data_7NGC # _model_server_result.job_id KixtcgR5NMQOUUy29OLZhg _model_server_result.datetime_utc '2024-11-05 04:13:26' _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 7ngc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1001}' # _entry.id 7NGC # _exptl.entry_id 7NGC _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 7NGC _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7NGC _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 O 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc2 H O2G AGS . A AGS 1001 1_555 I MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc3 H O1B AGS . A AGS 1001 1_555 I MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc4 B OG1 THR 424 B THR 530 1_555 K MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc5 J O2G AGS . B AGS 1001 1_555 K MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc6 J O1B AGS . B AGS 1001 1_555 K MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc7 J O1A AGS . B AGS 1001 1_555 K MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? metalc ? metalc8 C OG1 THR 424 C THR 530 1_555 M MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc9 L O2G AGS . C AGS 1001 1_555 M MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc10 L O1B AGS . C AGS 1001 1_555 M MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc11 L O1A AGS . C AGS 1001 1_555 M MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.916 ? metalc ? metalc12 E OG1 THR 424 E THR 530 1_555 P MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc13 O O2G AGS . E AGS 1001 1_555 P MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc14 O O1B AGS . E AGS 1001 1_555 P MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc15 F OG1 THR 424 F THR 530 1_555 R MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc16 Q O2G AGS . F AGS 1001 1_555 R MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc17 Q O1B AGS . F AGS 1001 1_555 R MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? # _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 7NGC _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 5 ADP D 1 1001 1001 ADP ADP . O 3 AGS E 1 1001 1001 AGS AGS . P 4 MG E 1 1002 1002 MG MG . 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 . . . J 3 240.925 201.198 242.048 1 186.09 ? PG AGS 1001 B 1 HETATM 2 S S1G AGS . . . J 3 239.504 199.943 241.6 1 186.09 ? S1G AGS 1001 B 1 HETATM 3 O O2G AGS . . . J 3 241.727 201.577 240.785 1 186.09 ? O2G AGS 1001 B 1 HETATM 4 O O3G AGS . . . J 3 240.291 202.46 242.693 1 186.09 ? O3G AGS 1001 B 1 HETATM 5 P PB AGS . . . J 3 242.699 199.282 242.719 1 186.09 ? PB AGS 1001 B 1 HETATM 6 O O1B AGS . . . J 3 242.249 198.734 241.426 1 186.09 ? O1B AGS 1001 B 1 HETATM 7 O O2B AGS . . . J 3 242.543 198.572 244.059 1 186.09 ? O2B AGS 1001 B 1 HETATM 8 O O3B AGS . . . J 3 242.045 200.673 242.968 1 186.09 ? O3B AGS 1001 B 1 HETATM 9 P PA AGS . . . J 3 244.575 199.274 241.041 1 186.09 ? PA AGS 1001 B 1 HETATM 10 O O1A AGS . . . J 3 244.022 200.36 240.22 1 186.09 ? O1A AGS 1001 B 1 HETATM 11 O O2A AGS . . . J 3 244.25 197.809 240.733 1 186.09 ? O2A AGS 1001 B 1 HETATM 12 O O3A AGS . . . J 3 244.197 199.519 242.506 1 186.09 ? O3A AGS 1001 B 1 HETATM 13 O O5' AGS . . . J 3 246.113 199.59 241.033 1 186.09 ? O5' AGS 1001 B 1 HETATM 14 C C5' AGS . . . J 3 246.535 200.94 241.332 1 186.09 ? C5' AGS 1001 B 1 HETATM 15 C C4' AGS . . . J 3 247.983 200.956 241.746 1 186.09 ? C4' AGS 1001 B 1 HETATM 16 O O4' AGS . . . J 3 248.295 199.756 242.479 1 186.09 ? O4' AGS 1001 B 1 HETATM 17 C C3' AGS . . . J 3 248.881 200.94 240.499 1 186.09 ? C3' AGS 1001 B 1 HETATM 18 O O3' AGS . . . J 3 249.687 202.112 240.451 1 186.09 ? O3' AGS 1001 B 1 HETATM 19 C C2' AGS . . . J 3 249.747 199.687 240.667 1 186.09 ? C2' AGS 1001 B 1 HETATM 20 O O2' AGS . . . J 3 251.091 199.975 240.3 1 186.09 ? O2' AGS 1001 B 1 HETATM 21 C C1' AGS . . . J 3 249.628 199.447 242.157 1 186.09 ? C1' AGS 1001 B 1 HETATM 22 N N9 AGS . . . J 3 249.909 198.104 242.635 1 186.09 ? N9 AGS 1001 B 1 HETATM 23 C C8 AGS . . . J 3 249.125 197.412 243.508 1 186.09 ? C8 AGS 1001 B 1 HETATM 24 N N7 AGS . . . J 3 249.525 196.184 243.725 1 186.09 ? N7 AGS 1001 B 1 HETATM 25 C C5 AGS . . . J 3 250.57 196.02 242.835 1 186.09 ? C5 AGS 1001 B 1 HETATM 26 C C6 AGS . . . J 3 251.414 194.93 242.55 1 186.09 ? C6 AGS 1001 B 1 HETATM 27 N N6 AGS . . . J 3 251.33 193.745 243.16 1 186.09 ? N6 AGS 1001 B 1 HETATM 28 N N1 AGS . . . J 3 252.355 195.099 241.596 1 186.09 ? N1 AGS 1001 B 1 HETATM 29 C C2 AGS . . . J 3 252.437 196.277 240.975 1 186.09 ? C2 AGS 1001 B 1 HETATM 30 N N3 AGS . . . J 3 251.718 197.38 241.179 1 186.09 ? N3 AGS 1001 B 1 HETATM 31 C C4 AGS . . . J 3 250.788 197.183 242.12 1 186.09 ? C4 AGS 1001 B 1 HETATM 32 H "H5'1" AGS . . . J 3 246.008 201.285 242.068 1 186.09 ? "H5'1" AGS 1001 B 1 HETATM 33 H "H5'2" AGS . . . J 3 246.377 201.515 240.563 1 186.09 ? "H5'2" AGS 1001 B 1 HETATM 34 H H4' AGS . . . J 3 248.171 201.74 242.288 1 186.09 ? H4' AGS 1001 B 1 HETATM 35 H H3' AGS . . . J 3 248.372 200.852 239.677 1 186.09 ? H3' AGS 1001 B 1 HETATM 36 H HO3' AGS . . . J 3 250.44 201.938 240.016 1 186.09 ? HO3' AGS 1001 B 1 HETATM 37 H H2' AGS . . . J 3 249.388 198.941 240.16 1 186.09 ? H2' AGS 1001 B 1 HETATM 38 H HO2' AGS . . . J 3 251.352 199.415 239.663 1 186.09 ? HO2' AGS 1001 B 1 HETATM 39 H H1' AGS . . . J 3 250.213 200.071 242.62 1 186.09 ? H1' AGS 1001 B 1 HETATM 40 H H8 AGS . . . J 3 248.429 197.849 244.018 1 186.09 ? H8 AGS 1001 B 1 HETATM 41 H HN61 AGS . . . J 3 250.515 193.39 243.351 1 186.09 ? HN61 AGS 1001 B 1 HETATM 42 H HN62 AGS . . . J 3 252.086 193.296 243.391 1 186.09 ? HN62 AGS 1001 B 1 HETATM 43 H H2 AGS . . . J 3 253.143 196.352 240.31 1 186.09 ? H2 AGS 1001 B 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 92 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #