data_3W8Q # _model_server_result.job_id 6hOFokhv99wfFC0p-i62MA _model_server_result.datetime_utc '2024-12-14 22:37:58' _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 3w8q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 3W8Q # _exptl.entry_id 3W8Q _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 90 _cell.entry_id 3W8Q _cell.length_a 47.815 _cell.length_b 96.191 _cell.length_c 138.617 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3W8Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_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 # 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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _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 3W8Q _atom_sites.fract_transf_matrix[1][1] 0.020914 _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] 0.010396 _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] 0.007214 _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 1 401 1 AGS AGS . C 3 HOH A 1 501 2 HOH HOH . C 3 HOH A 2 502 3 HOH HOH . C 3 HOH A 3 503 4 HOH HOH . C 3 HOH A 4 504 5 HOH HOH . C 3 HOH A 5 505 6 HOH HOH . C 3 HOH A 6 506 7 HOH HOH . C 3 HOH A 7 507 8 HOH HOH . C 3 HOH A 8 508 9 HOH HOH . C 3 HOH A 9 509 11 HOH HOH . C 3 HOH A 10 510 13 HOH HOH . C 3 HOH A 11 511 15 HOH HOH . C 3 HOH A 12 512 17 HOH HOH . C 3 HOH A 13 513 18 HOH HOH . C 3 HOH A 14 514 19 HOH HOH . C 3 HOH A 15 515 20 HOH HOH . C 3 HOH A 16 516 21 HOH HOH . C 3 HOH A 17 517 22 HOH HOH . C 3 HOH A 18 518 23 HOH HOH . C 3 HOH A 19 519 24 HOH HOH . C 3 HOH A 20 520 25 HOH HOH . C 3 HOH A 21 521 26 HOH HOH . C 3 HOH A 22 522 27 HOH HOH . C 3 HOH A 23 523 28 HOH HOH . C 3 HOH A 24 524 29 HOH HOH . C 3 HOH A 25 525 30 HOH HOH . C 3 HOH A 26 526 32 HOH HOH . C 3 HOH A 27 527 33 HOH HOH . C 3 HOH A 28 528 34 HOH HOH . C 3 HOH A 29 529 35 HOH HOH . C 3 HOH A 30 530 37 HOH HOH . C 3 HOH A 31 531 38 HOH HOH . C 3 HOH A 32 532 39 HOH HOH . C 3 HOH A 33 533 40 HOH HOH . C 3 HOH A 34 534 42 HOH HOH . C 3 HOH A 35 535 43 HOH HOH . C 3 HOH A 36 536 47 HOH HOH . C 3 HOH A 37 537 51 HOH HOH . C 3 HOH A 38 538 52 HOH HOH . C 3 HOH A 39 539 53 HOH HOH . C 3 HOH A 40 540 56 HOH HOH . C 3 HOH A 41 541 57 HOH HOH . C 3 HOH A 42 542 59 HOH HOH . C 3 HOH A 43 543 60 HOH HOH . C 3 HOH A 44 544 62 HOH HOH . C 3 HOH A 45 545 63 HOH HOH . C 3 HOH A 46 546 64 HOH HOH . C 3 HOH A 47 547 65 HOH HOH . C 3 HOH A 48 548 67 HOH HOH . C 3 HOH A 49 549 70 HOH HOH . C 3 HOH A 50 550 71 HOH HOH . C 3 HOH A 51 551 72 HOH HOH . C 3 HOH A 52 552 74 HOH HOH . C 3 HOH A 53 553 76 HOH HOH . C 3 HOH A 54 554 77 HOH HOH . C 3 HOH A 55 555 78 HOH HOH . C 3 HOH A 56 556 82 HOH HOH . C 3 HOH A 57 557 84 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 . . . B 2 29.827 5.705 7.677 1 29.58 ? PG AGS 401 A 1 HETATM 2 S S1G AGS . . . B 2 31.749 5.521 7.141 1 32.91 ? S1G AGS 401 A 1 HETATM 3 O O2G AGS . . . B 2 29.466 7.204 7.596 1 26.73 ? O2G AGS 401 A 1 HETATM 4 O O3G AGS . . . B 2 28.986 4.903 6.777 1 29.59 ? O3G AGS 401 A 1 HETATM 5 P PB AGS . . . B 2 28.812 5.567 10.395 1 27.93 ? PB AGS 401 A 1 HETATM 6 O O1B AGS . . . B 2 27.494 5.985 9.851 1 23.68 ? O1B AGS 401 A 1 HETATM 7 O O2B AGS . . . B 2 28.885 4.579 11.478 1 25.25 ? O2B AGS 401 A 1 HETATM 8 O O3B AGS . . . B 2 29.779 5.064 9.193 1 26.24 ? O3B AGS 401 A 1 HETATM 9 P PA AGS . . . B 2 29.087 8.049 11.94 1 21.9 ? PA AGS 401 A 1 HETATM 10 O O1A AGS . . . B 2 28.905 9.287 11.126 1 20.98 ? O1A AGS 401 A 1 HETATM 11 O O2A AGS . . . B 2 28.092 7.584 12.964 1 22.83 ? O2A AGS 401 A 1 HETATM 12 O O3A AGS . . . B 2 29.542 6.924 10.875 1 24.55 ? O3A AGS 401 A 1 HETATM 13 O O5' AGS . . . B 2 30.476 8.277 12.793 1 23.69 ? O5' AGS 401 A 1 HETATM 14 C C5' AGS . . . B 2 30.986 7.173 13.531 1 23.93 ? C5' AGS 401 A 1 HETATM 15 C C4' AGS . . . B 2 31.439 7.606 14.917 1 22.15 ? C4' AGS 401 A 1 HETATM 16 O O4' AGS . . . B 2 32.435 8.625 14.782 1 21.76 ? O4' AGS 401 A 1 HETATM 17 C C3' AGS . . . B 2 30.345 8.201 15.743 1 21.06 ? C3' AGS 401 A 1 HETATM 18 O O3' AGS . . . B 2 29.683 7.172 16.436 1 20.99 ? O3' AGS 401 A 1 HETATM 19 C C2' AGS . . . B 2 31.102 9.163 16.66 1 21.47 ? C2' AGS 401 A 1 HETATM 20 O O2' AGS . . . B 2 31.685 8.509 17.782 1 20.85 ? O2' AGS 401 A 1 HETATM 21 C C1' AGS . . . B 2 32.225 9.637 15.781 1 21.45 ? C1' AGS 401 A 1 HETATM 22 N N9 AGS . . . B 2 31.944 10.935 15.077 1 21.84 ? N9 AGS 401 A 1 HETATM 23 C C8 AGS . . . B 2 31.45 11.103 13.837 1 21.96 ? C8 AGS 401 A 1 HETATM 24 N N7 AGS . . . B 2 31.318 12.409 13.499 1 20.43 ? N7 AGS 401 A 1 HETATM 25 C C5 AGS . . . B 2 31.774 13.064 14.57 1 20.88 ? C5 AGS 401 A 1 HETATM 26 C C6 AGS . . . B 2 31.97 14.482 14.822 1 20.12 ? C6 AGS 401 A 1 HETATM 27 N N6 AGS . . . B 2 31.604 15.351 13.828 1 18.2 ? N6 AGS 401 A 1 HETATM 28 N N1 AGS . . . B 2 32.446 14.811 16.035 1 22.68 ? N1 AGS 401 A 1 HETATM 29 C C2 AGS . . . B 2 32.774 13.91 16.987 1 22.34 ? C2 AGS 401 A 1 HETATM 30 N N3 AGS . . . B 2 32.645 12.574 16.757 1 23.52 ? N3 AGS 401 A 1 HETATM 31 C C4 AGS . . . B 2 32.186 12.13 15.579 1 20.81 ? C4 AGS 401 A 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 31 #