data_3AR8 # _model_server_result.job_id b5F1VnNNvyNMqkedBK3cLQ _model_server_result.datetime_utc '2024-11-23 12:42:32' _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 3ar8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1002}' # _entry.id 3AR8 # _exptl.entry_id 3AR8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 558.31 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2',3'-O-[(1r)-2,4,6-trinitrocyclohexa-2,5-diene-1,1-diyl]adenosine 5'-(dihydrogen phosphate)" _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 106.71 _cell.angle_gamma 90 _cell.entry_id 3AR8 _cell.length_a 176.864 _cell.length_b 69.873 _cell.length_c 141.813 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3AR8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _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 _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 E _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 disulf ? disulf1 A SG CYS 877 A CYS 876 1_555 A SG CYS 889 A CYS 888 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A C ACE 1 A ACE 1 1_555 A N MET 2 A MET 1 1_555 A ? ? ? ? ? ? ? ? ? ? ? 1.326 ? metalc ? metalc1 A OD1 ASP 352 A ASP 351 1_555 C MG MG . A MG 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc2 A O THR 354 A THR 353 1_555 C MG MG . A MG 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc3 A OD1 ASP 704 A ASP 703 1_555 C MG MG . A MG 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.883 ? metalc ? metalc4 A O LEU 712 A LEU 711 1_555 B NA NA . A NA 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc5 A O LYS 713 A LYS 712 1_555 B NA NA . A NA 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc6 A O ALA 715 A ALA 714 1_555 B NA NA . A NA 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc7 A OE2 GLU 733 A GLU 732 1_555 B NA NA . A NA 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc8 C MG MG . A MG 995 1_555 G O HOH . A HOH 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc9 C MG MG . A MG 995 1_555 G O HOH . A HOH 4002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? # _chem_comp.formula 'C16 H15 N8 O13 P' _chem_comp.formula_weight 558.31 _chem_comp.id TM1 _chem_comp.mon_nstd_flag . _chem_comp.name "2',3'-O-[(1r)-2,4,6-trinitrocyclohexa-2,5-diene-1,1-diyl]adenosine 5'-(dihydrogen phosphate)" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 N1 C2 TM1 doub 414 n y N1 C6 TM1 sing 415 n y C2 N3 TM1 sing 416 n y C2 H2 TM1 sing 417 n n N3 C4 TM1 doub 418 n y C4 C5 TM1 sing 419 n y C4 N9 TM1 sing 420 n y C5 C6 TM1 doub 421 n y C5 N7 TM1 sing 422 n y C6 N6 TM1 sing 423 n n N6 HN6 TM1 sing 424 n n N6 HN6A TM1 sing 425 n n N7 C8 TM1 doub 426 n y C8 N9 TM1 sing 427 n y C8 H8 TM1 sing 428 n n N9 C1' TM1 sing 429 n n PA O1A TM1 sing 430 n n PA O2A TM1 doub 431 n n PA O3A TM1 sing 432 n n PA O5' TM1 sing 433 n n C1' C2' TM1 sing 434 n n C1' O4' TM1 sing 435 n n C1' H1' TM1 sing 436 n n O1A HO1A TM1 sing 437 n n C1F O2' TM1 sing 438 n n C1F C2F TM1 sing 439 n n C1F O3' TM1 sing 440 n n C1F C6F TM1 sing 441 n n C2' O2' TM1 sing 442 n n C2' C3' TM1 sing 443 n n C2' H2' TM1 sing 444 n n C2F N2F TM1 sing 445 n n C2F C3F TM1 doub 446 n n N2F O2F TM1 sing 447 n n N2F O3F TM1 doub 448 n n C3' O3' TM1 sing 449 n n C3' C4' TM1 sing 450 n n C3' H3' TM1 sing 451 n n O3A HO3A TM1 sing 452 n n C3F C4F TM1 sing 453 n n C3F H3F TM1 sing 454 n n C4' O4' TM1 sing 455 n n C4' C5' TM1 sing 456 n n C4' H4' TM1 sing 457 n n C4F N4F TM1 sing 458 n n C4F C5F TM1 sing 459 n n C4F H4F TM1 sing 460 n n N4F O4F TM1 sing 461 n n N4F O5F TM1 doub 462 n n C5' O5' TM1 sing 463 n n C5' H5' TM1 sing 464 n n C5' "H5'A" TM1 sing 465 n n C5F C6F TM1 doub 466 n n C5F H5F TM1 sing 467 n n C6F N6F TM1 sing 468 n n N6F O6F TM1 sing 469 n n N6F O7F TM1 doub 470 n n # _atom_sites.entry_id 3AR8 _atom_sites.fract_transf_matrix[1][1] 0.005654 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001697 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014312 _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] 0.007362 _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 NA A 1 1000 1000 NA NA . C 3 MG A 1 995 995 MG MG . D 4 ALF A 1 998 998 ALF ALF . E 5 TM1 A 1 1002 1002 TM1 TM1 . F 6 TG1 A 1 1003 1003 TG1 TG1 . G 7 HOH A 1 4001 4001 HOH HOH . G 7 HOH A 2 4002 4002 HOH HOH . G 7 HOH A 3 4003 4003 HOH HOH . G 7 HOH A 4 4004 4004 HOH HOH . G 7 HOH A 5 4005 4005 HOH HOH . G 7 HOH A 6 4006 4006 HOH HOH . G 7 HOH A 7 4007 4007 HOH HOH . G 7 HOH A 8 4008 4008 HOH HOH . G 7 HOH A 9 4009 4009 HOH HOH . G 7 HOH A 10 4010 4010 HOH HOH . G 7 HOH A 11 4011 4011 HOH HOH . G 7 HOH A 12 4012 4012 HOH HOH . G 7 HOH A 13 4013 4013 HOH HOH . G 7 HOH A 14 4014 4014 HOH HOH . G 7 HOH A 15 4015 4015 HOH HOH . G 7 HOH A 16 4016 4016 HOH HOH . G 7 HOH A 17 4017 4017 HOH HOH . G 7 HOH A 18 4018 4018 HOH HOH . G 7 HOH A 19 4019 4019 HOH HOH . G 7 HOH A 20 4020 4020 HOH HOH . G 7 HOH A 21 4021 4021 HOH HOH . G 7 HOH A 22 4022 4022 HOH HOH . G 7 HOH A 23 4023 4023 HOH HOH . G 7 HOH A 24 4024 4024 HOH HOH . G 7 HOH A 25 4025 4025 HOH HOH . G 7 HOH A 26 4026 4026 HOH HOH . G 7 HOH A 27 4027 4027 HOH HOH . G 7 HOH A 28 4028 4028 HOH HOH . G 7 HOH A 29 4029 4029 HOH HOH . G 7 HOH A 30 4030 4030 HOH HOH . G 7 HOH A 31 4031 4031 HOH HOH . G 7 HOH A 32 4032 4032 HOH HOH . G 7 HOH A 33 4034 4034 HOH HOH . G 7 HOH A 34 4036 4036 HOH HOH . G 7 HOH A 35 4037 4037 HOH HOH . G 7 HOH A 36 4038 4038 HOH HOH . G 7 HOH A 37 4039 4039 HOH HOH . G 7 HOH A 38 4040 4040 HOH HOH . G 7 HOH A 39 4041 4041 HOH HOH . G 7 HOH A 40 4042 4042 HOH HOH . G 7 HOH A 41 4043 4043 HOH HOH . G 7 HOH A 42 4044 4044 HOH HOH . G 7 HOH A 43 4045 4045 HOH HOH . G 7 HOH A 44 4046 4046 HOH HOH . G 7 HOH A 45 4047 4047 HOH HOH . G 7 HOH A 46 4048 4048 HOH HOH . G 7 HOH A 47 4049 4049 HOH HOH . G 7 HOH A 48 4050 4050 HOH HOH . G 7 HOH A 49 4051 4051 HOH HOH . G 7 HOH A 50 4052 4052 HOH HOH . G 7 HOH A 51 4054 4054 HOH HOH . G 7 HOH A 52 4055 4055 HOH HOH . G 7 HOH A 53 4056 4056 HOH HOH . G 7 HOH A 54 4057 4057 HOH HOH . G 7 HOH A 55 4058 4058 HOH HOH . G 7 HOH A 56 4059 4059 HOH HOH . G 7 HOH A 57 4060 4060 HOH HOH . G 7 HOH A 58 4061 4061 HOH HOH . G 7 HOH A 59 4062 4062 HOH HOH . G 7 HOH A 60 4063 4063 HOH HOH . G 7 HOH A 61 4064 4064 HOH HOH . G 7 HOH A 62 4065 4065 HOH HOH . G 7 HOH A 63 4066 4066 HOH HOH . G 7 HOH A 64 4067 4067 HOH HOH . G 7 HOH A 65 4068 4068 HOH HOH . G 7 HOH A 66 4069 4069 HOH HOH . G 7 HOH A 67 4070 4070 HOH HOH . G 7 HOH A 68 4071 4071 HOH HOH . G 7 HOH A 69 4072 4072 HOH HOH . G 7 HOH A 70 4073 4073 HOH HOH . G 7 HOH A 71 4074 4074 HOH HOH . G 7 HOH A 72 4075 4075 HOH HOH . G 7 HOH A 73 4076 4076 HOH HOH . G 7 HOH A 74 4077 4077 HOH HOH . G 7 HOH A 75 4078 4078 HOH HOH . G 7 HOH A 76 4079 4079 HOH HOH . G 7 HOH A 77 4080 4080 HOH HOH . G 7 HOH A 78 4081 4081 HOH HOH . G 7 HOH A 79 4083 4083 HOH HOH . G 7 HOH A 80 4084 4084 HOH HOH . G 7 HOH A 81 4085 4085 HOH HOH . G 7 HOH A 82 4086 4086 HOH HOH . G 7 HOH A 83 4087 4087 HOH HOH . G 7 HOH A 84 4088 4088 HOH HOH . G 7 HOH A 85 4089 4089 HOH HOH . G 7 HOH A 86 4090 4090 HOH HOH . G 7 HOH A 87 4091 4091 HOH HOH . G 7 HOH A 88 4092 4092 HOH HOH . G 7 HOH A 89 4093 4093 HOH HOH . G 7 HOH A 90 4094 4094 HOH HOH . G 7 HOH A 91 4095 4095 HOH HOH . G 7 HOH A 92 4099 4099 HOH HOH . G 7 HOH A 93 4100 4100 HOH HOH . G 7 HOH A 94 4101 4101 HOH HOH . G 7 HOH A 95 4103 4103 HOH HOH . G 7 HOH A 96 4104 4104 HOH HOH . G 7 HOH A 97 4105 4105 HOH HOH . G 7 HOH A 98 4106 4106 HOH HOH . G 7 HOH A 99 4107 4107 HOH HOH . G 7 HOH A 100 4108 4108 HOH HOH . G 7 HOH A 101 4109 4109 HOH HOH . G 7 HOH A 102 4111 4111 HOH HOH . G 7 HOH A 103 4112 4112 HOH HOH . G 7 HOH A 104 4113 4113 HOH HOH . G 7 HOH A 105 9001 9001 HOH HOH . G 7 HOH A 106 9002 9002 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 N N1 TM1 . . . E 5 22.782 61.87 136.703 1 146.95 ? N1 TM1 1002 A 1 HETATM 2 C C2 TM1 . . . E 5 22.324 63.183 136.742 1 147.55 ? C2 TM1 1002 A 1 HETATM 3 N N3 TM1 . . . E 5 23.172 64.241 136.488 1 147.78 ? N3 TM1 1002 A 1 HETATM 4 C C4 TM1 . . . E 5 24.537 64.08 136.178 1 147.96 ? C4 TM1 1002 A 1 HETATM 5 C C5 TM1 . . . E 5 25.043 62.769 136.126 1 147.08 ? C5 TM1 1002 A 1 HETATM 6 C C6 TM1 . . . E 5 24.162 61.636 136.393 1 146.95 ? C6 TM1 1002 A 1 HETATM 7 N N6 TM1 . . . E 5 24.661 60.399 136.34 1 146.87 ? N6 TM1 1002 A 1 HETATM 8 N N7 TM1 . . . E 5 26.328 62.779 135.826 1 147.06 ? N7 TM1 1002 A 1 HETATM 9 C C8 TM1 . . . E 5 26.657 64.065 135.683 1 148.06 ? C8 TM1 1002 A 1 HETATM 10 N N9 TM1 . . . E 5 25.574 64.873 135.894 1 148.57 ? N9 TM1 1002 A 1 HETATM 11 P PA TM1 . . . E 5 22.423 68.318 131.642 1 150.57 ? PA TM1 1002 A 1 HETATM 12 C C1' TM1 . . . E 5 25.551 66.479 135.82 1 150.26 ? C1' TM1 1002 A 1 HETATM 13 O O1A TM1 . . . E 5 21.214 68.025 132.622 1 150.74 ? O1A TM1 1002 A 1 HETATM 14 C C1F TM1 . . . E 5 27.701 69.205 135.62 1 154.74 ? C1F TM1 1002 A 1 HETATM 15 C C2' TM1 . . . E 5 26.921 67.094 135.365 1 151.86 ? C2' TM1 1002 A 1 HETATM 16 O O2' TM1 . . . E 5 27.608 67.897 136.363 1 153.45 ? O2' TM1 1002 A 1 HETATM 17 O O2A TM1 . . . E 5 21.909 68.397 130.212 1 149.35 ? O2A TM1 1002 A 1 HETATM 18 C C2F TM1 . . . E 5 29.245 69.383 135.606 1 154.97 ? C2F TM1 1002 A 1 HETATM 19 N N2F TM1 . . . E 5 30.189 68.423 134.984 1 154.86 ? N2F TM1 1002 A 1 HETATM 20 O O2F TM1 . . . E 5 29.911 67.405 134.396 1 155.46 ? O2F TM1 1002 A 1 HETATM 21 C C3' TM1 . . . E 5 26.661 67.824 134.074 1 152.22 ? C3' TM1 1002 A 1 HETATM 22 O O3' TM1 . . . E 5 27.03 69.21 134.269 1 153.9 ? O3' TM1 1002 A 1 HETATM 23 O O3A TM1 . . . E 5 23.092 69.699 132.03 1 151.62 ? O3A TM1 1002 A 1 HETATM 24 C C3F TM1 . . . E 5 29.841 70.492 136.191 1 155.84 ? C3F TM1 1002 A 1 HETATM 25 O O3F TM1 . . . E 5 31.415 68.591 135.002 1 155.37 ? O3F TM1 1002 A 1 HETATM 26 C C4' TM1 . . . E 5 25.279 67.734 133.669 1 151.32 ? C4' TM1 1002 A 1 HETATM 27 O O4' TM1 . . . E 5 24.735 66.936 134.743 1 151.35 ? O4' TM1 1002 A 1 HETATM 28 C C4F TM1 . . . E 5 29.21 71.537 136.83 1 157.1 ? C4F TM1 1002 A 1 HETATM 29 N N4F TM1 . . . E 5 29.831 72.58 137.377 1 158.25 ? N4F TM1 1002 A 1 HETATM 30 O O4F TM1 . . . E 5 30.222 72.598 138.522 1 157.86 ? O4F TM1 1002 A 1 HETATM 31 C C5' TM1 . . . E 5 24.978 67.178 132.17 1 150.03 ? C5' TM1 1002 A 1 HETATM 32 O O5' TM1 . . . E 5 23.545 67.097 131.768 1 150 ? O5' TM1 1002 A 1 HETATM 33 C C5F TM1 . . . E 5 27.783 71.474 136.893 1 156.32 ? C5F TM1 1002 A 1 HETATM 34 O O5F TM1 . . . E 5 30.056 73.574 136.758 1 159.29 ? O5F TM1 1002 A 1 HETATM 35 C C6F TM1 . . . E 5 26.956 70.343 136.312 1 155.33 ? C6F TM1 1002 A 1 HETATM 36 N N6F TM1 . . . E 5 25.55 70.459 136.476 1 155.3 ? N6F TM1 1002 A 1 HETATM 37 O O6F TM1 . . . E 5 25.04 71.414 137.022 1 156.18 ? O6F TM1 1002 A 1 HETATM 38 O O7F TM1 . . . E 5 24.746 69.687 136.123 1 155.42 ? O7F TM1 1002 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 38 #