data_2R8F # _model_server_result.job_id sgRAwiE0T69nh6_4WPrhvA _model_server_result.datetime_utc '2025-04-28 05:45:53' _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 2r8f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":400}' # _entry.id 2R8F # _exptl.entry_id 2R8F _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 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 2R8F _cell.length_a 108.644 _cell.length_b 108.644 _cell.length_c 155.664 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2R8F _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8 # 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_465 -x-1,-y+1,z -1 0 0 0 -1 0 0 0 1 -108.644 108.644 0 3 'crystal symmetry operation' 3_565 -y,x+1,z 0 -1 0 1 0 0 0 0 1 0 108.644 0 4 'crystal symmetry operation' 4_455 y-1,-x,z 0 1 0 -1 0 0 0 0 1 -108.644 0 0 5 'crystal symmetry operation' 5_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -108.644 0 0 6 'crystal symmetry operation' 6_565 x,-y+1,-z 1 0 0 0 -1 0 0 0 -1 0 108.644 0 7 'crystal symmetry operation' 7_465 y-1,x+1,-z 0 1 0 1 0 0 0 0 -1 -108.644 108.644 0 8 'crystal symmetry operation' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 2R8F _atom_sites.fract_transf_matrix[1][1] 0.009204 _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] 0.009204 _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] 0.006424 _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 PO4 A 1 318 1 PO4 PO4 . C 3 AGS A 1 400 400 AGS AGS . D 4 HOH A 1 401 1 HOH HOH . D 4 HOH A 2 402 2 HOH HOH . D 4 HOH A 3 403 3 HOH HOH . D 4 HOH A 4 404 4 HOH HOH . D 4 HOH A 5 405 5 HOH HOH . D 4 HOH A 6 406 6 HOH HOH . D 4 HOH A 7 407 7 HOH HOH . D 4 HOH A 8 408 8 HOH HOH . D 4 HOH A 9 409 9 HOH HOH . D 4 HOH A 10 410 10 HOH HOH . D 4 HOH A 11 411 11 HOH HOH . D 4 HOH A 12 412 12 HOH HOH . D 4 HOH A 13 413 13 HOH HOH . D 4 HOH A 14 414 14 HOH HOH . D 4 HOH A 15 415 15 HOH HOH . D 4 HOH A 16 416 16 HOH HOH . D 4 HOH A 17 417 17 HOH HOH . D 4 HOH A 18 418 18 HOH HOH . D 4 HOH A 19 419 19 HOH HOH . D 4 HOH A 20 420 20 HOH HOH . D 4 HOH A 21 421 21 HOH HOH . D 4 HOH A 22 422 22 HOH HOH . D 4 HOH A 23 423 23 HOH HOH . D 4 HOH A 24 424 24 HOH HOH . D 4 HOH A 25 425 25 HOH HOH . D 4 HOH A 26 426 26 HOH HOH . D 4 HOH A 27 427 27 HOH HOH . D 4 HOH A 28 428 28 HOH HOH . D 4 HOH A 29 429 29 HOH HOH . D 4 HOH A 30 430 30 HOH HOH . D 4 HOH A 31 431 31 HOH HOH . D 4 HOH A 32 432 32 HOH HOH . D 4 HOH A 33 433 33 HOH HOH . D 4 HOH A 34 434 34 HOH HOH . D 4 HOH A 35 435 35 HOH HOH . D 4 HOH A 36 436 36 HOH HOH . D 4 HOH A 37 437 37 HOH HOH . D 4 HOH A 38 438 38 HOH HOH . D 4 HOH A 39 439 39 HOH HOH . D 4 HOH A 40 440 40 HOH HOH . D 4 HOH A 41 441 41 HOH HOH . D 4 HOH A 42 442 42 HOH HOH . D 4 HOH A 43 443 43 HOH HOH . D 4 HOH A 44 444 44 HOH HOH . D 4 HOH A 45 445 45 HOH HOH . D 4 HOH A 46 446 46 HOH HOH . D 4 HOH A 47 447 47 HOH HOH . D 4 HOH A 48 448 48 HOH HOH . D 4 HOH A 49 449 49 HOH HOH . D 4 HOH A 50 450 50 HOH HOH . D 4 HOH A 51 451 51 HOH HOH . D 4 HOH A 52 452 52 HOH HOH . D 4 HOH A 53 453 53 HOH HOH . D 4 HOH A 54 454 54 HOH HOH . D 4 HOH A 55 455 55 HOH HOH . D 4 HOH A 56 456 56 HOH HOH . D 4 HOH A 57 457 57 HOH HOH . D 4 HOH A 58 458 58 HOH HOH . D 4 HOH A 59 459 59 HOH HOH . D 4 HOH A 60 460 60 HOH HOH . D 4 HOH A 61 461 61 HOH HOH . D 4 HOH A 62 462 62 HOH HOH . D 4 HOH A 63 463 63 HOH HOH . D 4 HOH A 64 464 64 HOH HOH . D 4 HOH A 65 465 65 HOH HOH . D 4 HOH A 66 466 66 HOH HOH . D 4 HOH A 67 467 67 HOH HOH . D 4 HOH A 68 468 68 HOH HOH . D 4 HOH