data_9D7A
#
_model_server_result.job_id            i4-fWYDeINXQUdVRhcbP7Q 
_model_server_result.datetime_utc      '2024-12-22 08:38:16' 
_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          9d7a 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":301}' 
#
_entry.id    9D7A 
#
_exptl.entry_id    9D7A 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              401.478 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(5R)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-5-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid' 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          91.12 
_cell.angle_gamma         90 
_cell.entry_id            9D7A 
_cell.length_a            37.065 
_cell.length_b            66.257 
_cell.length_c            193.061 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9D7A 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
PISA monomeric 1 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,I 1 1 
B,F,J 2 1 
C,G,K 3 1 
D,H,L 4 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 E N N 
? 3 F N N 
? 3 G N N 
? 3 H 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
covale ? covale1 A OG SER 83 A SER 83 1_555 E C7 Y33 . A Y33 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? 
covale ? covale2 A C PHE 85 A PHE 85 1_555 A N KCX 86 A KCX 86 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.326 ? 
covale ? covale3 A C KCX 86 A KCX 86 1_555 A N ILE 87 A ILE 87 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale4 B OG SER 83 B SER 83 1_555 F C7 Y33 . B Y33 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? 
covale ? covale5 B C PHE 85 B PHE 85 1_555 B N KCX 86 B KCX 86 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.332 ? 
covale ? covale6 B C KCX 86 B KCX 86 1_555 B N ILE 87 B ILE 87 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.338 ? 
covale ? covale7 C OG SER 83 C SER 83 1_555 G C7 Y33 . C Y33 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale8 C C PHE 85 C PHE 85 1_555 C N KCX 86 C KCX 86 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.322 ? 
covale ? covale9 C C KCX 86 C KCX 86 1_555 C N ILE 87 C ILE 87 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.334 ? 
covale ? covale10 D OG SER 83 D SER 83 1_555 H C7 Y33 . D Y33 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? 
#
_chem_comp.formula           'C17 H27 N3 O6 S' 
_chem_comp.formula_weight    401.478 
_chem_comp.id                Y33 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(5R)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-5-methyl-4,5-dihydro-1H-pyrrole-2-carboxylic acid' 
_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
O31 C31 Y33 doub 402 n n 
C31 O32 Y33 sing 403 n n 
C31 C3 Y33 sing 404 n n 
C7 O7 Y33 doub 405 n n 
C7 C6 Y33 sing 406 n n 
N4 C3 Y33 sing 407 n n 
N4 C5 Y33 sing 408 n n 
C3 C2 Y33 doub 409 n n 
C26 C5 Y33 sing 410 n n 
C5 C6 Y33 sing 411 n n 
C5 C1 Y33 sing 412 n n 
C6 C61 Y33 sing 413 n n 
C62 C61 Y33 sing 414 n n 
C61 O62 Y33 sing 415 n n 
C2 C1 Y33 sing 416 n n 
C2 S21 Y33 sing 417 n n 
N3A C2A Y33 sing 418 n n 
N3A C5A Y33 sing 419 n n 
O6A C6A Y33 doub 420 n n 
C2A C1A Y33 sing 421 n n 
S21 C1A Y33 sing 422 n n 
C6A C5A Y33 sing 423 n n 
C6A N7A Y33 sing 424 n n 
C5A C4A Y33 sing 425 n n 
C1A C4A Y33 sing 426 n n 
C8A N7A Y33 sing 427 n n 
N7A C9A Y33 sing 428 n n 
C1 H1 Y33 sing 429 n n 
C1 H2 Y33 sing 430 n n 
N4 H5 Y33 sing 431 n n 
C6 H7 Y33 sing 432 n n 
C26 H9 Y33 sing 433 n n 
C26 H10 Y33 sing 434 n n 
C26 H11 Y33 sing 435 n n 
C61 H12 Y33 sing 436 n n 
C62 H13 Y33 sing 437 n n 
C62 H14 Y33 sing 438 n n 
C62 H15 Y33 sing 439 n n 
O32 H16 Y33 sing 440 n n 
O62 H17 Y33 sing 441 n n 
C1A H18 Y33 sing 442 n n 
C2A H19 Y33 sing 443 n n 
C2A H20 Y33 sing 444 n n 
C4A H21 Y33 sing 445 n n 
C4A H22 Y33 sing 446 n n 
C5A H23 Y33 sing 447 n n 
C8A H24 Y33 sing 448 n n 
C8A H25 Y33 sing 449 n n 
C8A H26 Y33 sing 450 n n 
C9A H27 Y33 sing 451 n n 
C9A H28 Y33 sing 452 n n 
C9A H29 Y33 sing 453 n n 
N3A H30 Y33 sing 454 n n 
C7 O7A Y33 sing 455 n n 
O7A H8 Y33 sing 456 n n 
#
_atom_sites.entry_id                     9D7A 
_atom_sites.fract_transf_matrix[1][1]    0.02698 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000528 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015093 
_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]    0.005181 
_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
E 3 Y33 A 1 301 301 Y33 Y33 . 
