data_3VSX # _model_server_result.job_id M3Zl6azwpX4iadiiMr5O6w _model_server_result.datetime_utc '2024-11-22 08:25:19' _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 3vsx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 3VSX # _exptl.entry_id 3VSX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 524.096 _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)-6-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]-4-hydroxy-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 3VSX _cell.length_a 138.188 _cell.length_b 138.188 _cell.length_c 138.188 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VSX _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 # 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 # 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_533 z+1/2,-x-3/2,-y-2 0 0 1 -1 0 0 0 -1 0 69.094 -207.282 -276.376 3 'crystal symmetry operation' 12_334 -y-3/2,-z-2,x-1/2 0 -1 0 0 0 -1 1 0 0 -207.282 -276.376 -69.094 # 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? disulf ? disulf2 A SG CYS 217 A CYS 217 1_555 A SG CYS 221 A CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.898 ? disulf ? disulf3 A SG CYS 259 A CYS 259 1_555 A SG CYS 296 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.677 ? disulf ? disulf4 B SG CYS 51 B CYS 51 1_555 B SG CYS 58 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? disulf ? disulf5 B SG CYS 217 B CYS 217 1_555 B SG CYS 221 B CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.745 ? disulf ? disulf6 B SG CYS 259 B CYS 259 1_555 B SG CYS 296 B CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? covale ? covale1 A ND2 ASN 75 A ASN 75 1_555 C C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale2 B ND2 ASN 75 B ASN 75 1_555 E C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? # _chem_comp.formula 'C26 H42 Cl N5 O4' _chem_comp.formula_weight 524.096 _chem_comp.id R32 _chem_comp.mon_nstd_flag . _chem_comp.name (2S,4S,5S)-5-amino-N-(3-amino-2,2-dimethyl-3-oxopropyl)-6-[4-(2-chlorophenyl)-2,2-dimethyl-5-oxopiperazin-1-yl]-4-hydroxy-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 N35 C32 R32 sing 305 n n O36 C32 R32 doub 306 n n C32 C25 R32 sing 307 n n C33 C25 R32 sing 308 n n C25 C34 R32 sing 309 n n C25 C24 R32 sing 310 n n C24 N23 R32 sing 311 n n N23 C22 R32 sing 312 n n O27 C19 R32 sing 313 n n C15 C10 R32 sing 314 n n C22 C21 R32 sing 315 n n C22 O29 R32 doub 316 n n C19 C18 R32 sing 317 n n C19 C20 R32 sing 318 n n C31 C28 R32 sing 319 n n C21 C28 R32 sing 320 n n C21 C20 R32 sing 321 n n C17 C18 R32 sing 322 n n C17 N11 R32 sing 323 n n C16 C10 R32 sing 324 n n C10 N11 R32 sing 325 n n C10 C9 R32 sing 326 n n N26 C18 R32 sing 327 n n C28 C30 R32 sing 328 n n N11 C12 R32 sing 329 n n C9 N7 R32 sing 330 n n C12 C13 R32 sing 331 n n N7 C13 R32 sing 332 n n N7 C2 R32 sing 333 n n C13 O14 R32 doub 334 n n CL1 C3 R32 sing 335 n n C2 C3 R32 doub 336 n y C2 C1 R32 sing 337 n y C3 C4 R32 sing 338 n y C1 C6 R32 doub 339 n y C4 C5 R32 doub 340 n y C6 C5 R32 sing 341 n y C1 H1 R32 sing 342 n n C4 H2 R32 sing 343 n n C5 H3 R32 sing 344 n n C6 H4 R32 sing 345 n n C9 H5 R32 sing 346 n n C9 H6 R32 sing 347 n n C12 H8 R32 sing 348 n n C12 H9 R32 sing 349 n n C15 H10 R32 sing 350 n n C15 H11 R32 sing 351 n n C15 H12 R32 sing 352 n n C16 H13 R32 sing 353 n n C16 H14 R32 sing 354 n n C16 H15 R32 sing 355 n n C17 H16 R32 sing 356 n n C17 H17 R32 sing 357 n n C18 H18 R32 sing 358 n n C19 H19 R32 sing 359 n n C20 H20 R32 sing 360 n n C20 H21 R32 sing 361 n n C21 H22 R32 sing 362 n n N23 H23 R32 sing 363 n n C24 H24 R32 sing 364 n n C24 H25 R32 sing 365 n n N26 H26 R32 sing 366 n n N26 H27 R32 sing 367 n n O27 H29 R32 sing 368 n n C28 H30 R32 sing 369 n n C30 H31 R32 sing 370 n n C30 H32 R32 sing 371 n n C30 H33 R32 sing 372 n n C31 H34 R32 sing 373 n n C31 H35 R32 sing 374 n n C31 H36 R32 sing 375 n n C33 H37 R32 sing 376 n n C33 H38 R32 sing 377 n n C33 H39 R32 sing 378 n n C34 H40 R32 sing 379 n n C34 H41 R32 sing 380 n n C34 H42 R32 sing 381 n n N35 H43 R32 sing 382 n n N35 H44 R32 sing 383 n n # _atom_sites.entry_id 3VSX _atom_sites.fract_transf_matrix[1][1] 0.007237 _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] 0.007237 _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] 0.007237 _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 R32 A 1 402 501 R32 R32 . E 2 NAG B 1 401 401 NAG NAG . F 3 R32 B 1 402 501 R32 R32 . # 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 R32 . . . D 3 -57.835 -161.078 -136.486 1 28.23 ? C1 R32 402 A 1 HETATM 2 C C2 R32 . . . D 3 -58.646 -160.112 -137.069 1 27.87 ? C2 R32 402 A 1 HETATM 3 C C3 R32 . . . D 3 -58.424 -158.782 -136.762 1 29.19 ? C3 R32 402 A 1 HETATM 4 C C4 R32 . . . D 3 -57.424 -158.383 -135.894 1 29.95 ? C4 R32 402 A 1 HETATM 5 C C5 R32 . . . D 3 -56.616 -159.352 -135.314 1 28.93 ? C5 R32 402 A 1 HETATM 6 C C6 R32 . . . D 3 -56.822 -160.696 -135.609 1 27.54 ? C6 R32 402 A 1 HETATM 7 N N7 R32 . . . D 3 -59.649 -160.527 -137.938 1 25.7 ? N7 R32 402 A 1 HETATM 8 CL CL1 R32 . . . D 3 -59.429 -157.577 -137.482 1 33.95 ? CL1 R32 402 A 1 HETATM 9 C C9 R32 . . . D 3 -59.284 -160.969 -139.294 1 24.74 ? C9 R32 402 A 1 HETATM 10 C C10 R32 . . . D 3 -60.38 -160.778 -140.322 1 25.93 ? C10 R32 402 A 1 HETATM 11 N N11 R32 . . . D 3 -61.595 -161.379 -139.786 1 25.57 ? N11 R32 402 A 1 HETATM 12 C C12 R32 . . . D 3 -62.048 -160.965 -138.474 1 24.8 ? C12 R32 402 A 1 HETATM 13 C C13 R32 . . . D 3 -60.955 -160.509 -137.498 1 24.82 ? C13 R32 402 A 1 HETATM 14 O O14 R32 . . . D 3 -61.272 -160.148 -136.377 1 25.01 ? O14 R32 402 A 1 HETATM 15 C C15 R32 . . . D 3 -59.984 -161.468 -141.631 1 25.59 ? C15 R32 402 A 1 HETATM 16 C C16 R32 . . . D 3 -60.595 -159.286 -140.582 1 27.66 ? C16 R32 402 A 1 HETATM 17 C C17 R32 . . . D 3 -62.628 -161.818 -140.711 1 24.87 ? C17 R32 402 A 1 HETATM 18 C C18 R32 . . . D 3 -63.431 -162.994 -140.143 1 23.57 ? C18 R32 402 A 1 HETATM 19 C C19 R32 . . . D 3 -64.804 -163.138 -140.801 1 22.71 ? C19 R32 402 A 1 HETATM 20 C C20 R32 . . . D 3 -65.789 -164.005 -139.999 1 24.58 ? C20 R32 402 A 1 HETATM 21 C C21 R32 . . . D 3 -67.11 -164.238 -140.755 1 26.42 ? C21 R32 402 A 1 HETATM 22 C C22 R32 . . . D 3 -67.818 -162.89 -140.985 1 26.54 ? C22 R32 402 A 1 HETATM 23 N N23 R32 . . . D 3 -67.945 -162.583 -142.289 1 25.08 ? N23 R32 402 A 1 HETATM 24 C C24 R32 . . . D 3 -68.592 -161.33 -142.617 1 26.24 ? C24 R32 402 A 1 HETATM 25 C C25 R32 . . . D 3 -69.871 -161.598 -143.417 1 27.01 ? C25 R32 402 A 1 HETATM 26 N N26 R32 . . . D 3 -62.667 -164.234 -140.155 1 22.01 ? N26 R32 402 A 1 HETATM 27 O O27 R32 . . . D 3 -64.672 -163.624 -142.111 1 20.53 ? O27 R32 402 A 1 HETATM 28 C C28 R32 . . . D 3 -68.051 -165.26 -140.084 1 25.02 ? C28 R32 402 A 1 HETATM 29 O O29 R32 . . . D 3 -68.207 -162.189 -140.054 1 26.23 ? O29 R32 402 A 1 HETATM 30 C C30 R32 . . . D 3 -67.401 -166.628 -139.874 1 23.59 ? C30 R32 402 A 1 HETATM 31 C C31 R32 . . . D 3 -69.394 -165.377 -140.799 1 25.63 ? C31 R32 402 A 1 HETATM 32 C C32 R32 . . . D 3 -69.46 -162.154 -144.786 1 26.27 ? C32 R32 402 A 1 HETATM 33 C C33 R32 . . . D 3 -70.651 -160.297 -143.637 1 26.87 ? C33 R32 402 A 1 HETATM 34 C C34 R32 . . . D 3 -70.755 -162.643 -142.72 1 25.33 ? C34 R32 402 A 1 HETATM 35 N N35 R32 . . . D 3 -68.722 -161.287 -145.515 1 25.14 ? N35 R32 402 A 1 HETATM 36 O O36 R32 . . . D 3 -69.776 -163.284 -145.141 1 25.52 ? O36 R32 402 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 36 #