data_7NFY # _model_server_result.job_id umS4sUR5PleyAbXyQDsJkg _model_server_result.datetime_utc '2024-11-21 17:56:59' _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 7nfy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1001}' # _entry.id 7NFY # _exptl.entry_id 7NFY _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 5 _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 7NFY _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7NFY _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 PISA _pdbx_struct_assembly.oligomeric_details heptameric _pdbx_struct_assembly.oligomeric_count 7 _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 _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 H N N ? 3 J N N ? 3 L N N ? 3 N N N ? 3 Q 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 424 A THR 530 1_555 I MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc2 H O2G AGS . A AGS 1001 1_555 I MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc3 H O1B AGS . A AGS 1001 1_555 I MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc4 B OG1 THR 424 B THR 530 1_555 K MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc5 J O2G AGS . B AGS 1001 1_555 K MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc6 J O1B AGS . B AGS 1001 1_555 K MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc7 C OG1 THR 424 C THR 530 1_555 M MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc8 L O2G AGS . C AGS 1001 1_555 M MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc9 L O1B AGS . C AGS 1001 1_555 M MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc10 D OG1 THR 424 D THR 530 1_555 O MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc11 N O2G AGS . D AGS 1001 1_555 O MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc12 N O1B AGS . D AGS 1001 1_555 O MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc13 F OG1 THR 424 F THR 530 1_555 R MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc14 Q O2G AGS . F AGS 1001 1_555 R MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc15 Q O1B AGS . F AGS 1001 1_555 R MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? # _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 45 n n PG O2G AGS sing 46 n n PG O3G AGS sing 47 n n PG O3B AGS sing 48 n n PB O1B AGS doub 49 n n PB O2B AGS sing 50 n n PB O3B AGS sing 51 n n PB O3A AGS sing 52 n n PA O1A AGS doub 53 n n PA O2A AGS sing 54 n n PA O3A AGS sing 55 n n PA O5' AGS sing 56 n n O5' C5' AGS sing 57 n n C5' C4' AGS sing 58 n n C4' O4' AGS sing 59 n n C4' C3' AGS sing 60 n n O4' C1' AGS sing 61 n n C3' O3' AGS sing 62 n n C3' C2' AGS sing 63 n n C2' O2' AGS sing 64 n n C2' C1' AGS sing 65 n n C1' N9 AGS sing 66 n n N9 C8 AGS sing 67 n y N9 C4 AGS sing 68 n y C8 N7 AGS doub 69 n y N7 C5 AGS sing 70 n y C5 C6 AGS sing 71 n y C5 C4 AGS doub 72 n y C6 N6 AGS sing 73 n n C6 N1 AGS doub 74 n y N1 C2 AGS sing 75 n y C2 N3 AGS doub 76 n y N3 C4 AGS sing 77 n y O2G HOG2 AGS sing 78 n n O3G H21 AGS sing 79 n n O2B HOB2 AGS sing 80 n n O2A HOA2 AGS sing 81 n n C5' "H5'1" AGS sing 82 n n C5' "H5'2" AGS sing 83 n n C4' H4' AGS sing 84 n n C3' H3' AGS sing 85 n n O3' HO3' AGS sing 86 n n C2' H2' AGS sing 87 n n O2' HO2' AGS sing 88 n n C1' H1' AGS sing 89 n n C8 H8 AGS sing 90 n n N6 HN61 AGS sing 91 n n N6 HN62 AGS sing 92 n n C2 H2 AGS sing 93 n n # _atom_sites.entry_id 7NFY _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 H 3 AGS A 1 1001 1001 AGS AGS . I 4 MG A 1 1002 1002 MG MG . J 3 AGS B 1 1001 1001 AGS AGS . K 4 MG B 1 1002 1002 MG MG . L 3 AGS C 1 1001 1001 AGS AGS . M 4 MG C 1 1002 1002 MG MG . N 3 AGS D 1 1001 1001 AGS AGS . O 4 MG D 1 1002 1002 MG MG . P 5 ADP E 1 1001 1001 ADP ADP . Q 