A 69 469 69 HOH HOH . D 4 HOH A 70 470 70 HOH HOH . D 4 HOH A 71 471 71 HOH HOH . D 4 HOH A 72 472 72 HOH HOH . D 4 HOH A 73 473 73 HOH HOH . D 4 HOH A 74 474 74 HOH HOH . D 4 HOH A 75 475 75 HOH HOH . D 4 HOH A 76 476 76 HOH HOH . D 4 HOH A 77 477 77 HOH HOH . D 4 HOH A 78 478 78 HOH HOH . D 4 HOH A 79 479 79 HOH HOH . D 4 HOH A 80 480 80 HOH HOH . D 4 HOH A 81 481 81 HOH HOH . D 4 HOH A 82 482 82 HOH HOH . D 4 HOH A 83 483 83 HOH HOH . D 4 HOH A 84 484 84 HOH HOH . D 4 HOH A 85 485 85 HOH HOH . D 4 HOH A 86 486 86 HOH HOH . D 4 HOH A 87 487 87 HOH HOH . D 4 HOH A 88 488 88 HOH HOH . D 4 HOH A 89 489 89 HOH HOH . D 4 HOH A 90 490 90 HOH HOH . D 4 HOH A 91 491 92 HOH HOH . D 4 HOH A 92 492 93 HOH HOH . D 4 HOH A 93 493 94 HOH HOH . D 4 HOH A 94 494 95 HOH HOH . D 4 HOH A 95 495 96 HOH HOH . D 4 HOH A 96 496 97 HOH HOH . D 4 HOH A 97 497 98 HOH HOH . D 4 HOH A 98 498 99 HOH HOH . D 4 HOH A 99 499 100 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 . . . C 3 -18.115 39.072 18.583 0.75 95.25 ? PG AGS 400 A 1 HETATM 2 S S1G AGS . . . C 3 -18.136 37.353 17.444 0.75 93.23 ? S1G AGS 400 A 1 HETATM 3 O O2G AGS . . . C 3 -17.372 38.724 19.796 0.75 94.88 ? O2G AGS 400 A 1 HETATM 4 O O3G AGS . . . C 3 -19.49 39.509 18.935 0.75 94.9 ? O3G AGS 400 A 1 HETATM 5 P PB AGS . . . C 3 -17.514 41.847 18.221 0.75 94.44 ? PB AGS 400 A 1 HETATM 6 O O1B AGS . . . C 3 -18.9 42.37 18.403 0.75 93.33 ? O1B AGS 400 A 1 HETATM 7 O O2B AGS . . . C 3 -16.688 42.02 19.418 0.75 93.55 ? O2B AGS 400 A 1 HETATM 8 O O3B AGS . . . C 3 -17.398 40.294 17.839 0.75 94.26 ? O3B AGS 400 A 1 HETATM 9 P PA AGS . . . C 3 -17.736 43.36 15.918 0.75 95.57 ? PA AGS 400 A 1 HETATM 10 O O1A AGS . . . C 3 -18.848 42.48 15.436 0.75 94.07 ? O1A AGS 400 A 1 HETATM 11 O O2A AGS . . . C 3 -18.212 44.648 16.49 0.75 95.23 ? O2A AGS 400 A 1 HETATM 12 O O3A AGS . . . C 3 -16.834 42.646 17.048 0.75 94.77 ? O3A AGS 400 A 1 HETATM 13 O O5' AGS . . . C 3 -16.704 43.761 14.728 0.75 94.6 ? O5' AGS 400 A 1 HETATM 14 C C5' AGS . . . C 3 -15.279 43.683 14.814 0.75 94.2 ? C5' AGS 400 A 1 HETATM 15 C C4' AGS . . . C 3 -14.757 44.931 15.516 0.75 95.3 ? C4' AGS 400 A 1 HETATM 16 O O4' AGS . . . C 3 -15.528 46.08 15.117 0.75 95.6 ? O4' AGS 400 A 1 HETATM 17 C C3' AGS . . . C 3 -13.307 45.347 15.222 0.75 95.54 ? C3' AGS 400 A 1 HETATM 18 O O3' AGS . . . C 3 -12.622 45.401 16.471 0.75 97.5 ? O3' AGS 400 A 1 HETATM 19 C C2' AGS . . . C 3 -13.416 46.718 14.697 0.75 95.6 ? C2' AGS 400 A 1 HETATM 20 O O2' AGS . . . C 3 -12.356 46.933 13.769 0.75 95.46 ? O2' AGS 400 A 1 HETATM 21 C C1' AGS . . . C 3 -14.757 46.719 14.113 0.75 95.46 ? C1' AGS 400 A 1 HETATM 22 N N9 AGS . . . C 3 -15.361 47.987 13.51 0.75 95.53 ? N9 AGS 400 A 1 HETATM 23 C C8 AGS . . . C 3 -14.875 49.242 13.495 0.75 94.79 ? C8 AGS 400 A 1 HETATM 24 N N7 AGS . . . C 3 -15.78 50.023 12.839 0.75 94.8 ? N7 AGS 400 A 1 HETATM 25 C C5 AGS . . . C 3 -16.835 49.269 12.446 0.75 94.52 ? C5 AGS 400 A 1 HETATM 26 C C6 AGS . . . C 3 -18.049 49.491 11.747 0.75 94.22 ? C6 AGS 400 A 1 HETATM 27 N N6 AGS . . . C 3 -18.436 50.705 11.282 0.75 92.89 ? N6 AGS 400 A 1 HETATM 28 N N1 AGS . . . C 3 -18.9 48.449 11.523 0.75 93.7 ? N1 AGS 400 A 1 HETATM 29 C C2 AGS . . . C 3 -18.599 47.205 11.952 0.75 93.36 ? C2 AGS 400 A 1 HETATM 30 N N3 AGS . . . C 3 -17.451 46.976 12.614 0.75 93.92 ? N3 AGS 400 A 1 HETATM 31 C C4 AGS . . . C 3 -16.554 47.986 12.871 0.75 94.91 ? C4 AGS 400 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 407 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #