data_7LYI
#
_model_server_result.job_id            owjsbG_kfmCG561DGYx7xg 
_model_server_result.datetime_utc      '2024-11-16 08:33:55' 
_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          7lyi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":503}' 
#
_entry.id    7LYI 
#
_exptl.entry_id    7LYI 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              429.509 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'benzyl (1R,2S,5S)-2-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-3-carboxylate' 
_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          101.1 
_cell.angle_gamma         90 
_cell.entry_id            7LYI 
_cell.length_a            113.9 
_cell.length_b            54.31 
_cell.length_c            45.17 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7LYI 
_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,E 
_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_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_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
covale ? covale1 A SG CYS 147 A CYS 145 1_555 D C29 YHI . A YHI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.706 ? 
metalc ? metalc1 A O VAL 79 A VAL 77 1_555 C NA NA . A NA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.777 ? 
metalc ? metalc2 C NA NA . A NA 502 1_555 E O HOH . A HOH 637 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.011 ? 
metalc ? metalc3 C NA NA . A NA 502 1_555 E O HOH . A HOH 665 1_544 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? 
#
_chem_comp.formula           'C23 H31 N3 O5' 
_chem_comp.formula_weight    429.509 
_chem_comp.id                YHI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'benzyl (1R,2S,5S)-2-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-3-carboxylate' 
_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
C01 C02 YHI sing 389 n n 
C01 C16 YHI sing 390 n n 
C01 C15 YHI sing 391 n n 
C02 N03 YHI sing 392 n n 
C18 C16 YHI sing 393 n n 
C11 C12 YHI doub 394 n y 
C11 C10 YHI sing 395 n y 
C12 C07 YHI sing 396 n y 
C16 C15 YHI sing 397 n n 
C16 C17 YHI sing 398 n n 
C10 C09 YHI doub 399 n y 
C15 C14 YHI sing 400 n n 
O05 C06 YHI sing 401 n n 
O05 C04 YHI sing 402 n n 
C07 C06 YHI sing 403 n n 
C07 C08 YHI doub 404 n y 
O31 C19 YHI doub 405 n n 
N03 C04 YHI sing 406 n n 
N03 C14 YHI sing 407 n n 
C09 C08 YHI sing 408 n y 
C04 O13 YHI doub 409 n n 
C14 C19 YHI sing 410 n n 
C19 N20 YHI sing 411 n n 
N20 C21 YHI sing 412 n n 
C24 C25 YHI sing 413 n n 
C24 C23 YHI sing 414 n n 
C21 C29 YHI sing 415 n n 
C21 C22 YHI sing 416 n n 
C25 N26 YHI sing 417 n n 
C29 O30 YHI sing 418 n n 
C23 C22 YHI sing 419 n n 
C23 C27 YHI sing 420 n n 
N26 C27 YHI sing 421 n n 
C27 O28 YHI doub 422 n n 
C10 H1 YHI sing 423 n n 
C15 H2 YHI sing 424 n n 
C17 H3 YHI sing 425 n n 
C17 H4 YHI sing 426 n n 
C17 H5 YHI sing 427 n n 
C21 H6 YHI sing 428 n n 
C22 H7 YHI sing 429 n n 
C22 H8 YHI sing 430 n n 
C24 H9 YHI sing 431 n n 
C24 H10 YHI sing 432 n n 
C01 H11 YHI sing 433 n n 
C02 H12 YHI sing 434 n n 
C02 H13 YHI sing 435 n n 
C06 H14 YHI sing 436 n n 
C06 H15 YHI sing 437 n n 
C08 H16 YHI sing 438 n n 
C09 H17 YHI sing 439 n n 
C11 H18 YHI sing 440 n n 
C12 H19 YHI sing 441 n n 
C14 H20 YHI sing 442 n n 
C18 H21 YHI sing 443 n n 
C18 H22 YHI sing 444 n n 
C18 H23 YHI sing 445 n n 
N20 H24 YHI sing 446 n n 
C23 H25 YHI sing 447 n n 
C25 H26 YHI sing 448 n n 
C29 H27 YHI sing 449 n n 
C29 H28 YHI sing 450 n n 
O30 H29 YHI sing 451 n n 
C25 H30 YHI sing 452 n n 
N26 H31 YHI sing 453 n n 
#
_atom_sites.entry_id                     7LYI 
_atom_sites.fract_transf_matrix[1][1]    0.00878 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001722 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018413 
_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]    0.022561 
_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 GOL A 1 501 501 GOL GOL . 
C 3 NA A 1 502 502 NA NA . 
D 4 YHI A 1 503 601 YHI LIG . 
E 5 HOH A 1 601 233 HOH HOH . 
E 5 HOH A 2 602 234 HOH HOH . 
E 5 HOH A 3 603 238 HOH HOH . 
E 5 HOH A 4 604 91 HOH HOH . 
E 5 HOH A 5 605 241 HOH HOH . 
E 5 HOH A 6 606 243 HOH HOH . 
E 5 HOH A 7 607 26 HOH HOH . 
E 5 HOH A 8 608 129 HOH HOH . 
E 5 HOH A 9 609 235 HOH HOH . 
E 5 HOH A 10 610 42 HOH HOH . 
E 5 HOH A 11 611 237 HOH HOH . 
E 5 HOH A 12 612 4 HOH HOH . 
E 5 HOH A 13 613 101 HOH HOH . 
E 5 HOH A 14 614 95 HOH HOH . 
E 5 HOH A 15 615 17 HOH HOH . 
E 5 HOH A 16 616 43 HOH HOH . 
E 5 HOH A 17 617 56 HOH HOH . 
E 5 HOH A 18 618 24 HOH HOH . 
E 5 HOH A 19 619 9 HOH HOH . 
E 5 HOH A 20 620 166 HOH HOH . 
E 5 HOH A 21 621 45 HOH HOH . 
E 5 HOH A 22 622 53 HOH HOH . 
E 5 HOH A 23 623 94 HOH HOH . 
E 5 HOH A 24 624 21 HOH HOH . 
E 5 HOH A 25 625 71 HOH HOH . 
E 5 HOH A 26 626 92 HOH HOH . 
E 5 HOH A 27 627 16 HOH HOH . 
E 5 HOH A 28 628 20 HOH HOH . 
E 5 HOH A 29 629 87 HOH HOH . 
E 5 HOH A 30 630 76 HOH HOH . 
E 5 HOH A 31 631 15 HOH HOH . 
E 5 HOH A 32 632 22 HOH HOH . 
E 5 HOH A 33 633 39 HOH HOH . 
E 5 HOH A 34 634 63 HOH HOH . 
E 5 HOH A 35 635 28 HOH HOH . 
E 5 HOH A 36 636 2 HOH HOH . 
E 5 HOH A 37 637 64 HOH HOH . 
E 5 HOH A 38 638 31 HOH HOH . 
E 5 HOH A 39 639 34 HOH HOH . 
E 5 HOH A 40 640 12 HOH HOH . 
E 5 HOH A 41 641 23 HOH HOH . 
E 5 HOH A 42 642 38 HOH HOH . 
E 5 HOH A 43 643 75 HOH HOH . 
E 5 HOH A 44 644 33 HOH HOH . 
E 5 HOH A 45 645 1 HOH HOH . 
E 5 HOH A 46 646 127 HOH HOH . 
E 5 HOH A 47 647 82 HOH HOH . 
E 5 HOH A 48 648 67 HOH HOH . 
E 5 HOH A 49 649 112 HOH HOH . 
E 5 HOH A 50 650 5 HOH HOH . 
E 5 HOH A 51 651 35 HOH HOH . 
E 5 HOH A 52 652 44 HOH HOH . 
E 5 HOH A 53 653 242 HOH HOH . 
E 5 HOH A 54 654 230 HOH HOH . 
E 5 HOH A 55 655 10 HOH HOH . 
E 5 HOH A 56 656 29 HOH HOH . 
E 5 HOH A 57 657 47 HOH HOH . 
E 5 HOH A 58 658 70 HOH HOH . 
E 5 HOH A 59 659 3 HOH HOH . 
E 5 HOH A 60 660 223 HOH HOH . 
E 5 HOH A 61 661 65 HOH HOH . 
E 5 HOH A 62 662 186 HOH HOH . 
E 5 HOH A 63 663 58 HOH HOH . 
E 5 HOH A 64 664 128 HOH HOH . 
E 5 HOH A 65 665 231 HOH HOH . 
E 5 HOH A 66 666 57 HOH HOH . 
E 5 HOH A 67 667 136 HOH HOH . 
E 5 HOH A 68 668 60 HOH HOH . 
E 5 HOH A 69 669 48 HOH HOH . 
E 5 HOH A 70 670 25 HOH HOH . 
E 5 HOH A 71 671 147 HOH HOH . 
E 5 HOH A 72 672 96 HOH HOH . 
E 5 HOH A 73 673 69 HOH HOH . 
E 5 HOH A 74 674 232 HOH HOH . 
E 5 HOH A 75 675 228 HOH HOH . 
E 5 HOH A 76 676 18 HOH HOH . 
E 5 HOH A 77 677 74 HOH HOH . 
E 5 HOH A 78 678 116 HOH HOH . 
E 5 HOH A 79 679 13 HOH HOH . 
E 5 HOH A 80 680 37 HOH HOH . 
E 5 HOH A 81 681 7 HOH HOH . 
E 5 HOH A 82 682 27 HOH HOH . 
E 5 HOH A 83 683 8 HOH HOH . 
E 5 HOH A 84 684 14 HOH HOH . 
E 5 HOH A 85 685 244 HOH HOH . 
E 5 HOH A 86 686 246 HOH HOH . 
E 5 HOH A 87 687 226 HOH HOH . 
E 5 HOH A 88 688 124 HOH HOH . 
E 5 HOH A 89 689 221 HOH HOH . 
E 5 HOH A 90 690 229 HOH HOH . 
E 5 HOH A 91 691 148 HOH HOH . 
E 5 HOH A 92 692 40 HOH HOH . 
E 5 HOH A 93 693 236 HOH HOH . 
E 5 HOH A 94 694 114 HOH HOH . 
E 5 HOH A 95 695 83 HOH HOH . 
E 5 HOH A 96 696 109 HOH HOH . 
E 5 HOH A 97 697 49 HOH HOH . 
E 5 HOH A 98 698 99 HOH HOH . 
E 5 HOH A 99 699 152 HOH HOH . 
E 5 HOH A 100 700 239 HOH HOH . 
E 5 HOH A 101 701 104 HOH HOH . 
E 5 HOH A 102 702 219 HOH HOH . 
E 5 HOH A 103 703 247 HOH HOH . 
E 5 HOH A 104 704 220 HOH HOH . 
E 5 HOH A 105 705 222 HOH HOH . 
E 5 HOH A 106 706 225 HOH HOH . 
E 5 HOH A 107 707 121 HOH HOH . 
E 5 HOH A 108 708 245 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 C10 YHI . . . D 4 -5.099 -23.86 -23.141 1 20 ? C10 YHI 503 A 1 
HETATM 2 C C15 YHI . . . D 4 -11.89 -28.471 -23.012 1 20 ? C15 YHI 503 A 1 
HETATM 3 C C17 YHI . . . D 4 -14.194 -27.465 -22.503 1 20 ? C17 YHI 503 A 1 
HETATM 4 C C21 YHI . . . D 4 -7.903 -29.094 -20.115 1 20 ? C21 YHI 503 A 1 
HETATM 5 C C22 YHI . . . D 4 -7.291 -28.139 -19.042 1 20 ? C22 YHI 503 A 1 
HETATM 6 C C24 YHI . . . D 4 -6.072 -26.357 -20.457 1 20 ? C24 YHI 503 A 1 
HETATM 7 C C01 YHI . . . D 4 -12.122 -27.621 -24.252 1 20 ? C01 YHI 503 A 1 
HETATM 8 C C02 YHI . . . D 4 -11.247 -26.41 -24.104 1 20 ? C02 YHI 503 A 1 
HETATM 9 N N03 YHI . . . D 4 -10.942 -26.308 -22.665 1 20 ? N03 YHI 503 A 1 
HETATM 10 C C04 YHI . . . D 4 -10.407 -25.256 -22.144 1 20 ? C04 YHI 503 A 1 
HETATM 11 O O05 YHI . . . D 4 -10.297 -24.126 -22.95 1 20 ? O05 YHI 503 A 1 
HETATM 12 C C06 YHI . . . D 4 -9.303 -23.119 -22.611 1 20 ? C06 YHI 503 A 1 
HETATM 13 C C07 YHI . . . D 4 -7.827 -23.476 -22.782 1 20 ? C07 YHI 503 A 1 
HETATM 14 C C08 YHI . . . D 4 -6.841 -22.546 -22.289 1 20 ? C08 YHI 503 A 1 
HETATM 15 C C09 YHI . . . D 4 -5.513 -22.745 -22.442 1 20 ? C09 YHI 503 A 1 
HETATM 16 C C11 YHI . . . D 4 -5.968 -24.812 -23.67 1 20 ? C11 YHI 503 A 1 
HETATM 17 C C12 YHI . . . D 4 -7.334 -24.597 -23.534 1 20 ? C12 YHI 503 A 1 
HETATM 18 O O13 YHI . . . D 4 -9.998 -25.185 -21.019 1 20 ? O13 YHI 503 A 1 
HETATM 19 C C14 YHI . . . D 4 -11.029 -27.661 -22.114 1 20 ? C14 YHI 503 A 1 
HETATM 20 C C16 YHI . . . D 4 -13.337 -28.364 -23.496 1 20 ? C16 YHI 503 A 1 
HETATM 21 C C18 YHI . . . D 4 -14.004 -29.462 -24.034 1 20 ? C18 YHI 503 A 1 
HETATM 22 C C19 YHI . . . D 4 -9.551 -28.16 -21.837 1 20 ? C19 YHI 503 A 1 
HETATM 23 N N20 YHI . . . D 4 -9.237 -28.657 -20.495 1 20 ? N20 YHI 503 A 1 
HETATM 24 C C23 YHI . . . D 4 -7.126 -26.653 -19.344 1 20 ? C23 YHI 503 A 1 
HETATM 25 C C25 YHI . . . D 4 -5.16 -25.291 -19.973 1 20 ? C25 YHI 503 A 1 
HETATM 26 N N26 YHI . . . D 4 -5.535 -25.095 -18.491 1 20 ? N26 YHI 503 A 1 
HETATM 27 C C27 YHI . . . D 4 -6.683 -25.835 -18.144 1 20 ? C27 YHI 503 A 1 
HETATM 28 O O28 YHI . . . D 4 -7.214 -25.823 -17.054 1 20 ? O28 YHI 503 A 1 
HETATM 29 C C29 YHI . . . D 4 -8.028 -30.456 -19.676 1 20 ? C29 YHI 503 A 1 
HETATM 30 O O30 YHI . . . D 4 -6.614 -30.844 -19.427 1 20 ? O30 YHI 503 A 1 
HETATM 31 O O31 YHI . . . D 4 -8.63 -28.129 -22.667 1 20 ? O31 YHI 503 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           28 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           31 
#