data_8CVT
#
_model_server_result.job_id            jGIo_Z1ZoucgpHcQD9I6Lw 
_model_server_result.datetime_utc      '2025-09-12 16:23:45' 
_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          8cvt 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"DB","auth_seq_id":301}' 
#
_entry.id    8CVT 
#
_exptl.entry_id    8CVT 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              475.621 
_entity.id                          34 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-yl]-L-leucinamide 
_entity.pdbx_number_of_molecules    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    46-meric 
_pdbx_struct_assembly.oligomeric_count      46 
_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,AB,BB,CB,DB,EB 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 34 YA N N 
? 34 ZA N N 
? 34 AB N N 
? 34 CB N N 
? 34 DB N N 
? 34 EB N 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 H SG CYS 137 H CYS 137 1_555 H SG CYS 213 H CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
disulf ? disulf2 M SG CYS 42 M CYS 41 1_555 M SG CYS 187 M CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf3 U SG CYS 633 U CYS 633 1_555 U SG CYS 659 U CYS 659 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
disulf ? disulf4 MA SG CYS 42 m CYS 41 1_555 MA SG CYS 187 m CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
metalc ? metalc1 CA NE2 HIS 113 c HIS 113 1_555 BB ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
metalc ? metalc2 CA OD1 ASP 126 c ASP 126 1_555 BB ZN ZN . c ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? 
#
_chem_comp.formula           'C26 H41 N3 O5' 
_chem_comp.formula_weight    475.621 
_chem_comp.id                LDZ 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-yl]-L-leucinamide 
_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
C5 C4 LDZ doub 220 n y 
C5 C6 LDZ sing 221 n y 
C4 C3 LDZ sing 222 n y 
C6 C1 LDZ doub 223 n y 
C3 C7 LDZ sing 224 n n 
C3 C2 LDZ doub 225 n y 
C7 O8 LDZ sing 226 n n 
C1 C2 LDZ sing 227 n y 
O8 C9 LDZ sing 228 n n 
O31 C9 LDZ doub 229 n n 
C9 N10 LDZ sing 230 n n 
N10 C11 LDZ sing 231 n n 
C33 C31 LDZ sing 232 n n 
C31 C30 LDZ sing 233 n n 
C31 C32 LDZ sing 234 n n 
C11 C30 LDZ sing 235 n n 
C11 C12 LDZ sing 236 n n 
C27 C25 LDZ sing 237 n n 
C26 C25 LDZ sing 238 n n 
O32 C12 LDZ doub 239 n n 
C25 C24 LDZ sing 240 n n 
C12 N13 LDZ sing 241 n n 
N13 C14 LDZ sing 242 n n 
C24 C14 LDZ sing 243 n n 
C14 C15 LDZ sing 244 n n 
C15 O34 LDZ doub 245 n n 
C15 N16 LDZ sing 246 n n 
N16 C17 LDZ sing 247 n n 
C17 C22 LDZ sing 248 n n 
C17 C18 LDZ sing 249 n n 
O33 C22 LDZ doub 250 n n 
C19 C21 LDZ sing 251 n n 
C19 C18 LDZ sing 252 n n 
C19 C20 LDZ sing 253 n n 
C1 H1 LDZ sing 254 n n 
C2 H2 LDZ sing 255 n n 
C4 H3 LDZ sing 256 n n 
C5 H4 LDZ sing 257 n n 
C6 H5 LDZ sing 258 n n 
C7 H6 LDZ sing 259 n n 
C7 H7 LDZ sing 260 n n 
N10 H8 LDZ sing 261 n n 
C11 H9 LDZ sing 262 n n 
N13 H10 LDZ sing 263 n n 
C14 H11 LDZ sing 264 n n 
N16 H12 LDZ sing 265 n n 
C17 H13 LDZ sing 266 n n 
C18 H14 LDZ sing 267 n n 
C18 H15 LDZ sing 268 n n 
C19 H16 LDZ sing 269 n n 
C20 H17 LDZ sing 270 n n 
C20 H18 LDZ sing 271 n n 
C20 H19 LDZ sing 272 n n 
C21 H20 LDZ sing 273 n n 
C21 H21 LDZ sing 274 n n 
C21 H22 LDZ sing 275 n n 
C22 H23 LDZ sing 276 n n 
C24 H25 LDZ sing 277 n n 
C24 H26 LDZ sing 278 n n 
C25 H27 LDZ sing 279 n n 
C26 H28 LDZ sing 280 n n 
C26 H29 LDZ sing 281 n n 
C26 H30 LDZ sing 282 n n 
C27 H31 LDZ sing 283 n n 
C27 H32 LDZ sing 284 n n 
C27 H33 LDZ sing 285 n n 
C30 H34 LDZ sing 286 n n 
C30 H35 LDZ sing 287 n n 
C31 H36 LDZ sing 288 n n 
C32 H37 LDZ sing 289 n n 
C32 H38 LDZ sing 290 n n 
C32 H39 LDZ sing 291 n n 
C33 H40 LDZ sing 292 n n 
C33 H41 LDZ sing 293 n n 
C33 H42 LDZ sing 294 n n 
#
_atom_sites.entry_id                     8CVT 
_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
UA 33 ATP A 1 501 501 ATP ATP . 
VA 33 ATP C 1 501 501 ATP ATP . 
WA 33 ATP D 1 501 501 ATP ATP . 
XA 33 ATP F 1 501 501 ATP ATP . 
YA 34 LDZ N 1 301 1 LDZ MGG . 
ZA 34 LDZ O 1 301 1 LDZ MGG . 
AB 34 LDZ R 1 301 1 LDZ MGG . 
BB 35 ZN c 1 401 401 ZN ZN . 
CB 34 LDZ n 1 301 1 LDZ MGG . 
DB 34 LDZ o 1 301 1 LDZ MGG . 
EB 34 LDZ r 1 301 1 LDZ MGG . 
#
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 C4 LDZ . . . DB 34 199.253 182.737 88.891 1 0.5 ? C4 LDZ 301 o 1 
HETATM 2 C C5 LDZ . . . DB 34 198.034 183.34 88.624 1 0.5 ? C5 LDZ 301 o 1 
HETATM 3 C C6 LDZ . . . DB 34 196.939 182.57 88.273 1 0.5 ? C6 LDZ 301 o 1 
HETATM 4 C C1 LDZ . . . DB 34 197.066 181.195 88.196 1 0.5 ? C1 LDZ 301 o 1 
HETATM 5 C C2 LDZ . . . DB 34 198.284 180.591 88.462 1 0.5 ? C2 LDZ 301 o 1 
HETATM 6 C C3 LDZ . . . DB 34 199.381 181.361 88.807 1 0.5 ? C3 LDZ 301 o 1 
HETATM 7 C C7 LDZ . . . DB 34 200.724 180.696 89.106 1 0.5 ? C7 LDZ 301 o 1 
HETATM 8 O O8 LDZ . . . DB 34 201.722 181.299 88.332 1 0.5 ? O8 LDZ 301 o 1 
HETATM 9 C C9 LDZ . . . DB 34 202.047 180.612 87.157 1 0.5 ? C9 LDZ 301 o 1 
HETATM 10 O O31 LDZ . . . DB 34 201.324 179.774 86.741 1 0.5 ? O31 LDZ 301 o 1 
HETATM 11 N N10 LDZ . . . DB 34 203.284 180.912 86.46 1 0.5 ? N10 LDZ 301 o 1 
HETATM 12 C C11 LDZ . . . DB 34 204.541 180.692 87.146 1 0.5 ? C11 LDZ 301 o 1 
HETATM 13 C C12 LDZ . . . DB 34 204.849 181.897 88.001 1 0.5 ? C12 LDZ 301 o 1 
HETATM 14 O O32 LDZ . . . DB 34 205.487 181.738 88.98 1 0.5 ? O32 LDZ 301 o 1 
HETATM 15 C C30 LDZ . . . DB 34 205.684 180.585 86.144 1 0.5 ? C30 LDZ 301 o 1 
HETATM 16 C C31 LDZ . . . DB 34 206.631 179.452 86.518 1 0.5 ? C31 LDZ 301 o 1 
HETATM 17 C C32 LDZ . . . DB 34 207.261 178.806 85.289 1 0.5 ? C32 LDZ 301 o 1 
HETATM 18 C C33 LDZ . . . DB 34 205.919 178.417 87.376 1 0.5 ? C33 LDZ 301 o 1 
HETATM 19 N N13 LDZ . . . DB 34 204.356 183.189 87.57 1 0.5 ? N13 LDZ 301 o 1 
HETATM 20 C C14 LDZ . . . DB 34 204.615 184.415 88.292 1 0.5 ? C14 LDZ 301 o 1 
HETATM 21 C C15 LDZ . . . DB 34 206.088 184.758 88.137 1 0.5 ? C15 LDZ 301 o 1 
HETATM 22 O O34 LDZ . . . DB 34 206.93 184.189 88.741 1 0.5 ? O34 LDZ 301 o 1 
HETATM 23 C C24 LDZ . . . DB 34 204.206 184.399 89.761 1 0.5 ? C24 LDZ 301 o 1 
HETATM 24 C C25 LDZ . . . DB 34 204.542 185.725 90.431 1 0.5 ? C25 LDZ 301 o 1 
HETATM 25 C C26 LDZ . . . DB 34 204.594 185.574 91.946 1 0.5 ? C26 LDZ 301 o 1 
HETATM 26 C C27 LDZ . . . DB 34 203.561 186.815 90.005 1 0.5 ? C27 LDZ 301 o 1 
HETATM 27 N N16 LDZ . . . DB 34 206.452 185.801 87.213 1 0.5 ? N16 LDZ 301 o 1 
HETATM 28 C C17 LDZ . . . DB 34 207.84 186.145 87.06 1 0.5 ? C17 LDZ 301 o 1 
HETATM 29 C C22 LDZ . . . DB 34 208.179 187.013 88.258 1 0.5 ? C22 LDZ 301 o 1 
HETATM 30 C C18 LDZ . . . DB 34 207.963 186.997 85.808 1 0.5 ? C18 LDZ 301 o 1 
HETATM 31 C C19 LDZ . . . DB 34 207.679 186.162 84.58 1 0.5 ? C19 LDZ 301 o 1 
HETATM 32 C C20 LDZ . . . DB 34 207.903 186.935 83.289 1 0.5 ? C20 LDZ 301 o 1 
HETATM 33 C C21 LDZ . . . DB 34 208.489 184.878 84.629 1 0.5 ? C21 LDZ 301 o 1 
HETATM 34 O O33 LDZ . . . DB 34 207.514 187.972 88.453 1 0.5 ? O33 LDZ 301 o 1 
#
_model_server_stats.io_time_ms              83 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    114 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           34 
#