F 3 Y33 B 1 301 301 Y33 Y33 . 
G 3 Y33 C 1 301 301 Y33 Y33 . 
H 3 Y33 D 1 301 301 Y33 Y33 . 
I 4 HOH A 1 401 54 HOH HOH . 
I 4 HOH A 2 402 7 HOH HOH . 
I 4 HOH A 3 403 73 HOH HOH . 
I 4 HOH A 4 404 53 HOH HOH . 
I 4 HOH A 5 405 38 HOH HOH . 
I 4 HOH A 6 406 52 HOH HOH . 
I 4 HOH A 7 407 33 HOH HOH . 
I 4 HOH A 8 408 89 HOH HOH . 
I 4 HOH A 9 409 84 HOH HOH . 
I 4 HOH A 10 410 56 HOH HOH . 
I 4 HOH A 11 411 93 HOH HOH . 
I 4 HOH A 12 412 78 HOH HOH . 
I 4 HOH A 13 413 109 HOH HOH . 
I 4 HOH A 14 414 88 HOH HOH . 
J 4 HOH B 1 401 102 HOH HOH . 
J 4 HOH B 2 402 59 HOH HOH . 
J 4 HOH B 3 403 6 HOH HOH . 
J 4 HOH B 4 404 26 HOH HOH . 
J 4 HOH B 5 405 21 HOH HOH . 
J 4 HOH B 6 406 55 HOH HOH . 
J 4 HOH B 7 407 103 HOH HOH . 
J 4 HOH B 8 408 91 HOH HOH . 
J 4 HOH B 9 409 20 HOH HOH . 
J 4 HOH B 10 410 85 HOH HOH . 
J 4 HOH B 11 411 19 HOH HOH . 
J 4 HOH B 12 412 65 HOH HOH . 
J 4 HOH B 13 413 16 HOH HOH . 
J 4 HOH B 14 414 22 HOH HOH . 
J 4 HOH B 15 415 28 HOH HOH . 
J 4 HOH B 16 416 86 HOH HOH . 
J 4 HOH B 17 417 9 HOH HOH . 
J 4 HOH B 18 418 64 HOH HOH . 
J 4 HOH B 19 419 61 HOH HOH . 
J 4 HOH B 20 420 68 HOH HOH . 
J 4 HOH B 21 421 104 HOH HOH . 
K 4 HOH C 1 401 35 HOH HOH . 
K 4 HOH C 2 402 46 HOH HOH . 
K 4 HOH C 3 403 34 HOH HOH . 
K 4 HOH C 4 404 3 HOH HOH . 
K 4 HOH C 5 405 110 HOH HOH . 
K 4 HOH C 6 406 40 HOH HOH . 
K 4 HOH C 7 407 60 HOH HOH . 
K 4 HOH C 8 408 48 HOH HOH . 
K 4 HOH C 9 409 47 HOH HOH . 
K 4 HOH C 10 410 43 HOH HOH . 
K 4 HOH C 11 411 100 HOH HOH . 
K 4 HOH C 12 412 44 HOH HOH . 
K 4 HOH C 13 413 62 HOH HOH . 
K 4 HOH C 14 414 83 HOH HOH . 
K 4 HOH C 15 415 96 HOH HOH . 
K 4 HOH C 16 416 17 HOH HOH . 
K 4 HOH C 17 417 15 HOH HOH . 
K 4 HOH C 18 418 95 HOH HOH . 
K 4 HOH C 19 419 72 HOH HOH . 
K 4 HOH C 20 420 76 HOH HOH . 
K 4 HOH C 21 421 80 HOH HOH . 
K 4 HOH C 22 422 45 HOH HOH . 
K 4 HOH C 23 423 49 HOH HOH . 
K 4 HOH C 24 424 99 HOH HOH . 
K 4 HOH C 25 425 50 HOH HOH . 
K 4 HOH C 26 426 74 HOH HOH . 
K 4 HOH C 27 427 5 HOH HOH . 
K 4 HOH C 28 428 70 HOH HOH . 
K 4 HOH C 29 429 82 HOH HOH . 
K 4 HOH C 30 430 66 HOH HOH . 
K 4 HOH C 31 431 67 HOH HOH . 
K 4 HOH C 32 432 57 HOH HOH . 
K 4 HOH C 33 433 71 HOH HOH . 
K 4 HOH C 34 434 69 HOH HOH . 
L 4 HOH D 1 401 36 HOH HOH . 
L 4 HOH D 2 402 101 HOH HOH . 
L 4 HOH D 3 403 4 HOH HOH . 
L 4 HOH D 4 404 90 HOH HOH . 
L 4 HOH D 5 405 81 HOH HOH . 
L 4 HOH D 6 406 58 HOH HOH . 
L 4 HOH D 7 407 87 HOH HOH . 
L 4 HOH D 8 408 108 HOH HOH . 
L 4 HOH D 9 409 37 HOH HOH . 
L 4 HOH D 10 410 107 HOH HOH . 
L 4 HOH D 11 411 77 HOH HOH . 
L 4 HOH D 12 412 97 HOH HOH . 
L 4 HOH D 13 413 106 HOH HOH . 
L 4 HOH D 14 414 24 HOH HOH . 
L 4 HOH D 15 415 25 HOH HOH . 
L 4 HOH D 16 416 105 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 C1 Y33 . . . H 3 14.666 40.701 83.793 0.73 47.03 ? C1 Y33 301 D 1 
HETATM 2 C C2 Y33 . . . H 3 14.299 40.845 82.333 0.73 50.02 ? C2 Y33 301 D 1 
HETATM 3 C C3 Y33 . . . H 3 13.736 39.718 81.922 0.73 51.48 ? C3 Y33 301 D 1 
HETATM 4 N N4 Y33 . . . H 3 13.329 38.988 82.958 0.73 50.31 ? N4 Y33 301 D 1 
HETATM 5 C C5 Y33 . . . H 3 13.969 39.384 84.2 0.73 48.2 ? C5 Y33 301 D 1 
HETATM 6 C C6 Y33 . . . H 3 14.901 38.217 84.562 0.73 45.64 ? C6 Y33 301 D 1 
HETATM 7 C C7 Y33 . . . H 3 14.146 36.899 84.416 0.73 44.85 ? C7 Y33 301 D 1 
HETATM 8 C C26 Y33 . . . H 3 12.893 39.635 85.243 0.73 48.22 ? C26 Y33 301 D 1 
HETATM 9 C C31 Y33 . . . H 3 13.555 39.311 80.535 0.73 49.32 ? C31 Y33 301 D 1 
HETATM 10 C C61 Y33 . . . H 3 15.56 38.184 85.95 0.73 45.45 ? C61 Y33 301 D 1 
HETATM 11 C C62 Y33 . . . H 3 16.175 39.485 86.47 0.73 43.29 ? C62 Y33 301 D 1 
HETATM 12 O O31 Y33 . . . H 3 12.551 38.625 80.261 0.73 51.23 ? O31 Y33 301 D 1 
HETATM 13 O O32 Y33 . . . H 3 14.403 39.645 79.679 0.73 50.54 ? O32 Y33 301 D 1 
HETATM 14 O O62 Y33 . . . H 3 14.638 37.646 86.906 0.73 46.78 ? O62 Y33 301 D 1 
HETATM 15 O O7 Y33 . . . H 3 14.715 36.003 83.814 0.73 39.04 ? O7 Y33 301 D 1 
HETATM 16 C C1A Y33 . . . H 3 13.065 43.267 81.571 0.73 55.29 ? C1A Y33 301 D 1 
HETATM 17 C C2A Y33 . . . H 3 11.95 42.534 82.28 0.73 54.28 ? C2A Y33 301 D 1 
HETATM 18 C C4A Y33 . . . H 3 12.472 43.676 80.225 0.73 55.9 ? C4A Y33 301 D 1 
HETATM 19 C C5A Y33 . . . H 3 11.24 42.799 80.036 0.73 56.03 ? C5A Y33 301 D 1 
HETATM 20 C C6A Y33 . . . H 3 11.287 42.021 78.734 0.73 55.76 ? C6A Y33 301 D 1 
HETATM 21 C C8A Y33 . . . H 3 11.099 42.14 76.283 0.73 56.67 ? C8A Y33 301 D 1 
HETATM 22 C C9A Y33 . . . H 3 9.655 43.558 77.707 0.73 56.84 ? C9A Y33 301 D 1 
HETATM 23 N N3A Y33 . . . H 3 11.177 41.911 81.221 0.73 53.46 ? N3A Y33 301 D 1 
HETATM 24 N N7A Y33 . . . H 3 10.717 42.552 77.639 0.73 57.91 ? N7A Y33 301 D 1 
HETATM 25 O O6A Y33 . . . H 3 11.766 40.911 78.689 0.73 53.87 ? O6A Y33 301 D 1 
HETATM 26 S S21 Y33 . . . H 3 14.493 42.225 81.394 0.73 53.88 ? S21 Y33 301 D 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           225 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           26 
#