data_3KU9
#
_model_server_result.job_id            n9jacbFqjomxElB6lZIHyQ 
_model_server_result.datetime_utc      '2024-11-18 18:41:44' 
_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          3ku9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":700}' 
#
_entry.id    3KU9 
#
_exptl.entry_id    3KU9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              202.34 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            SPERMINE 
_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         120 
_cell.entry_id            3KU9 
_cell.length_a            138.957 
_cell.length_b            138.957 
_cell.length_c            189.8 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KU9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 2 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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
PISA dimeric 2 software_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,E,F,K 1 1 
B,C,G,H,I,J,L 2 1 
A,B,C,D,E,F,G,H,I,J,K,L 3 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
? 5 F N N 
? 5 H N N 
#
_pdbx_entity_branch.entity_id    2 
_pdbx_entity_branch.type         oligosaccharide 
#
_pdbx_entity_branch_link.link_id                     1 
_pdbx_entity_branch_link.details                     ? 
_pdbx_entity_branch_link.entity_id                   2 
_pdbx_entity_branch_link.entity_branch_list_num_1    2 
_pdbx_entity_branch_link.entity_branch_list_num_2    1 
_pdbx_entity_branch_link.comp_id_1                   NAG 
_pdbx_entity_branch_link.comp_id_2                   NAG 
_pdbx_entity_branch_link.atom_id_1                   C1 
_pdbx_entity_branch_link.leaving_atom_id_1           O1 
_pdbx_entity_branch_link.atom_stereo_config_1        . 
_pdbx_entity_branch_link.atom_id_2                   O4 
_pdbx_entity_branch_link.leaving_atom_id_2           HO4 
_pdbx_entity_branch_link.atom_stereo_config_2        . 
_pdbx_entity_branch_link.value_order                 sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
2 n C NAG 1 C 1 NAG B 600 NAG 
2 n C NAG 2 C 2 NAG B 601 NAG 
#
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 457 A CYS 457 1_555 A SG CYS 463 A CYS 463 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? 
disulf ? disulf2 B SG CYS 457 B CYS 457 1_555 B SG CYS 463 B CYS 463 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.995 ? 
covale ? covale1 A ND2 ASN 77 A ASN 77 1_555 E C1 NAG . A NAG 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.521 ? 
covale ? covale2 B ND2 ASN 77 B ASN 77 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? 
covale ? covale3 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? 
#
_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 415 n n 
N1 HN11 SPM sing 416 n n 
N1 HN12 SPM sing 417 n n 
C2 C3 SPM sing 418 n n 
C2 H21 SPM sing 419 n n 
C2 H22 SPM sing 420 n n 
C3 C4 SPM sing 421 n n 
C3 H31 SPM sing 422 n n 
C3 H32 SPM sing 423 n n 
C4 N5 SPM sing 424 n n 
C4 H41 SPM sing 425 n n 
C4 H42 SPM sing 426 n n 
N5 C6 SPM sing 427 n n 
N5 HN5 SPM sing 428 n n 
C6 C7 SPM sing 429 n n 
C6 H61 SPM sing 430 n n 
C6 H62 SPM sing 431 n n 
C7 C8 SPM sing 432 n n 
C7 H71 SPM sing 433 n n 
C7 H72 SPM sing 434 n n 
C8 C9 SPM sing 435 n n 
C8 H81 SPM sing 436 n n 
C8 H82 SPM sing 437 n n 
C9 N10 SPM sing 438 n n 
C9 H91 SPM sing 439 n n 
C9 H92 SPM sing 440 n n 
N10 C11 SPM sing 441 n n 
N10 HN0 SPM sing 442 n n 
C11 C12 SPM sing 443 n n 
C11 H111 SPM sing 444 n n 
C11 H112 SPM sing 445 n n 
C12 C13 SPM sing 446 n n 
C12 H121 SPM sing 447 n n 
C12 H122 SPM sing 448 n n 
C13 N14 SPM sing 449 n n 
C13 H131 SPM sing 450 n n 
C13 H132 SPM sing 451 n n 
N14 HN41 SPM sing 452 n n 
N14 HN42 SPM sing 453 n n 
#
_atom_sites.entry_id                     3KU9 
_atom_sites.fract_transf_matrix[1][1]    0.007196 
_atom_sites.fract_transf_matrix[1][2]    0.004155 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00831 
_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]    0.005269 
_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 3 FAD A 1 500 500 FAD FAD . 
E 4 NAG A 1 600 600 NAG NAG . 
F 5 SPM A 1 700 700 SPM SPM . 
G 3 FAD B 1 500 500 FAD FAD . 
H 5 SPM B 1 700 700 SPM SPM . 
I 6 CL B 1 479 1 CL CL . 
J 7 SO4 B 1 480 1 SO4 SO4 . 
K 8 HOH A 1 479 1 HOH HOH . 
K 8 HOH A 2 480 2 HOH HOH . 
K 8 HOH A 3 481 3 HOH HOH . 
K 8 HOH A 4 482 4 HOH HOH . 
K 8 HOH A 5 483 5 HOH HOH . 
K 8 HOH A 6 484 11 HOH HOH . 
K 8 HOH A 7 485 12 HOH HOH . 
K 8 HOH A 8 486 22 HOH HOH . 
K 8 HOH A 9 487 23 HOH HOH . 
K 8 HOH A 10 488 25 HOH HOH . 
K 8 HOH A 11 489 26 HOH HOH . 
K 8 HOH A 12 490 27 HOH HOH . 
K 8 HOH A 13 491 28 HOH HOH . 
K 8 HOH A 14 492 30 HOH HOH . 
K 8 HOH A 15 493 31 HOH HOH . 
K 8 HOH A 16 494 35 HOH HOH . 
K 8 HOH A 17 495 37 HOH HOH . 
K 8 HOH A 18 496 38 HOH HOH . 
K 8 HOH A 19 497 40 HOH HOH . 
K 8 HOH A 20 498 44 HOH HOH . 
K 8 HOH A 21 499 46 HOH HOH . 
K 8 HOH A 22 501 48 HOH HOH . 
K 8 HOH A 23 502 52 HOH HOH . 
K 8 HOH A 24 503 53 HOH HOH . 
L 8 HOH B 1 481 6 HOH HOH . 
L 8 HOH B 2 482 7 HOH HOH . 
L 8 HOH B 3 483 8 HOH HOH . 
L 8 HOH B 4 484 9 HOH HOH . 
L 8 HOH B 5 485 10 HOH HOH . 
L 8 HOH B 6 486 13 HOH HOH . 
L 8 HOH B 7 487 14 HOH HOH . 
L 8 HOH B 8 488 15 HOH HOH . 
L 8 HOH B 9 489 16 HOH HOH . 
L 8 HOH B 10 490 17 HOH HOH . 
L 8 HOH B 11 491 18 HOH HOH . 
L 8 HOH B 12 492 19 HOH HOH . 
L 8 HOH B 13 493 20 HOH HOH . 
L 8 HOH B 14 494 21 HOH HOH . 
L 8 HOH B 15 495 24 HOH HOH . 
L 8 HOH B 16 496 29 HOH HOH . 
L 8 HOH B 17 497 32 HOH HOH . 
L 8 HOH B 18 498 33 HOH HOH . 
L 8 HOH B 19 499 34 HOH HOH . 
L 8 HOH B 20 501 36 HOH HOH . 
L 8 HOH B 21 502 39 HOH HOH . 
L 8 HOH B 22 503 41 HOH HOH . 
L 8 HOH B 23 504 42 HOH HOH . 
L 8 HOH B 24 505 43 HOH HOH . 
L 8 HOH B 25 506 45 HOH HOH . 
L 8 HOH B 26 507 49 HOH HOH . 
L 8 HOH B 27 508 54 HOH HOH . 
L 8 HOH B 28 509 55 HOH HOH . 
L 8 HOH B 29 510 56 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 SPM . . . F 5 -61.317 31.225 35.847 1 33.85 ? N1 SPM 700 A 1 
HETATM 2 C C2 SPM . . . F 5 -61.239 31.033 34.418 1 34.63 ? C2 SPM 700 A 1 
HETATM 3 C C3 SPM . . . F 5 -59.818 30.684 34.046 1 34.81 ? C3 SPM 700 A 1 
HETATM 4 C C4 SPM . . . F 5 -59.775 30.17 32.633 1 35.92 ? C4 SPM 700 A 1 
HETATM 5 N N5 SPM . . . F 5 -59.241 31.202 31.798 1 37.58 ? N5 SPM 700 A 1 
HETATM 6 C C6 SPM . . . F 5 -58.762 30.923 30.474 1 38.97 ? C6 SPM 700 A 1 
HETATM 7 C C7 SPM . . . F 5 -59.178 32.053 29.558 1 40.35 ? C7 SPM 700 A 1 
HETATM 8 C C8 SPM . . . F 5 -58.25 33.237 29.715 1 42.04 ? C8 SPM 700 A 1 
HETATM 9 C C9 SPM . . . F 5 -58.332 34.137 28.503 1 43.99 ? C9 SPM 700 A 1 
HETATM 10 N N10 SPM . . . F 5 -59.304 35.194 28.66 1 45.78 ? N10 SPM 700 A 1 
HETATM 11 C C11 SPM . . . F 5 -58.908 36.437 29.285 1 46.64 ? C11 SPM 700 A 1 
HETATM 12 C C12 SPM . . . F 5 -58.594 37.537 28.282 1 47.22 ? C12 SPM 700 A 1 
HETATM 13 C C13 SPM . . . F 5 -58.07 38.798 28.953 1 46.89 ? C13 SPM 700 A 1 
HETATM 14 N N14 SPM . . . F 5 -59.157 39.629 29.428 1 46.74 ? N14 SPM 700 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           257 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           14 
#