data_3VHH
#
_model_server_result.job_id            pvknWMrdIzj2s1KJG0Oe8w 
_model_server_result.datetime_utc      '2024-11-15 18:48:08' 
_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          3vhh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":1124}' 
#
_entry.id    3VHH 
#
_exptl.entry_id    3VHH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              272.364 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '5-[(3aS,4S,6aR)-1,3-dimethyl-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic 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          119.64 
_cell.angle_gamma         90 
_cell.entry_id            3VHH 
_cell.length_a            129.967 
_cell.length_b            73.51 
_cell.length_c            81.473 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VHH 
_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    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 E N N 
? 2 I N N 
? 2 L N N 
? 2 P 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 4 A CYS 4 1_555 A SG CYS 83 A CYS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
disulf ? disulf2 B SG CYS 4 B CYS 4 1_555 B SG CYS 83 B CYS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf3 C SG CYS 4 C CYS 4 1_555 C SG CYS 83 C CYS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf4 D SG CYS 4 D CYS 4 1_555 D SG CYS 83 D CYS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
covale ? covale1 A ND2 ASN 17 A ASN 17 1_555 F C1 NAG . A NAG 1125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.738 ? 
covale ? covale2 B ND2 ASN 17 B ASN 17 1_555 J C1 NAG . B NAG 1125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? 
covale ? covale3 C ND2 ASN 17 C ASN 17 1_555 M C1 NAG . C NAG 1125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.616 ? 
covale ? covale4 D ND2 ASN 17 D ASN 17 1_555 Q C1 NAG . D NAG 1125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? 
#
_chem_comp.formula           'C12 H20 N2 O3 S' 
_chem_comp.formula_weight    272.364 
_chem_comp.id                VHH 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '5-[(3aS,4S,6aR)-1,3-dimethyl-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic 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
N1 C3 VHH sing 410 n n 
N1 C5 VHH sing 411 n n 
N1 C18 VHH sing 412 n n 
S1 C2 VHH sing 413 n n 
S1 C6 VHH sing 414 n n 
C2 C4 VHH sing 415 n n 
C2 C7 VHH sing 416 n n 
N2 C3 VHH sing 417 n n 
N2 C4 VHH sing 418 n n 
N2 C17 VHH sing 419 n n 
C3 O3 VHH doub 420 n n 
C4 C5 VHH sing 421 n n 
C5 C6 VHH sing 422 n n 
C7 C8 VHH sing 423 n n 
C8 C9 VHH sing 424 n n 
C9 C10 VHH sing 425 n n 
C10 C11 VHH sing 426 n n 
C11 O11 VHH sing 427 n n 
C11 O12 VHH doub 428 n n 
C2 H2 VHH sing 429 n n 
C4 H4 VHH sing 430 n n 
C5 H5 VHH sing 431 n n 
C6 H6 VHH sing 432 n n 
C6 H6A VHH sing 433 n n 
C7 H7 VHH sing 434 n n 
C7 H7A VHH sing 435 n n 
C8 H8 VHH sing 436 n n 
C8 H8A VHH sing 437 n n 
C9 H9 VHH sing 438 n n 
C9 H9A VHH sing 439 n n 
C10 H10 VHH sing 440 n n 
C10 H10A VHH sing 441 n n 
O11 HO11 VHH sing 442 n n 
C17 H17 VHH sing 443 n n 
C17 H17A VHH sing 444 n n 
C17 H17B VHH sing 445 n n 
C18 H18 VHH sing 446 n n 
C18 H18A VHH sing 447 n n 
C18 H18B VHH sing 448 n n 
#
_atom_sites.entry_id                     3VHH 
_atom_sites.fract_transf_matrix[1][1]    0.007694 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004378 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013604 
_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]    0.014122 
_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 2 VHH A 1 1124 1124 VHH DME . 
F 3 NAG A 1 1125 1125 NAG NAG . 
G 4 SO4 A 1 1126 1126 SO4 SO4 . 
H 4 SO4 A 1 1127 1127 SO4 SO4 . 
I 2 VHH B 1 1124 1124 VHH DME . 
J 3 NAG B 1 1125 1125 NAG NAG . 
K 4 SO4 B 1 1126 1126 SO4 SO4 . 
L 2 VHH C 1 1124 1124 VHH DME . 
M 3 NAG C 1 1125 1125 NAG NAG . 
N 4 SO4 C 1 1126 1126 SO4 SO4 . 
