data_5CSE
#
_model_server_result.job_id            n4oouQ3psD2XbFIVyC0QYg 
_model_server_result.datetime_utc      '2025-09-14 00:55:13' 
_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          5cse 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":201}' 
#
_entry.id    5CSE 
#
_exptl.entry_id    5CSE 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              673.606 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            chloro{di-tert-butyl[2-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)ethyl]-lambda~5~-phosphanyl}(1-phenylprop-1-ene-1,3-diyl-kappa~2~C~1~,C~3~)palladium 
_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            5CSE 
_cell.length_a            81.368 
_cell.length_b            81.46 
_cell.length_c            90.811 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5CSE 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA tetrameric 4 software_defined_assembly 1 
PISA dimeric 2 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H 1 1,2 
A,B,C,D,E,F,G,H 2 1 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 3_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 45.4055 
#
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 E N N 
#
_chem_comp.formula           'C29 H46 Cl N3 O2 P Pd S' 
_chem_comp.formula_weight    673.606 
_chem_comp.id                SVP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              chloro{di-tert-butyl[2-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)ethyl]-lambda~5~-phosphanyl}(1-phenylprop-1-ene-1,3-diyl-kappa~2~C~1~,C~3~)palladium 
_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
N35 C36 SVP sing 277 n n 
N35 C33 SVP sing 278 n n 
C37 C36 SVP sing 279 n n 
C37 S38 SVP sing 280 n n 
O34 C33 SVP doub 281 n n 
C36 C31 SVP sing 282 n n 
C33 N32 SVP sing 283 n n 
S38 C01 SVP sing 284 n n 
N32 C31 SVP sing 285 n n 
C31 C01 SVP sing 286 n n 
C01 C02 SVP sing 287 n n 
C02 C03 SVP sing 288 n n 
C03 C04 SVP sing 289 n n 
C04 C05 SVP sing 290 n n 
C05 C06 SVP sing 291 n n 
C29 C27 SVP sing 292 n n 
C28 C27 SVP sing 293 n n 
C06 N08 SVP sing 294 n n 
C06 O07 SVP doub 295 n n 
N08 C09 SVP sing 296 n n 
C10 C09 SVP sing 297 n n 
C10 P11 SVP sing 298 n n 
C27 C30 SVP sing 299 n n 
C27 P11 SVP sing 300 n n 
P11 C23 SVP sing 301 n n 
P11 PD SVP sing 302 n n 
C25 C23 SVP sing 303 n n 
C23 C26 SVP sing 304 n n 
C23 C24 SVP sing 305 n n 
PD CL SVP sing 306 n n 
C01 H1 SVP sing 307 n n 
C02 H2 SVP sing 308 n n 
C02 H3 SVP sing 309 n n 
C03 H4 SVP sing 310 n n 
C03 H5 SVP sing 311 n n 
C04 H6 SVP sing 312 n n 
C04 H7 SVP sing 313 n n 
C05 H8 SVP sing 314 n n 
C05 H9 SVP sing 315 n n 
N08 H10 SVP sing 316 n n 
C09 H11 SVP sing 317 n n 
C09 H12 SVP sing 318 n n 
C10 H13 SVP sing 319 n n 
C10 H14 SVP sing 320 n n 
C24 H15 SVP sing 321 n n 
C24 H16 SVP sing 322 n n 
C24 H17 SVP sing 323 n n 
C25 H18 SVP sing 324 n n 
C25 H19 SVP sing 325 n n 
C25 H20 SVP sing 326 n n 
C26 H21 SVP sing 327 n n 
C26 H22 SVP sing 328 n n 
C26 H23 SVP sing 329 n n 
C28 H24 SVP sing 330 n n 
C28 H25 SVP sing 331 n n 
C28 H26 SVP sing 332 n n 
C29 H27 SVP sing 333 n n 
C29 H28 SVP sing 334 n n 
C29 H29 SVP sing 335 n n 
C30 H30 SVP sing 336 n n 
C30 H31 SVP sing 337 n n 
C30 H32 SVP sing 338 n n 
C31 H33 SVP sing 339 n n 
N32 H34 SVP sing 340 n n 
N35 H35 SVP sing 341 n n 
C36 H36 SVP sing 342 n n 
C37 H37 SVP sing 343 n n 
C37 H38 SVP sing 344 n n 
C1 C2 SVP sing 345 n n 
C2 C3 SVP doub 346 n n 
C3 C4 SVP sing 347 n n 
C4 C5 SVP doub 348 n y 
C4 C6 SVP sing 349 n y 
C6 C11 SVP doub 350 n y 
C5 C8 SVP sing 351 n y 
C8 C9 SVP doub 352 n y 
C9 C11 SVP sing 353 n y 
PD C1 SVP sing 354 n n 
PD C3 SVP sing 355 n n 
C1 H39 SVP sing 356 n n 
C1 H40 SVP sing 357 n n 
C2 H41 SVP sing 358 n n 
C5 H42 SVP sing 359 n n 
C6 H43 SVP sing 360 n n 
C8 H44 SVP sing 361 n n 
C9 H45 SVP sing 362 n n 
C11 H46 SVP sing 363 n n 
#
_atom_sites.entry_id                     5CSE 
_atom_sites.fract_transf_matrix[1][1]    0.01229 
_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]    0.012276 
_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]    0.011012 
_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 SVP A 1 201 1000 SVP SVP . 
D 3 CL A 1 202 2 CL CL . 
E 2 SVP B 1 201 1000 SVP SVP . 
F 3 CL B 1 202 1 CL CL . 
G 4 HOH A 1 301 52 HOH HOH . 
G 4 HOH A 2 302 15 HOH HOH . 
G 4 HOH A 3 303 18 HOH HOH . 
G 4 HOH A 4 304 33 HOH HOH . 
G 4 HOH A 5 305 41 HOH HOH . 
G 4 HOH A 6 306 39 HOH HOH . 
G 4 HOH A 7 307 25 HOH HOH . 
G 4 HOH A 8 308 1 HOH HOH . 
G 4 HOH A 9 309 2 HOH HOH . 
G 4 HOH A 10 310 14 HOH HOH . 
G 4 HOH A 11 311 10 HOH HOH . 
G 4 HOH A 12 312 6 HOH HOH . 
G 4 HOH A 13 313 11 HOH HOH . 
G 4 HOH A 14 314 40 HOH HOH . 
G 4 HOH A 15 315 30 HOH HOH . 
G 4 HOH A 16 316 3 HOH HOH . 
G 4 HOH A 17 317 34 HOH HOH . 
G 4 HOH A 18 318 31 HOH HOH . 
G 4 HOH A 19 319 44 HOH HOH . 
G 4 HOH A 20 320 50 HOH HOH . 
G 4 HOH A 21 321 5 HOH HOH . 
G 4 HOH A 22 322 29 HOH HOH . 
H 4 HOH B 1 301 37 HOH HOH . 
H 4 HOH B 2 302 12 HOH HOH . 
H 4 HOH B 3 303 42 HOH HOH . 
H 4 HOH B 4 304 36 HOH HOH . 
H 4 HOH B 5 305 20 HOH HOH . 
H 4 HOH B 6 306 46 HOH HOH . 
H 4 HOH B 7 307 35 HOH HOH . 
H 4 HOH B 8 308 45 HOH HOH . 
H 4 HOH B 9 309 8 HOH HOH . 
H 4 HOH B 10 310 9 HOH HOH . 
H 4 HOH B 11 311 28 HOH HOH . 
H 4 HOH B 12 312 22 HOH HOH . 
H 4 HOH B 13 313 21 HOH HOH . 
H 4 HOH B 14 314 53 HOH HOH . 
H 4 HOH B 15 315 7 HOH HOH . 
H 4 HOH B 16 316 4 HOH HOH . 
H 4 HOH B 17 317 13 HOH HOH . 
H 4 HOH B 18 318 43 HOH HOH . 
H 4 HOH B 19 319 48 HOH HOH . 
H 4 HOH B 20 320 55 HOH HOH . 
H 4 HOH B 21 321 47 HOH HOH . 
H 4 HOH B 22 322 24 HOH HOH . 
H 4 HOH B 23 323 38 HOH HOH . 
H 4 HOH B 24 324 51 HOH HOH . 
H 4 HOH B 25 325 23 HOH HOH . 
H 4 HOH B 26 326 49 HOH HOH . 
H 4 HOH B 27 327 54 HOH HOH . 
H 4 HOH B 28 328 19 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 C01 SVP . . . E 2 8.387 -1.319 12.639 1 15.3 ? C01 SVP 201 B 1 
HETATM 2 C C02 SVP . . . E 2 9.325 -1.318 11.41 1 19.36 ? C02 SVP 201 B 1 
HETATM 3 C C03 SVP . . . E 2 9.463 0.081 10.767 1 20.5 ? C03 SVP 201 B 1 
HETATM 4 C C04 SVP . . . E 2 10.603 0.144 9.731 1 18.53 ? C04 SVP 201 B 1 
HETATM 5 C C05 SVP . . . E 2 10.677 1.54 9.077 1 23.18 ? C05 SVP 201 B 1 
HETATM 6 C C06 SVP . . . E 2 9.486 1.855 8.196 1 31.28 ? C06 SVP 201 B 1 
HETATM 7 O O07 SVP . . . E 2 8.833 1 7.624 1 27.36 ? O07 SVP 201 B 1 
HETATM 8 N N08 SVP . . . E 2 9.208 3.178 8.112 1 30.4 ? N08 SVP 201 B 1 
HETATM 9 C C09 SVP . . . E 2 8.121 3.773 7.325 1 33.91 ? C09 SVP 201 B 1 
HETATM 10 C C10 SVP . . . E 2 6.711 3.324 7.77 1 33.36 ? C10 SVP 201 B 1 
HETATM 11 P P11 SVP . . . E 2 5.382 3.638 6.545 1 65.35 ? P11 SVP 201 B 1 
HETATM 12 PD PD SVP . . . E 2 5.858 5.434 5.144 1 53.43 ? PD SVP 201 B 1 
HETATM 13 CL CL SVP . . . E 2 5.177 4.826 2.953 1 81.02 ? CL SVP 201 B 1 
HETATM 14 C C23 SVP . . . E 2 5.47 2.18 5.396 1 51.2 ? C23 SVP 201 B 1 
HETATM 15 C C24 SVP . . . E 2 6.687 2.303 4.443 1 59.91 ? C24 SVP 201 B 1 
HETATM 16 C C25 SVP . . . E 2 5.689 0.859 6.175 1 46.27 ? C25 SVP 201 B 1 
HETATM 17 C C26 SVP . . . E 2 4.223 2.009 4.496 1 53.25 ? C26 SVP 201 B 1 
HETATM 18 C C27 SVP . . . E 2 3.787 3.896 7.45 1 57.81 ? C27 SVP 201 B 1 
HETATM 19 C C28 SVP . . . E 2 2.77 4.537 6.469 1 41.52 ? C28 SVP 201 B 1 
HETATM 20 C C29 SVP . . . E 2 3.119 2.608 7.987 1 54.19 ? C29 SVP 201 B 1 
HETATM 21 C C30 SVP . . . E 2 3.981 4.875 8.64 1 39.06 ? C30 SVP 201 B 1 
HETATM 22 C C31 SVP . . . E 2 7.934 -2.727 13.073 1 21.98 ? C31 SVP 201 B 1 
HETATM 23 N N32 SVP . . . E 2 9.006 -3.726 13.165 1 27.65 ? N32 SVP 201 B 1 
HETATM 24 C C33 SVP . . . E 2 9.176 -4.254 14.396 1 25.83 ? C33 SVP 201 B 1 
HETATM 25 O O34 SVP . . . E 2 10.002 -5.107 14.718 1 17.81 ? O34 SVP 201 B 1 
HETATM 26 N N35 SVP . . . E 2 8.267 -3.652 15.201 1 23.32 ? N35 SVP 201 B 1 
HETATM 27 C C36 SVP . . . E 2 7.426 -2.653 14.536 1 22.93 ? C36 SVP 201 B 1 
HETATM 28 C C37 SVP . . . E 2 7.695 -1.208 15.028 1 14.85 ? C37 SVP 201 B 1 
HETATM 29 S S38 SVP . . . E 2 9.118 -0.576 14.111 1 17.13 ? S38 SVP 201 B 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           358 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           29 
#