data_8SS6
#
_model_server_result.job_id            hILG5_ksa_gQAru_RTBWKw 
_model_server_result.datetime_utc      '2024-11-25 21:51:35' 
_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          8ss6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"KA","auth_seq_id":1111}' 
#
_entry.id    8SS6 
#
_exptl.entry_id    8SS6 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              145.246 
_entity.id                          8 
_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            8SS6 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8SS6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA 
_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    ? 
_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                      8 
_struct_asym.id                             KA 
_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 54 A CYS 63 1_555 A SG CYS 306 A CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
disulf ? disulf2 A SG CYS 580 A CYS 589 1_555 D SG CYS 580 D CYS 589 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
disulf ? disulf3 A SG CYS 709 A CYS 718 1_555 A SG CYS 764 A CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf4 A SG CYS 881 A CYS 890 1_555 A SG CYS 891 A CYS 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf5 B SG CYS 54 B CYS 63 1_555 B SG CYS 306 B CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf6 B SG CYS 580 B CYS 589 1_555 C SG CYS 580 C CYS 589 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? 
disulf ? disulf7 B SG CYS 709 B CYS 718 1_555 B SG CYS 764 B CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf8 C SG CYS 54 C CYS 63 1_555 C SG CYS 306 C CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf9 C SG CYS 709 C CYS 718 1_555 C SG CYS 764 C CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf10 C SG CYS 881 C CYS 890 1_555 C SG CYS 891 C CYS 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf11 D SG CYS 54 D CYS 63 1_555 D SG CYS 306 D CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf12 D SG CYS 709 D CYS 718 1_555 D SG CYS 764 D CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
#
_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 548 n n 
N1 HN11 SPD sing 549 n n 
N1 HN12 SPD sing 550 n n 
C2 C3 SPD sing 551 n n 
C2 H21 SPD sing 552 n n 
C2 H22 SPD sing 553 n n 
C3 C4 SPD sing 554 n n 
C3 H31 SPD sing 555 n n 
C3 H32 SPD sing 556 n n 
C4 C5 SPD sing 557 n n 
C4 H41 SPD sing 558 n n 
C4 H42 SPD sing 559 n n 
C5 N6 SPD sing 560 n n 
C5 H51 SPD sing 561 n n 
C5 H52 SPD sing 562 n n 
N6 C7 SPD sing 563 n n 
N6 HN6 SPD sing 564 n n 
C7 C8 SPD sing 565 n n 
C7 H71 SPD sing 566 n n 
C7 H72 SPD sing 567 n n 
C8 C9 SPD sing 568 n n 
C8 H81 SPD sing 569 n n 
C8 H82 SPD sing 570 n n 
C9 N10 SPD sing 571 n n 
C9 H91 SPD sing 572 n n 
C9 H92 SPD sing 573 n n 
N10 H101 SPD sing 574 n n 
N10 H102 SPD sing 575 n n 
#
_atom_sites.entry_id                     8SS6 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 3 6ZP A 1 1101 1100 6ZP 6ZP . 
H 4 ZK1 A 1 1102 1101 ZK1 ZK1 . 
I 5 PCW A 1 1103 1102 PCW PCW . 
J 5 PCW A 1 1104 1103 PCW PCW . 
K 5 PCW A 1 1105 1105 PCW PCW . 
L 5 PCW A 1 1106 1106 PCW PCW . 
M 6 CLR A 1 1107 1108 CLR CLR . 
N 6 CLR A 1 1108 1109 CLR CLR . 
O 5 PCW A 1 1109 1104 PCW PCW . 
P 5 PCW A 1 1110 1110 PCW PCW . 
Q 7 NA A 1 1111 1 NA NA . 
R 3 6ZP B 1 1101 1100 6ZP 6ZP . 
S 4 ZK1 B 1 1102 1101 ZK1 ZK1 . 
T 5 PCW B 1 1103 1102 PCW PCW . 
U 5 PCW B 1 1104 1105 PCW PCW . 
V 5 PCW B 1 1105 1106 PCW PCW . 
W 5 PCW B 1 1106 1107 PCW PCW . 
X 6 CLR B 1 1107 1108 CLR CLR . 
Y 6 CLR B 1 1108 1109 CLR CLR . 
Z 5 PCW B 1 1109 1104 PCW PCW . 
AA 3 6ZP C 1 1101 1100 6ZP 6ZP . 
BA 4 ZK1 C 1 1102 1101 ZK1 ZK1 . 
CA 5 PCW C 1 1103 1102 PCW PCW . 
DA 5 PCW C 1 1104 1103 PCW PCW . 
EA 5 PCW C 1 1105 1105 PCW PCW . 
FA 5 PCW C 1 1106 1106 PCW PCW . 
GA 6 CLR C 1 1107 1108 CLR CLR . 
HA 6 CLR C 1 1108 1109 CLR CLR . 
IA 5 PCW C 1 1109 1104 PCW PCW . 
JA 5 PCW C 1 1110 1110 PCW PCW . 
KA 8 SPD C 1 1111 2 SPD SPD . 
LA 5 PCW D 1 1101 1104 PCW PCW . 
MA 3 6ZP D 1 1102 1100 6ZP 6ZP . 
NA 4 ZK1 D 1 1103 1101 ZK1 ZK1 . 
OA 5 PCW D 1 1104 1102 PCW PCW . 
PA 5 PCW D 1 1105 1105 PCW PCW . 
QA 5 PCW D 1 1106 1106 PCW PCW . 
RA 5 PCW D 1 1107 1107 PCW PCW . 
SA 6 CLR D 1 1108 1108 CLR CLR . 
TA 6 CLR D 1 1109 1109 CLR CLR . 
UA 5 PCW E 1 201 1107 PCW PCW . 
VA 5 PCW E 1 202 1110 PCW PCW . 
WA 5 PCW E 1 203 1103 PCW PCW . 
XA 5 PCW F 1 201 1103 PCW PCW . 
YA 5 PCW F 1 202 1107 PCW PCW . 
ZA 5 PCW F 1 203 1110 PCW PCW . 
#
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 . . . KA 8 192.19 192.184 145.594 1 0 ? N1 SPD 1111 C 1 
HETATM 2 C C2 SPD . . . KA 8 192.73 192.799 146.793 1 0 ? C2 SPD 1111 C 1 
HETATM 3 C C3 SPD . . . KA 8 192.15 192.143 148.044 1 0 ? C3 SPD 1111 C 1 
HETATM 4 C C4 SPD . . . KA 8 192.803 192.68 149.316 1 0 ? C4 SPD 1111 C 1 
HETATM 5 C C5 SPD . . . KA 8 192.108 192.197 150.585 1 0 ? C5 SPD 1111 C 1 
HETATM 6 N N6 SPD . . . KA 8 192.597 192.926 151.74 1 0 ? N6 SPD 1111 C 1 
HETATM 7 C C7 SPD . . . KA 8 192.419 192.094 152.91 1 0 ? C7 SPD 1111 C 1 
HETATM 8 C C8 SPD . . . KA 8 192.583 192.89 154.196 1 0 ? C8 SPD 1111 C 1 
HETATM 9 C C9 SPD . . . KA 8 192.251 192.042 155.419 1 0 ? C9 SPD 1111 C 1 
HETATM 10 N N10 SPD . . . KA 8 192.586 192.752 156.637 1 0 ? N10 SPD 1111 C 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    62 
_model_server_stats.query_time_ms           280 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           10 
#