data_5DHT # _model_server_result.job_id Mn1LLvdKYLzxRHQfiUfN1Q _model_server_result.datetime_utc '2024-11-12 21:09:22' _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 5dht # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":303}' # _entry.id 5DHT # _exptl.entry_id 5DHT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 564.416 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-azido-8-[(2-{[2-(3-bromophenyl)ethyl]amino}-2-oxoethyl)sulfanyl]-5'-deoxyadenosine" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.03 _cell.angle_gamma 90 _cell.entry_id 5DHT _cell.length_a 66.781 _cell.length_b 119.072 _cell.length_c 67.347 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DHT _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,K,L,M,N,O,P _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 G N N ? 4 I N N ? 4 J N N ? 4 L N N # _chem_comp.formula 'C20 H22 Br N9 O4 S' _chem_comp.formula_weight 564.416 _chem_comp.id 5A9 _chem_comp.mon_nstd_flag . _chem_comp.name "5'-azido-8-[(2-{[2-(3-bromophenyl)ethyl]amino}-2-oxoethyl)sulfanyl]-5'-deoxyadenosine" _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 OBF CBA 5A9 sing 1 n n NBB CAU 5A9 sing 2 n n NBB NBG 5A9 doub 3 n n CBA CAT 5A9 sing 4 n n CBA CAZ 5A9 sing 5 n n CAU CAT 5A9 sing 6 n n OAY CAZ 5A9 sing 7 n n CAT OAS 5A9 sing 8 n n NBG NBI 5A9 doub 9 n n CAZ CAR 5A9 sing 10 n n OAS CAR 5A9 sing 11 n n CAR N9 5A9 sing 12 n n SAH C8 5A9 sing 13 n n SAH CAI 5A9 sing 14 n n N9 C8 5A9 sing 15 n y N9 C4 5A9 sing 16 n y C8 N7 5A9 doub 17 n y N3 C4 5A9 doub 18 n y N3 C2 5A9 sing 19 n y C4 C5 5A9 sing 20 n y CAI CAJ 5A9 sing 21 n n CAX CBE 5A9 doub 22 n y CAX CAW 5A9 sing 23 n y CBE CBD 5A9 sing 24 n y C2 N1 5A9 doub 25 n y OAB CAJ 5A9 doub 26 n n N7 C5 5A9 sing 27 n y C5 C6 5A9 doub 28 n y CAJ NAK 5A9 sing 29 n n CAW CAV 5A9 doub 30 n y CBD BR 5A9 sing 31 n n CBD CBC 5A9 doub 32 n y N1 C6 5A9 sing 33 n y C6 N6 5A9 sing 34 n n NAK CAL 5A9 sing 35 n n CAV CBC 5A9 sing 36 n y CAV CAM 5A9 sing 37 n n CAL CAM 5A9 sing 38 n n CBC H1 5A9 sing 39 n n CBE H2 5A9 sing 40 n n CAX H3 5A9 sing 41 n n CAW H4 5A9 sing 42 n n CAM H5 5A9 sing 43 n n CAM H6 5A9 sing 44 n n CAL H7 5A9 sing 45 n n CAL H8 5A9 sing 46 n n NAK H9 5A9 sing 47 n n CAI H10 5A9 sing 48 n n CAI H11 5A9 sing 49 n n N6 H12 5A9 sing 50 n n N6 H13 5A9 sing 51 n n C2 H14 5A9 sing 52 n n CAR H15 5A9 sing 53 n n CAZ H16 5A9 sing 54 n n OAY H17 5A9 sing 55 n n CBA H18 5A9 sing 56 n n OBF H19 5A9 sing 57 n n CAT H20 5A9 sing 58 n n CAU H21 5A9 sing 59 n n CAU H22 5A9 sing 60 n n # _atom_sites.entry_id 5DHT _atom_sites.fract_transf_matrix[1][1] 0.014974 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00265 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008398 _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] 0.015079 _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 E 2 CIT A 1 301 3 CIT CIT . F 3 GOL A 1 302 1 GOL GOL . G 4 5A9 A 1 303 1 5A9 DRG . H 2 CIT B 1 301 2 CIT CIT . I 4 5A9 B 1 302 1 5A9 DRG . J 4 5A9 C 1 301 1 5A9 DRG . K 3 GOL D 1 301 1 GOL GOL . L 4 5A9 D 1 302 1 5A9 DRG . M 5 HOH A 1 401 58 HOH HOH . M 5 HOH A 2 402 211 HOH HOH . M 5 HOH A 3 403 77 HOH HOH . M 5 HOH A 4 404 31 HOH HOH . M 5 HOH A 5 405 26 HOH HOH . M 5 HOH A 6 406 76 HOH HOH . M 5 HOH A 7 407 201 HOH HOH . M 5 HOH A 8 408 38 HOH HOH . M 5 HOH A 9 409 29 HOH HOH . M 5 HOH A 10 410 210 HOH HOH . M 5 HOH A 11 411 162 HOH HOH . M 5 HOH A 12 412 46 HOH HOH . M 5 HOH A 13 413 7 HOH HOH . M 5 HOH A 14 414 35 HOH HOH . M 5 HOH A 15 415 63 HOH HOH . M 5 HOH A 16 416 3 HOH HOH . M 5 HOH A 17 417 65 HOH HOH . M 5 HOH A 18 418 68 HOH HOH . M 5 HOH A 19 419 110 HOH HOH . M 5 HOH A 20 420 1 HOH HOH . M 5 HOH A 21 421 44 HOH HOH . M 5 HOH A 22 422 179 HOH HOH . M 5 HOH A 23 423 5 HOH HOH . M 5 HOH A 24 424 4 HOH HOH . M 5 HOH A 25 425 183 HOH HOH . M 5 HOH A 26 426 70 HOH HOH . M 5 HOH A 27 427 8 HOH HOH . M 5 HOH A 28 428 142 HOH HOH . M 5 HOH A 29 429 203 HOH HOH . M 5 HOH A 30 430 30 HOH HOH . M 5 HOH A 31 431 28 HOH HOH . M 5 HOH A 32 432 163 HOH HOH . M 5 HOH A 33 433 27 HOH HOH . M 5 HOH A 34 434 139 HOH HOH . M 5 HOH A 35 435 90 HOH HOH . M 5 HOH A 36 436 207 HOH HOH . M 5 HOH A 37 437 108 HOH HOH . M 5 HOH A 38 438 118 HOH HOH . M 5 HOH A 39 439 102 HOH HOH . M 5 HOH A 40 440 130 HOH HOH . M 5 HOH A 41 441 82 HOH HOH . M 5 HOH A 42 442 168 HOH HOH . M 5 HOH A 43 443 164 HOH HOH . M 5 HOH A 44 444 181 HOH HOH . M 5 HOH A 45 445 204 HOH HOH . M 5 HOH A 46 446 194 HOH HOH . M 5 HOH A 47 447 135 HOH HOH . M 5 HOH A 48 448 81 HOH HOH . M 5 HOH A 49 449 174 HOH HOH . M 5 HOH A 50 450 141 HOH HOH . M 5 HOH A 51 451 79 HOH HOH . M 5 HOH A 52 452 202 HOH HOH . M 5 HOH A 53 453 169 HOH HOH . M 5 HOH A 54 454 143 HOH HOH . M 5 HOH A 55 455 172 HOH HOH . M 5 HOH A 56 456 158 HOH HOH . M 5 HOH A 57 457 144 HOH HOH . M 5 HOH A 58 458 113 HOH HOH . M 5 HOH A 59 459 105 HOH HOH . M 5 HOH A 60 460 153 HOH HOH . M 5 HOH A 61 461 117 HOH HOH . N 5 HOH B 1 401 151 HOH HOH . N 5 HOH B 2 402 212 HOH HOH . N 5 HOH B 3 403 59 HOH HOH . N 5 HOH B 4 404 21 HOH HOH . N 5 HOH B 5 405 145 HOH HOH . N 5 HOH B 6 406 123 HOH HOH . N 5 HOH B 7 407 23 HOH HOH . N 5 HOH B 8 408 24 HOH HOH . N 5 HOH B 9 409 48 HOH HOH . N 5 HOH B 10 410 69 HOH HOH . N 5 HOH B 11 411 84 HOH HOH . N 5 HOH B 12 412 32 HOH HOH . N 5 HOH B 13 413 60 HOH HOH . N 5 HOH B 14 414 136 HOH HOH . N 5 HOH B 15 415 200 HOH HOH . N 5 HOH B 16 416 25 HOH HOH . N 5 HOH B 17 417 20 HOH HOH . N 5 HOH B 18 418 50 HOH HOH . N 5 HOH B 19 419 92 HOH HOH . N 5 HOH B 20 420 22 HOH HOH . N 5 HOH B 21 421 66 HOH HOH . N 5 HOH B 22 422 89 HOH HOH . N 5 HOH B 23 423 57 HOH HOH . N 5 HOH B 24 424 19 HOH HOH . N 5 HOH B 25 425 178 HOH HOH . N 5 HOH B 26 426 88 HOH HOH . N 5 HOH B 27 427 43 HOH HOH . N 5 HOH B 28 428 112 HOH HOH . N 5 HOH B 29 429 173 HOH HOH . N 5 HOH B 30 430 87 HOH HOH . N 5 HOH B 31 431 192 HOH HOH . N 5 HOH B 32 432 93 HOH HOH . N 5 HOH B 33 433 170 HOH HOH . N 5 HOH B 34 434 114 HOH HOH . N 5 HOH B 35 435 128 HOH HOH . N 5 HOH B 36 436 160 HOH HOH . N 5 HOH B 37 437 83 HOH HOH . N 5 HOH B 38 438 184 HOH HOH . N 5 HOH B 39 439 214 HOH HOH . N 5 HOH B 40 440 137 HOH HOH . N 5 HOH B 41 441 182 HOH HOH . N 5 HOH B 42 442 205 HOH HOH . N 5 HOH B 43 443 165 HOH HOH . N 5 HOH B 44 444 111 HOH HOH . O 5 HOH C 1 401 106 HOH HOH . O 5 HOH C 2 402 75 HOH HOH . O 5 HOH C 3 403 193 HOH HOH . O 5 HOH C 4 404 17 HOH HOH . O 5 HOH C 5 405 41 HOH HOH . O 5 HOH C 6 406 126 HOH HOH . O 5 HOH C 7 407 171 HOH HOH . O 5 HOH C 8 408 147 HOH HOH . O 5 HOH C 9 409 64 HOH HOH . O 5 HOH C 10 410 54 HOH HOH . O 5 HOH C 11 411 37 HOH HOH . O 5 HOH C 12 412 52 HOH HOH . O 5 HOH C 13 413 14 HOH HOH . O 5 HOH C 14 414 115 HOH HOH . O 5 HOH C 15 415 125 HOH HOH . O 5 HOH C 16 416 16 HOH HOH . O 5 HOH C 17 417 180 HOH HOH . O 5 HOH C 18 418 129 HOH HOH . O 5 HOH C 19 419 67 HOH HOH . O 5 HOH C 20 420 86 HOH HOH . O 5 HOH C 21 421 140 HOH HOH . O 5 HOH C 22 422 185 HOH HOH . O 5 HOH C 23 423 159 HOH HOH . O 5 HOH C 24 424 96 HOH HOH . O 5 HOH C 25 425 152 HOH HOH . O 5 HOH C 26 426 104 HOH HOH . O 5 HOH C 27 427 6 HOH HOH . O 5 HOH C 28 428 109 HOH HOH . O 5 HOH C 29 429 146 HOH HOH . O 5 HOH C 30 430 206 HOH HOH . O 5 HOH C 31 431 132 HOH HOH . O 5 HOH C 32 432 154 HOH HOH . O 5 HOH C 33 433 186 HOH HOH . O 5 HOH C 34 434 199 HOH HOH . O 5 HOH C 35 435 188 HOH HOH . O 5 HOH C 36 436 98 HOH HOH . O 5 HOH C 37 437 148 HOH HOH . O 5 HOH C 38 438 138 HOH HOH . O 5 HOH C 39 439 103 HOH HOH . O 5 HOH C 40 440 187 HOH HOH . O 5 HOH C 41 441 208 HOH HOH . O 5 HOH C 42 442 190 HOH HOH . O 5 HOH C 43 443 99 HOH HOH . O 5 HOH C 44 444 195 HOH HOH . P 5 HOH D 1 401 149 HOH HOH . P 5 HOH D 2 402 18 HOH HOH . P 5 HOH D 3 403 177 HOH HOH . P 5 HOH D 4 404 36 HOH HOH . P 5 HOH D 5 405 53 HOH HOH . P 5 HOH D 6 406 34 HOH HOH . P 5 HOH D 7 407 15 HOH HOH . P 5 HOH D 8 408 39 HOH HOH . P 5 HOH D 9 409 80 HOH HOH . P 5 HOH D 10 410 40 HOH HOH . P 5 HOH D 11 411 191 HOH HOH . P 5 HOH D 12 412 13 HOH HOH . P 5 HOH D 13 413 131 HOH HOH . P 5 HOH D 14 414 107 HOH HOH . P 5 HOH D 15 415 120 HOH HOH . P 5 HOH D 16 416 197 HOH HOH . P 5 HOH D 17 417 95 HOH HOH . P 5 HOH D 18 418 33 HOH HOH . P 5 HOH D 19 419 74 HOH HOH . P 5 HOH D 20 420 11 HOH HOH . P 5 HOH D 21 421 121 HOH HOH . P 5 HOH D 22 422 155 HOH HOH . P 5 HOH D 23 423 175 HOH HOH . P 5 HOH D 24 424 116 HOH HOH . P 5 HOH D 25 425 189 HOH HOH . P 5 HOH D 26 426 101 HOH HOH . P 5 HOH D 27 427 166 HOH HOH . P 5 HOH D 28 428 157 HOH HOH . P 5 HOH D 29 429 198 HOH HOH . P 5 HOH D 30 430 97 HOH HOH . P 5 HOH D 31 431 122 HOH HOH . P 5 HOH D 32 432 156 HOH HOH . P 5 HOH D 33 433 167 HOH HOH . P 5 HOH D 34 434 176 HOH HOH . P 5 HOH D 35 435 209 HOH HOH . P 5 HOH D 36 436 213 HOH HOH . P 5 HOH D 37 437 100 HOH HOH . P 5 HOH D 38 438 119 HOH HOH . P 5 HOH D 39 439 196 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 C C4 5A9 . . . G 4 11.397 -19.519 -44.731 1 46.57 ? C4 5A9 303 A 1 HETATM 2 C C5 5A9 . . . G 4 11.394 -19.123 -46.009 1 44.26 ? C5 5A9 303 A 1 HETATM 3 C C6 5A9 . . . G 4 12.513 -19.151 -46.731 1 39.81 ? C6 5A9 303 A 1 HETATM 4 C C8 5A9 . . . G 4 9.415 -18.916 -45.241 1 49.62 ? C8 5A9 303 A 1 HETATM 5 N N1 5A9 . . . G 4 13.677 -19.571 -46.22 1 39.66 ? N1 5A9 303 A 1 HETATM 6 N N3 5A9 . . . G 4 12.527 -19.952 -44.153 1 44.99 ? N3 5A9 303 A 1 HETATM 7 C CBC 5A9 . . . G 4 9.715 -21.393 -48.523 1 42.36 ? CBC 5A9 303 A 1 HETATM 8 C CBD 5A9 . . . G 4 9.944 -22.115 -47.357 1 41.45 ? CBD 5A9 303 A 1 HETATM 9 BR BR 5A9 . . . G 4 11.656 -22.786 -46.99 0.5 38.92 ? BR 5A9 303 A 1 HETATM 10 C CBE 5A9 . . . G 4 8.903 -22.34 -46.463 1 41.55 ? CBE 5A9 303 A 1 HETATM 11 C CAX 5A9 . . . G 4 7.634 -21.842 -46.735 1 43.04 ? CAX 5A9 303 A 1 HETATM 12 C CAW 5A9 . . . G 4 7.405 -21.121 -47.901 1 43.9 ? CAW 5A9 303 A 1 HETATM 13 C CAV 5A9 . . . G 4 8.446 -20.896 -48.794 1 44 ? CAV 5A9 303 A 1 HETATM 14 C CAM 5A9 . . . G 4 8.217 -20.174 -49.96 1 43.42 ? CAM 5A9 303 A 1 HETATM 15 C CAL 5A9 . . . G 4 7.396 -18.925 -49.634 1 47.02 ? CAL 5A9 303 A 1 HETATM 16 N NAK 5A9 . . . G 4 7.805 -18.397 -48.325 1 48.21 ? NAK 5A9 303 A 1 HETATM 17 C CAJ 5A9 . . . G 4 7.012 -17.591 -47.605 1 50.72 ? CAJ 5A9 303 A 1 HETATM 18 O OAB 5A9 . . . G 4 5.894 -17.226 -47.965 1 55.97 ? OAB 5A9 303 A 1 HETATM 19 C CAI 5A9 . . . G 4 7.597 -17.136 -46.266 1 51.16 ? CAI 5A9 303 A 1 HETATM 20 S SAH 5A9 . . . G 4 7.704 -18.566 -45.129 1 41.59 ? SAH 5A9 303 A 1 HETATM 21 N N7 5A9 . . . G 4 10.156 -18.746 -46.328 1 46.78 ? N7 5A9 303 A 1 HETATM 22 N N6 5A9 . . . G 4 12.411 -18.738 -47.991 1 37.62 ? N6 5A9 303 A 1 HETATM 23 C C2 5A9 . . . G 4 13.714 -19.991 -44.89 1 41.97 ? C2 5A9 303 A 1 HETATM 24 N N9 5A9 . . . G 4 10.161 -19.389 -44.253 1 52.2 ? N9 5A9 303 A 1 HETATM 25 C CAR 5A9 . . . G 4 9.708 -19.712 -42.882 1 60.13 ? CAR 5A9 303 A 1 HETATM 26 O OAS 5A9 . . . G 4 8.644 -20.672 -42.942 1 63.52 ? OAS 5A9 303 A 1 HETATM 27 C CAZ 5A9 . . . G 4 9.072 -18.501 -42.219 1 66.9 ? CAZ 5A9 303 A 1 HETATM 28 O OAY 5A9 . . . G 4 10.029 -17.869 -41.357 1 70.4 ? OAY 5A9 303 A 1 HETATM 29 C CBA 5A9 . . . G 4 7.945 -19.087 -41.383 1 66.9 ? CBA 5A9 303 A 1 HETATM 30 O OBF 5A9 . . . G 4 8.199 -18.836 -39.993 1 67.76 ? OBF 5A9 303 A 1 HETATM 31 C CAT 5A9 . . . G 4 8.024 -20.582 -41.651 1 66.14 ? CAT 5A9 303 A 1 HETATM 32 C CAU 5A9 . . . G 4 6.61 -21.163 -41.721 0.6 66.94 ? CAU 5A9 303 A 1 HETATM 33 N NBB 5A9 . . . G 4 6.681 -22.631 -41.697 0.6 67.86 ? NBB 5A9 303 A 1 HETATM 34 N NBG 5A9 . . . G 4 6.824 -23.132 -42.689 0.6 68.63 ? NBG 5A9 303 A 1 HETATM 35 N NBI 5A9 . . . G 4 6.966 -23.633 -43.68 0.6 68.38 ? NBI 5A9 303 A 1 # _model_server_stats.io_time_ms 121 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 35 #