data_1XP8 # _model_server_result.job_id tNoU0a3UPMLb4CuYS3MtlA _model_server_result.datetime_utc '2024-11-14 11:22:03' _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 1xp8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":400}' # _entry.id 1XP8 # _exptl.entry_id 1XP8 _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 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 120 _cell.entry_id 1XP8 _cell.length_a 111.38 _cell.length_b 111.38 _cell.length_c 67.49 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XP8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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_555 -y,x-y,z+1/3 -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 22.496667 3 'crystal symmetry operation' 3_555 -x+y,-x,z+2/3 -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 44.993333 4 'crystal symmetry operation' 4_555 -x,-y,z+1/2 -1 0 0 0 -1 0 0 0 1 0 0 33.745 5 'crystal symmetry operation' 5_555 y,-x+y,z+5/6 0.5 0.866025 0 -0.866025 0.5 0 0 0 1 0 0 56.241667 6 'crystal symmetry operation' 6_555 x-y,x,z+1/6 0.5 -0.866025 0 0.866025 0.5 0 0 0 1 0 0 11.248333 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 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 1XP8 _atom_sites.fract_transf_matrix[1][1] 0.008978 _atom_sites.fract_transf_matrix[1][2] 0.005184 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010367 _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] 0.014817 _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 AGS A 1 400 400 AGS SAP . C 3 HOH A 1 501 501 HOH WAT . C 3 HOH A 2 502 502 HOH WAT . C 3 HOH A 3 503 503 HOH WAT . C 3 HOH A 4 504 504 HOH WAT . C 3 HOH A 5 505 505 HOH WAT . C 3 HOH A 6 506 506 HOH WAT . C 3 HOH A 7 507 507 HOH WAT . C 3 HOH A 8 508 508 HOH WAT . C 3 HOH A 9 509 509 HOH WAT . C 3 HOH A 10 510 510 HOH WAT . C 3 HOH A 11 511 511 HOH WAT . C 3 HOH A 12 512 512 HOH WAT . C 3 HOH A 13 513 513 HOH WAT . C 3 HOH A 14 514 514 HOH WAT . C 3 HOH A 15 515 515 HOH WAT . C 3 HOH A 16 516 516 HOH WAT . C 3 HOH A 17 517 517 HOH WAT . C 3 HOH A 18 518 518 HOH WAT . C 3 HOH A 19 519 519 HOH WAT . C 3 HOH A 20 520 520 HOH WAT . C 3 HOH A 21 521 521 HOH WAT . C 3 HOH A 22 522 522 HOH WAT . C 3 HOH A 23 523 523 HOH WAT . C 3 HOH A 24 524 524 HOH WAT . C 3 HOH A 25 525 525 HOH WAT . C 3 HOH A 26 526 526 HOH WAT . C 3 HOH A 27 527 527 HOH WAT . # 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 . . . B 2 18.551 14.88 7.948 1 81.55 ? PG AGS 400 A 1 HETATM 2 S S1G AGS . . . B 2 19.139 14.212 6.229 1 81.24 ? S1G AGS 400 A 1 HETATM 3 O O2G AGS . . . B 2 17.505 13.976 8.479 1 80.65 ? O2G AGS 400 A 1 HETATM 4 O O3G AGS . . . B 2 19.733 15.156 8.796 1 81.98 ? O3G AGS 400 A 1 HETATM 5 P PB AGS . . . B 2 18.64 17.69 7.623 1 67.06 ? PB AGS 400 A 1 HETATM 6 O O1B AGS . . . B 2 17.696 18.739 8.07 1 69.54 ? O1B AGS 400 A 1 HETATM 7 O O2B AGS . . . B 2 19.907 17.531 8.371 1 68.88 ? O2B AGS 400 A 1 HETATM 8 O O3B AGS . . . B 2 17.851 16.286 7.585 1 74.52 ? O3B AGS 400 A 1 HETATM 9 P PA AGS . . . B 2 20.472 18.401 5.587 1 60.89 ? PA AGS 400 A 1 HETATM 10 O O1A AGS . . . B 2 21.213 17.182 5.984 1 61.16 ? O1A AGS 400 A 1 HETATM 11 O O2A AGS . . . B 2 20.527 19.701 6.291 1 62.8 ? O2A AGS 400 A 1 HETATM 12 O O3A AGS . . . B 2 18.999 17.956 6.073 1 64.95 ? O3A AGS 400 A 1 HETATM 13 O O5' AGS . . . B 2 20.051 18.417 4.031 1 62.94 ? O5' AGS 400 A 1 HETATM 14 C C5' AGS . . . B 2 19.258 19.48 3.494 1 61.83 ? C5' AGS 400 A 1 HETATM 15 C C4' AGS . . . B 2 19.685 19.821 2.065 1 62.03 ? C4' AGS 400 A 1 HETATM 16 O O4' AGS . . . B 2 21.054 20.26 1.991 1 62.99 ? O4' AGS 400 A 1 HETATM 17 C C3' AGS . . . B 2 19.585 18.646 1.093 1 62.17 ? C3' AGS 400 A 1 HETATM 18 O O3' AGS . . . B 2 18.251 18.494 0.599 1 61.69 ? O3' AGS 400 A 1 HETATM 19 C C2' AGS . . . B 2 20.475 19.182 -0.025 1 62.8 ? C2' AGS 400 A 1 HETATM 20 O O2' AGS . . . B 2 19.85 20.262 -0.724 1 63.11 ? O2' AGS 400 A 1 HETATM 21 C C1' AGS . . . B 2 21.651 19.708 0.801 1 63.1 ? C1' AGS 400 A 1 HETATM 22 N N9 AGS . . . B 2 22.563 18.612 1.208 1 63.22 ? N9 AGS 400 A 1 HETATM 23 C C8 AGS . . . B 2 22.526 17.943 2.359 1 63.44 ? C8 AGS 400 A 1 HETATM 24 N N7 AGS . . . B 2 23.527 17.067 2.405 1 63.47 ? N7 AGS 400 A 1 HETATM 25 C C5 AGS . . . B 2 24.211 17.174 1.271 1 63.73 ? C5 AGS 400 A 1 HETATM 26 C C6 AGS . . . B 2 25.333 16.54 0.746 1 63.84 ? C6 AGS 400 A 1 HETATM 27 N N6 AGS . . . B 2 25.958 15.588 1.433 1 63.17 ? N6 AGS 400 A 1 HETATM 28 N N1 AGS . . . B 2 25.777 16.9 -0.468 1 63.92 ? N1 AGS 400 A 1 HETATM 29 C C2 AGS . . . B 2 25.168 17.841 -1.17 1 64.45 ? C2 AGS 400 A 1 HETATM 30 N N3 AGS . . . B 2 24.1 18.463 -0.7 1 64.45 ? N3 AGS 400 A 1 HETATM 31 C C4 AGS . . . B 2 23.598 18.158 0.506 1 63.56 ? C4 AGS 400 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 124 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 457 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #