data_1VJ9 # _model_server_result.job_id Ci5B2k1naTtJp1AVfOpuGA _model_server_result.datetime_utc '2025-03-12 04:56:08' _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 1vj9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":300}' # _entry.id 1VJ9 # _exptl.entry_id 1VJ9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 567.657 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-(BENZYLSULFONYL)-L-SERYL-N~1~-{4-[AMINO(IMINO)METHYL]BENZYL}-O-BENZYL-L-SERINAMIDE _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 1VJ9 _cell.length_a 53.23 _cell.length_b 54.9 _cell.length_c 82.28 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VJ9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 x,y,z _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 3 _struct_asym.id D _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 disulf ? disulf1 A SG CYS 46 U CYS 42 1_555 A SG CYS 62 U CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 A SG CYS 54 U CYS 50 1_555 A SG CYS 125 U CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 150 U CYS 136 1_555 A SG CYS 219 U CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf4 A SG CYS 182 U CYS 168 1_555 A SG CYS 198 U CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf5 A SG CYS 209 U CYS 191 1_555 A SG CYS 237 U CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? # _chem_comp.formula 'C28 H33 N5 O6 S' _chem_comp.formula_weight 567.657 _chem_comp.id 5IN _chem_comp.mon_nstd_flag . _chem_comp.name N-(BENZYLSULFONYL)-L-SERYL-N~1~-{4-[AMINO(IMINO)METHYL]BENZYL}-O-BENZYL-L-SERINAMIDE _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 C1 O2 5IN sing 1 n n C1 C35 5IN sing 2 n n C1 H11 5IN sing 3 n n C1 H12A 5IN sing 4 n n O2 C3 5IN sing 5 n n C3 C4 5IN sing 6 n n C3 H31A 5IN sing 7 n n C3 H32 5IN sing 8 n n C4 N5 5IN sing 9 n n C4 C22 5IN sing 10 n n C4 H4 5IN sing 11 n n N5 C6 5IN sing 12 n n N5 HN5 5IN sing 13 n n C6 C7 5IN sing 14 n n C6 O21 5IN doub 15 n n C7 N8 5IN sing 16 n n C7 C19 5IN sing 17 n n C7 H7 5IN sing 18 n n N8 S9 5IN sing 19 n n N8 HN8 5IN sing 20 n n S9 C10 5IN sing 21 n n S9 O17 5IN doub 22 n n S9 O18 5IN doub 23 n n C10 C11 5IN sing 24 n n C10 H101 5IN sing 25 n n C10 H102 5IN sing 26 n n C11 C12 5IN doub 27 n y C11 C16 5IN sing 28 n y C12 C13 5IN sing 29 n y C12 H12 5IN sing 30 n n C13 C14 5IN doub 31 n y C13 H13 5IN sing 32 n n C14 C15 5IN sing 33 n y C14 H14 5IN sing 34 n n C15 C16 5IN doub 35 n y C15 H15 5IN sing 36 n n C16 H16 5IN sing 37 n n C19 O20 5IN sing 38 n n C19 H191 5IN sing 39 n n C19 H192 5IN sing 40 n n O20 H20 5IN sing 41 n n C22 O23 5IN doub 42 n n C22 N24 5IN sing 43 n n N24 C25 5IN sing 44 n n N24 H24 5IN sing 45 n n C25 C26 5IN sing 46 n n C25 H251 5IN sing 47 n n C25 H252 5IN sing 48 n n C26 C27 5IN doub 49 n y C26 C31 5IN sing 50 n y C27 C28 5IN sing 51 n y C27 H27 5IN sing 52 n n C28 C29 5IN doub 53 n y C28 H28 5IN sing 54 n n C29 C30 5IN sing 55 n y C29 C32 5IN sing 56 n n C30 C31 5IN doub 57 n y C30 H30 5IN sing 58 n n C31 H31 5IN sing 59 n n C32 N33 5IN doub 60 n n C32 N34 5IN sing 61 n n N33 H33 5IN sing 62 n n N34 H341 5IN sing 63 n n N34 H342 5IN sing 64 n n C35 C36 5IN doub 65 n y C35 C40 5IN sing 66 n y C36 C37 5IN sing 67 n y C36 H36 5IN sing 68 n n C37 C38 5IN doub 69 n y C37 H37 5IN sing 70 n n C38 C39 5IN sing 71 n y C38 H38 5IN sing 72 n n C39 C40 5IN doub 73 n y C39 H39 5IN sing 74 n n C40 H40 5IN sing 75 n n # _atom_sites.entry_id 1VJ9 _atom_sites.fract_transf_matrix[1][1] 0.018786 _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] 0.018215 _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] 0.012154 _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 SO4 U 1 401 401 SO4 SO4 . C 2 SO4 U 1 403 403 SO4 SO4 . D 3 5IN U 1 300 300 5IN 5IN . E 4 HOH U 1 404 1 HOH WAT . E 4 HOH U 2 405 2 HOH WAT . E 4 HOH U 3 406 3 HOH WAT . E 4 HOH U 4 407 4 HOH WAT . E 4 HOH U 5 408 5 HOH WAT . E 4 HOH U 6 409 6 HOH WAT . E 4 HOH U 7 410 7 HOH WAT . E 4 HOH U 8 411 8 HOH WAT . E 4 HOH U 9 412 9 HOH WAT . E 4 HOH U 10 413 10 HOH WAT . E 4 HOH U 11 414 11 HOH WAT . E 4 HOH U 12 415 12 HOH WAT . E 4 HOH U 13 416 13 HOH WAT . E 4 HOH U 14 417 14 HOH WAT . E 4 HOH U 15 418 15 HOH WAT . E 4 HOH U 16 419 16 HOH WAT . E 4 HOH U 17 420 17 HOH WAT . E 4 HOH U 18 421 18 HOH WAT . E 4 HOH U 19 422 19 HOH WAT . E 4 HOH U 20 423 20 HOH WAT . E 4 HOH U 21 424 21 HOH WAT . E 4 HOH U 22 425 22 HOH WAT . E 4 HOH U 23 426 23 HOH WAT . E 4 HOH U 24 427 24 HOH WAT . E 4 HOH U 25 428 25 HOH WAT . E 4 HOH U 26 429 26 HOH WAT . E 4 HOH U 27 430 27 HOH WAT . E 4 HOH U 28 431 28 HOH WAT . E 4 HOH U 29 432 29 HOH WAT . E 4 HOH U 30 433 30 HOH WAT . E 4 HOH U 31 434 31 HOH WAT . E 4 HOH U 32 435 32 HOH WAT . E 4 HOH U 33 436 33 HOH WAT . E 4 HOH U 34 437 34 HOH WAT . E 4 HOH U 35 438 35 HOH WAT . E 4 HOH U 36 439 36 HOH WAT . E 4 HOH U 37 440 37 HOH WAT . E 4 HOH U 38 441 38 HOH WAT . E 4 HOH U 39 442 39 HOH WAT . E 4 HOH U 40 443 40 HOH WAT . E 4 HOH U 41 444 45 HOH WAT . E 4 HOH U 42 445 46 HOH WAT . E 4 HOH U 43 446 47 HOH WAT . E 4 HOH U 44 447 48 HOH WAT . E 4 HOH U 45 448 50 HOH WAT . E 4 HOH U 46 449 52 HOH WAT . E 4 HOH U 47 450 53 HOH WAT . E 4 HOH U 48 451 54 HOH WAT . E 4 HOH U 49 452 55 HOH WAT . E 4 HOH U 50 453 57 HOH WAT . E 4 HOH U 51 454 62 HOH WAT . E 4 HOH U 52 455 63 HOH WAT . E 4 HOH U 53 456 65 HOH WAT . E 4 HOH U 54 457 66 HOH WAT . E 4 HOH U 55 458 67 HOH WAT . E 4 HOH U 56 459 70 HOH WAT . E 4 HOH U 57 460 72 HOH WAT . E 4 HOH U 58 461 73 HOH WAT . E 4 HOH U 59 462 75 HOH WAT . E 4 HOH U 60 463 76 HOH WAT . E 4 HOH U 61 464 78 HOH WAT . E 4 HOH U 62 465 79 HOH WAT . E 4 HOH U 63 466 80 HOH WAT . E 4 HOH U 64 467 81 HOH WAT . E 4 HOH U 65 468 87 HOH WAT . E 4 HOH U 66 469 89 HOH WAT . E 4 HOH U 67 470 90 HOH WAT . E 4 HOH U 68 471 93 HOH WAT . E 4 HOH U 69 472 94 HOH WAT . E 4 HOH U 70 473 97 HOH WAT . E 4 HOH U 71 474 101 HOH WAT . E 4 HOH U 72 475 102 HOH WAT . E 4 HOH U 73 476 103 HOH WAT . E 4 HOH U 74 477 104 HOH WAT . E 4 HOH U 75 478 105 HOH WAT . E 4 HOH U 76 479 108 HOH WAT . E 4 HOH U 77 480 109 HOH WAT . E 4 HOH U 78 481 110 HOH WAT . E 4 HOH U 79 482 115 HOH WAT . E 4 HOH U 80 483 117 HOH WAT . E 4 HOH U 81 484 119 HOH WAT . E 4 HOH U 82 485 120 HOH WAT . E 4 HOH U 83 486 125 HOH WAT . E 4 HOH U 84 487 126 HOH WAT . E 4 HOH U 85 488 127 HOH WAT . E 4 HOH U 86 489 128 HOH WAT . E 4 HOH U 87 490 129 HOH WAT . E 4 HOH U 88 491 154 HOH WAT . E 4 HOH U 89 492 159 HOH WAT . E 4 HOH U 90 493 160 HOH WAT . E 4 HOH U 91 494 167 HOH WAT . E 4 HOH U 92 495 168 HOH WAT . # 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 5IN . . . D 3 26.954 13.356 31.673 1 44.28 ? C1 5IN 300 U 1 HETATM 2 O O2 5IN . . . D 3 27.772 12.234 32.014 1 40.78 ? O2 5IN 300 U 1 HETATM 3 C C3 5IN . . . D 3 27.81 11.352 30.907 1 37.08 ? C3 5IN 300 U 1 HETATM 4 C C4 5IN . . . D 3 29.08 10.488 30.934 1 35.16 ? C4 5IN 300 U 1 HETATM 5 N N5 5IN . . . D 3 30.226 11.378 30.958 1 32.66 ? N5 5IN 300 U 1 HETATM 6 C C6 5IN . . . D 3 31.537 10.876 30.994 1 32.16 ? C6 5IN 300 U 1 HETATM 7 C C7 5IN . . . D 3 32.673 11.903 31.009 1 32.66 ? C7 5IN 300 U 1 HETATM 8 N N8 5IN . . . D 3 33.638 11.76 29.954 1 33.87 ? N8 5IN 300 U 1 HETATM 9 S S9 5IN . . . D 3 33.49 12.02 28.329 1 37.19 ? S9 5IN 300 U 1 HETATM 10 C C10 5IN . . . D 3 32.171 10.96 27.708 1 38.13 ? C10 5IN 300 U 1 HETATM 11 C C11 5IN . . . D 3 32.015 11.202 26.153 1 41.27 ? C11 5IN 300 U 1 HETATM 12 C C12 5IN . . . D 3 31.018 12.155 25.794 1 43.87 ? C12 5IN 300 U 1 HETATM 13 C C13 5IN . . . D 3 30.772 12.454 24.421 1 44.75 ? C13 5IN 300 U 1 HETATM 14 C C14 5IN . . . D 3 31.528 11.792 23.426 1 44.96 ? C14 5IN 300 U 1 HETATM 15 C C15 5IN . . . D 3 32.522 10.844 23.777 1 42.05 ? C15 5IN 300 U 1 HETATM 16 C C16 5IN . . . D 3 32.767 10.547 25.141 1 42.15 ? C16 5IN 300 U 1 HETATM 17 O O17 5IN . . . D 3 33.092 13.395 28.2 1 37.06 ? O17 5IN 300 U 1 HETATM 18 O O18 5IN . . . D 3 34.854 11.718 27.843 1 39.52 ? O18 5IN 300 U 1 HETATM 19 C C19 5IN . . . D 3 33.527 11.878 32.287 1 31.15 ? C19 5IN 300 U 1 HETATM 20 O O20 5IN . . . D 3 32.669 12.099 33.38 1 36.23 ? O20 5IN 300 U 1 HETATM 21 O O21 5IN . . . D 3 31.778 9.683 31.007 1 31.39 ? O21 5IN 300 U 1 HETATM 22 C C22 5IN . . . D 3 29.022 9.598 29.721 1 32.58 ? C22 5IN 300 U 1 HETATM 23 O O23 5IN . . . D 3 29.253 10.054 28.628 1 37.71 ? O23 5IN 300 U 1 HETATM 24 N N24 5IN . . . D 3 28.687 8.286 29.985 1 27.67 ? N24 5IN 300 U 1 HETATM 25 C C25 5IN . . . D 3 28.577 7.327 28.921 1 26.26 ? C25 5IN 300 U 1 HETATM 26 C C26 5IN . . . D 3 29.858 6.574 28.601 1 26.55 ? C26 5IN 300 U 1 HETATM 27 C C27 5IN . . . D 3 29.948 5.203 28.949 1 23.57 ? C27 5IN 300 U 1 HETATM 28 C C28 5IN . . . D 3 31.11 4.458 28.664 1 22.93 ? C28 5IN 300 U 1 HETATM 29 C C29 5IN . . . D 3 32.248 5.048 28.017 1 22.68 ? C29 5IN 300 U 1 HETATM 30 C C30 5IN . . . D 3 32.186 6.436 27.653 1 24.07 ? C30 5IN 300 U 1 HETATM 31 C C31 5IN . . . D 3 30.993 7.178 27.949 1 25.08 ? C31 5IN 300 U 1 HETATM 32 C C32 5IN . . . D 3 33.373 4.228 27.755 1 21.79 ? C32 5IN 300 U 1 HETATM 33 N N33 5IN . . . D 3 33.36 2.92 28.094 1 18.48 ? N33 5IN 300 U 1 HETATM 34 N N34 5IN . . . D 3 34.517 4.629 27.166 1 19.33 ? N34 5IN 300 U 1 HETATM 35 C C35 5IN . . . D 3 26.481 14.044 32.954 1 48.27 ? C35 5IN 300 U 1 HETATM 36 C C36 5IN . . . D 3 25.187 13.749 33.485 1 46.09 ? C36 5IN 300 U 1 HETATM 37 C C37 5IN . . . D 3 24.747 14.392 34.682 1 47.59 ? C37 5IN 300 U 1 HETATM 38 C C38 5IN . . . D 3 25.598 15.327 35.346 1 46.5 ? C38 5IN 300 U 1 HETATM 39 C C39 5IN . . . D 3 26.889 15.621 34.815 1 46.34 ? C39 5IN 300 U 1 HETATM 40 C C40 5IN . . . D 3 27.333 14.982 33.621 1 47.46 ? C40 5IN 300 U 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 40 #