data_3WR7 # _model_server_result.job_id o0aLYCRxYNEBKqoSYNg2gw _model_server_result.datetime_utc '2024-11-22 15:46:24' _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 3wr7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":201}' # _entry.id 3WR7 # _exptl.entry_id 3WR7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 145.246 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPERMIDINE _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 90 _cell.angle_gamma 90 _cell.entry_id 3WR7 _cell.length_a 148.688 _cell.length_b 148.688 _cell.length_c 148.688 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3WR7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 195 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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 1,2,3 # 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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 G N N ? 2 I N N ? 2 K N N # _chem_comp.formula 'C7 H19 N3' _chem_comp.formula_weight 145.246 _chem_comp.id SPD _chem_comp.mon_nstd_flag . _chem_comp.name SPERMIDINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE;PA(34) # 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 SPD sing 376 n n N1 HN11 SPD sing 377 n n N1 HN12 SPD sing 378 n n C2 C3 SPD sing 379 n n C2 H21 SPD sing 380 n n C2 H22 SPD sing 381 n n C3 C4 SPD sing 382 n n C3 H31 SPD sing 383 n n C3 H32 SPD sing 384 n n C4 C5 SPD sing 385 n n C4 H41 SPD sing 386 n n C4 H42 SPD sing 387 n n C5 N6 SPD sing 388 n n C5 H51 SPD sing 389 n n C5 H52 SPD sing 390 n n N6 C7 SPD sing 391 n n N6 HN6 SPD sing 392 n n C7 C8 SPD sing 393 n n C7 H71 SPD sing 394 n n C7 H72 SPD sing 395 n n C8 C9 SPD sing 396 n n C8 H81 SPD sing 397 n n C8 H82 SPD sing 398 n n C9 N10 SPD sing 399 n n C9 H91 SPD sing 400 n n C9 H92 SPD sing 401 n n N10 H101 SPD sing 402 n n N10 H102 SPD sing 403 n n # _atom_sites.entry_id 3WR7 _atom_sites.fract_transf_matrix[1][1] 0.006725 _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] 0.006725 _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] 0.006725 _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 SPD A 1 201 201 SPD SPD . F 3 COA A 1 202 202 COA COA . G 2 SPD C 1 201 201 SPD SPD . H 3 COA C 1 202 202 COA COA . I 2 SPD B 1 201 201 SPD SPD . J 3 COA B 1 202 202 COA COA . K 2 SPD D 1 201 201 SPD SPD . L 3 COA D 1 202 202 COA COA . M 4 HOH A 1 301 3 HOH HOH . M 4 HOH A 2 302 7 HOH HOH . M 4 HOH A 3 303 16 HOH HOH . M 4 HOH A 4 304 18 HOH HOH . M 4 HOH A 5 305 19 HOH HOH . M 4 HOH A 6 306 21 HOH HOH . M 4 HOH A 7 307 23 HOH HOH . M 4 HOH A 8 308 24 HOH HOH . M 4 HOH A 9 309 26 HOH HOH . M 4 HOH A 10 310 27 HOH HOH . M 4 HOH A 11 311 29 HOH HOH . M 4 HOH A 12 312 32 HOH HOH . M 4 HOH A 13 313 37 HOH HOH . M 4 HOH A 14 314 46 HOH HOH . M 4 HOH