data_4QF8
#
_model_server_result.job_id            '_TcRGvqJoEYmOiJCz6QRoA' 
_model_server_result.datetime_utc      '2024-12-26 22:32:46' 
_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          4qf8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    4QF8 
#
_exptl.entry_id    4QF8 
_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    1 
_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            4QF8 
_cell.length_a            51.555 
_cell.length_b            51.555 
_cell.length_c            47.417 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4QF8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        78 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43' 
#
_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 
_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                      2 
_struct_asym.id                             B 
_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 26 A CYS 27 1_555 A SG CYS 115 A CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
disulf ? disulf2 A SG CYS 28 A CYS 29 1_555 A SG CYS 44 A CYS 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf3 A SG CYS 43 A CYS 44 1_555 A SG CYS 95 A CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf4 A SG CYS 49 A CYS 50 1_555 A SG CYS 121 A CYS 133 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
disulf ? disulf5 A SG CYS 50 A CYS 51 1_555 A SG CYS 88 A CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? 
disulf ? disulf6 A SG CYS 57 A CYS 61 1_555 A SG CYS 81 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
disulf ? disulf7 A SG CYS 75 A CYS 84 1_555 A SG CYS 86 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
#
_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 294 n n 
N1 HN11 SPD sing 295 n n 
N1 HN12 SPD sing 296 n n 
C2 C3 SPD sing 297 n n 
C2 H21 SPD sing 298 n n 
C2 H22 SPD sing 299 n n 
C3 C4 SPD sing 300 n n 
C3 H31 SPD sing 301 n n 
C3 H32 SPD sing 302 n n 
C4 C5 SPD sing 303 n n 
C4 H41 SPD sing 304 n n 
C4 H42 SPD sing 305 n n 
C5 N6 SPD sing 306 n n 
C5 H51 SPD sing 307 n n 
C5 H52 SPD sing 308 n n 
N6 C7 SPD sing 309 n n 
N6 HN6 SPD sing 310 n n 
C7 C8 SPD sing 311 n n 
C7 H71 SPD sing 312 n n 
C7 H72 SPD sing 313 n n 
C8 C9 SPD sing 314 n n 
C8 H81 SPD sing 315 n n 
C8 H82 SPD sing 316 n n 
C9 N10 SPD sing 317 n n 
C9 H91 SPD sing 318 n n 
C9 H92 SPD sing 319 n n 
N10 H101 SPD sing 320 n n 
N10 H102 SPD sing 321 n n 
#
_atom_sites.entry_id                     4QF8 
_atom_sites.fract_transf_matrix[1][1]    0.019397 
_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]    0.019397 
_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]    0.021089 
_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 SPD A 1 201 1 SPD SPD . 
C 3 SO4 A 1 202 1 SO4 SO4 . 
D 4 HOH A 1 301 1 HOH HOH . 
D 4 HOH A 2 302 2 HOH HOH . 
D 4 HOH A 3 303 3 HOH HOH . 
D 4 HOH A 4 304 4 HOH HOH . 
D 4 HOH A 5 305 5 HOH HOH . 
D 4 HOH A 6 306 6 HOH HOH . 
D 4 HOH A 7 307 7 HOH HOH . 
D 4 HOH A 8 308 8 HOH HOH . 
D 4 HOH A 9 309 9 HOH HOH . 
D 4 HOH A 10 310 10 HOH HOH . 
D 4 HOH A 11 311 11 HOH HOH . 
D 4 HOH A 12 312 12 HOH HOH . 
D 4 HOH A 13 313 13 HOH HOH . 
D 4 HOH A 14 314 14 HOH HOH . 
D 4 HOH A 15 315 15 HOH HOH . 
D 4 HOH A 16 316 16 HOH HOH . 
D 4 HOH A 17 317 17 HOH HOH . 
D 4 HOH A 18 318 18 HOH HOH . 
D 4 HOH A 19 319 19 HOH HOH . 
D 4 HOH A 20 320 20 HOH HOH . 
D 4 HOH A 21 321 21 HOH HOH . 
D 4 HOH A 22 322 22 HOH HOH . 
D 4 HOH A 23 323 23 HOH HOH . 
D 4 HOH A 24 324 24 HOH HOH . 
D 4 HOH A 25 325 25 HOH HOH . 
D 4 HOH A 26 326 26 HOH HOH . 
D 4 HOH A 27 327 27 HOH HOH . 
D 4 HOH A 28 328 28 HOH HOH . 
