data_1GJV # _model_server_result.job_id mHT5YtaLDNnkh1y6xUaobA _model_server_result.datetime_utc '2024-11-15 05:41:16' _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 1gjv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1383}' # _entry.id 1GJV # _exptl.entry_id 1GJV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 1 _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 1GJV _cell.length_a 127.722 _cell.length_b 127.722 _cell.length_c 74.314 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1GJV _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 42 21 2' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 OD1 ASN 249 A ASN 249 1_555 E MG MG . A MG 1379 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc2 A O VAL 298 A VAL 298 1_555 F K K . A K 1380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.87 ? metalc ? metalc3 A O ASP 300 A ASP 300 1_555 F K K . A K 1380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.803 ? metalc ? metalc4 A N PHE 303 A PHE 303 1_555 F K K . A K 1380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.712 ? metalc ? metalc5 A O PHE 303 A PHE 303 1_555 F K K . A K 1380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.871 ? metalc ? metalc6 A O GLY 337 A GLY 337 1_555 F K K . A K 1380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.105 ? metalc ? metalc7 E MG MG . A MG 1379 1_555 I O2B AGS . A AGS 1383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc8 E MG MG . A MG 1379 1_555 I O1A AGS . A AGS 1383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc9 E MG MG . A MG 1379 1_555 I O2G AGS . A AGS 1383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc10 E MG MG . A MG 1379 1_555 J O HOH . A HOH 2039 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc11 E MG MG . A MG 1379 1_555 J O HOH . A HOH 2069 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc12 F K K . A K 1380 1_555 I O2A AGS . A AGS 1383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.043 ? # _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 1GJV _atom_sites.fract_transf_matrix[1][1] 0.007829 _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] 0.007829 _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] 0.013456 _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 B 2 CL A 1 502 502 CL CL . C 2 CL A 1 504 504 CL CL . D 2 CL A 1 505 505 CL CL . E 3 MG A 1 1379 1379 MG MG . F 4 K A 1 1380 1380 K K . G 2 CL A 1 1381 1381 CL CL . H 2 CL A 1 1382 1382 CL CL . I 5 AGS A 1 1383 1383 AGS AGS . J 6 HOH A 1 2001 2001 HOH HOH . J 6 HOH A 2 2002 2002 HOH HOH . J 6 HOH A 3 2003 2003 HOH HOH . J 6 HOH A 4 2004 2004 HOH HOH . J 6 HOH A 5 2005 2005 HOH HOH . J 6 HOH A 6 2006 2006 HOH HOH . J 6 HOH A 7 2007 2007 HOH HOH . J 6 HOH A 8 2008 2008 HOH HOH . J 6 HOH A 9 2009 2009 HOH HOH . J 6 HOH A 10 2010 2010 HOH HOH . J 6 HOH A 11 2011 2011 HOH HOH . J 6 HOH A 12 2012 2012 HOH HOH . J 6 HOH A 13 2013 2013 HOH HOH . J 6 HOH A 14 2014 2014 HOH HOH . J 6 HOH A 15 2015 2015 HOH HOH . J 6 HOH A 16 2016 2016 HOH HOH . J 6 HOH A 17 2017 2017 HOH HOH . J 6 HOH A 18 2018 2018 HOH HOH . J 6 HOH A 19 2019 2019 HOH HOH . J 6 HOH A 20 2020 2020 HOH HOH . J 6 HOH A 21 2021 2021 HOH HOH . J 6 HOH A 22 2022 2022 HOH HOH . J 6 HOH A 23 2023 2023 HOH HOH . J 6 HOH A 24 2024 2024 HOH HOH . J 6 HOH A 25 2025 2025 HOH HOH . J 6 HOH A 26 2026 2026 HOH HOH . J 6 HOH A 27 2027 2027 HOH HOH . J 6 HOH A 28 2028 2028 HOH HOH . J 6 HOH A 29 2029 2029 HOH HOH . J 6 HOH A 30 2030 2030 HOH HOH . J 6 HOH A 31 2031 2031 HOH HOH . J 6 HOH A 32 2032 2032 HOH HOH . J 6 HOH A 33 2033 2033 HOH HOH . J 6 HOH A 34 2034 2034 HOH HOH . J 6 HOH A 35 2035 2035 HOH HOH . J 6 HOH A 36 2036 2036 HOH HOH . J 6 HOH A 37 2037 2037 HOH HOH . J 6 HOH A 38 2038 2038 HOH HOH . J 6 HOH A 39 2039 2039 HOH HOH . J 6 HOH A 40 2040 2040 HOH HOH . J 6 HOH A 41 2041 2041 HOH HOH . J 6 HOH A 42 2042 2042 HOH HOH . J 6 HOH A 43 2043 2043 HOH HOH . J 6 HOH A 44 2044 2044 HOH HOH . J 6 HOH A 45 2045 2045 HOH HOH . J 6 HOH A 46 2046 2046 HOH HOH . J 6 HOH A 47 2047 2047 HOH HOH . J 6 HOH A 48 2048 2048 HOH HOH . J 6 HOH A 49 2049 2049 HOH HOH . J 6 HOH A 50 2050 2050 HOH HOH . J 6 HOH A 51 2051 2051 HOH HOH . J 6 HOH A 52 2052 2052 HOH HOH . J 6 HOH A 53 2053 2053 HOH HOH . J 6 HOH A 54 2054 2054 HOH HOH . J 6 HOH A 55 2055 2055 HOH HOH . J 6 HOH A 56 2056 2056 HOH HOH . J 6 HOH A 57 2057 2057 HOH HOH . J 6 HOH A 58 2058 2058 HOH HOH . J 6 HOH A 59 2059 2059 HOH HOH . J 6 HOH A 60 2060 2060 HOH HOH . J 6 HOH A 61 2061 2061 HOH HOH . J 6 HOH A 62 2062 2062 HOH HOH . J 6 HOH A 63 2063 2063 HOH HOH . J 6 HOH A 64 2064 2064 HOH HOH . J 6 HOH A 65 2065 2065 HOH HOH . J 6 HOH A 66 2066 2066 HOH HOH . J 6 HOH A 67 2067 2067 HOH HOH . J 6 HOH A 68 2068 2068 HOH HOH . J 6 HOH A 69 2069 2069 HOH HOH . J 6 HOH A 70 2070 2070 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 . . . I 5 93.562 124.34 34.881 1 77.83 ? PG AGS 1383 A 1 HETATM 2 S S1G AGS . . . I 5 93.767 125.834 35.066 1 73.3 ? S1G AGS 1383 A 1 HETATM 3 O O2G AGS . . . I 5 94.349 123.402 35.742 1 75.18 ? O2G AGS 1383 A 1 HETATM 4 O O3G AGS . . . I 5 92.176 123.77 35.053 1 74.78 ? O3G AGS 1383 A 1 HETATM 5 P PB AGS . . . I 5 94.784 122.77 32.75 1 63.86 ? PB AGS 1383 A 1 HETATM 6 O O1B AGS . . . I 5 94.959 123.044 31.308 1 66.18 ? O1B AGS 1383 A 1 HETATM 7 O O2B AGS . . . I 5 94.178 121.485 33.18 1 62.92 ? O2B AGS 1383 A 1 HETATM 8 O O3B AGS . . . I 5 93.969 123.991 33.372 1 70.12 ? O3B AGS 1383 A 1 HETATM 9 P PA AGS . . . I 5 97.308 122.104 34.078 1 57.26 ? PA AGS 1383 A 1 HETATM 10 O O1A AGS . . . I 5 96.699 121.157 35.045 1 57.42 ? O1A AGS 1383 A 1 HETATM 11 O O2A AGS . . . I 5 98.485 122.893 34.48 1 53.25 ? O2A AGS 1383 A 1 HETATM 12 O O3A AGS . . . I 5 96.174 123.064 33.49 1 61.36 ? O3A AGS 1383 A 1 HETATM 13 O O5' AGS . . . I 5 97.598 121.266 32.757 1 55.27 ? O5' AGS 1383 A 1 HETATM 14 C C5' AGS . . . I 5 98.596 121.645 31.822 1 52.92 ? C5' AGS 1383 A 1 HETATM 15 C C4' AGS . . . I 5 98.438 120.829 30.565 1 52.56 ? C4' AGS 1383 A 1 HETATM 16 O O4' AGS . . . I 5 99.141 119.557 30.705 1 53.29 ? O4' AGS 1383 A 1 HETATM 17 C C3' AGS . . . I 5 97.005 120.428 30.265 1 51.54 ? C3' AGS 1383 A 1 HETATM 18 O O3' AGS . . . I 5 96.358 121.479 29.572 1 51.58 ? O3' AGS 1383 A 1 HETATM 19 C C2' AGS . . . I 5 97.185 119.188 29.398 1 51.75 ? C2' AGS 1383 A 1 HETATM 20 O O2' AGS . . . I 5 97.516 119.517 28.068 1 54.64 ? O2' AGS 1383 A 1 HETATM 21 C C1' AGS . . . I 5 98.405 118.53 30.047 1 51.35 ? C1' AGS 1383 A 1 HETATM 22 N N9 AGS . . . I 5 98.093 117.464 31.01 1 49.42 ? N9 AGS 1383 A 1 HETATM 23 C C8 AGS . . . I 5 97.997 117.553 32.385 1 47.61 ? C8 AGS 1383 A 1 HETATM 24 N N7 AGS . . . I 5 97.718 116.412 32.97 1 45.61 ? N7 AGS 1383 A 1 HETATM 25 C C5 AGS . . . I 5 97.622 115.512 31.92 1 45.33 ? C5 AGS 1383 A 1 HETATM 26 C C6 AGS . . . I 5 97.356 114.142 31.88 1 44.69 ? C6 AGS 1383 A 1 HETATM 27 N N6 AGS . . . I 5 97.143 113.396 32.967 1 41.41 ? N6 AGS 1383 A 1 HETATM 28 N N1 AGS . . . I 5 97.322 113.545 30.668 1 45.96 ? N1 AGS 1383 A 1 HETATM 29 C C2 AGS . . . I 5 97.558 114.283 29.584 1 46.06 ? C2 AGS 1383 A 1 HETATM 30 N N3 AGS . . . I 5 97.832 115.577 29.491 1 46.61 ? N3 AGS 1383 A 1 HETATM 31 C C4 AGS . . . I 5 97.845 116.144 30.706 1 47.16 ? C4 AGS 1383 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #