data_5WKL # _model_server_result.job_id fu6zYPofJUQE3zAmwwW4SA _model_server_result.datetime_utc '2024-11-22 06:11:00' _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 5wkl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5WKL # _exptl.entry_id 5WKL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 668.799 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1R,2S)-2-{[N-({[4-benzyl-1-(tert-butoxycarbonyl)piperidin-4-yl]oxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid' _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 112 _cell.angle_gamma 90 _cell.entry_id 5WKL _cell.length_a 101.253 _cell.length_b 58.099 _cell.length_c 49.734 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WKL _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 2_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -18.630684 0 46.112562 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 covale ? covale1 A SG CYS 155 A CYS 148 1_555 B C19 AVY . A AVY 401 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.8 ? covale ? covale2 A SG CYS 155 A CYS 148 1_555 C C19 B3J . A B3J 402 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.821 ? # _chem_comp.formula 'C31 H48 N4 O10 S' _chem_comp.formula_weight 668.799 _chem_comp.id AVY _chem_comp.mon_nstd_flag . _chem_comp.name '(1R,2S)-2-{[N-({[4-benzyl-1-(tert-butoxycarbonyl)piperidin-4-yl]oxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'bound form' # 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 C07 C06 AVY sing 70 n n C06 C08 AVY sing 71 n n C06 C05 AVY sing 72 n n C05 C04 AVY sing 73 n n N03 C04 AVY sing 74 n n N03 C02 AVY sing 75 n n C04 C09 AVY sing 76 n n O22 C23 AVY sing 77 n n O22 C02 AVY sing 78 n n C23 C24 AVY sing 79 n n C02 O01 AVY doub 80 n n C09 O21 AVY doub 81 n n C09 N10 AVY sing 82 n n C24 C25 AVY sing 83 n n N10 C11 AVY sing 84 n n O20 C19 AVY sing 85 n n C26 C25 AVY doub 86 n y C26 C27 AVY sing 87 n y C25 C30 AVY sing 88 n y C19 C11 AVY sing 89 n n C27 C28 AVY doub 90 n y C11 C12 AVY sing 91 n n C30 C29 AVY doub 92 n y C28 C29 AVY sing 93 n y C12 C13 AVY sing 94 n n C13 C17 AVY sing 95 n n C13 C14 AVY sing 96 n n C17 C16 AVY sing 97 n n C14 O18 AVY doub 98 n n C14 N15 AVY sing 99 n n C16 N15 AVY sing 100 n n C11 H1 AVY sing 101 n n C12 H2 AVY sing 102 n n C12 H3 AVY sing 103 n n C13 H4 AVY sing 104 n n C24 H5 AVY sing 105 n n C24 H6 AVY sing 106 n n C16 H7 AVY sing 107 n n C16 H8 AVY sing 108 n n C04 H9 AVY sing 109 n n C05 H10 AVY sing 110 n n C05 H11 AVY sing 111 n n C06 H12 AVY sing 112 n n C07 H13 AVY sing 113 n n C07 H14 AVY sing 114 n n C07 H15 AVY sing 115 n n C08 H16 AVY sing 116 n n C08 H17 AVY sing 117 n n C08 H18 AVY sing 118 n n C17 H19 AVY sing 119 n n C17 H20 AVY sing 120 n n C19 H21 AVY sing 121 n n C26 H25 AVY sing 122 n n C27 H26 AVY sing 123 n n C28 H27 AVY sing 124 n n C29 H28 AVY sing 125 n n C30 H29 AVY sing 126 n n N03 H30 AVY sing 127 n n N10 H31 AVY sing 128 n n N15 H32 AVY sing 129 n n O20 H33 AVY sing 130 n n C19 S1 AVY sing 131 n n S1 O1 AVY sing 132 n n S1 O3 AVY doub 133 n n S1 O2 AVY doub 134 n n C23 C1 AVY sing 135 n n C23 C2 AVY sing 136 n n C2 C3 AVY sing 137 n n C3 N1 AVY sing 138 n n N1 C5 AVY sing 139 n n C5 C1 AVY sing 140 n n O1 H22 AVY sing 141 n n C1 H23 AVY sing 142 n n C1 H24 AVY sing 143 n n C2 H34 AVY sing 144 n n C2 H35 AVY sing 145 n n C3 H36 AVY sing 146 n n C3 H37 AVY sing 147 n n N1 C4 AVY sing 148 n n C5 H40 AVY sing 149 n n C5 H41 AVY sing 150 n n C4 O4 AVY doub 151 n n C4 O5 AVY sing 152 n n O5 C8 AVY sing 153 n n C8 C9 AVY sing 154 n n C8 C10 AVY sing 155 n n C8 C15 AVY sing 156 n n C9 H38 AVY sing 157 n n C9 H39 AVY sing 158 n n C9 H42 AVY sing 159 n n C10 H43 AVY sing 160 n n C10 H44 AVY sing 161 n n C10 H45 AVY sing 162 n n C15 H46 AVY sing 163 n n C15 H47 AVY sing 164 n n C15 H48 AVY sing 165 n n # _atom_sites.entry_id 5WKL _atom_sites.fract_transf_matrix[1][1] 0.009876 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003991 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017212 _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] 0.021687 _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 AVY A 1 401 1 AVY 167 . C 3 B3J A 1 402 1 B3J 167 . D 4 HOH A 1 501 51 HOH HOH . D 4 HOH A 2 502 17 HOH HOH . D 4 HOH A 3 503 126 HOH HOH . D 4 HOH A 4 504 124 HOH HOH . D 4 HOH A 5 505 99 HOH HOH . D 4 HOH A 6 506 81 HOH HOH . D 4 HOH A 7 507 84 HOH HOH . D 4 HOH A 8 508 33 HOH HOH . D 4 HOH A 9 509 6 HOH HOH . D 4 HOH A 10 510 100 HOH HOH . D 4 HOH A 11 511 3 HOH HOH . D 4 HOH A 12 512 103 HOH HOH . D 4 HOH A 13 513 49 HOH HOH . D 4 HOH A 14 514 94 HOH HOH . D 4 HOH A 15 515 39 HOH HOH . D 4 HOH A 16 516 101 HOH HOH . D 4 HOH A 17 517 55 HOH HOH . D 4 HOH A 18 518 54 HOH HOH . D 4 HOH A 19 519 45 HOH HOH . D 4 HOH A 20 520 44 HOH HOH . D 4 HOH A 21 521 128 HOH HOH . D 4 HOH A 22 522 38 HOH HOH . D 4 HOH A 23 523 10 HOH HOH . D 4 HOH A 24 524 36 HOH HOH . D 4 HOH A 25 525 1 HOH HOH . D 4 HOH A 26 526 23 HOH HOH . D 4 HOH A 27 527 76 HOH HOH . D 4 HOH A 28 528 52 HOH HOH . D 4 HOH A 29 529 9 HOH HOH . D 4 HOH A 30 530 104 HOH HOH . D 4 HOH A 31 531 42 HOH HOH . D 4 HOH A 32 532 86 HOH HOH . D 4 HOH A 33 533 72 HOH HOH . D 4 HOH A 34 534 16 HOH HOH . D 4 HOH A 35 535 5 HOH HOH . D 4 HOH A 36 536 20 HOH HOH . D 4 HOH A 37 537 24 HOH HOH . D 4 HOH A 38 538 12 HOH HOH . D 4 HOH A 39 539 92 HOH HOH . D 4 HOH A 40 540 27 HOH HOH . D 4 HOH A 41 541 108 HOH HOH . D 4 HOH A 42 542 4 HOH HOH . D 4 HOH A 43 543 107 HOH HOH . D 4 HOH A 44 544 59 HOH HOH . D 4 HOH A 45 545 111 HOH HOH . D 4 HOH A 46 546 25 HOH HOH . D 4 HOH A 47 547 30 HOH HOH . D 4 HOH A 48 548 22 HOH HOH . D 4 HOH A 49 549 95 HOH HOH . D 4 HOH A 50 550 46 HOH HOH . D 4 HOH A 51 551 98 HOH HOH . D 4 HOH A 52 552 74 HOH HOH . D 4 HOH A 53 553 11 HOH HOH . D 4 HOH A 54 554 122 HOH HOH . D 4 HOH A 55 555 18 HOH HOH . D 4 HOH A 56 556 75 HOH HOH . D 4 HOH A 57 557 63 HOH HOH . D 4 HOH A 58 558 64 HOH HOH . D 4 HOH A 59 559 40 HOH HOH . D 4 HOH A 60 560 34 HOH HOH . D 4 HOH A 61 561 105 HOH HOH . D 4 HOH A 62 562 2 HOH HOH . D 4 HOH A 63 563 56 HOH HOH . D 4 HOH A 64 564 58 HOH HOH . D 4 HOH A 65 565 61 HOH HOH . D 4 HOH A 66 566 68 HOH HOH . D 4 HOH A 67 567 7 HOH HOH . D 4 HOH A 68 568 73 HOH HOH . D 4 HOH A 69 569 87 HOH HOH . D 4 HOH A 70 570 41 HOH HOH . D 4 HOH A 71 571 43 HOH HOH . D 4 HOH A 72 572 113 HOH HOH . D 4 HOH A 73 573 91 HOH HOH . D 4 HOH A 74 574 102 HOH HOH . D 4 HOH A 75 575 57 HOH HOH . D 4 HOH A 76 576 32 HOH HOH . D 4 HOH A 77 577 31 HOH HOH . D 4 HOH A 78 578 93 HOH HOH . D 4 HOH A 79 579 90 HOH HOH . D 4 HOH A 80 580 13 HOH HOH . D 4 HOH A 81 581 85 HOH HOH . D 4 HOH A 82 582 71 HOH HOH . D 4 HOH A 83 583 109 HOH HOH . D 4 HOH A 84 584 21 HOH HOH . D 4 HOH A 85 585 29 HOH HOH . D 4 HOH A 86 586 28 HOH HOH . D 4 HOH A 87 587 67 HOH HOH . D 4 HOH A 88 588 37 HOH HOH . D 4 HOH A 89 589 19 HOH HOH . D 4 HOH A 90 590 123 HOH HOH . D 4 HOH A 91 591 82 HOH HOH . D 4 HOH A 92 592 79 HOH HOH . D 4 HOH A 93 593 127 HOH HOH . D 4 HOH A 94 594 80 HOH HOH . D 4 HOH A 95 595 118 HOH HOH . D 4 HOH A 96 596 14 HOH HOH . D 4 HOH A 97 597 106 HOH HOH . D 4 HOH A 98 598 121 HOH HOH . D 4 HOH A 99 599 47 HOH HOH . D 4 HOH A 100 600 112 HOH HOH . D 4 HOH A 101 601 83 HOH HOH . D 4 HOH A 102 602 8 HOH HOH . D 4 HOH A 103 603 77 HOH HOH . D 4 HOH A 104 604 62 HOH HOH . D 4 HOH A 105 605 114 HOH HOH . D 4 HOH A 106 606 96 HOH HOH . D 4 HOH A 107 607 89 HOH HOH . D 4 HOH A 108 608 88 HOH HOH . D 4 HOH A 109 609 26 HOH HOH . D 4 HOH A 110 610 116 HOH HOH . D 4 HOH A 111 611 97 HOH HOH . D 4 HOH A 112 612 78 HOH HOH . D 4 HOH A 113 613 66 HOH HOH . D 4 HOH A 114 614 53 HOH HOH . D 4 HOH A 115 615 65 HOH HOH . D 4 HOH A 116 616 15 HOH HOH . D 4 HOH A 117 617 35 HOH HOH . D 4 HOH A 118 618 120 HOH HOH . D 4 HOH A 119 619 70 HOH HOH . D 4 HOH A 120 620 125 HOH HOH . D 4 HOH A 121 621 69 HOH HOH . D 4 HOH A 122 622 110 HOH HOH . D 4 HOH A 123 623 50 HOH HOH . D 4 HOH A 124 624 48 HOH HOH . D 4 HOH A 125 625 115 HOH HOH . D 4 HOH A 126 626 119 HOH HOH . D 4 HOH A 127 627 117 HOH HOH . D 4 HOH A 128 628 60 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 C11 AVY . A . B 2 -20.983 -1.281 5.498 0.5 23.11 ? C11 AVY 401 A 1 HETATM 2 C C12 AVY . A . B 2 -20.284 -2.119 6.583 0.5 20.53 ? C12 AVY 401 A 1 HETATM 3 C C13 AVY . A . B 2 -20.761 -3.585 6.629 0.5 20.29 ? C13 AVY 401 A 1 HETATM 4 C C14 AVY . A . B 2 -20.141 -4.33 7.746 0.5 22.46 ? C14 AVY 401 A 1 HETATM 5 C C24 AVY . A . B 2 -22.144 -7.811 4.062 0.5 39.47 ? C24 AVY 401 A 1 HETATM 6 C C25 AVY . A . B 2 -23.311 -7.259 4.883 0.5 35.94 ? C25 AVY 401 A 1 HETATM 7 C C16 AVY . A . B 2 -22.491 -4.756 7.93 0.5 27.32 ? C16 AVY 401 A 1 HETATM 8 C C02 AVY . A . B 2 -21.55 -5.225 2.492 0.5 30.96 ? C02 AVY 401 A 1 HETATM 9 C C04 AVY . A . B 2 -20.925 -2.862 1.973 0.5 23.27 ? C04 AVY 401 A 1 HETATM 10 C C05 AVY . A . B 2 -21.133 -1.838 0.859 0.5 25.62 ? C05 AVY 401 A 1 HETATM 11 C C06 AVY . A . B 2 -20.501 -2.307 -0.455 0.5 26.59 ? C06 AVY 401 A 1 HETATM 12 C C07 AVY . A . B 2 -20.834 -1.392 -1.638 0.5 24.28 ? C07 AVY 401 A 1 HETATM 13 C C08 AVY . A . B 2 -18.981 -2.458 -0.352 0.5 28.37 ? C08 AVY 401 A 1 HETATM 14 C C09 AVY . A . B 2 -21.499 -2.36 3.294 0.5 26.74 ? C09 AVY 401 A 1 HETATM 15 C C17 AVY . A . B 2 -22.26 -3.627 6.886 0.5 23.39 ? C17 AVY 401 A 1 HETATM 16 C C19 AVY . A . B 2 -20.602 0.2 5.494 0.5 21.18 ? C19 AVY 401 A 1 HETATM 17 C C23 AVY . A . B 2 -22.28 -7.52 2.489 0.5 31.15 ? C23 AVY 401 A 1 HETATM 18 C C26 AVY . A . B 2 -23.801 -5.971 4.711 0.5 32.44 ? C26 AVY 401 A 1 HETATM 19 C C27 AVY . A . B 2 -24.846 -5.514 5.497 0.5 36.08 ? C27 AVY 401 A 1 HETATM 20 C C28 AVY . A . B 2 -25.403 -6.343 6.455 0.5 38.56 ? C28 AVY 401 A 1 HETATM 21 C C29 AVY . A . B 2 -24.911 -7.622 6.629 0.5 36.8 ? C29 AVY 401 A 1 HETATM 22 C C30 AVY . A . B 2 -23.862 -8.077 5.854 0.5 38.43 ? C30 AVY 401 A 1 HETATM 23 N N03 AVY . A . B 2 -21.6 -4.085 1.617 0.5 23.88 ? N03 AVY 401 A 1 HETATM 24 N N10 AVY . A . B 2 -20.551 -1.789 4.22 0.5 21.25 ? N10 AVY 401 A 1 HETATM 25 N N15 AVY . A . B 2 -21.209 -5.04 8.522 0.5 22.36 ? N15 AVY 401 A 1 HETATM 26 O O01 AVY . A . B 2 -20.729 -5.312 3.36 0.5 26.25 ? O01 AVY 401 A 1 HETATM 27 O O18 AVY . A . B 2 -18.992 -4.413 8.008 0.5 20.67 ? O18 AVY 401 A 1 HETATM 28 O O20 AVY . A . B 2 -21.243 0.821 4.41 0.5 19.71 ? O20 AVY 401 A 1 HETATM 29 O O21 AVY . A . B 2 -22.651 -2.442 3.568 0.5 25.24 ? O21 AVY 401 A 1 HETATM 30 O O22 AVY . A . B 2 -22.565 -6.167 2.272 0.5 28.36 ? O22 AVY 401 A 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 30 #