D 4 HOH A 29 329 29 HOH HOH . 
D 4 HOH A 30 330 30 HOH HOH . 
D 4 HOH A 31 331 31 HOH HOH . 
D 4 HOH A 32 332 32 HOH HOH . 
D 4 HOH A 33 333 33 HOH HOH . 
D 4 HOH A 34 334 34 HOH HOH . 
D 4 HOH A 35 335 35 HOH HOH . 
D 4 HOH A 36 336 36 HOH HOH . 
D 4 HOH A 37 337 37 HOH HOH . 
D 4 HOH A 38 338 38 HOH HOH . 
D 4 HOH A 39 339 39 HOH HOH . 
D 4 HOH A 40 340 40 HOH HOH . 
D 4 HOH A 41 341 41 HOH HOH . 
D 4 HOH A 42 342 42 HOH HOH . 
D 4 HOH A 43 343 43 HOH HOH . 
D 4 HOH A 44 344 44 HOH HOH . 
D 4 HOH A 45 345 45 HOH HOH . 
D 4 HOH A 46 346 46 HOH HOH . 
D 4 HOH A 47 347 47 HOH HOH . 
D 4 HOH A 48 348 48 HOH HOH . 
D 4 HOH A 49 349 49 HOH HOH . 
D 4 HOH A 50 350 51 HOH HOH . 
D 4 HOH A 51 351 52 HOH HOH . 
D 4 HOH A 52 352 53 HOH HOH . 
D 4 HOH A 53 353 54 HOH HOH . 
D 4 HOH A 54 354 55 HOH HOH . 
D 4 HOH A 55 355 56 HOH HOH . 
D 4 HOH A 56 356 57 HOH HOH . 
D 4 HOH A 57 357 58 HOH HOH . 
D 4 HOH A 58 358 59 HOH HOH . 
D 4 HOH A 59 359 60 HOH HOH . 
D 4 HOH A 60 360 61 HOH HOH . 
D 4 HOH A 61 361 62 HOH HOH . 
D 4 HOH A 62 362 63 HOH HOH . 
D 4 HOH A 63 363 64 HOH HOH . 
D 4 HOH A 64 364 65 HOH HOH . 
D 4 HOH A 65 365 66 HOH HOH . 
D 4 HOH A 66 366 67 HOH HOH . 
D 4 HOH A 67 367 68 HOH HOH . 
D 4 HOH A 68 368 69 HOH HOH . 
D 4 HOH A 69 369 70 HOH HOH . 
D 4 HOH A 70 370 71 HOH HOH . 
D 4 HOH A 71 371 72 HOH HOH . 
D 4 HOH A 72 372 73 HOH HOH . 
D 4 HOH A 73 373 74 HOH HOH . 
D 4 HOH A 74 374 75 HOH HOH . 
D 4 HOH A 75 375 76 HOH HOH . 
D 4 HOH A 76 376 77 HOH HOH . 
D 4 HOH A 77 377 78 HOH HOH . 
D 4 HOH A 78 378 79 HOH HOH . 
D 4 HOH A 79 379 80 HOH HOH . 
D 4 HOH A 80 380 81 HOH HOH . 
D 4 HOH A 81 381 82 HOH HOH . 
D 4 HOH A 82 382 83 HOH HOH . 
D 4 HOH A 83 383 84 HOH HOH . 
D 4 HOH A 84 384 85 HOH HOH . 
D 4 HOH A 85 385 86 HOH HOH . 
D 4 HOH A 86 386 87 HOH HOH . 
D 4 HOH A 87 387 88 HOH HOH . 
D 4 HOH A 88 388 90 HOH HOH . 
D 4 HOH A 89 389 91 HOH HOH . 
D 4 HOH A 90 390 92 HOH HOH . 
D 4 HOH A 91 391 93 HOH HOH . 
D 4 HOH A 92 392 94 HOH HOH . 
D 4 HOH A 93 393 95 HOH HOH . 
D 4 HOH A 94 394 96 HOH HOH . 
D 4 HOH A 95 395 97 HOH HOH . 
D 4 HOH A 96 396 98 HOH HOH . 
D 4 HOH A 97 397 99 HOH HOH . 
D 4 HOH A 98 398 100 HOH HOH . 
D 4 HOH A 99 399 101 HOH HOH . 
D 4 HOH A 100 400 102 HOH HOH . 
D 4 HOH A 101 401 104 HOH HOH . 
D 4 HOH A 102 402 105 HOH HOH . 
