS AGS . T 3 MG D 1 902 808 MG MG . U 2 AGS D 1 903 809 AGS AGS . V 3 MG D 1 904 810 MG MG . W 2 AGS E 1 901 807 AGS AGS . X 3 MG E 1 902 808 MG MG . Y 2 AGS E 1 903 809 AGS AGS . Z 3 MG E 1 904 810 MG MG . AA 2 AGS F 1 901 807 AGS AGS . BA 3 MG F 1 902 808 MG MG . CA 2 AGS F 1 903 809 AGS AGS . DA 3 MG F 1 904 810 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 . . . I 2 184.296 184.757 141.65 1 26.02 ? PG AGS 903 A 1 HETATM 2 S S1G AGS . . . I 2 186.112 184.407 141.097 1 26.02 ? S1G AGS 903 A 1 HETATM 3 O O2G AGS . . . I 2 184.181 185.065 143.156 1 26.02 ? O2G AGS 903 A 1 HETATM 4 O O3G AGS . . . I 2 183.444 183.521 141.344 1 26.02 ? O3G AGS 903 A 1 HETATM 5 P PB AGS . . . I 2 183.715 187.327 141.598 1 26.02 ? PB AGS 903 A 1 HETATM 6 O O1B AGS . . . I 2 183.271 187.153 142.975 1 26.02 ? O1B AGS 903 A 1 HETATM 7 O O2B AGS . . . I 2 182.786 188.141 140.725 1 26.02 ? O2B AGS 903 A 1 HETATM 8 O O3B AGS . . . I 2 183.754 185.965 140.873 1 26.02 ? O3B AGS 903 A 1 HETATM 9 P PA AGS . . . I 2 185.866 188.643 142.661 1 26.02 ? PA AGS 903 A 1 HETATM 10 O O1A AGS . . . I 2 185.84 187.896 143.864 1 26.02 ? O1A AGS 903 A 1 HETATM 11 O O2A AGS . . . I 2 185.409 190.07 142.825 1 26.02 ? O2A AGS 903 A 1 HETATM 12 O O3A AGS . . . I 2 185.085 188.032 141.489 1 26.02 ? O3A AGS 903 A 1 HETATM 13 O O5' AGS . . . I 2 187.294 188.661 142.119 1 26.02 ? O5' AGS 903 A 1 HETATM 14 C C5' AGS . . . I 2 188.14 187.523 141.992 1 26.02 ? C5' AGS 903 A 1 HETATM 15 C C4' AGS . . . I 2 189.548 188.052 142.055 1 26.02 ? C4' AGS 903 A 1 HETATM 16 O O4' AGS . . . I 2 189.944 188.505 140.749 1 26.02 ? O4' AGS 903 A 1 HETATM 17 C C3' AGS . . . I 2 189.694 189.255 142.972 1 26.02 ? C3' AGS 903 A 1 HETATM 18 O O3' AGS . . . I 2 190.139 188.827 144.249 1 26.02 ? O3' AGS 903 A 1 HETATM 19 C C2' AGS . . . I 2 190.774 190.082 142.296 1 26.02 ? C2' AGS 903 A 1 HETATM 20 O O2' AGS . . . I 2 192.035 189.612 142.732 1 26.02 ? O2' AGS 903 A 1 HETATM 21 C C1' AGS . . . I 2 190.561 189.771 140.821 1 26.02 ? C1' AGS 903 A 1 HETATM 22 N N9 AGS . . . I 2 189.72 190.714 140.105 1 26.02 ? N9 AGS 903 A 1 HETATM 23 C C8 AGS . . . I 2 188.538 190.416 139.496 1 26.02 ? C8 AGS 903 A 1 HETATM 24 N N7 AGS . . . I 2 187.975 191.435 138.903 1 26.02 ? N7 AGS 903 A 1 HETATM 25 C C5 AGS . . . I 2 188.852 192.474 139.131 1 26.02 ? C5 AGS 903 A 1 HETATM 26 C C6 AGS . . . I 2 188.831 193.826 138.761 1 26.02 ? C6 AGS 903 A 1 HETATM 27 N N6 AGS . . . I 2 187.85 194.381 138.05 1 26.02 ? N6 AGS 903 A 1 HETATM 28 N N1 AGS . . . I 2 189.859 194.598 139.149 1 26.02 ? N1 AGS 903 A 1 HETATM 29 C C2 AGS . . . I 2 190.843 194.047 139.858 1 26.02 ? C2 AGS 903 A 1 HETATM 30 N N3 AGS . . . I 2 190.974 192.786 140.264 1 26.02 ? N3 AGS 903 A 1 HETATM 31 C C4 AGS . . . I 2 189.937 192.047 139.869 1 26.02 ? C4 AGS 903 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #