data_7ZK5
#
_model_server_result.job_id            bBzmy0n19stdQ627tLabEA 
_model_server_result.datetime_utc      '2025-09-18 04:52:29' 
_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          7zk5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":2010}' 
#
_entry.id    7ZK5 
#
_exptl.entry_id    7ZK5 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              494.634 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4~{S},11~{S},18~{S})-4,11-dimethyl-18-(sulfanylmethyl)-6,13,20-trithia-3,10,17,22,23,24-hexazatetracyclo[17.2.1.1^{5,8}.1^{12,15}]tetracosa-1(21),5(24),7,12(23),14,19(22)-hexaene-2,9,16-trione 
_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            7ZK5 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7ZK5 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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                      5 
_struct_asym.id                             K 
_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
covale ? covale1 A SG CYS 335 A CYS 335 1_555 K S04 JIZ . A JIZ 2010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
metalc ? metalc1 A OG SER 430 A SER 430 1_555 C MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc2 A OE1 GLN 471 A GLN 471 1_555 C MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc3 A OG SER 1073 A SER 1073 1_555 E MG MG . A MG 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
metalc ? metalc4 A OE1 GLN 1114 A GLN 1114 1_555 E MG MG . A MG 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? 
metalc ? metalc5 B O1G ATP . A ATP 2001 1_555 C MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? 
metalc ? metalc6 B O2B ATP . A ATP 2001 1_555 C MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? 
metalc ? metalc7 C MG MG . A MG 2002 1_555 L O HOH . A HOH 2107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc8 C MG MG . A MG 2002 1_555 L O HOH . A HOH 2111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc9 D O2G ATP . A ATP 2003 1_555 E MG MG . A MG 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? 
metalc ? metalc10 D O2B ATP . A ATP 2003 1_555 E MG MG . A MG 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? 
metalc ? metalc11 E MG MG . A MG 2004 1_555 L O HOH . A HOH 2104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
metalc ? metalc12 E MG MG . A MG 2004 1_555 L O HOH . A HOH 2109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
#
_chem_comp.formula           'C18 H18 N6 O3 S4' 
_chem_comp.formula_weight    494.634 
_chem_comp.id                JIZ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (4~{S},11~{S},18~{S})-4,11-dimethyl-18-(sulfanylmethyl)-6,13,20-trithia-3,10,17,22,23,24-hexazatetracyclo[17.2.1.1^{5,8}.1^{12,15}]tetracosa-1(21),5(24),7,12(23),14,19(22)-hexaene-2,9,16-trione 
_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
S03 C14 JIZ sing 222 n y 
S03 C12 JIZ sing 223 n y 
C17 C11 JIZ sing 224 n n 
C14 C13 JIZ doub 225 n y 
C11 C12 JIZ sing 226 n n 
C11 N05 JIZ sing 227 n n 
C12 N06 JIZ doub 228 n y 
O02 C10 JIZ doub 229 n n 
N05 C10 JIZ sing 230 n n 
C13 N06 JIZ sing 231 n y 
C13 C15 JIZ sing 232 n n 
C10 C08 JIZ sing 233 n n 
O03 C15 JIZ doub 234 n n 
C15 N01 JIZ sing 235 n n 
C08 C09 JIZ doub 236 n y 
C08 N04 JIZ sing 237 n y 
C09 S02 JIZ sing 238 n y 
N01 C01 JIZ sing 239 n n 
N04 C07 JIZ doub 240 n y 
S02 C07 JIZ sing 241 n y 
S04 C18 JIZ sing 242 n n 
C01 C18 JIZ sing 243 n n 
C01 C02 JIZ sing 244 n n 
C07 C06 JIZ sing 245 n n 
N02 C02 JIZ doub 246 n y 
N02 C03 JIZ sing 247 n y 
C02 S01 JIZ sing 248 n y 
N03 C06 JIZ sing 249 n n 
N03 C05 JIZ sing 250 n n 
C06 C16 JIZ sing 251 n n 
C03 C05 JIZ sing 252 n n 
C03 C04 JIZ doub 253 n y 
S01 C04 JIZ sing 254 n y 
C05 O01 JIZ doub 255 n n 
C17 H1 JIZ sing 256 n n 
C17 H2 JIZ sing 257 n n 
C17 H3 JIZ sing 258 n n 
C01 H4 JIZ sing 259 n n 
C04 H5 JIZ sing 260 n n 
C06 H6 JIZ sing 261 n n 
C09 H7 JIZ sing 262 n n 
C11 H8 JIZ sing 263 n n 
C14 H9 JIZ sing 264 n n 
C16 H11 JIZ sing 265 n n 
C16 H12 JIZ sing 266 n n 
C18 H13 JIZ sing 267 n n 
C18 H14 JIZ sing 268 n n 
N01 H15 JIZ sing 269 n n 
N03 H16 JIZ sing 270 n n 
N05 H17 JIZ sing 271 n n 
S04 H18 JIZ sing 272 n n 
C16 H10 JIZ sing 273 n n 
#
_atom_sites.entry_id                     7ZK5 
_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
B 2 ATP A 1 2001 2001 ATP ATP . 
C 3 MG A 1 2002 2002 MG MG . 
D 2 ATP A 1 2003 2005 ATP ATP . 
E 3 MG A 1 2004 2006 MG MG . 
F 4 Y01 A 1 2005 2013 Y01 Y01 . 
G 4 Y01 A 1 2006 2014 Y01 Y01 . 
H 4 Y01 A 1 2007 2015 Y01 Y01 . 
I 4 Y01 A 1 2008 2017 Y01 Y01 . 
J 4 Y01 A 1 2009 2018 Y01 Y01 . 
K 5 JIZ A 1 2010 2000 JIZ LIG . 
L 6 HOH A 1 2101 2031 HOH HOH . 
L 6 HOH A 2 2102 2022 HOH HOH . 
L 6 HOH A 3 2103 2019 HOH HOH . 
L 6 HOH A 4 2104 2007 HOH HOH . 
L 6 HOH A 5 2105 2034 HOH HOH . 
L 6 HOH A 6 2106 2024 HOH HOH . 
L 6 HOH A 7 2107 2004 HOH HOH . 
L 6 HOH A 8 2108 2038 HOH HOH . 
L 6 HOH A 9 2109 2008 HOH HOH . 
L 6 HOH A 10 2110 2010 HOH HOH . 
L 6 HOH A 11 2111 2003 HOH HOH . 
L 6 HOH A 12 2112 2015 HOH HOH . 
L 6 HOH A 13 2113 2017 HOH HOH . 
L 6 HOH A 14 2114 2033 HOH HOH . 
L 6 HOH A 15 2115 2028 HOH HOH . 
L 6 HOH A 16 2116 2012 HOH HOH . 
L 6 HOH A 17 2117 2029 HOH HOH . 
L 6 HOH A 18 2118 2023 HOH HOH . 
L 6 HOH A 19 2119 2037 HOH HOH . 
L 6 HOH A 20 2120 2032 HOH HOH . 
L 6 HOH A 21 2121 2014 HOH HOH . 
L 6 HOH A 22 2122 2026 HOH HOH . 
L 6 HOH A 23 2123 2036 HOH HOH . 
L 6 HOH A 24 2124 2021 HOH HOH . 
L 6 HOH A 25 2125 2016 HOH HOH . 
L 6 HOH A 26 2126 2018 HOH HOH . 
L 6 HOH A 27 2127 2027 HOH HOH . 
L 6 HOH A 28 2128 2030 HOH HOH . 
L 6 HOH A 29 2129 2013 HOH HOH . 
L 6 HOH A 30 2130 2020 HOH HOH . 
L 6 HOH A 31 2131 2025 HOH HOH . 
L 6 HOH A 32 2132 2009 HOH HOH . 
L 6 HOH A 33 2133 2035 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 C C10 JIZ . . . K 5 117.622 123.383 138.303 1 48.38 ? C10 JIZ 2010 A 1 
HETATM 2 C C13 JIZ . . . K 5 120.432 118.577 138.133 1 48.38 ? C13 JIZ 2010 A 1 
HETATM 3 C C15 JIZ . . . K 5 120.701 117.599 139.275 1 48.38 ? C15 JIZ 2010 A 1 
HETATM 4 C C17 JIZ . . . K 5 120.469 123.047 136.363 1 48.38 ? C17 JIZ 2010 A 1 
HETATM 5 C C01 JIZ . . . K 5 120.964 117.257 141.792 1 48.38 ? C01 JIZ 2010 A 1 
HETATM 6 C C02 JIZ . . . K 5 120.251 117.921 142.967 1 48.38 ? C02 JIZ 2010 A 1 
HETATM 7 C C03 JIZ . . . K 5 118.898 119.452 144.264 1 48.38 ? C03 JIZ 2010 A 1 
HETATM 8 C C04 JIZ . . . K 5 119.414 118.42 145.251 1 48.38 ? C04 JIZ 2010 A 1 
HETATM 9 C C05 JIZ . . . K 5 117.998 120.657 144.535 1 48.38 ? C05 JIZ 2010 A 1 
HETATM 10 C C06 JIZ . . . K 5 117.085 122.861 143.601 1 48.38 ? C06 JIZ 2010 A 1 
HETATM 11 C C07 JIZ . . . K 5 116.96 123.42 142.187 1 48.38 ? C07 JIZ 2010 A 1 
HETATM 12 C C08 JIZ . . . K 5 117.176 123.713 139.727 1 48.38 ? C08 JIZ 2010 A 1 
HETATM 13 C C09 JIZ . . . K 5 116.373 124.847 140.17 1 48.38 ? C09 JIZ 2010 A 1 
HETATM 14 C C11 JIZ . . . K 5 119.321 122.159 136.833 1 48.38 ? C11 JIZ 2010 A 1 
HETATM 15 C C12 JIZ . . . K 5 119.782 120.718 137.041 1 48.38 ? C12 JIZ 2010 A 1 
HETATM 16 C C14 JIZ . . . K 5 120.542 118.323 136.699 1 48.38 ? C14 JIZ 2010 A 1 
HETATM 17 C C16 JIZ . . . K 5 117.767 123.881 144.509 1 48.38 ? C16 JIZ 2010 A 1 
HETATM 18 C C18 JIZ . . . K 5 122.45 117.076 142.102 1 48.38 ? C18 JIZ 2010 A 1 
HETATM 19 N N01 JIZ . . . K 5 120.739 118.108 140.636 1 48.38 ? N01 JIZ 2010 A 1 
HETATM 20 N N02 JIZ . . . K 5 119.495 119.049 142.792 1 48.38 ? N02 JIZ 2010 A 1 
HETATM 21 N N03 JIZ . . . K 5 117.901 121.666 143.494 1 48.38 ? N03 JIZ 2010 A 1 
HETATM 22 N N04 JIZ . . . K 5 117.54 122.816 141.022 1 48.38 ? N04 JIZ 2010 A 1 
HETATM 23 N N05 JIZ . . . K 5 118.81 122.566 138.13 1 48.38 ? N05 JIZ 2010 A 1 
HETATM 24 N N06 JIZ . . . K 5 119.937 120.103 138.331 1 48.38 ? N06 JIZ 2010 A 1 
HETATM 25 O O01 JIZ . . . K 5 117.401 120.762 145.553 1 48.38 ? O01 JIZ 2010 A 1 
HETATM 26 O O02 JIZ . . . K 5 117.015 123.778 137.367 1 48.38 ? O02 JIZ 2010 A 1 
HETATM 27 O O03 JIZ . . . K 5 120.866 116.446 139.055 1 48.38 ? O03 JIZ 2010 A 1 
HETATM 28 S S01 JIZ . . . K 5 120.299 117.409 144.425 1 48.38 ? S01 JIZ 2010 A 1 
HETATM 29 S S02 JIZ . . . K 5 116.195 124.731 141.72 1 48.38 ? S02 JIZ 2010 A 1 
HETATM 30 S S03 JIZ . . . K 5 120.149 119.633 135.939 1 48.38 ? S03 JIZ 2010 A 1 
HETATM 31 S S04 JIZ . . . K 5 123.4 118.577 141.724 1 48.38 ? S04 JIZ 2010 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           346 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           31 
#