A 15 315 53 HOH HOH . M 4 HOH A 16 316 59 HOH HOH . M 4 HOH A 17 317 60 HOH HOH . M 4 HOH A 18 318 61 HOH HOH . M 4 HOH A 19 319 62 HOH HOH . M 4 HOH A 20 320 63 HOH HOH . M 4 HOH A 21 321 64 HOH HOH . M 4 HOH A 22 322 69 HOH HOH . M 4 HOH A 23 323 75 HOH HOH . M 4 HOH A 24 324 76 HOH HOH . M 4 HOH A 25 325 78 HOH HOH . M 4 HOH A 26 326 83 HOH HOH . M 4 HOH A 27 327 94 HOH HOH . M 4 HOH A 28 328 95 HOH HOH . M 4 HOH A 29 329 96 HOH HOH . M 4 HOH A 30 330 97 HOH HOH . M 4 HOH A 31 331 98 HOH HOH . M 4 HOH A 32 332 99 HOH HOH . M 4 HOH A 33 333 100 HOH HOH . M 4 HOH A 34 334 101 HOH HOH . M 4 HOH A 35 335 103 HOH HOH . M 4 HOH A 36 336 129 HOH HOH . M 4 HOH A 37 337 131 HOH HOH . M 4 HOH A 38 338 133 HOH HOH . M 4 HOH A 39 339 136 HOH HOH . M 4 HOH A 40 340 141 HOH HOH . M 4 HOH A 41 341 145 HOH HOH . M 4 HOH A 42 342 153 HOH HOH . M 4 HOH A 43 343 154 HOH HOH . M 4 HOH A 44 344 161 HOH HOH . M 4 HOH A 45 345 162 HOH HOH . M 4 HOH A 46 346 163 HOH HOH . M 4 HOH A 47 347 164 HOH HOH . M 4 HOH A 48 348 166 HOH HOH . N 4 HOH C 1 301 1 HOH HOH . N 4 HOH C 2 302 2 HOH HOH . N 4 HOH C 3 303 11 HOH HOH . N 4 HOH C 4 304 12 HOH HOH . N 4 HOH C 5 305 14 HOH HOH . N 4 HOH C 6 306 17 HOH HOH . N 4 HOH C 7 307 22 HOH HOH . N 4 HOH C 8 308 30 HOH HOH . N 4 HOH C 9 309 33 HOH HOH . N 4 HOH C 10 310 34 HOH HOH . N 4 HOH C 11 311 38 HOH HOH . N 4 HOH C 12 312 44 HOH HOH . N 4 HOH C 13 313 47 HOH HOH . N 4 HOH C 14 314 48 HOH HOH . N 4 HOH C 15 315 51 HOH HOH . N 4 HOH C 16 316 52 HOH HOH . N 4 HOH C 17 317 77 HOH HOH . N 4 HOH C 18 318 79 HOH HOH . N 4 HOH C 19 319 80 HOH HOH . N 4 HOH C 20 320 81 HOH HOH . N 4 HOH C 21 321 102 HOH HOH . N 4 HOH C 22 322 104 HOH HOH . N 4 HOH C 23 323 105 HOH HOH . N 4 HOH C 24 324 106 HOH HOH . N 4 HOH C 25 325 107 HOH HOH . N 4 HOH C 26 326 108 HOH HOH . N 4 HOH C 27 327 109 HOH HOH . N 4 HOH C 28 328 110 HOH HOH . N 4 HOH C 29 329 111 HOH HOH . N 4 HOH C 30 330 112 HOH HOH . N 4 HOH C 31 331 114 HOH HOH . N 4 HOH C 32 332 126 HOH HOH . N 4 HOH C 33 333 127 HOH HOH . N 4 HOH C 34 334 130 HOH HOH . N 4 HOH C 35 335 137 HOH HOH . N 4 HOH C 36 336 138 HOH HOH . N 4 HOH C 37 337 140 HOH HOH . N 4 HOH C 38 338 142 HOH HOH . N 4 HOH C 39 339 155 HOH HOH . N 4 HOH C 40 340 156 HOH HOH . N 4 HOH C 41 341 159 HOH HOH . N 4 HOH C 42 342 160 HOH HOH . O 4 HOH B 1 301 5 HOH HOH . O 4 HOH B 2 302 6 HOH HOH . O 4 HOH B 3 303 8 HOH HOH . O 4 HOH B 4 304 25 HOH HOH . O 4 HOH B 5 305 28 HOH HOH . O 4 HOH B 6 306 31 HOH HOH . O 4 HOH B 7 307 36 HOH HOH . O 4 HOH B 8 308 39 HOH HOH . O 4 HOH B 9 309 40 HOH HOH . O 4 HOH B 10 310 41 HOH HOH . O 4 HOH B 11 311 45 HOH HOH . O 4 HOH B 12 312 57 HOH HOH . O 4 HOH B 13 313 58 HOH HOH . O 4 HOH B 14 314 65 HOH HOH . O 4 HOH B 15 315 66 HOH HOH . O 4 HOH B 16 316 67 HOH HOH . O 4 HOH B 17 317 82 HOH HOH . O 4 HOH B 18 318 84 HOH HOH . O 4 HOH B 19 319 85 HOH HOH . O 4 HOH B 20 320 86 HOH HOH . O 4 HOH B 21 321 87 HOH HOH . O 4 HOH B 22 322 88 HOH HOH . O 4 HOH B 23 323 115 HOH HOH . O 4 HOH B 24 324 116 HOH HOH . O 4 HOH B 25 325 117 HOH HOH . O 4 HOH B 26 326 118 HOH HOH . O 4 HOH B 27 327 119 HOH HOH . O 4 HOH B 28 328 120 HOH HOH . O 4 HOH B 29 329 121 HOH HOH . O 4 HOH B 30 330 123 HOH HOH . O 4 HOH B 31 331 128 HOH HOH . O 4 HOH B 32 332 132 HOH HOH . O 4 HOH B 33 333 134 HOH HOH . O 4 HOH B 34 334 135 HOH HOH . O 4 HOH B 35 335 146 HOH HOH . O 4 HOH B 36 336 147 HOH HOH . O 4 HOH B 37 337 148 HOH HOH . O 4 HOH B 38 338 149 HOH HOH . O 4 HOH B 39 339 150 HOH HOH . O 4 HOH B 40 340 151 HOH HOH . O 4 HOH B 41 341 152 HOH HOH . O 4 HOH B 42 342 165 HOH HOH . P 4 HOH D 1 301 4 HOH HOH . P 4 HOH D 2 302 9 HOH HOH . P 4 HOH D 3 303 10 HOH HOH . P 4 HOH D 4 304 13 HOH HOH . P 4 HOH D 5 305 15 HOH HOH . P 4 HOH D 6 306 20 HOH HOH . P 4 HOH D 7 307 35 HOH HOH . P 4 HOH D 8 308 42 HOH HOH . P 4 HOH D 9 309 43 HOH HOH . P 4 HOH D 10 310 49 HOH HOH . P 4 HOH D 11 311 50 HOH HOH . P 4 HOH D 12 312 54 HOH HOH . P 4 HOH D 13 313 55 HOH HOH . P 4 HOH D 14 314 56 HOH HOH . P 4 HOH D 15 315 68 HOH HOH . P 4 HOH D 16 316 70 HOH HOH . P 4 HOH D 17 317 71 HOH HOH . P 4 HOH D 18 318 72 HOH HOH . P 4 HOH D 19 319 73 HOH HOH . P 4 HOH D 20 320 74 HOH HOH . P 4 HOH D 21 321 89 HOH HOH . P 4 HOH D 22 322 90 HOH HOH . P 4 HOH D 23 323 91 HOH HOH . P 4 HOH D 24 324 92 HOH HOH . P 4 HOH D 25 325 93 HOH HOH . P 4 HOH D 26 326 113 HOH HOH . P 4 HOH D 27 327 122 HOH HOH . P 4 HOH D 28 328 124 HOH HOH . P 4 HOH D 29 329 125 HOH HOH . P 4 HOH D 30 330 139 HOH HOH . P 4 HOH D 31 331 143 HOH HOH . P 4 HOH D 32 332 144 HOH HOH . P 4 HOH D 33 333 157 HOH HOH . P 4 HOH D 34 334 158 HOH HOH . P 4 HOH D 35 335 167 HOH HOH . P 4 HOH D 36 336 168 HOH HOH . P 4 HOH D 37 337 169 HOH HOH . P 4 HOH D 38 338 170 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 SPD . . . K 2 61.511 23.851 51.975 1 50.82 ? N1 SPD 201 D 1 HETATM 2 C C2 SPD . . . K 2 61.99 24.792 50.98 1 47.33 ? C2 SPD 201 D 1 HETATM 3 C C3 SPD . . . K 2 62.222 23.964 49.718 1 44.77 ? C3 SPD 201 D 1 HETATM 4 C C4 SPD . . . K 2 61.414 24.495 48.541 1 41.22 ? C4 SPD 201 D 1 HETATM 5 C C5 SPD . . . K 2 62.21 25.642 47.928 1 38.83 ? C5 SPD 201 D 1 HETATM 6 N N6 SPD . . . K 2 61.771 25.948 46.584 1 40.73 ? N6 SPD 201 D 1 HETATM 7 C C7 SPD . . . K 2 62.144 27.255 46.069 1 39.18 ? C7 SPD 201 D 1 HETATM 8 C C8 SPD . . . K 2 61.495 27.585 44.729 1 38.15 ? C8 SPD 201 D 1 HETATM 9 C C9 SPD . . . K 2 62.497 28.449 43.953 1 37.23 ? C9 SPD 201 D 1 HETATM 10 N N10 SPD . . . K 2 61.88 29.345 43.012 1 35.67 ? N10 SPD 201 D 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 10 #