3 AGS F 1 1001 1001 AGS AGS . R 4 MG F 1 1002 1002 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 . . . H 3 237.099 196.715 229.271 1 123.71 ? PG AGS 1001 A 1 HETATM 2 S S1G AGS . . . H 3 235.667 195.431 229.123 1 123.71 ? S1G AGS 1001 A 1 HETATM 3 O O2G AGS . . . H 3 237.415 197.224 227.857 1 123.71 ? O2G AGS 1001 A 1 HETATM 4 O O3G AGS . . . H 3 236.614 197.848 230.195 1 123.71 ? O3G AGS 1001 A 1 HETATM 5 P PB AGS . . . H 3 238.774 194.727 229.45 1 123.71 ? PB AGS 1001 A 1 HETATM 6 O O1B AGS . . . H 3 238.331 194.438 228.081 1 123.71 ? O1B AGS 1001 A 1 HETATM 7 O O2B AGS . . . H 3 238.138 193.934 230.583 1 123.71 ? O2B AGS 1001 A 1 HETATM 8 O O3B AGS . . . H 3 238.402 196.153 229.861 1 123.71 ? O3B AGS 1001 A 1 HETATM 9 P PA AGS . . . H 3 240.948 194.032 228.255 1 123.71 ? PA AGS 1001 A 1 HETATM 10 O O1A AGS . . . H 3 240.78 195.1 227.285 1 123.71 ? O1A AGS 1001 A 1 HETATM 11 O O2A AGS . . . H 3 240.331 192.671 227.929 1 123.71 ? O2A AGS 1001 A 1 HETATM 12 O O3A AGS . . . H 3 240.293 194.464 229.569 1 123.71 ? O3A AGS 1001 A 1 HETATM 13 O O5' AGS . . . H 3 242.468 193.897 228.541 1 123.71 ? O5' AGS 1001 A 1 HETATM 14 C C5' AGS . . . H 3 243.143 195.035 229.011 1 123.71 ? C5' AGS 1001 A 1 HETATM 15 C C4' AGS . . . H 3 244.43 194.6 229.639 1 123.71 ? C4' AGS 1001 A 1 HETATM 16 O O4' AGS . . . H 3 244.2 193.45 230.463 1 123.71 ? O4' AGS 1001 A 1 HETATM 17 C C3' AGS . . . H 3 245.522 194.196 228.65 1 123.71 ? C3' AGS 1001 A 1 HETATM 18 O O3' AGS . . . H 3 246.549 195.174 228.596 1 123.71 ? O3' AGS 1001 A 1 HETATM 19 C C2' AGS . . . H 3 246.098 192.898 229.225 1 123.71 ? C2' AGS 1001 A 1 HETATM 20 O O2' AGS . . . H 3 247.506 192.993 229.369 1 123.71 ? O2' AGS 1001 A 1 HETATM 21 C C1' AGS . . . H 3 245.439 192.803 230.593 1 123.71 ? C1' AGS 1001 A 1 HETATM 22 N N9 AGS . . . H 3 245.214 191.448 231.045 1 123.71 ? N9 AGS 1001 A 1 HETATM 23 C C8 AGS . . . H 3 244.054 190.905 231.514 1 123.71 ? C8 AGS 1001 A 1 HETATM 24 N N7 AGS . . . H 3 244.149 189.642 231.839 1 123.71 ? N7 AGS 1001 A 1 HETATM 25 C C5 AGS . . . H 3 245.469 189.338 231.573 1 123.71 ? C5 AGS 1001 A 1 HETATM 26 C C6 AGS . . . H 3 246.212 188.153 231.702 1 123.71 ? C6 AGS 1001 A 1 HETATM 27 N N6 AGS . . . H 3 245.712 187.007 232.166 1 123.71 ? N6 AGS 1001 A 1 HETATM 28 N N1 AGS . . . H 3 247.511 188.191 231.344 1 123.71 ? N1 AGS 1001 A 1 HETATM 29 C C2 AGS . . . H 3 248.018 189.337 230.885 1 123.71 ? C2 AGS 1001 A 1 HETATM 30 N N3 AGS . . . H 3 247.414 190.508 230.713 1 123.71 ? N3 AGS 1001 A 1 HETATM 31 C C4 AGS . . . H 3 246.134 190.44 231.076 1 123.71 ? C4 AGS 1001 A 1 HETATM 32 H "H5'1" AGS . . . H 3 242.6 195.493 229.676 1 123.71 ? "H5'1" AGS 1001 A 1 HETATM 33 H "H5'2" AGS . . . H 3 243.335 195.634 228.268 1 123.71 ? "H5'2" AGS 1001 A 1 HETATM 34 H H4' AGS . . . H 3 244.764 195.322 230.197 1 123.71 ? H4' AGS 1001 A 1 HETATM 35 H H3' AGS . . . H 3 245.141 194.041 227.77 1 123.71 ? H3' AGS 1001 A 1 HETATM 36 H HO3' AGS . . . H 3 247.226 194.869 228.11 1 123.71 ? HO3' AGS 1001 A 1 HETATM 37 H H2' AGS . . . H 3 245.853 192.14 228.67 1 123.71 ? H2' AGS 1001 A 1 HETATM 38 H HO2' AGS . . . H 3 247.904 192.597 228.683 1 123.71 ? HO2' AGS 1001 A 1 HETATM 39 H H1' AGS . . . H 3 245.984 193.276 231.246 1 123.71 ? H1' AGS 1001 A 1 HETATM 40 H H8 AGS . . . H 3 243.233 191.412 231.589 1 123.71 ? H8 AGS 1001 A 1 HETATM 41 H HN61 AGS . . . H 3 244.863 186.764 231.953 1 123.71 ? HN61 AGS 1001 A 1 HETATM 42 H HN62 AGS . . . H 3 246.22 186.47 232.693 1 123.71 ? HN62 AGS 1001 A 1 HETATM 43 H H2 AGS . . . H 3 248.955 189.331 230.629 1 123.71 ? H2 AGS 1001 A 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 72 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #