data_1NLY # _model_server_result.job_id PX7WB6WJw3SkjBNFs13PaA _model_server_result.datetime_utc '2025-03-05 01:47:06' _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 1nly # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":402}' # _entry.id 1NLY # _exptl.entry_id 1NLY _exptl.method 'X-RAY DIFFRACTION' # _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 2 _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 120 _cell.entry_id 1NLY _cell.length_a 110.82 _cell.length_b 110.82 _cell.length_c 230.91 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NLY _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63 2 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 55.41 95.972935 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -55.41 95.972935 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F 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 covale ? covale1 A C LYS 41 A LYS 41 1_555 A N MSE 42 A MSE 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale2 A C MSE 42 A MSE 42 1_555 A N GLU 43 A GLU 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale3 A C LEU 81 A LEU 81 1_555 A N MSE 82 A MSE 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale4 A C MSE 82 A MSE 82 1_555 A N HIS 83 A HIS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale5 A C ILE 191 A ILE 191 1_555 A N MSE 192 A MSE 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale6 A C MSE 192 A MSE 192 1_555 A N GLU 193 A GLU 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale7 A C ARG 238 A ARG 238 1_555 A N MSE 239 A MSE 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale8 A C MSE 239 A MSE 239 1_555 A N ARG 240 A ARG 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale9 A C ASN 286 A ASN 286 1_555 A N MSE 287 A MSE 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale10 A C MSE 287 A MSE 287 1_555 A N SER 288 A SER 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale11 A C ASP 311 A ASP 311 1_555 A N MSE 312 A MSE 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale12 A C MSE 312 A MSE 312 1_555 A N ILE 313 A ILE 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale13 B C LYS 41 B LYS 41 1_555 B N MSE 42 B MSE 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale14 B C MSE 42 B MSE 42 1_555 B N GLU 43 B GLU 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale15 B C LEU 81 B LEU 81 1_555 B N MSE 82 B MSE 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale16 B C MSE 82 B MSE 82 1_555 B N HIS 83 B HIS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale17 B C ILE 191 B ILE 191 1_555 B N MSE 192 B MSE 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale18 B C MSE 192 B MSE 192 1_555 B N GLU 193 B GLU 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale19 B C ARG 238 B ARG 238 1_555 B N MSE 239 B MSE 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale20 B C MSE 239 B MSE 239 1_555 B N ARG 240 B ARG 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale21 B C ASN 286 B ASN 286 1_555 B N MSE 287 B MSE 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale22 B