data_3BJ8
#
_model_server_result.job_id            1HLybKS-M3vfPdj0UsDsvA 
_model_server_result.datetime_utc      '2025-06-22 05:56:09' 
_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          3bj8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":500}' 
#
_entry.id    3BJ8 
#
_exptl.entry_id    3BJ8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              202.34 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            SPERMINE 
_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            3BJ8 
_cell.length_a            77.25 
_cell.length_b            97.12 
_cell.length_c            105.5 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3BJ8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,J,K 1 1 
C,D,G,H,I,L,M 2 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                      3 
_struct_asym.id                             G 
_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 120 A CYS 120 1_555 A SG CYS 122 A CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf2 B SG CYS 120 B CYS 120 1_555 B SG CYS 122 B CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
#
_chem_comp.formula           'C10 H26 N4' 
_chem_comp.formula_weight    202.34 
_chem_comp.id                SPM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              SPERMINE 
_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
N1 C2 SPM sing 376 n n 
N1 HN11 SPM sing 377 n n 
N1 HN12 SPM sing 378 n n 
C2 C3 SPM sing 379 n n 
C2 H21 SPM sing 380 n n 
C2 H22 SPM sing 381 n n 
C3 C4 SPM sing 382 n n 
C3 H31 SPM sing 383 n n 
C3 H32 SPM sing 384 n n 
C4 N5 SPM sing 385 n n 
C4 H41 SPM sing 386 n n 
C4 H42 SPM sing 387 n n 
N5 C6 SPM sing 388 n n 
N5 HN5 SPM sing 389 n n 
C6 C7 SPM sing 390 n n 
C6 H61 SPM sing 391 n n 
C6 H62 SPM sing 392 n n 
C7 C8 SPM sing 393 n n 
C7 H71 SPM sing 394 n n 
C7 H72 SPM sing 395 n n 
C8 C9 SPM sing 396 n n 
C8 H81 SPM sing 397 n n 
C8 H82 SPM sing 398 n n 
C9 N10 SPM sing 399 n n 
C9 H91 SPM sing 400 n n 
C9 H92 SPM sing 401 n n 
N10 C11 SPM sing 402 n n 
N10 HN0 SPM sing 403 n n 
C11 C12 SPM sing 404 n n 
C11 H111 SPM sing 405 n n 
C11 H112 SPM sing 406 n n 
C12 C13 SPM sing 407 n n 
C12 H121 SPM sing 408 n n 
C12 H122 SPM sing 409 n n 
C13 N14 SPM sing 410 n n 
C13 H131 SPM sing 411 n n 
C13 H132 SPM sing 412 n n 
N14 HN41 SPM sing 413 n n 
N14 HN42 SPM sing 414 n n 
#
_atom_sites.entry_id                     3BJ8 
_atom_sites.fract_transf_matrix[1][1]    0.012945 
_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]    0.010297 
_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]    0.009479 
_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 COA A 1 400 400 COA COA . 
F 2 COA B 1 401 401 COA COA . 
G 3 SPM C 1 500 500 SPM SPM . 
H 2 COA C 1 402 402 COA COA . 
I 2 COA D 1 403 403 COA COA . 
J 4 HOH A 1 401 1 HOH TIP . 
J 4 HOH A 2 402 2 HOH TIP . 
J 4 HOH A 3 403 3 HOH TIP . 
J 4 HOH A 4 404 4 HOH TIP . 
J 4 HOH A 5 405 5 HOH TIP . 
J 4 HOH A 6 406 6 HOH TIP . 
J 4 HOH A 7 407 8 HOH TIP . 
J 4 HOH A 8 408 9 HOH TIP . 
J 4 HOH A 9 409 10 HOH TIP . 
J 4 HOH A 10 410 11 HOH TIP . 
J 4 HOH A 11 411 12 HOH TIP . 
J 4 HOH A 12 412 13 HOH TIP . 
J 4 HOH A 13 413 14 HOH TIP . 
J 4 HOH A 14 414 15 HOH TIP . 
J 4 HOH A 15 415 16 HOH TIP . 
J 4 HOH A 16 416 18 HOH TIP . 
J 4 HOH A 17 417 21 HOH TIP . 
J 4 HOH A 18 418 22 HOH TIP . 
J 4 HOH A 19 419 23 HOH TIP . 
J 4 HOH A 20 420 24 HOH TIP . 
J 4 HOH A 21 421 26 HOH TIP . 
J 4 HOH A 22 422 54 HOH TIP . 
J 4 HOH A 23 423 55 HOH TIP . 
J 4 HOH A 24 424 110 HOH TIP . 
J 4 HOH A 25 425 111 HOH TIP . 
J 4 HOH A 26 426 112 HOH TIP . 
J 4 HOH A 27 427 113 HOH TIP . 
J 4 HOH A 28 428 114 HOH TIP . 
J 4 HOH A 29 429 115 HOH TIP . 
J 4 HOH A 30 430 116 HOH TIP . 
J 4 HOH A 31 431 117 HOH TIP . 
J 4 HOH A 32 432 118 HOH TIP . 
J 4 HOH A 33 433 120 HOH TIP . 
J 4 HOH A 34 434 123 HOH TIP . 
J 4 HOH A 35 435 124 HOH TIP . 
J 4 HOH A 36 436 125 HOH TIP . 
J 4 HOH A 37 437 126 HOH TIP . 
J 4 HOH A 38 438 127 HOH TIP . 
J 4 HOH A 39 439 128 HOH TIP . 
J 4 HOH A 40 440 129 HOH TIP . 
J 4 HOH A 41 441 130 HOH TIP . 
J 4 HOH A 42 442 131 HOH TIP . 
J 4 HOH A 43 443 214 HOH TIP . 
K 4 HOH B 1 402 7 HOH TIP . 
K 4 HOH B 2 403 17 HOH TIP . 
K 4 HOH B 3 404 19 HOH TIP . 
K 4 HOH B 4 405 20 HOH TIP . 
K 4 HOH B 5 406 27 HOH TIP . 
K 4 HOH B 6 407 28 HOH TIP . 
K 4 HOH B 7 408 29 HOH TIP . 
K 4 HOH B 8 409 30 HOH TIP . 
K 4 HOH B 9 410 31 HOH TIP . 
K 4 HOH B 10 411 32 HOH TIP . 
K 4 HOH B 11 412 33 HOH TIP . 
K 4 HOH B 12 413 34 HOH TIP . 
K 4 HOH B 13 414 35 HOH TIP . 
K 4 HOH B 14 415 36 HOH TIP . 
K 4 HOH B 15 416 37 HOH TIP . 
K 4 HOH B 16 417 38 HOH TIP . 
K 4 HOH B 17 418 39 HOH TIP . 
K 4 HOH B 18 419 40 HOH TIP . 
K 4 HOH B 19 420 41 HOH TIP . 
K 4 HOH B 20 421 42 HOH TIP . 
K 4 HOH B 21 422 43 HOH TIP . 
K 4 HOH B 22 423 44 HOH TIP . 
K 4 HOH B 23 424 45 HOH TIP . 
K 4 HOH B 24 425 46 HOH TIP . 
K 4 HOH B 25 426 47 HOH TIP . 
K 4 HOH B 26 427 48 HOH TIP . 
K 4 HOH B 27 428 49 HOH TIP . 
K 4 HOH B 28 429 50 HOH TIP . 
K 4 HOH B 29 430 51 HOH TIP . 
K 4 HOH B 30 431 52 HOH TIP . 
K 4 HOH B 31 432 53 HOH TIP . 
K 4 HOH B 32 433 56 HOH TIP . 
K 4 HOH B 33 434 107 HOH TIP . 
K 4 HOH B 34 435 108 HOH TIP . 
K 4 HOH B 35 436 109 HOH TIP . 
K 4 HOH B 36 437 119 HOH TIP . 
K 4 HOH B 37 438 121 HOH TIP . 
K 4 HOH B 38 439 122 HOH TIP . 
K 4 HOH B 39 440 132 HOH TIP . 
K 4 HOH B 40 441 133 HOH TIP . 
K 4 HOH B 41 442 134 HOH TIP . 
K 4 HOH B 42 443 135 HOH TIP . 
K 4 HOH B 43 444 136 HOH TIP . 
K 4 HOH B 44 445 137 HOH TIP . 
K 4 HOH B 45 446 138 HOH TIP . 
K 4 HOH B 46 447 139 HOH TIP . 
K 4 HOH B 47 448 140 HOH TIP . 
K 4 HOH B 48 449 141 HOH TIP . 
K 4 HOH B 49 450 142 HOH TIP . 
K 4 HOH B 50 451 143 HOH TIP . 
K 4 HOH B 51 452 144 HOH TIP . 
K 4 HOH B 52 453 145 HOH TIP . 
K 4 HOH B 53 454 146 HOH TIP . 
K 4 HOH B 54 455 147 HOH TIP . 
K 4 HOH B 55 456 212 HOH TIP . 
K 4 HOH B 56 457 213 HOH TIP . 
K 4 HOH B 57 458 86 HOH TIP . 
L 4 HOH C 1 501 25 HOH TIP . 
L 4 HOH C 2 502 57 HOH TIP . 
L 4 HOH C 3 503 58 HOH TIP . 
L 4 HOH C 4 504 59 HOH TIP . 
L 4 HOH C 5 505 60 HOH TIP . 
L 4 HOH C 6 506 61 HOH TIP . 
L 4 HOH C 7 507 62 HOH TIP . 
L 4 HOH C 8 508 63 HOH TIP . 
L 4 HOH C 9 509 64 HOH TIP . 
L 4 HOH C 10 510 65 HOH TIP . 
L 4 HOH C 11 511 66 HOH TIP . 
L 4 HOH C 12 512 68 HOH TIP . 
L 4 HOH C 13 513 69 HOH TIP . 
L 4 HOH C 14 514 75 HOH TIP . 
L 4 HOH C 15 515 76 HOH TIP . 
L 4 HOH C 16 516 77 HOH TIP . 
L 4 HOH C 17 517 78 HOH TIP . 
L 4 HOH C 18 518 79 HOH TIP . 
L 4 HOH C 19 519 80 HOH TIP . 
L 4 HOH C 20 520 81 HOH TIP . 
L 4 HOH C 21 521 82 HOH TIP . 
L 4 HOH C 22 522 100 HOH TIP . 
L 4 HOH C 23 523 101 HOH TIP . 
L 4 HOH C 24 524 148 HOH TIP . 
L 4 HOH C 25 525 149 HOH TIP . 
L 4 HOH C 26 526 150 HOH TIP . 
L 4 HOH C 27 527 151 HOH TIP . 
L 4 HOH C 28 528 152 HOH TIP . 
L 4 HOH C 29 529 153 HOH TIP . 
L 4 HOH C 30 530 155 HOH TIP . 
L 4 HOH C 31 531 156 HOH TIP . 
L 4 HOH C 32 532 157 HOH TIP . 
L 4 HOH C 33 533 161 HOH TIP . 
L 4 HOH C 34 534 162 HOH TIP . 
L 4 HOH C 35 535 164 HOH TIP . 
L 4 HOH C 36 536 165 HOH TIP . 
L 4 HOH C 37 537 166 HOH TIP . 
L 4 HOH C 38 538 167 HOH TIP . 
L 4 HOH C 39 539 168 HOH TIP . 
L 4 HOH C 40 540 169 HOH TIP . 
L 4 HOH C 41 541 170 HOH TIP . 
L 4 HOH C 42 542 171 HOH TIP . 
L 4 HOH C 43 543 172 HOH TIP . 
L 4 HOH C 44 544 173 HOH TIP . 
L 4 HOH C 45 545 195 HOH TIP . 
L 4 HOH C 46 546 201 HOH TIP . 
L 4 HOH C 47 547 207 HOH TIP . 
L 4 HOH C 48 548 208 HOH TIP . 
L 4 HOH C 49 549 209 HOH TIP . 
L 4 HOH C 50 550 210 HOH TIP . 
L 4 HOH C 51 551 211 HOH TIP . 
M 4 HOH D 1 404 67 HOH TIP . 
M 4 HOH D 2 405 70 HOH TIP . 
M 4 HOH D 3 406 71 HOH TIP . 
M 4 HOH D 4 407 72 HOH TIP . 
M 4 HOH D 5 408 73 HOH TIP . 
M 4 HOH D 6 409 74 HOH TIP . 
M 4 HOH D 7 410 83 HOH TIP . 
M 4 HOH D 8 411 84 HOH TIP . 
M 4 HOH D 9 412 85 HOH TIP . 
M 4 HOH D 10 414 87 HOH TIP . 
M 4 HOH D 11 415 88 HOH TIP . 
M 4 HOH D 12 416 89 HOH TIP . 
M 4 HOH D 13 417 90 HOH TIP . 
M 4 HOH D 14 418 91 HOH TIP . 
M 4 HOH D 15 419 92 HOH TIP . 
M 4 HOH D 16 420 93 HOH TIP . 
M 4 HOH D 17 421 94 HOH TIP . 
M 4 HOH D 18 422 95 HOH TIP . 
M 4 HOH D 19 423 96 HOH TIP . 
M 4 HOH D 20 424 97 HOH TIP . 
