data_7OBZ
#
_model_server_result.job_id            VVpg3Uz07fKWppzoRLVEDA 
_model_server_result.datetime_utc      '2024-10-10 08:21:50' 
_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          7obz 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"EA","auth_seq_id":203}' 
#
_entry.id    7OBZ 
#
_exptl.entry_id    7OBZ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              145.246 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            SPERMIDINE 
_entity.pdbx_number_of_molecules    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          94 
_cell.angle_gamma         90 
_cell.entry_id            7OBZ 
_cell.length_a            90.96 
_cell.length_b            65.8 
_cell.length_c            122.72 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7OBZ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    'P 2yb' 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? dimeric 2 author_defined_assembly 1 
? dimeric 2 author_defined_assembly 2 
? dimeric 2 author_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,G,H,I,J,K,L,M,N,O,Y,Z,AA,BA,HA,KA 1 1 
B,C,P,Q,R,S,T,U,V,W,X,IA,JA 2 1 
E,CA,DA,EA,FA,LA 3 1 
F,GA 3 2 
#
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' 1_545 x,y-1,z 1 0 0 0 1 0 0 0 1 0 -65.8 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 N N N 
? 4 O N N 
? 4 S N N 
? 4 EA N N 
? 4 FA N 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
metalc ? metalc1 C OD2 ASP 112 C ASP 112 1_555 X NA NA . C NA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.108 ? 
metalc ? metalc2 D O GLU 120 D GLU 120 1_555 BA NA NA . D NA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? 
metalc ? metalc3 D OG SER 124 D SER 124 1_555 BA NA NA . D NA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? 
metalc ? metalc4 D OE1 GLU 128 D GLU 128 1_555 BA NA NA . D NA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? 
#
_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 344 n n 
N1 HN11 SPD sing 345 n n 
N1 HN12 SPD sing 346 n n 
C2 C3 SPD sing 347 n n 
C2 H21 SPD sing 348 n n 
C2 H22 SPD sing 349 n n 
C3 C4 SPD sing 350 n n 
C3 H31 SPD sing 351 n n 
C3 H32 SPD sing 352 n n 
C4 C5 SPD sing 353 n n 
C4 H41 SPD sing 354 n n 
C4 H42 SPD sing 355 n n 
C5 N6 SPD sing 356 n n 
C5 H51 SPD sing 357 n n 
C5 H52 SPD sing 358 n n 
N6 C7 SPD sing 359 n n 
N6 HN6 SPD sing 360 n n 
C7 C8 SPD sing 361 n n 
C7 H71 SPD sing 362 n n 
C7 H72 SPD sing 363 n n 
C8 C9 SPD sing 364 n n 
C8 H81 SPD sing 365 n n 
C8 H82 SPD sing 366 n n 
C9 N10 SPD sing 367 n n 
C9 H91 SPD sing 368 n n 
C9 H92 SPD sing 369 n n 
N10 H101 SPD sing 370 n n 
N10 H102 SPD sing 371 n n 
#
_atom_sites.entry_id                     7OBZ 
_atom_sites.fract_transf_matrix[1][1]    0.010994 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000769 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015198 
_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]    0.008169 
_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
G 2 FMN A 1 201 1 FMN FMN . 
H 3 CL A 1 202 1 CL CL . 
I 3 CL A 1 203 6 CL CL . 
J 3 CL A 1 204 7 CL CL . 
K 3 CL A 1 205 8 CL CL . 
L 3 CL A 1 206 9 CL CL . 
M 3 CL A 1 207 11 CL CL . 
N 4 SPD A 1 208 1 SPD SPD . 
O 4 SPD A 1 209 4 SPD SPD . 
P 2 FMN B 1 201 2 FMN FMN . 
Q 3 CL B 1 202 3 CL CL . 
R 5 NA B 1 203 41 NA NA . 
S 4 SPD B 1 204 2 SPD SPD . 
T 2 FMN C 1 201 3 FMN FMN . 
U 3 CL C 1 202 4 CL CL . 
V 3 CL C 1 203 5 CL CL . 
W 3 CL C 1 204 13 CL CL . 
X 5 NA C 1 205 40 NA NA . 
Y 2 FMN D 1 201 4 FMN FMN . 
Z 3 CL D 1 202 2 CL CL . 
AA 3 CL D 1 203 10 CL CL . 
BA 5 NA D 1 204 42 NA NA . 
CA 2 FMN E 1 201 5 FMN FMN . 
DA 3 CL E 1 202 12 CL CL . 
EA 4 SPD E 1 203 3 SPD SPD . 
FA 4 SPD E 1 204 5 SPD SPD . 
GA 2 FMN F 1 201 6 FMN FMN . 
HA 6 HOH A 1 301 176 HOH HOH . 
HA 6 HOH A 2 302 31 HOH HOH . 
HA 6 HOH A 3 303 305 HOH HOH . 
HA 6 HOH A 4 304 11 HOH HOH . 
HA 6 HOH A 5 305 324 HOH HOH . 
HA 6 HOH A 6 306 20 HOH HOH . 
HA 6 HOH A 7 307 13 HOH HOH . 
HA 6 HOH A 8 308 473 HOH HOH . 
HA 6 HOH A 9 309 34 HOH HOH . 
HA 6 HOH A 10 310 420 HOH HOH . 
HA 6 HOH A 11 311 189 HOH HOH . 
HA 6 HOH A 12 312 175 HOH HOH . 
HA 6 HOH A 13 313 195 HOH HOH . 
HA 6 HOH A 14 314 260 HOH HOH . 
HA 6 HOH A 15 315 174 HOH HOH . 
HA 6 HOH A 16 316 166 HOH HOH . 
HA 6 HOH A 17 317 414 HOH HOH . 
HA 6 HOH A 18 318 276 HOH HOH . 
HA 6 HOH A 19 319 339 HOH HOH . 
HA 6 HOH A 20 320 10 HOH HOH . 
HA 6 HOH A 21 321 197 HOH HOH . 
HA 6 HOH A 22 322 467 HOH HOH . 
HA 6 HOH A 23 323 178 HOH HOH . 
HA 6 HOH A 24 324 44 HOH HOH . 
HA 6 HOH A 25 325 185 HOH HOH . 
HA 6 HOH A 26 326 183 HOH HOH . 
HA 6 HOH A 27 327 180 HOH HOH . 
HA 6 HOH A 28 328 187 HOH HOH . 
HA 6 HOH A 29 329 181 HOH HOH . 
HA 6 HOH A 30 330 3 HOH HOH . 
HA 6 HOH A 31 331 403 HOH HOH . 
HA 6 HOH A 32 332 170 HOH HOH . 
HA 6 HOH A 33 333 33 HOH HOH . 
HA 6 HOH A 34 334 1 HOH HOH . 
HA 6 HOH A 35 335 26 HOH HOH . 
HA 6 HOH A 36 336 425 HOH HOH . 
HA 6 HOH A 37 337 17 HOH HOH . 
HA 6 HOH A 38 338 171 HOH HOH . 
HA 6 HOH A 39 339 61 HOH HOH . 
HA 6 HOH A 40 340 27 HOH HOH . 
HA 6 HOH A 41 341 335 HOH HOH . 
HA 6 HOH A 42 342 278 HOH HOH . 
HA 6 HOH A 43 343 401 HOH HOH . 
HA 6 HOH A 44 344 193 HOH HOH . 
HA 6 HOH A 45 345 379 HOH HOH . 
HA 6 HOH A 46 346 396 HOH HOH . 
HA 6 HOH A 47 347 24 HOH HOH . 
HA 6 HOH A 48 348 300 HOH HOH . 
HA 6 HOH A 49 349 320 HOH HOH . 
HA 6 HOH A 50 350 63 HOH HOH . 
HA 6 HOH A 51 351 177 HOH HOH . 
HA 6 HOH A 52 352 448 HOH HOH . 
HA 6 HOH A 53 353 461 HOH HOH . 
HA 6 HOH A 54 354 14 HOH HOH . 
HA 6 HOH A 55 355 398 HOH HOH . 
HA 6 HOH A 56 356 309 HOH HOH . 
HA 6 HOH A 57 357 428 HOH HOH . 
HA 6 HOH A 58 358 402 HOH HOH . 
HA 6 HOH A 59 359 190 HOH HOH . 
HA 6 HOH A 60 360 432 HOH HOH . 
HA 6 HOH A 61 361 184 HOH HOH . 
HA 6 HOH A 62 362 332 HOH HOH . 
HA 6 HOH A 63 363 186 HOH HOH . 
IA 6 HOH B 1 301 204 HOH HOH . 
IA 6 HOH B 2 302 261 HOH HOH . 
IA 6 HOH B 3 303 202 HOH HOH . 
IA 6 HOH B 4 304 188 HOH HOH . 
IA 6 HOH B 5 305 60 HOH HOH . 
IA 6 HOH B 6 306 412 HOH HOH . 
IA 6 HOH B 7 307 51 HOH HOH . 
IA 6 HOH B 8 308 436 HOH HOH . 
IA 6 HOH B 9 309 269 HOH HOH . 
IA 6 HOH B 10 310 264 HOH HOH . 
IA 6 HOH B 11 311 395 HOH HOH . 
IA 6 HOH B 12 312 211 HOH HOH . 
IA 6 HOH B 13 313 413 HOH HOH . 
IA 6 HOH B 14 314 49 HOH HOH . 
IA 6 HOH B 15 315 201 HOH HOH . 
IA 6 HOH B 16 316 9 HOH HOH . 
IA 6 HOH B 17 317 206 HOH HOH . 
IA 6 HOH B 18 318 323 HOH HOH . 
IA 6 HOH B 19 319 208 HOH HOH . 
IA 6 HOH B 20 320 2 HOH HOH . 
IA 6 HOH B 21 321 118 HOH HOH . 
IA 6 HOH B 22 322 266 HOH HOH . 
IA 6 HOH B 23 323 32 HOH HOH . 
IA 6 HOH B 24 324 73 HOH HOH . 
IA 6 HOH B 25 325 468 HOH HOH . 
IA 6 HOH B 26 326 437 HOH HOH . 
IA 6 HOH B 27 327 8 HOH HOH . 
IA 6 HOH B 28 328 408 HOH HOH . 
IA 6 HOH B 29 329 80 HOH HOH . 
IA 6 HOH B 30 330 295 HOH HOH . 
IA 6 HOH B 31 331 30 HOH HOH . 
IA 6 HOH B 32 332 135 HOH HOH . 
IA 6 HOH B 33 333 207 HOH HOH . 
IA 6 HOH B 34 334 407 HOH HOH . 
IA 6 HOH B 35 335 213 HOH HOH . 
IA 6 HOH B 36 336 59 HOH HOH . 
IA 6 HOH B 37 337 434 HOH HOH . 
IA 6 HOH B 38 338 199 HOH HOH . 
IA 6 HOH B 39 339 22 HOH HOH . 
IA 6 HOH B 40 340 198 HOH HOH . 
IA 6 HOH B 41 341 325 HOH HOH . 
IA 6 HOH B 42 342 310 HOH HOH . 
IA 6 HOH B 43 343 357 HOH HOH . 
IA 6 HOH B 44 344 438 HOH HOH . 
IA 6 HOH B 45 345 452 HOH HOH . 
IA 6 HOH B 46 346 167 HOH HOH . 
IA 6 HOH B 47 347 458 HOH HOH . 
IA 6 HOH B 48 348 168 HOH HOH . 
IA 6 HOH B 49 349 433 HOH HOH . 
IA 6 HOH B 50 350 200 HOH HOH . 
IA 6 HOH B 51 351 392 HOH HOH . 
IA 6 HOH B 52 352 203 HOH HOH . 
IA 6 HOH B 53 353 164 HOH HOH . 
JA 6 HOH C 1 301 209 HOH HOH . 
JA 6 HOH C 2 302 222 HOH HOH . 
