data_4MHD # _model_server_result.job_id cIaGl5kR5jdNFBacI751ow _model_server_result.datetime_utc '2024-11-13 08:43:02' _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 4mhd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 4MHD # _exptl.entry_id 4MHD _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 3 _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 4MHD _cell.length_a 73.453 _cell.length_b 136.012 _cell.length_c 139.831 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4MHD _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 0 0 139.831 4 'crystal symmetry operation' 4_556 x,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 139.831 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F 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 290 n n N1 HN11 SPD sing 291 n n N1 HN12 SPD sing 292 n n C2 C3 SPD sing 293 n n C2 H21 SPD sing 294 n n C2 H22 SPD sing 295 n n C3 C4 SPD sing 296 n n C3 H31 SPD sing 297 n n C3 H32 SPD sing 298 n n C4 C5 SPD sing 299 n n C4 H41 SPD sing 300 n n C4 H42 SPD sing 301 n n C5 N6 SPD sing 302 n n C5 H51 SPD sing 303 n n C5 H52 SPD sing 304 n n N6 C7 SPD sing 305 n n N6 HN6 SPD sing 306 n n C7 C8 SPD sing 307 n n C7 H71 SPD sing 308 n n C7 H72 SPD sing 309 n n C8 C9 SPD sing 310 n n C8 H81 SPD sing 311 n n C8 H82 SPD sing 312 n n C9 N10 SPD sing 313 n n C9 H91 SPD sing 314 n n C9 H92 SPD sing 315 n n N10 H101 SPD sing 316 n n N10 H102 SPD sing 317 n n # _atom_sites.entry_id 4MHD _atom_sites.fract_transf_matrix[1][1] 0.013614 _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] 0.007352 _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] 0.007151 _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 D 2 SPD A 1 201 2 SPD SPD . E 2 SPD B 1 201 1 SPD SPD . F 2 SPD C 1 201 3 SPD SPD . G 3 HOH A 1 301 8 HOH HOH . G 3 HOH A 2 302 12 HOH HOH . G 3 HOH A 3 303 15 HOH HOH . G 3 HOH A 4 304 21 HOH HOH . G 3 HOH A 5 305 33 HOH HOH . G 3 HOH A 6 306 47 HOH HOH . G 3 HOH A 7 307 48 HOH HOH . G 3 HOH A 8 308 77 HOH HOH . G 3 HOH A 9 309 83 HOH HOH . G 3 HOH A 10 310 84 HOH HOH . G 3 HOH A 11 311 129 HOH HOH . G 3 HOH A 12 312 203 HOH HOH . G 3 HOH A 13 313 249 HOH HOH . G 3 HOH A 14 314 250 HOH HOH . G 3 HOH A 15 315 254 HOH HOH . G 3 HOH A 16 316 255 HOH HOH . G 3 HOH A 17 317 256 HOH HOH . G 3 HOH A 18 318 257 HOH HOH . G 3 HOH A 19 319 258 HOH HOH . G 3 HOH A 20 320 259 HOH HOH . G 3 HOH A 21 321 260 HOH HOH . G 3 HOH A 22 322 294 HOH HOH . G 3 HOH A 23 323 295 HOH HOH . G 3 HOH A 24 324 296 HOH HOH . G 3 HOH A 25 325 297 HOH HOH . G 3 HOH A 26 326 298 HOH HOH . G 3 HOH A 27 327 299 HOH HOH . G 3 HOH A 28 328 300 HOH HOH . G 3 HOH A 29 329 309 HOH HOH . G 3 HOH A 30 330 310 HOH HOH . G 3 HOH A 31 331 311 HOH HOH . G 3 HOH A 32 332 312 HOH HOH . G 3 HOH A 33 333 314 HOH HOH . G 3 HOH A 34 334 328 HOH HOH . G 3 HOH A 35 335 330 HOH HOH . G 3 HOH A 36 336 331 HOH HOH . G 3 HOH A 37 337 332 HOH HOH . G 3 HOH A 38 338 333 HOH HOH . H 3 HOH B 1 301 6 HOH HOH . H 3 HOH B 2 302 9 HOH HOH . H 3 HOH B 3 303 16 HOH HOH . H 3 HOH B 4 304 20 HOH HOH . H 3 HOH B 5 305 49 HOH HOH . H 3 HOH B 6 306 50 HOH HOH . H 3 HOH B 7 307 54 HOH HOH . H 3 HOH B 8 308 56 HOH HOH . H 3 HOH B 9 309 60 HOH HOH . H 3 HOH B 10 310 63 HOH HOH . H 3 HOH B 11 311 88 HOH HOH . H 3 HOH B 12 312 100 HOH HOH . H 3 HOH B 13 313 104 HOH HOH . H 3 HOH B 14 314 113 HOH HOH . H 3 HOH B 15 315 131 HOH HOH . H 3 HOH B 16 316 152 HOH HOH . H 3 HOH B 17 317 261 HOH HOH . H 3 HOH B 18 318 262 HOH HOH . H 3 HOH B 19 319 263 HOH HOH . H 3 HOH B 20 320 267 HOH HOH . H 3 HOH B 21 321 268 HOH HOH . H 3 HOH B 22 322 269 HOH HOH . H 3 HOH B 23 323 270 HOH HOH . H 3 HOH B 24 324 271 HOH HOH . H 3 HOH B 25 325 273 HOH HOH . H 3 HOH B 26 326 274 HOH HOH . H 3 HOH B 27 327 277 HOH HOH . H 3 HOH B 28 328 278 HOH HOH . H 3 HOH B 29 329 279 HOH HOH . H 3 HOH B 30 330 280 HOH HOH . H 3 HOH B 31 331 281 HOH HOH . H 3 HOH B 32 332 282 HOH HOH . H 3 HOH B 33 333 287 HOH HOH . H 3 HOH B 34 334 301 HOH HOH . H 3 HOH B 35 335 302 HOH HOH . H 3 HOH B 36 336 303 HOH HOH . H 3 HOH B 37 337 304 HOH HOH . H 3 HOH B 38 338 305 HOH HOH . H 3 HOH B 39 339 306 HOH HOH . H 3 HOH B 40 340 316 HOH HOH . H 3 HOH B 41 341 317 HOH HOH . H 3 HOH B 42 342 318 HOH HOH . H 3 HOH B 43 343 319 HOH HOH . H 3 HOH B 44 344 320 HOH HOH . H 3 HOH B 45 345 321 HOH HOH . H 3 HOH B 46 346 324 HOH HOH . H 3 HOH B 47 347 325 HOH HOH . H 3 HOH B 48 348 337 HOH HOH . H 3 HOH B 49 349 338 HOH HOH . H 3 HOH B 50 350 339 HOH HOH . H 3 HOH B 51 351 341 HOH HOH . I 3 HOH C 1 301 1 HOH HOH . I 3 HOH C 2 302 2 HOH HOH . I 3 HOH C 3 303 14 HOH HOH . I 3 HOH C 4 304 19 HOH HOH . I 3 HOH C 5 305 26 HOH HOH . I 3 HOH C 6 306 27 HOH HOH . I 3 HOH C 7 307 28 HOH HOH . I 3 HOH C 8 308 37 HOH HOH . I 3 HOH C 9 309 41 HOH HOH . I 3 HOH C 10 310 42 HOH HOH . I 3 HOH C 11 311 57 HOH HOH . I 3 HOH C 12 312 62 HOH HOH . I 3 HOH C 13 313 71 HOH HOH . I 3 HOH C 14 314 98 HOH HOH . I 3 HOH C 15 315 160 HOH HOH . I 3 HOH C 16 316 238 HOH HOH . I 3 HOH C 17 317 239 HOH HOH . I 3 HOH C 18 318 264 HOH HOH . I 3 HOH C 19 319 265 HOH HOH . I 3 HOH C 20 320 266 HOH HOH . I 3 HOH C 21 321 283 HOH HOH . I 3 HOH C 22 322 284 HOH HOH . I 3 HOH C 23 323 285 HOH HOH . I 3 HOH C 24 324 286 HOH HOH . I 3 HOH C 25 325 288 HOH HOH . I 3 HOH C 26 326 289 HOH HOH . I 3 HOH C 27 327 290 HOH HOH . I 3 HOH C 28 328 291 HOH HOH . I 3 HOH C 29 329 292 HOH HOH . I 3 HOH C 30 330 308 HOH HOH . I 3 HOH C 31 331 313 HOH HOH . I 3 HOH C 32 332 315 HOH HOH . I 3 HOH C 33 333 322 HOH HOH . I 3 HOH C 34 334 323 HOH HOH . I 3 HOH C 35 335 326 HOH HOH . I 3 HOH C 36 336 329 HOH HOH . I 3 HOH C 37 337 335 HOH HOH . I 3 HOH C 38 338 336 HOH HOH . I 3 HOH C 39 339 340 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 . . . D 2 -10.569 -20.439 51.226 1 34.97 ? N1 SPD 201 A 1 HETATM 2 C C2 SPD . . . D 2 -9.92 -20.056 52.465 1 38.04 ? C2 SPD 201 A 1 HETATM 3 C C3 SPD . . . D 2 -10.143 -21.142 53.512 1 41.06 ? C3 SPD 201 A 1 HETATM 4 C C4 SPD . . . D 2 -8.981 -21.199 54.496 1 54.39 ? C4 SPD 201 A 1 HETATM 5 C C5 SPD . . . D 2 -9.438 -21.73 55.849 1 50.6 ? C5 SPD 201 A 1 HETATM 6 N N6 SPD . . . D 2 -8.786 -21.045 56.949 1 67.36 ? N6 SPD 201 A 1 HETATM 7 C C7 SPD . . . D 2 -8.717 -21.672 58.255 1 71.59 ? C7 SPD 201 A 1 HETATM 8 C C8 SPD . . . D 2 -9.906 -21.295 59.132 1 46.13 ? C8 SPD 201 A 1 HETATM 9 C C9 SPD . . . D 2 -9.9 -22.092 60.431 1 53.05 ? C9 SPD 201 A 1 HETATM 10 N N10 SPD . . . D 2 -9.081 -21.409 61.413 1 42.79 ? N10 SPD 201 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 10 #