data_5XDO
#
_model_server_result.job_id            nv5epWyY7sJuvUqJgIvKWg 
_model_server_result.datetime_utc      '2024-12-23 06:35:09' 
_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          5xdo 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":301}' 
#
_entry.id    5XDO 
#
_exptl.entry_id    5XDO 
_exptl.method      'X-RAY DIFFRACTION' 
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_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    2 
_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            5XDO 
_cell.length_a            121.62 
_cell.length_b            146.33 
_cell.length_c            77.53 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5XDO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        21 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_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 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 I 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 350 n n 
N1 HN11 SPD sing 351 n n 
N1 HN12 SPD sing 352 n n 
C2 C3 SPD sing 353 n n 
C2 H21 SPD sing 354 n n 
C2 H22 SPD sing 355 n n 
C3 C4 SPD sing 356 n n 
C3 H31 SPD sing 357 n n 
C3 H32 SPD sing 358 n n 
C4 C5 SPD sing 359 n n 
C4 H41 SPD sing 360 n n 
C4 H42 SPD sing 361 n n 
C5 N6 SPD sing 362 n n 
C5 H51 SPD sing 363 n n 
C5 H52 SPD sing 364 n n 
N6 C7 SPD sing 365 n n 
N6 HN6 SPD sing 366 n n 
C7 C8 SPD sing 367 n n 
C7 H71 SPD sing 368 n n 
C7 H72 SPD sing 369 n n 
C8 C9 SPD sing 370 n n 
C8 H81 SPD sing 371 n n 
C8 H82 SPD sing 372 n n 
C9 N10 SPD sing 373 n n 
C9 H91 SPD sing 374 n n 
C9 H92 SPD sing 375 n n 
N10 H101 SPD sing 376 n n 
N10 H102 SPD sing 377 n n 
#
_atom_sites.entry_id                     5XDO 
_atom_sites.fract_transf_matrix[1][1]    0.008222 
_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]    0.006834 
_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]    0.012898 
_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
C 2 SPD A 1 301 2 SPD SPD . 
D 3 OCT A 1 302 2 OCT OCT . 
E 3 OCT A 1 303 4 OCT OCT . 
F 4 LNK A 1 304 1 LNK LNK . 
G 4 LNK A 1 305 2 LNK LNK . 
H 5 HEX A 1 306 1 HEX HEX . 
I 2 SPD B 1 301 1 SPD SPD . 
J 3 OCT B 1 302 1 OCT OCT . 
K 3 OCT B 1 303 3 OCT OCT . 
L 6 HOH A 1 401 6 HOH HOH . 
L 6 HOH A 2 402 2 HOH HOH . 
L 6 HOH A 3 403 13 HOH HOH . 
L 6 HOH A 4 404 12 HOH HOH . 
L 6 HOH A 5 405 1 HOH HOH . 
L 6 HOH A 6 406 5 HOH HOH . 
L 6 HOH A 7 407 10 HOH HOH . 
L 6 HOH A 8 408 3 HOH HOH . 
L 6 HOH A 9 409 4 HOH HOH . 
L 6 HOH A 10 410 17 HOH HOH . 
L 6 HOH A 11 411 11 HOH HOH . 
M 6 HOH B 1 401 14 HOH HOH . 
M 6 HOH B 2 402 8 HOH HOH . 
M 6 HOH B 3 403 9 HOH HOH . 
M 6 HOH B 4 404 7 HOH HOH . 
M 6 HOH B 5 405 15 HOH HOH . 
M 6 HOH B 6 406 16 HOH HOH . 
M 6 HOH B 7 407 18 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 . . . I 2 -58.544 -44.023 12.287 1 88.76 ? N1 SPD 301 B 1 
HETATM 2 C C2 SPD . . . I 2 -58.554 -43.667 13.695 1 87.69 ? C2 SPD 301 B 1 
HETATM 3 C C3 SPD . . . I 2 -57.572 -42.523 13.933 1 94.01 ? C3 SPD 301 B 1 
HETATM 4 C C4 SPD . . . I 2 -58.056 -41.682 15.111 1 86.95 ? C4 SPD 301 B 1 
HETATM 5 C C5 SPD . . . I 2 -56.975 -41.632 16.188 1 71.35 ? C5 SPD 301 B 1 
HETATM 6 N N6 SPD . . . I 2 -57.33 -40.618 17.164 1 69.22 ? N6 SPD 301 B 1 
HETATM 7 C C7 SPD . . . I 2 -57.213 -39.304 16.558 1 64.71 ? C7 SPD 301 B 1 
HETATM 8 C C8 SPD . . . I 2 -55.744 -38.894 16.543 1 53.2 ? C8 SPD 301 B 1 
HETATM 9 C C9 SPD . . . I 2 -55.536 -37.697 17.466 1 47.74 ? C9 SPD 301 B 1 
HETATM 10 N N10 SPD . . . I 2 -54.407 -37.965 18.337 1 51.99 ? N10 SPD 301 B 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           281 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           10 
#