JA 6 HOH C 3 303 399 HOH HOH . 
JA 6 HOH C 4 304 443 HOH HOH . 
JA 6 HOH C 5 305 221 HOH HOH . 
JA 6 HOH C 6 306 470 HOH HOH . 
JA 6 HOH C 7 307 229 HOH HOH . 
JA 6 HOH C 8 308 230 HOH HOH . 
JA 6 HOH C 9 309 225 HOH HOH . 
JA 6 HOH C 10 310 109 HOH HOH . 
JA 6 HOH C 11 311 163 HOH HOH . 
JA 6 HOH C 12 312 214 HOH HOH . 
JA 6 HOH C 13 313 272 HOH HOH . 
JA 6 HOH C 14 314 219 HOH HOH . 
JA 6 HOH C 15 315 47 HOH HOH . 
JA 6 HOH C 16 316 4 HOH HOH . 
JA 6 HOH C 17 317 410 HOH HOH . 
JA 6 HOH C 18 318 232 HOH HOH . 
JA 6 HOH C 19 319 257 HOH HOH . 
JA 6 HOH C 20 320 223 HOH HOH . 
JA 6 HOH C 21 321 409 HOH HOH . 
JA 6 HOH C 22 322 411 HOH HOH . 
JA 6 HOH C 23 323 326 HOH HOH . 
JA 6 HOH C 24 324 228 HOH HOH . 
JA 6 HOH C 25 325 475 HOH HOH . 
JA 6 HOH C 26 326 173 HOH HOH . 
JA 6 HOH C 27 327 220 HOH HOH . 
JA 6 HOH C 28 328 215 HOH HOH . 
JA 6 HOH C 29 329 397 HOH HOH . 
JA 6 HOH C 30 330 430 HOH HOH . 
JA 6 HOH C 31 331 435 HOH HOH . 
JA 6 HOH C 32 332 81 HOH HOH . 
JA 6 HOH C 33 333 453 HOH HOH . 
JA 6 HOH C 34 334 442 HOH HOH . 
JA 6 HOH C 35 335 417 HOH HOH . 
JA 6 HOH C 36 336 12 HOH HOH . 
JA 6 HOH C 37 337 456 HOH HOH . 
JA 6 HOH C 38 338 450 HOH HOH . 
JA 6 HOH C 39 339 464 HOH HOH . 
JA 6 HOH C 40 340 56 HOH HOH . 
JA 6 HOH C 41 341 41 HOH HOH . 
JA 6 HOH C 42 342 393 HOH HOH . 
JA 6 HOH C 43 343 463 HOH HOH . 
JA 6 HOH C 44 344 474 HOH HOH . 
JA 6 HOH C 45 345 455 HOH HOH . 
KA 6 HOH D 1 301 297 HOH HOH . 
KA 6 HOH D 2 302 25 HOH HOH . 
KA 6 HOH D 3 303 472 HOH HOH . 
KA 6 HOH D 4 304 465 HOH HOH . 
KA 6 HOH D 5 305 153 HOH HOH . 
KA 6 HOH D 6 306 314 HOH HOH . 
KA 6 HOH D 7 307 451 HOH HOH . 
KA 6 HOH D 8 308 471 HOH HOH . 
KA 6 HOH D 9 309 446 HOH HOH . 
LA 6 HOH E 1 301 252 HOH HOH . 
LA 6 HOH E 2 302 447 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 N6 SPD . . . EA 4 38.338 -0.054 -64.841 1 65.83 ? N6 SPD 203 E 1 
HETATM 2 C C7 SPD . . . EA 4 38.642 -0.738 -63.597 1 70.38 ? C7 SPD 203 E 1 
HETATM 3 C C8 SPD . . . EA 4 38.549 0.226 -62.415 1 70.1 ? C8 SPD 203 E 1 
HETATM 4 C C9 SPD . . . EA 4 39.211 -0.422 -61.195 1 84.24 ? C9 SPD 203 E 1 
#
_model_server_stats.io_time_ms              27 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           262 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           4 
#