D 4 HOH A 103 403 106 HOH HOH . 
D 4 HOH A 104 404 107 HOH HOH . 
D 4 HOH A 105 405 108 HOH HOH . 
D 4 HOH A 106 406 109 HOH HOH . 
D 4 HOH A 107 407 110 HOH HOH . 
D 4 HOH A 108 408 111 HOH HOH . 
D 4 HOH A 109 409 112 HOH HOH . 
D 4 HOH A 110 410 113 HOH HOH . 
D 4 HOH A 111 411 114 HOH HOH . 
D 4 HOH A 112 412 115 HOH HOH . 
D 4 HOH A 113 413 116 HOH HOH . 
D 4 HOH A 114 414 117 HOH HOH . 
D 4 HOH A 115 415 118 HOH HOH . 
D 4 HOH A 116 416 119 HOH HOH . 
D 4 HOH A 117 417 120 HOH HOH . 
D 4 HOH A 118 418 122 HOH HOH . 
D 4 HOH A 119 419 123 HOH HOH . 
D 4 HOH A 120 420 124 HOH HOH . 
D 4 HOH A 121 421 126 HOH HOH . 
D 4 HOH A 122 422 127 HOH HOH . 
D 4 HOH A 123 423 128 HOH HOH . 
D 4 HOH A 124 424 129 HOH HOH . 
D 4 HOH A 125 425 131 HOH HOH . 
D 4 HOH A 126 426 132 HOH HOH . 
D 4 HOH A 127 427 133 HOH HOH . 
D 4 HOH A 128 428 134 HOH HOH . 
D 4 HOH A 129 429 135 HOH HOH . 
D 4 HOH A 130 430 136 HOH HOH . 
D 4 HOH A 131 431 137 HOH HOH . 
D 4 HOH A 132 432 138 HOH HOH . 
D 4 HOH A 133 433 139 HOH HOH . 
D 4 HOH A 134 434 140 HOH HOH . 
D 4 HOH A 135 435 141 HOH HOH . 
D 4 HOH A 136 436 142 HOH HOH . 
D 4 HOH A 137 437 143 HOH HOH . 
D 4 HOH A 138 438 144 HOH HOH . 
D 4 HOH A 139 439 145 HOH HOH . 
D 4 HOH A 140 440 146 HOH HOH . 
D 4 HOH A 141 441 147 HOH HOH . 
D 4 HOH A 142 442 148 HOH HOH . 
D 4 HOH A 143 443 149 HOH HOH . 
D 4 HOH A 144 444 150 HOH HOH . 
D 4 HOH A 145 445 151 HOH HOH . 
D 4 HOH A 146 446 152 HOH HOH . 
D 4 HOH A 147 447 153 HOH HOH . 
D 4 HOH A 148 448 154 HOH HOH . 
D 4 HOH A 149 449 155 HOH HOH . 
D 4 HOH A 150 450 156 HOH HOH . 
D 4 HOH A 151 451 157 HOH HOH . 
D 4 HOH A 152 452 158 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 . . . B 2 17.023 -0.697 -3.405 1 30.59 ? N1 SPD 201 A 1 
HETATM 2 C C2 SPD . . . B 2 18.018 -0.742 -4.485 1 45.96 ? C2 SPD 201 A 1 
HETATM 3 C C3 SPD . . . B 2 18.531 0.651 -4.844 1 39.65 ? C3 SPD 201 A 1 
HETATM 4 C C4 SPD . . . B 2 19.911 0.849 -4.285 1 41.58 ? C4 SPD 201 A 1 
HETATM 5 C C5 SPD . . . B 2 19.944 1.943 -3.234 1 44.08 ? C5 SPD 201 A 1 
HETATM 6 N N6 SPD . . . B 2 20.963 2.91 -3.52 1 51.13 ? N6 SPD 201 A 1 
HETATM 7 C C7 SPD . . . B 2 20.876 3.842 -4.637 1 50.77 ? C7 SPD 201 A 1 
HETATM 8 C C8 SPD . . . B 2 21.909 4.912 -4.295 1 48.8 ? C8 SPD 201 A 1 
HETATM 9 C C9 SPD . . . B 2 21.568 6.286 -4.862 1 49.29 ? C9 SPD 201 A 1 
HETATM 10 N N10 SPD . . . B 2 20.709 6.976 -3.908 1 55.69 ? N10 SPD 201 A 1 
#
_model_server_stats.io_time_ms              50 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           904 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           10 
#