C MSE 287 B MSE 287 1_555 B N SER 288 B SER 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale23 B C ASP 311 B ASP 311 1_555 B N MSE 312 B MSE 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale24 B C MSE 312 B MSE 312 1_555 B N ILE 313 B ILE 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? metalc ? metalc1 A OG1 THR 185 A THR 185 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.718 ? metalc ? metalc2 C MG MG . A MG 401 1_555 D O2B AGS . A AGS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.582 ? metalc ? metalc3 C MG MG . A MG 401 1_555 H O HOH . A HOH 1022 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? # _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 66 n n PG O2G AGS sing 67 n n PG O3G AGS sing 68 n n PG O3B AGS sing 69 n n PB O1B AGS doub 70 n n PB O2B AGS sing 71 n n PB O3B AGS sing 72 n n PB O3A AGS sing 73 n n PA O1A AGS doub 74 n n PA O2A AGS sing 75 n n PA O3A AGS sing 76 n n PA O5' AGS sing 77 n n O5' C5' AGS sing 78 n n C5' C4' AGS sing 79 n n C4' O4' AGS sing 80 n n C4' C3' AGS sing 81 n n O4' C1' AGS sing 82 n n C3' O3' AGS sing 83 n n C3' C2' AGS sing 84 n n C2' O2' AGS sing 85 n n C2' C1' AGS sing 86 n n C1' N9 AGS sing 87 n n N9 C8 AGS sing 88 n y N9 C4 AGS sing 89 n y C8 N7 AGS doub 90 n y N7 C5 AGS sing 91 n y C5 C6 AGS sing 92 n y C5 C4 AGS doub 93 n y C6 N6 AGS sing 94 n n C6 N1 AGS doub 95 n y N1 C2 AGS sing 96 n y C2 N3 AGS doub 97 n y N3 C4 AGS sing 98 n y O2G HOG2 AGS sing 99 n n O3G H21 AGS sing 100 n n O2B HOB2 AGS sing 101 n n O2A HOA2 AGS sing 102 n n C5' "H5'1" AGS sing 103 n n C5' "H5'2" AGS sing 104 n n C4' H4' AGS sing 105 n n C3' H3' AGS sing 106 n n O3' HO3' AGS sing 107 n n C2' H2' AGS sing 108 n n O2' HO2' AGS sing 109 n n C1' H1' AGS sing 110 n n C8 H8 AGS sing 111 n n N6 HN61 AGS sing 112 n n N6 HN62 AGS sing 113 n n C2 H2 AGS sing 114 n n # _atom_sites.entry_id 1NLY _atom_sites.fract_transf_matrix[1][1] 0.009024 _atom_sites.fract_transf_matrix[1][2] 0.00521 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01042 _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] 0.004331 _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 C 2 MG A 1 401 700 MG MG2 . D 3 AGS A 1 402 400 AGS ATG . E 4 SO4 B 1 401 800 SO4 SO4 . F 3 AGS B 1 402 500 AGS ATG . G 5 2PE B 1 403 600 2PE PEG . H 6 HOH A 1 1001 1001 HOH HOH . H 6 HOH A 2 1002 1002 HOH HOH . H 6 HOH A 3 1003 1003 HOH HOH . H 6 HOH A 4 1004 1004 HOH HOH . H 6 HOH A 5 1005 1005 HOH HOH . H 6 HOH A 6 1006 1006 HOH HOH . H 6 HOH A 7 1007 1007 HOH HOH . H 6 HOH A 8 1008 1008 HOH HOH . H 6 HOH A 9 1009 1010 HOH HOH . H 6 HOH A 10 1010 1011 HOH HOH . H 6 HOH A 11 1011 1012 HOH HOH . H 6 HOH A 12 1012 1013 HOH HOH . H 6 HOH A 13 1013 1015 HOH HOH . H 6 HOH A 14 1014 1025 HOH HOH . H 6 HOH A 15 1015 1027 HOH HOH . H 6 HOH A 16 1016 1032 HOH HOH . H 6 HOH A 17 1017 1033 HOH HOH . H 6 HOH A 18 1018 1034 HOH HOH . H 6 HOH A 19 1019 1035 HOH HOH . H 6 HOH A 20 1020 1036 HOH HOH . H 6 HOH A 21 1021 1041 HOH HOH . H 6 HOH A 22 1022 1042 HOH HOH . I 6 HOH B 1 501 1009 HOH HOH . I 6 HOH B 2 502 1014 HOH HOH . I 6 HOH B 3 503 1016 HOH HOH . I 6 HOH B 4 504 1017 HOH HOH . I 6 HOH B 5 505 1018 HOH HOH . I 6 HOH B 6 506 1019 HOH HOH . I 6 HOH B 7 507 1020 HOH HOH . I 6 HOH B 8 508 1021 HOH HOH . I 6 HOH B 9 509 1022 HOH HOH . I 6 HOH B 10 510 1023 HOH HOH . I 6 HOH B 11 511 1024 HOH HOH . I 6 HOH B 12 512 1026 HOH HOH . I 6 HOH B 13 513 1028 HOH HOH . I 6 HOH B 14 514 1029 HOH HOH . I 6 HOH B 15 515 1030 HOH HOH . I 6 HOH B 16 516 1031 HOH HOH . I 6 HOH B 17 517 1037 HOH HOH . I 6 HOH B 18 518 1038 HOH HOH . I 6 HOH B 19 519 1039 HOH HOH . I 6 HOH B 20 520 1040 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 . . . F 3 -10.923 30.981 24.143 0.5 66.19 ? PG AGS 402 B 1 HETATM 2 S S1G AGS . . . F 3 -9.081 30.909 24.145 0.5 65.82 ? S1G AGS 402 B 1 HETATM 3 O O2G AGS . . . F 3 -11.377 30.941 25.559 0.5 65.37 ? O2G AGS 402 B 1 HETATM 4 O O3G AGS . . . F 3 -11.515 32.094 23.376 0.5 66.26 ? O3G AGS 402 B 1 HETATM 5 P PB AGS . . . F 3 -11.148 28.764 22.295 0.5 65.11 ? PB AGS 402 B 1 HETATM 6 O O1B AGS . . . F 3 -11.756 29.163 21.024 0.5 64.18 ? O1B AGS 402 B 1 HETATM 7 O O2B AGS . . . F 3 -9.671 28.743 22.368 0.5 64.65 ? O2B AGS 402 B 1 HETATM 8 O O3B AGS . . . F 3 -11.677 29.74 23.405 0.5 64.73 ? O3B AGS 402 B 1 HETATM 9 P PA AGS . . . F 3 -10.757 25.906 22.749 0.5 57.27 ? PA AGS 402 B 1 HETATM 10 O O1A AGS . . . F 3 -9.916 25.487 21.59 0.5 54.26 ? O1A AGS 402 B 1 HETATM 11 O O2A AGS . . . F 3 -10.259 26.158 24.08 0.5 56.99 ? O2A AGS 402 B 1 HETATM 12 O O3A AGS . . . F 3 -11.661 27.296 22.398 0.5 60.41 ? O3A AGS 402 B 1 HETATM 13 O O5' AGS . . . F 3 -11.921 24.892 22.77 0.5 51.84 ? O5' AGS 402 B 1 HETATM 14 C C5' AGS . . . F 3 -11.776 23.734 23.458 0.5 46.62 ? C5' AGS 402 B 1 HETATM 15 C C4' AGS . . . F 3 -13.038 22.954 23.353 0.5 41.55 ? C4' AGS 402 B 1 HETATM 16 O O4' AGS . . . F 3 -13.344 22.749 22.045 0.5 39.58 ? O4' AGS 402 B 1 HETATM 17 C C3' AGS . . . F 3 -12.974 21.582 24.065 0.5 38.86 ? C3' AGS 402 B 1 HETATM 18 O O3' AGS . . . F 3 -14.259 21.304 24.599 0.5 38.77 ? O3' AGS 402 B 1 HETATM 19 C C2' AGS . . . F 3 -12.723 20.652 22.876 0.5 37.9 ? C2' AGS 402 B 1 HETATM 20 O O2' AGS . . . F 3 -13.119 19.297 23.095 0.5 37.75 ? O2' AGS 402 B 1 HETATM 21 C C1' AGS . . . F 3 -13.528 21.411 21.753 0.5 38.1 ? C1' AGS 402 B 1 HETATM 22 N N9 AGS . . . F 3 -12.924 21.159 20.4 0.5 37.3 ? N9 AGS 402 B 1 HETATM 23 C C8 AGS . . . F 3 -11.945 21.847 19.707 0.5 36.85 ? C8 AGS 402 B 1 HETATM 24 N N7 AGS . . . F 3 -11.561 21.417 18.519 0.5 36.82 ? N7 AGS 402 B 1 HETATM 25 C C5 AGS . . . F 3 -12.347 20.299 18.4 0.5 37.23 ? C5 AGS 402 B 1 HETATM 26 C C6 AGS . . . F 3 -12.512 19.336 17.345 0.5 36.8 ? C6 AGS 402 B 1 HETATM 27 N N6 AGS . . . F 3 -11.715 19.395 16.129 0.5 35.32 ? N6 AGS 402 B 1 HETATM 28 N N1 AGS . . . F 3 -13.414 18.312 17.513 0.5 36.13 ? N1 AGS 402 B 1 HETATM 29 C C2 AGS . . . F 3 -14.185 18.231 18.657 0.5 36.85 ? C2 AGS 402 B 1 HETATM 30 N N3 AGS . . . F 3 -14.15 19.091 19.737 0.5 37.99 ? N3 AGS 402 B 1 HETATM 31 C C4 AGS . . . F 3 -13.22 20.116 19.541 0.5 37.99 ? C4 AGS 402 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #