data_4NAH # _model_server_result.job_id Omz2kHw-ce2HiQWNcjwUsQ _model_server_result.datetime_utc '2025-07-07 17:06:58' _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 4nah # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":201}' # _entry.id 4NAH # _exptl.entry_id 4NAH _exptl.method 'X-RAY DIFFRACTION' # _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 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 94.69 _cell.angle_gamma 90 _cell.entry_id 4NAH _cell.length_a 68.476 _cell.length_b 105.36 _cell.length_c 79.98 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NAH _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,S,T,U,V,W,X _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 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 # 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 J N N ? 2 L N N ? 2 M N N ? 2 O N N ? 2 P N 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 64 n n PG O2G AGS sing 65 n n PG O3G AGS sing 66 n n PG O3B AGS sing 67 n n PB O1B AGS doub 68 n n PB O2B AGS sing 69 n n PB O3B AGS sing 70 n n PB O3A AGS sing 71 n n PA O1A AGS doub 72 n n PA O2A AGS sing 73 n n PA O3A AGS sing 74 n n PA O5' AGS sing 75 n n O5' C5' AGS sing 76 n n C5' C4' AGS sing 77 n n C4' O4' AGS sing 78 n n C4' C3' AGS sing 79 n n O4' C1' AGS sing 80 n n C3' O3' AGS sing 81 n n C3' C2' AGS sing 82 n n C2' O2' AGS sing 83 n n C2' C1' AGS sing 84 n n C1' N9 AGS sing 85 n n N9 C8 AGS sing 86 n y N9 C4 AGS sing 87 n y C8 N7 AGS doub 88 n y N7 C5 AGS sing 89 n y C5 C6 AGS sing 90 n y C5 C4 AGS doub 91 n y C6 N6 AGS sing 92 n n C6 N1 AGS doub 93 n y N1 C2 AGS sing 94 n y C2 N3 AGS doub 95 n y N3 C4 AGS sing 96 n y O2G HOG2 AGS sing 97 n n O3G H21 AGS sing 98 n n O2B HOB2 AGS sing 99 n n O2A HOA2 AGS sing 100 n n C5' "H5'1" AGS sing 101 n n C5' "H5'2" AGS sing 102 n n C4' H4' AGS sing 103 n n C3' H3' AGS sing 104 n n O3' HO3' AGS sing 105 n n C2' H2' AGS sing 106 n n O2' HO2' AGS sing 107 n n C1' H1' AGS sing 108 n n C8 H8 AGS sing 109 n n N6 HN61 AGS sing 110 n n N6 HN62 AGS sing 111 n n C2 H2 AGS sing 112 n n # _atom_sites.entry_id 4NAH _atom_sites.fract_transf_matrix[1][1] 0.014604 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001198 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009491 _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] 0.012545 _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 1 201 1 AGS AGS . H 3 2VJ A 1 202 1 2VJ INH . I 3 2VJ A 1 203 1 2VJ INH . J 2 AGS B 1 201 1 AGS AGS . K 3 2VJ B 1 202 1 2VJ INH . L 2 AGS C 1 201 1 AGS AGS . M 2 AGS D 1 201 1 AGS AGS . N 3 2VJ D 1 202 1 2VJ INH . O 2 AGS E 1 201 1 AGS AGS . P 2 AGS F 1 201 1 AGS AGS . Q 3 2VJ F 1 202 1 2VJ INH . R 3 2VJ F 1 203 1 2VJ INH . S 4 HOH A 1 301 2 HOH HOH . S 4 HOH A 2 302 11 HOH HOH . S 4 HOH A 3 303 14 HOH HOH . S 4 HOH A 4 304 17 HOH HOH . S 4 HOH A 5 305 20 HOH HOH . S 4 HOH A 6 306 22 HOH HOH . S 4 HOH A 7 307 26 HOH HOH . S 4 HOH A 8 308 27 HOH HOH . S 4 HOH A 9 309 37 HOH HOH . S 4 HOH A 10 310 40 HOH HOH . S 4 HOH A 11 311 41 HOH HOH . S 4 HOH A 12 312 48 HOH HOH . S 4 HOH A 13 313 51 HOH HOH . S 4 HOH A 14 314 57 HOH HOH . S 4 HOH A 15 315 61 HOH HOH . S 4 HOH A 16 316 71 HOH HOH . S 4 HOH A 17 317 75 HOH HOH . T 4 HOH B 1 301 4 HOH HOH . T 4 HOH B 2 302 5 HOH HOH . T 4 HOH B 3 303 10 HOH HOH . T 4 HOH B 4 304 12 HOH HOH . T 4 HOH B 5 305 16 HOH HOH . T 4 HOH B 6 306 24 HOH HOH . T 4 HOH B 7 307 36 HOH HOH . T 4 HOH B 8 308 39 HOH HOH . T 4 HOH B 9 309 44 HOH HOH . T 4 HOH B 10 310 45 HOH HOH . T 4 HOH B 11 311 46 HOH HOH . T 4 HOH B 12 312 50 HOH HOH . T 4 HOH B 13 313 55 HOH HOH . T 4 HOH B 14 314 56 HOH HOH . T 4 HOH B 15 315 58 HOH HOH . T 4 HOH B 16 316 62 HOH HOH . T 4 HOH B 17 317 65 HOH HOH . T 4 HOH B 18 318 67 HOH HOH . T 4 HOH B 19 319 68 HOH HOH . T 4 HOH B 20 320 69 HOH HOH . T 4 HOH B 21 321 74 HOH HOH . T 4 HOH B 22 322 76 HOH HOH . U 4 HOH C 1 301 1 HOH HOH . U 4 HOH C 2 302 3 HOH HOH . U 4 HOH C 3 303 13 HOH HOH . U 4 HOH C 4 304 19 HOH HOH . U 4 HOH C 5 305 25 HOH HOH . U 4 HOH C 6 306 34 HOH HOH . U 4 HOH C 7 307 38 HOH HOH . U 4 HOH C 8 308 49 HOH HOH . U 4 HOH C 9 309 53 HOH HOH . U 4 HOH C 10 310 54 HOH HOH . U 4 HOH C 11 311 63 HOH HOH . U 4 HOH C 12 312 64 HOH HOH . U 4 HOH C 13 313 70 HOH HOH . V 4 HOH D 1 301 6 HOH HOH . V 4 HOH D 2 302 9 HOH HOH . V 4 HOH D 3 303 21 HOH HOH . V 4 HOH D 4 304 29 HOH HOH . V 4 HOH D 5 305 30 HOH HOH . V 4 HOH D 6 306 31 HOH HOH . V 4 HOH D 7 307 32 HOH HOH . V 4 HOH D 8 308 60 HOH HOH . V 4 HOH D 9 309 72 HOH HOH . V 4 HOH D 10 310 78 HOH HOH . W 4 HOH E 1 301 33 HOH HOH . W 4 HOH E 2 302 43 HOH HOH . W 4 HOH E 3 303 77 HOH HOH . X 4 HOH F 1 301 7 HOH HOH . X 4 HOH F 2 302 8 HOH HOH . X 4 HOH F 3 303 15 HOH HOH . X 4 HOH F 4 304 18 HOH HOH . X 4 HOH F 5 305 23 HOH HOH . X 4 HOH F 6 306 28 HOH HOH . X 4 HOH F 7 307 35 HOH HOH . X 4 HOH F 8 308 42 HOH HOH . X 4 HOH F 9 309 47 HOH HOH . X 4 HOH F 10 310 52 HOH HOH . X 4 HOH F 11 311 59 HOH HOH . X 4 HOH F 12 312 66 HOH HOH . X 4 HOH F 13 313 73 HOH HOH . # 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 . . . P 2 -32.144 -33.297 -16.816 1 50 ? PG AGS 201 F 1 HETATM 2 S S1G AGS . . . P 2 -30.592 -32.441 -17.424 1 50 ? S1G AGS 201 F 1 HETATM 3 O O2G AGS . . . P 2 -33.258 -33.299 -17.976 1 50 ? O2G AGS 201 F 1 HETATM 4 O O3G AGS . . . P 2 -32.664 -32.502 -15.455 1 45.08 ? O3G AGS 201 F 1 HETATM 5 P PB AGS . . . P 2 -31.578 -34.777 -14.786 1 50 ? PB AGS 201 F 1 HETATM 6 O O1B AGS . . . P 2 -30.884 -36.085 -14.729 1 48.41 ? O1B AGS 201 F 1 HETATM 7 O O2B AGS . . . P 2 -30.635 -33.451 -14.611 1 50 ? O2B AGS 201 F 1 HETATM 8 O O3B AGS . . . P 2 -31.808 -34.814 -16.394 1 50 ? O3B AGS 201 F 1 HETATM 9 P PA AGS . . . P 2 -33.045 -33.458 -12.516 1 47.37 ? PA AGS 201 F 1 HETATM 10 O O1A AGS . . . P 2 -32.317 -32.362 -13.191 1 50 ? O1A AGS 201 F 1 HETATM 11 O O2A AGS . . . P 2 -34.438 -32.804 -12.169 1 46.67 ? O2A AGS 201 F 1 HETATM 12 O O3A AGS . . . P 2 -32.916 -34.648 -13.699 1 50 ? O3A AGS 201 F 1 HETATM 13 O O5' AGS . . . P 2 -32.611 -33.753 -10.994 1 46.19 ? O5' AGS 201 F 1 HETATM 14 C C5' AGS . . . P 2 -31.295 -33.278 -10.973 1 43.71 ? C5' AGS 201 F 1 HETATM 15 C C4' AGS . . . P 2 -30.564 -33.121 -9.637 1 43.62 ? C4' AGS 201 F 1 HETATM 16 O O4' AGS . . . P 2 -29.687 -34.26 -9.346 1 42.47 ? O4' AGS 201 F 1 HETATM 17 C C3' AGS . . . P 2 -29.575 -31.955 -9.948 1 40.5 ? C3' AGS 201 F 1 HETATM 18 O O3' AGS . . . P 2 -28.86 -31.539 -8.783 1 39.3 ? O3' AGS 201 F 1 HETATM 19 C C2' AGS . . . P 2 -28.674 -32.71 -10.938 1 38.53 ? C2' AGS 201 F 1 HETATM 20 O O2' AGS . . . P 2 -27.437 -32.079 -11.202 1 45.71 ? O2' AGS 201 F 1 HETATM 21 C C1' AGS . . . P 2 -28.471 -34.017 -10.132 1 39.73 ? C1' AGS 201 F 1 HETATM 22 N N9 AGS . . . P 2 -28.079 -35.029 -11.093 1 38.22 ? N9 AGS 201 F 1 HETATM 23 C C8 AGS . . . P 2 -28.619 -35.3 -12.328 1 36.86 ? C8 AGS 201 F 1 HETATM 24 N N7 AGS . . . P 2 -27.975 -36.256 -12.925 1 34.26 ? N7 AGS 201 F 1 HETATM 25 C C5 AGS . . . P 2 -26.966 -36.655 -12.137 1 35.87 ? C5 AGS 201 F 1 HETATM 26 C C6 AGS . . . P 2 -25.963 -37.619 -12.289 1 36.32 ? C6 AGS 201 F 1 HETATM 27 N N6 AGS . . . P 2 -25.88 -38.361 -13.453 1 38.32 ? N6 AGS 201 F 1 HETATM 28 N N1 AGS . . . P 2 -25.096 -37.763 -11.303 1 35.24 ? N1 AGS 201 F 1 HETATM 29 C C2 AGS . . . P 2 -25.171 -37.004 -10.202 1 37.4 ? C2 AGS 201 F 1 HETATM 30 N N3 AGS . . . P 2 -26.106 -36.078 -10 1 36.47 ? N3 AGS 201 F 1 HETATM 31 C C4 AGS . . . P 2 -27.01 -35.869 -10.952 1 38.6 ? C4 AGS 201 F 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #