data_5DHS # _model_server_result.job_id Qwv-tMBJGbCGI9pQNIoWlQ _model_server_result.datetime_utc '2024-11-12 21:14:01' _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 5dhs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":301}' # _entry.id 5DHS # _exptl.entry_id 5DHS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 509.541 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-azido-5'-deoxy-8-[(2-{[2-(3-ethynylphenyl)ethyl]amino}-2-oxoethyl)sulfanyl]adenosine" _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 100.14 _cell.angle_gamma 90 _cell.entry_id 5DHS _cell.length_a 66.77 _cell.length_b 118.95 _cell.length_c 66.9 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DHS _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 _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 K N N # _chem_comp.formula 'C22 H23 N9 O4 S' _chem_comp.formula_weight 509.541 _chem_comp.id 5AG _chem_comp.mon_nstd_flag . _chem_comp.name "5'-azido-5'-deoxy-8-[(2-{[2-(3-ethynylphenyl)ethyl]amino}-2-oxoethyl)sulfanyl]adenosine" _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 CAG CAF 5AG sing 1 n n CAG NAH 5AG sing 2 n n CAF CAE 5AG sing 3 n n OBG CAI 5AG doub 4 n n N6 C6 5AG sing 5 n n NAH CAI 5AG sing 6 n n CAE CBH 5AG doub 7 n y CAE CAD 5AG sing 8 n y CAI CAJ 5AG sing 9 n n CBH CBI 5AG sing 10 n y CAD CAC 5AG doub 11 n y C6 N1 5AG doub 12 n y C6 C5 5AG sing 13 n y N1 C2 5AG sing 14 n y CBI CBJ 5AG doub 15 n y N7 C5 5AG sing 16 n y N7 C8 5AG doub 17 n y CAJ SAK 5AG sing 18 n n C5 C4 5AG doub 19 n y CAC CBJ 5AG sing 20 n y CAC CAB 5AG sing 21 n n C2 N3 5AG doub 22 n y C8 SAK 5AG sing 23 n n C8 N9 5AG sing 24 n y CAB CAA 5AG trip 25 n n C4 N3 5AG sing 26 n y C4 N9 5AG sing 27 n y N9 CAV 5AG sing 28 n n OBF CAV 5AG sing 29 n n OBF CBA 5AG sing 30 n n CAV CAW 5AG sing 31 n n NBE NBD 5AG doub 32 n n NBD NBC 5AG doub 33 n n CBB CBA 5AG sing 34 n n CBB NBC 5AG sing 35 n n CBA CAY 5AG sing 36 n n CAW CAY 5AG sing 37 n n CAW OAX 5AG sing 38 n n CAY OAZ 5AG sing 39 n n C2 H1 5AG sing 40 n n CAA H2 5AG sing 41 n n CAD H3 5AG sing 42 n n CBJ H4 5AG sing 43 n n CBI H5 5AG sing 44 n n CBH H6 5AG sing 45 n n CAF H7 5AG sing 46 n n CAF H8 5AG sing 47 n n CAG H9 5AG sing 48 n n CAG H10 5AG sing 49 n n NAH H11 5AG sing 50 n n CAJ H12 5AG sing 51 n n CAJ H13 5AG sing 52 n n N6 H14 5AG sing 53 n n N6 H15 5AG sing 54 n n CAV H16 5AG sing 55 n n CAW H17 5AG sing 56 n n OAX H18 5AG sing 57 n n CAY H19 5AG sing 58 n n OAZ H20 5AG sing 59 n n CBA H21 5AG sing 60 n n CBB H22 5AG sing 61 n n CBB H23 5AG sing 62 n n # _atom_sites.entry_id 5DHS _atom_sites.fract_transf_matrix[1][1] 0.014977 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002679 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008407 _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] 0.015185 _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 5AG A 1 303 1 5AG PDB . H 2 CIT B 1 301 2 CIT CIT . I 4 5AG B 1 302 1 5AG PDB . J 4 5AG C 1 301 1 5AG PDB . K 4 5AG D 1 301 1 5AG PDB . L 5 HOH A 1 401 154 HOH HOH . L 5 HOH A 2 402 133 HOH HOH . L 5 HOH A 3 403 62 HOH HOH . L 5 HOH A 4 404 7 HOH HOH . L 5 HOH A 5 405 6 HOH HOH . L 5 HOH A 6 406 34 HOH HOH . L 5 HOH A 7 407 82 HOH HOH . L 5 HOH A 8 408 172 HOH HOH . L 5 HOH A 9 409 30 HOH HOH . L 5 HOH A 10 410 56 HOH HOH . L 5 HOH A 11 411 75 HOH HOH . L 5 HOH A 12 412 13 HOH HOH . L 5 HOH A 13 413 92 HOH HOH . L 5 HOH A 14 414 38 HOH HOH . L 5 HOH A 15 415 182 HOH HOH . L 5 HOH A 16 416 10 HOH HOH . L 5 HOH A 17 417 121 HOH HOH . L 5 HOH A 18 418 150 HOH HOH . L 5 HOH A 19 419 41 HOH HOH . L 5 HOH A 20 420 55 HOH HOH . L 5 HOH A 21 421 5 HOH HOH . L 5 HOH A 22 422 72 HOH HOH . L 5 HOH A 23 423 28 HOH HOH . L 5 HOH A 24 424 65 HOH HOH . L 5 HOH A 25 425 44 HOH HOH . L 5 HOH A 26 426 84 HOH HOH . L 5 HOH A 27 427 194 HOH HOH . L 5 HOH A 28 428 1 HOH HOH . L 5 HOH A 29 429 14 HOH HOH . L 5 HOH A 30 430 89 HOH HOH . L 5 HOH A 31 431 183 HOH HOH . L 5 HOH A 32 432 12 HOH HOH . L 5 HOH A 33 433 40 HOH HOH . L 5 HOH A 34 434 152 HOH HOH . L 5 HOH A 35 435 135 HOH HOH . L 5 HOH A 36 436 109 HOH HOH . L 5 HOH A 37 437 106 HOH HOH . L 5 HOH A 38 438 53 HOH HOH . L 5 HOH A 39 439 169 HOH HOH . L 5 HOH A 40 440 21 HOH HOH . L 5 HOH A 41 441 95 HOH HOH . L 5 HOH A 42 442 63 HOH HOH . L 5 HOH A 43 443 79 HOH HOH . L 5 HOH A 44 444 107 HOH HOH . L 5 HOH A 45 445 186 HOH HOH . L 5 HOH A 46 446 145 HOH HOH . L 5 HOH A 47 447 159 HOH HOH . L 5 HOH A 48 448 93 HOH HOH . L 5 HOH A 49 449 149 HOH HOH . L 5 HOH A 50 450 196 HOH HOH . L 5 HOH A 51 451 122 HOH HOH . L 5 HOH A 52 452 111 HOH HOH . L 5 HOH A 53 453 164 HOH HOH . L 5 HOH A 54 454 48 HOH HOH . M 5 HOH B 1 401 189 HOH HOH . M 5 HOH B 2 402 54 HOH HOH . M 5 HOH B 3 403 131 HOH HOH . M 5 HOH B 4 404 4 HOH HOH . M 5 HOH B 5 405 17 HOH HOH . M 5 HOH B 6 406 195 HOH HOH . M 5 HOH B 7 407 3 HOH HOH . M 5 HOH B 8 408 148 HOH HOH . M 5 HOH B 9 409 71 HOH HOH . M 5 HOH B 10 410 103 HOH HOH . M 5 HOH B 11 411 15 HOH HOH . M 5 HOH B 12 412 176 HOH HOH . M 5 HOH B 13 413 114 HOH HOH . M 5 HOH B 14 414 52 HOH HOH . M 5 HOH B 15 415 25 HOH HOH . M 5 HOH B 16 416 68 HOH HOH . M 5 HOH B 17 417 124 HOH HOH . M 5 HOH B 18 418 23 HOH HOH . M 5 HOH B 19 419 146 HOH HOH . M 5 HOH B 20 420 87 HOH HOH . M 5 HOH B 21 421 174 HOH HOH . M 5 HOH B 22 422 86 HOH HOH . M 5 HOH B 23 423 188 HOH HOH . M 5 HOH B 24 424 108 HOH HOH . M 5 HOH B 25 425 42 HOH HOH . M 5 HOH B 26 426 115 HOH HOH . M 5 HOH B 27 427 125 HOH HOH . M 5 HOH B 28 428 165 HOH HOH . M 5 HOH B 29 429 201 HOH HOH . M 5 HOH B 30 430 175 HOH HOH . M 5 HOH B 31 431 173 HOH HOH . M 5 HOH B 32 432 170 HOH HOH . N 5 HOH C 1 401 20 HOH HOH . N 5 HOH C 2 402 16 HOH HOH . N 5 HOH C 3 403 120 HOH HOH . N 5 HOH C 4 404 99 HOH HOH . N 5 HOH C 5 405 91 HOH HOH . N 5 HOH C 6 406 46 HOH HOH . N 5 HOH C 7 407 9 HOH HOH . N 5 HOH C 8 408 57 HOH HOH . N 5 HOH C 9 409 26 HOH HOH . N 5 HOH C 10 410 50 HOH HOH . N 5 HOH C 11 411 19 HOH HOH . N 5 HOH C 12 412 2 HOH HOH . N 5 HOH C 13 413 18 HOH HOH . N 5 HOH C 14 414 49 HOH HOH . N 5 HOH C 15 415 78 HOH HOH . N 5 HOH C 16 416 37 HOH HOH . N 5 HOH C 17 417 187 HOH HOH . N 5 HOH C 18 418 102 HOH HOH . N 5 HOH C 19 419 181 HOH HOH . N 5 HOH C 20 420 163 HOH HOH . N 5 HOH C 21 421 83 HOH HOH . N 5 HOH C 22 422 129 HOH HOH . N 5 HOH C 23 423 123 HOH HOH . N 5 HOH C 24 424 70 HOH HOH . N 5 HOH C 25 425 119 HOH HOH . N 5 HOH C 26 426 171 HOH HOH . N 5 HOH C 27 427 47 HOH HOH . N 5 HOH C 28 428 77 HOH HOH . N 5 HOH C 29 429 179 HOH HOH . N 5 HOH C 30 430 51 HOH HOH . N 5 HOH C 31 431 105 HOH HOH . N 5 HOH C 32 432 64 HOH HOH . N 5 HOH C 33 433 200 HOH HOH . N 5 HOH C 34 434 180 HOH HOH . N 5 HOH C 35 435 177 HOH HOH . N 5 HOH C 36 436 198 HOH HOH . N 5 HOH C 37 437 199 HOH HOH . O 5 HOH D 1 401 8 HOH HOH . O 5 HOH D 2 402 147 HOH HOH . O 5 HOH D 3 403 197 HOH HOH . O 5 HOH D 4 404 191 HOH HOH . O 5 HOH D 5 405 127 HOH HOH . O 5 HOH D 6 406 88 HOH HOH . O 5 HOH D 7 407 112 HOH HOH . O 5 HOH D 8 408 90 HOH HOH . O 5 HOH D 9 409 60 HOH HOH . O 5 HOH D 10 410 80 HOH HOH . O 5 HOH D 11 411 74 HOH HOH . O 5 HOH D 12 412 141 HOH HOH . O 5 HOH D 13 413 58 HOH HOH . O 5 HOH D 14 414 61 HOH HOH . O 5 HOH D 15 415 24 HOH HOH . O 5 HOH D 16 416 11 HOH HOH . O 5 HOH D 17 417 35 HOH HOH . O 5 HOH D 18 418 156 HOH HOH . O 5 HOH D 19 419 136 HOH HOH . O 5 HOH D 20 420 27 HOH HOH . O 5 HOH D 21 421 140 HOH HOH . O 5 HOH D 22 422 128 HOH HOH . O 5 HOH D 23 423 117 HOH HOH . O 5 HOH D 24 424 113 HOH HOH . O 5 HOH D 25 425 66 HOH HOH . O 5 HOH D 26 426 116 HOH HOH . O 5 HOH D 27 427 104 HOH HOH . O 5 HOH D 28 428 110 HOH HOH . O 5 HOH D 29 429 134 HOH HOH . O 5 HOH D 30 430 160 HOH HOH . O 5 HOH D 31 431 190 HOH HOH . O 5 HOH D 32 432 192 HOH HOH . O 5 HOH D 33 433 157 HOH HOH . O 5 HOH D 34 434 130 HOH HOH . O 5 HOH D 35 435 193 HOH HOH . O 5 HOH D 36 436 155 HOH HOH . O 5 HOH D 37 437 137 HOH HOH . O 5 HOH D 38 438 144 HOH HOH . O 5 HOH D 39 439 158 HOH HOH . O 5 HOH D 40 440 178 HOH HOH . O 5 HOH D 41 441 166 HOH HOH . O 5 HOH D 42 442 85 HOH HOH . O 5 HOH D 43 443 126 HOH HOH . O 5 HOH D 44 444 139 HOH HOH . O 5 HOH D 45 445 184 HOH HOH . O 5 HOH D 46 446 32 HOH HOH . O 5 HOH D 47 447 142 HOH HOH . O 5 HOH D 48 448 39 HOH HOH . O 5 HOH D 49 449 143 HOH HOH . O 5 HOH D 50 450 138 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 C2 5AG . . . J 4 12.43 -1.666 -57.238 1 36.13 ? C2 5AG 301 C 1 HETATM 2 C C4 5AG . . . J 4 10.846 -2.704 -58.457 1 40.51 ? C4 5AG 301 C 1 HETATM 3 C C5 5AG . . . J 4 10.401 -3.344 -57.359 1 43.42 ? C5 5AG 301 C 1 HETATM 4 C C6 5AG . . . J 4 10.986 -3.136 -56.17 1 47.39 ? C6 5AG 301 C 1 HETATM 5 N N9 5AG . . . J 4 10.089 -3.093 -59.434 1 41.08 ? N9 5AG 301 C 1 HETATM 6 C CAA 5AG . . . J 4 9.562 0.701 -56.289 1 56.7 ? CAA 5AG 301 C 1 HETATM 7 C CAB 5AG . . . J 4 8.729 -0.074 -56.487 1 49.5 ? CAB 5AG 301 C 1 HETATM 8 C CAC 5AG . . . J 4 7.717 -1.019 -56.705 1 39.16 ? CAC 5AG 301 C 1 HETATM 9 C CAD 5AG . . . J 4 7.509 -2.005 -55.787 1 36.94 ? CAD 5AG 301 C 1 HETATM 10 C CBJ 5AG . . . J 4 6.948 -0.94 -57.827 1 36.81 ? CBJ 5AG 301 C 1 HETATM 11 C CBI 5AG . . . J 4 5.958 -1.854 -58.047 1 36.85 ? CBI 5AG 301 C 1 HETATM 12 C CBH 5AG . . . J 4 5.756 -2.836 -57.13 1 37.09 ? CBH 5AG 301 C 1 HETATM 13 C CAE 5AG . . . J 4 6.524 -2.91 -56.008 1 37.28 ? CAE 5AG 301 C 1 HETATM 14 C CAF 5AG . . . J 4 6.287 -4.009 -55.03 1 38.01 ? CAF 5AG 301 C 1 HETATM 15 C CAG 5AG . . . J 4 6.808 -5.366 -55.493 1 42.33 ? CAG 5AG 301 C 1 HETATM 16 N NAH 5AG . . . J 4 7.513 -5.319 -56.775 1 51.71 ? NAH 5AG 301 C 1 HETATM 17 C CAI 5AG . . . J 4 7.526 -6.353 -57.561 1 55.91 ? CAI 5AG 301 C 1 HETATM 18 O OBG 5AG . . . J 4 6.99 -7.392 -57.27 1 67 ? OBG 5AG 301 C 1 HETATM 19 C CAJ 5AG . . . J 4 8.247 -6.258 -58.868 1 49.68 ? CAJ 5AG 301 C 1 HETATM 20 S SAK 5AG . . . J 4 8.096 -4.706 -59.754 1 60.39 ? SAK 5AG 301 C 1 HETATM 21 C C8 5AG . . . J 4 9.241 -3.927 -58.928 1 37.15 ? C8 5AG 301 C 1 HETATM 22 N N7 5AG . . . J 4 9.415 -4.103 -57.679 1 36.55 ? N7 5AG 301 C 1 HETATM 23 N N6 5AG . . . J 4 10.514 -3.779 -55.146 1 56.05 ? N6 5AG 301 C 1 HETATM 24 N N1 5AG . . . J 4 12.027 -2.284 -56.097 1 36.3 ? N1 5AG 301 C 1 HETATM 25 N N3 5AG . . . J 4 11.855 -1.881 -58.371 1 36.44 ? N3 5AG 301 C 1 HETATM 26 C CAV 5AG . . . J 4 10.183 -2.716 -60.811 1 44.42 ? CAV 5AG 301 C 1 HETATM 27 O OBF 5AG . . . J 4 8.891 -2.453 -61.18 1 47.55 ? OBF 5AG 301 C 1 HETATM 28 C CAW 5AG . . . J 4 10.484 -4.042 -61.486 1 44.4 ? CAW 5AG 301 C 1 HETATM 29 O OAX 5AG . . . J 4 11.669 -3.981 -62.208 1 41.1 ? OAX 5AG 301 C 1 HETATM 30 C CAY 5AG . . . J 4 9.396 -4.198 -62.472 1 44.69 ? CAY 5AG 301 C 1 HETATM 31 O OAZ 5AG . . . J 4 10.051 -4.461 -63.662 1 44.11 ? OAZ 5AG 301 C 1 HETATM 32 C CBA 5AG . . . J 4 8.826 -2.825 -62.515 1 53.06 ? CBA 5AG 301 C 1 HETATM 33 C CBB 5AG . . . J 4 7.37 -3.018 -62.891 1 61.48 ? CBB 5AG 301 C 1 HETATM 34 N NBC 5AG . . . J 4 6.524 -1.899 -62.494 1 66.03 ? NBC 5AG 301 C 1 HETATM 35 N NBD 5AG . . . J 4 7.001 -0.711 -62.448 1 70.57 ? NBD 5AG 301 C 1 HETATM 36 N NBE 5AG . . . J 4 7.489 0.514 -62.392 1 68.65 ? NBE 5AG 301 C 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #