data_3VSW
#
_model_server_result.job_id            5PDJWwvyOQ3F5_mLhl3nAg 
_model_server_result.datetime_utc      '2024-11-22 05:02:45' 
_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          3vsw 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":402}' 
#
_entry.id    3VSW 
#
_exptl.entry_id    3VSW 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              549.703 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (2S,4S,5S)-5-amino-N-(3-amino-2,2-dimethyl-3-oxopropyl)-4-hydroxy-6-{4-[2-(3-methoxypropoxy)phenyl]-3-oxopiperazin-1-yl}-2-(propan-2-yl)hexanamide 
_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            3VSW 
_cell.length_a            140.762 
_cell.length_b            140.762 
_cell.length_c            140.762 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VSW 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        198 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 3' 
#
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 hexameric 6 software_defined_assembly 3 
PISA trimeric 3 software_defined_assembly 4 
PISA trimeric 3 software_defined_assembly 5 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D 1 1 
B,E,F 2 1 
A,B,C,D,E,F 3 1,2,3 
A,C,D 4 1,2,3 
B,E,F 5 1,2,3 
#
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' 6_577 z+1/2,-x+5/2,-y+2 0 0 1 -1 0 0 0 -1 0 70.381 351.905 281.524 
3 'crystal symmetry operation' 12_774 -y+5/2,-z+2,x-1/2 0 -1 0 0 0 -1 1 0 0 351.905 281.524 -70.381 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 F 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 A SG CYS 51 A CYS 51 1_555 A SG CYS 58 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? 
disulf ? disulf2 A SG CYS 217 A CYS 217 1_555 A SG CYS 221 A CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? 
disulf ? disulf3 A SG CYS 259 A CYS 259 1_555 A SG CYS 296 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? 
disulf ? disulf4 B SG CYS 51 B CYS 51 1_555 B SG CYS 58 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? 
disulf ? disulf5 B SG CYS 217 B CYS 217 1_555 B SG CYS 221 B CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? 
disulf ? disulf6 B SG CYS 259 B CYS 259 1_555 B SG CYS 296 B CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? 
covale ? covale1 A ND2 ASN 75 A ASN 75 1_555 C C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? 
covale ? covale2 B ND2 ASN 75 B ASN 75 1_555 E C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? 
#
_chem_comp.formula           'C28 H47 N5 O6' 
_chem_comp.formula_weight    549.703 
_chem_comp.id                R31 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (2S,4S,5S)-5-amino-N-(3-amino-2,2-dimethyl-3-oxopropyl)-4-hydroxy-6-{4-[2-(3-methoxypropoxy)phenyl]-3-oxopiperazin-1-yl}-2-(propan-2-yl)hexanamide 
_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
C18 O17 R31 sing 305 n n 
O17 C16 R31 sing 306 n n 
C16 C15 R31 sing 307 n n 
C14 C15 R31 sing 308 n n 
C14 O13 R31 sing 309 n n 
C9 C10 R31 doub 310 n y 
C9 C8 R31 sing 311 n y 
C10 C11 R31 sing 312 n y 
O13 C8 R31 sing 313 n n 
C8 C7 R31 doub 314 n y 
C11 C12 R31 doub 315 n y 
C12 C7 R31 sing 316 n y 
C7 N5 R31 sing 317 n n 
C4 N5 R31 sing 318 n n 
C4 C3 R31 sing 319 n n 
N5 C6 R31 sing 320 n n 
C3 N2 R31 sing 321 n n 
C6 O39 R31 doub 322 n n 
C6 C1 R31 sing 323 n n 
N2 C1 R31 sing 324 n n 
N2 C19 R31 sing 325 n n 
C19 C20 R31 sing 326 n n 
N22 C20 R31 sing 327 n n 
C20 C21 R31 sing 328 n n 
O24 C21 R31 sing 329 n n 
C21 C23 R31 sing 330 n n 
C23 C25 R31 sing 331 n n 
C38 C29 R31 sing 332 n n 
C25 C29 R31 sing 333 n n 
C25 C26 R31 sing 334 n n 
C29 C37 R31 sing 335 n n 
C26 N27 R31 sing 336 n n 
C26 O28 R31 doub 337 n n 
N27 C30 R31 sing 338 n n 
C30 C31 R31 sing 339 n n 
N33 C32 R31 sing 340 n n 
C31 C32 R31 sing 341 n n 
C31 C35 R31 sing 342 n n 
C31 C34 R31 sing 343 n n 
C32 O36 R31 doub 344 n n 
C1 H1 R31 sing 345 n n 
C1 H2 R31 sing 346 n n 
C3 H4 R31 sing 347 n n 
C3 H5 R31 sing 348 n n 
C4 H6 R31 sing 349 n n 
C4 H7 R31 sing 350 n n 
C9 H8 R31 sing 351 n n 
C10 H9 R31 sing 352 n n 
C11 H10 R31 sing 353 n n 
C12 H11 R31 sing 354 n n 
C14 H12 R31 sing 355 n n 
C14 H13 R31 sing 356 n n 
C15 H14 R31 sing 357 n n 
C15 H15 R31 sing 358 n n 
C16 H16 R31 sing 359 n n 
C16 H17 R31 sing 360 n n 
C18 H18 R31 sing 361 n n 
C18 H19 R31 sing 362 n n 
C18 H20 R31 sing 363 n n 
C19 H21 R31 sing 364 n n 
C19 H22 R31 sing 365 n n 
C20 H23 R31 sing 366 n n 
C21 H24 R31 sing 367 n n 
N22 H25 R31 sing 368 n n 
N22 H26 R31 sing 369 n n 
C23 H28 R31 sing 370 n n 
C23 H29 R31 sing 371 n n 
O24 H30 R31 sing 372 n n 
C25 H31 R31 sing 373 n n 
N27 H32 R31 sing 374 n n 
C29 H33 R31 sing 375 n n 
C30 H34 R31 sing 376 n n 
C30 H35 R31 sing 377 n n 
N33 H36 R31 sing 378 n n 
N33 H37 R31 sing 379 n n 
C34 H38 R31 sing 380 n n 
C34 H39 R31 sing 381 n n 
C34 H40 R31 sing 382 n n 
C35 H41 R31 sing 383 n n 
C35 H42 R31 sing 384 n n 
C35 H43 R31 sing 385 n n 
C37 H44 R31 sing 386 n n 
C37 H45 R31 sing 387 n n 
C37 H46 R31 sing 388 n n 
C38 H47 R31 sing 389 n n 
C38 H48 R31 sing 390 n n 
C38 H49 R31 sing 391 n n 
#
_atom_sites.entry_id                     3VSW 
_atom_sites.fract_transf_matrix[1][1]    0.007104 
_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]    0.007104 
_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]    0.007104 
_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 NAG A 1 401 401 NAG NAG . 
D 3 R31 A 1 402 501 R31 R31 . 
E 2 NAG B 1 401 401 NAG NAG . 
F 3 R31 B 1 402 501 R31 R31 . 
#
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 C1 R31 . . . D 3 176.58 198.788 97.173 1 18.74 ? C1 R31 402 A 1 
HETATM 2 N N2 R31 . . . D 3 177.808 199.383 96.686 1 18.11 ? N2 R31 402 A 1 
HETATM 3 C C3 R31 . . . D 3 178.331 198.91 95.442 1 17.61 ? C3 R31 402 A 1 
HETATM 4 C C4 R31 . . . D 3 177.282 198.976 94.306 1 18.16 ? C4 R31 402 A 1 
HETATM 5 N N5 R31 . . . D 3 175.992 198.363 94.718 1 19.31 ? N5 R31 402 A 1 
HETATM 6 C C6 R31 . . . D 3 175.579 198.456 96.043 1 19.61 ? C6 R31 402 A 1 
HETATM 7 C C7 R31 . . . D 3 175.206 197.721 93.79 1 19.4 ? C7 R31 402 A 1 
HETATM 8 C C8 R31 . . . D 3 174.45 198.475 92.87 1 20.46 ? C8 R31 402 A 1 
HETATM 9 C C9 R31 . . . D 3 173.599 197.819 91.943 1 21.17 ? C9 R31 402 A 1 
HETATM 10 C C10 R31 . . . D 3 173.413 196.401 92.051 1 21.91 ? C10 R31 402 A 1 
HETATM 11 C C11 R31 . . . D 3 174.203 195.648 92.951 1 20.9 ? C11 R31 402 A 1 
HETATM 12 C C12 R31 . . . D 3 175.148 196.308 93.765 1 19.75 ? C12 R31 402 A 1 
HETATM 13 O O13 R31 . . . D 3 174.505 199.816 92.856 1 20.65 ? O13 R31 402 A 1 
HETATM 14 C C14 R31 . . . D 3 174.811 200.677 91.8 1 20.56 ? C14 R31 402 A 1 
HETATM 15 C C15 R31 . . . D 3 175.49 201.95 92.322 1 19 ? C15 R31 402 A 1 
HETATM 16 C C16 R31 . . . D 3 175.661 202.924 91.153 1 18.19 ? C16 R31 402 A 1 
HETATM 17 O O17 R31 . . . D 3 176.966 202.815 90.62 1 15.34 ? O17 R31 402 A 1 
HETATM 18 C C18 R31 . . . D 3 177.42 204.099 90.238 1 15.68 ? C18 R31 402 A 1 
HETATM 19 C C19 R31 . . . D 3 178.7 199.998 97.617 1 17.94 ? C19 R31 402 A 1 
HETATM 20 C C20 R31 . . . D 3 178.102 201.168 98.437 1 18.53 ? C20 R31 402 A 1 
HETATM 21 C C21 R31 . . . D 3 178.805 201.31 99.823 1 18.51 ? C21 R31 402 A 1 
HETATM 22 N N22 R31 . . . D 3 178.279 202.401 97.655 1 17.14 ? N22 R31 402 A 1 
HETATM 23 C C23 R31 . . . D 3 178.057 202.201 100.849 1 19.76 ? C23 R31 402 A 1 
HETATM 24 O O24 R31 . . . D 3 180.106 201.839 99.633 1 18.48 ? O24 R31 402 A 1 
HETATM 25 C C25 R31 . . . D 3 178.728 202.691 102.167 1 20.94 ? C25 R31 402 A 1 
HETATM 26 C C26 R31 . . . D 3 179.115 201.475 103.032 1 22.05 ? C26 R31 402 A 1 
HETATM 27 N N27 R31 . . . D 3 180.389 201.108 103.209 1 22.64 ? N27 R31 402 A 1 
HETATM 28 O O28 R31 . . . D 3 178.223 200.805 103.571 1 22.85 ? O28 R31 402 A 1 
HETATM 29 C C29 R31 . . . D 3 177.891 203.781 102.952 1 20.94 ? C29 R31 402 A 1 
HETATM 30 C C30 R31 . . . D 3 180.795 199.762 103.629 1 24.29 ? C30 R31 402 A 1 
HETATM 31 C C31 R31 . . . D 3 181.499 199.638 104.989 1 25.59 ? C31 R31 402 A 1 
HETATM 32 C C32 R31 . . . D 3 182.528 200.804 105.058 1 27.98 ? C32 R31 402 A 1 
HETATM 33 N N33 R31 . . . D 3 183.616 200.761 104.238 1 28.24 ? N33 R31 402 A 1 
HETATM 34 C C34 R31 . . . D 3 180.481 199.766 106.158 1 22.15 ? C34 R31 402 A 1 
HETATM 35 C C35 R31 . . . D 3 182.298 198.302 105.104 1 25 ? C35 R31 402 A 1 
HETATM 36 O O36 R31 . . . D 3 182.352 201.753 105.815 1 32.31 ? O36 R31 402 A 1 
HETATM 37 C C37 R31 . . . D 3 178.595 204.326 104.246 1 20.67 ? C37 R31 402 A 1 
HETATM 38 C C38 R31 . . . D 3 177.3 204.963 102.152 1 19.67 ? C38 R31 402 A 1 
HETATM 39 O O39 R31 . . . D 3 174.429 198.258 96.383 1 20.76 ? O39 R31 402 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           296 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           39 
#