M 4 HOH D 21 425 98 HOH TIP . 
M 4 HOH D 22 426 102 HOH TIP . 
M 4 HOH D 23 427 103 HOH TIP . 
M 4 HOH D 24 428 104 HOH TIP . 
M 4 HOH D 25 429 105 HOH TIP . 
M 4 HOH D 26 430 106 HOH TIP . 
M 4 HOH D 27 431 154 HOH TIP . 
M 4 HOH D 28 432 158 HOH TIP . 
M 4 HOH D 29 433 159 HOH TIP . 
M 4 HOH D 30 434 160 HOH TIP . 
M 4 HOH D 31 435 163 HOH TIP . 
M 4 HOH D 32 436 174 HOH TIP . 
M 4 HOH D 33 437 175 HOH TIP . 
M 4 HOH D 34 438 176 HOH TIP . 
M 4 HOH D 35 439 177 HOH TIP . 
M 4 HOH D 36 440 178 HOH TIP . 
M 4 HOH D 37 441 179 HOH TIP . 
M 4 HOH D 38 442 180 HOH TIP . 
M 4 HOH D 39 443 181 HOH TIP . 
M 4 HOH D 40 444 182 HOH TIP . 
M 4 HOH D 41 445 183 HOH TIP . 
M 4 HOH D 42 446 184 HOH TIP . 
M 4 HOH D 43 447 185 HOH TIP . 
M 4 HOH D 44 448 186 HOH TIP . 
M 4 HOH D 45 449 187 HOH TIP . 
M 4 HOH D 46 450 188 HOH TIP . 
M 4 HOH D 47 451 189 HOH TIP . 
M 4 HOH D 48 452 190 HOH TIP . 
M 4 HOH D 49 453 191 HOH TIP . 
M 4 HOH D 50 454 192 HOH TIP . 
M 4 HOH D 51 455 193 HOH TIP . 
M 4 HOH D 52 456 194 HOH TIP . 
M 4 HOH D 53 457 196 HOH TIP . 
M 4 HOH D 54 458 197 HOH TIP . 
M 4 HOH D 55 459 198 HOH TIP . 
M 4 HOH D 56 460 199 HOH TIP . 
M 4 HOH D 57 461 200 HOH TIP . 
M 4 HOH D 58 462 202 HOH TIP . 
M 4 HOH D 59 463 203 HOH TIP . 
M 4 HOH D 60 464 204 HOH TIP . 
M 4 HOH D 61 465 205 HOH TIP . 
M 4 HOH D 62 466 206 HOH TIP . 
#
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 SPM . . . G 3 40.203 32.184 32.615 1 35.63 ? N1 SPM 500 C 1 
HETATM 2 C C2 SPM . . . G 3 39.793 33.344 33.43 1 41.64 ? C2 SPM 500 C 1 
HETATM 3 C C3 SPM . . . G 3 38.822 34.284 32.669 1 41.65 ? C3 SPM 500 C 1 
HETATM 4 C C4 SPM . . . G 3 39.171 34.399 31.171 1 41.52 ? C4 SPM 500 C 1 
HETATM 5 N N5 SPM . . . G 3 38.243 35.346 30.526 1 44.01 ? N5 SPM 500 C 1 
HETATM 6 C C6 SPM . . . G 3 38.737 35.591 29.161 1 44.88 ? C6 SPM 500 C 1 
HETATM 7 C C7 SPM . . . G 3 37.674 36.321 28.328 1 45.81 ? C7 SPM 500 C 1 
HETATM 8 C C8 SPM . . . G 3 38.241 36.625 26.936 1 48.42 ? C8 SPM 500 C 1 
HETATM 9 C C9 SPM . . . G 3 37.122 37.044 25.972 1 50 ? C9 SPM 500 C 1 
HETATM 10 N N10 SPM . . . G 3 37.507 36.712 24.646 1 50.41 ? N10 SPM 500 C 1 
HETATM 11 C C11 SPM . . . G 3 36.858 36.553 23.331 1 50.3 ? C11 SPM 500 C 1 
HETATM 12 C C12 SPM . . . G 3 37.805 35.758 22.502 1 48.95 ? C12 SPM 500 C 1 
HETATM 13 C C13 SPM . . . G 3 37.094 35.217 21.26 1 46.6 ? C13 SPM 500 C 1 
HETATM 14 N N14 SPM . . . G 3 37.969 34.245 20.572 1 44.92 ? N14 SPM 500 C 1 
#
_model_server_stats.io_time_ms              42 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           238 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           14 
#