O 4 SO4 C 1 1127 1127 SO4 SO4 . 
P 2 VHH D 1 1124 1124 VHH DME . 
Q 3 NAG D 1 1125 1125 NAG NAG . 
R 4 SO4 D 1 1126 1126 SO4 SO4 . 
S 5 HOH A 1 124 124 HOH HOH . 
S 5 HOH A 2 125 125 HOH HOH . 
S 5 HOH A 3 126 3 HOH HOH . 
S 5 HOH A 4 127 13 HOH HOH . 
S 5 HOH A 5 128 14 HOH HOH . 
S 5 HOH A 6 129 15 HOH HOH . 
S 5 HOH A 7 130 16 HOH HOH . 
S 5 HOH A 8 131 17 HOH HOH . 
S 5 HOH A 9 132 132 HOH HOH . 
S 5 HOH A 10 133 21 HOH HOH . 
S 5 HOH A 11 134 22 HOH HOH . 
S 5 HOH A 12 135 23 HOH HOH . 
S 5 HOH A 13 136 24 HOH HOH . 
S 5 HOH A 14 137 25 HOH HOH . 
S 5 HOH A 15 138 32 HOH HOH . 
S 5 HOH A 16 139 33 HOH HOH . 
S 5 HOH A 17 140 34 HOH HOH . 
S 5 HOH A 18 141 35 HOH HOH . 
S 5 HOH A 19 142 36 HOH HOH . 
S 5 HOH A 20 143 37 HOH HOH . 
S 5 HOH A 21 144 42 HOH HOH . 
S 5 HOH A 22 145 43 HOH HOH . 
S 5 HOH A 23 146 46 HOH HOH . 
S 5 HOH A 24 147 47 HOH HOH . 
S 5 HOH A 25 148 48 HOH HOH . 
S 5 HOH A 26 149 51 HOH HOH . 
S 5 HOH A 27 150 57 HOH HOH . 
S 5 HOH A 28 151 58 HOH HOH . 
S 5 HOH A 29 152 59 HOH HOH . 
S 5 HOH A 30 153 61 HOH HOH . 
S 5 HOH A 31 154 123 HOH HOH . 
T 5 HOH B 1 124 19 HOH HOH . 
T 5 HOH B 2 125 27 HOH HOH . 
T 5 HOH B 3 126 126 HOH HOH . 
T 5 HOH B 4 127 28 HOH HOH . 
T 5 HOH B 5 128 29 HOH HOH . 
T 5 HOH B 6 129 30 HOH HOH . 
T 5 HOH B 7 130 44 HOH HOH . 
T 5 HOH B 8 131 45 HOH HOH . 
T 5 HOH B 9 132 49 HOH HOH . 
T 5 HOH B 10 133 50 HOH HOH . 
T 5 HOH B 11 134 52 HOH HOH . 
T 5 HOH B 12 135 53 HOH HOH . 
T 5 HOH B 13 136 54 HOH HOH . 
T 5 HOH B 14 137 55 HOH HOH . 
T 5 HOH B 15 138 56 HOH HOH . 
T 5 HOH B 16 139 63 HOH HOH . 
T 5 HOH B 17 140 65 HOH HOH . 
T 5 HOH B 18 141 66 HOH HOH . 
T 5 HOH B 19 142 67 HOH HOH . 
T 5 HOH B 20 143 69 HOH HOH . 
T 5 HOH B 21 144 70 HOH HOH . 
T 5 HOH B 22 145 71 HOH HOH . 
T 5 HOH B 23 146 72 HOH HOH . 
T 5 HOH B 24 147 73 HOH HOH . 
T 5 HOH B 25 148 74 HOH HOH . 
T 5 HOH B 26 149 77 HOH HOH . 
T 5 HOH B 27 150 78 HOH HOH . 
T 5 HOH B 28 151 83 HOH HOH . 
U 5 HOH C 1 124 1 HOH HOH . 
U 5 HOH C 2 125 2 HOH HOH . 
U 5 HOH C 3 126 4 HOH HOH . 
U 5 HOH C 4 127 127 HOH HOH . 
U 5 HOH C 5 128 128 HOH HOH . 
U 5 HOH C 6 129 129 HOH HOH . 
U 5 HOH C 7 130 5 HOH HOH . 
U 5 HOH C 8 131 6 HOH HOH . 
U 5 HOH C 9 132 7 HOH HOH . 
U 5 HOH C 10 133 133 HOH HOH . 
U 5 HOH C 11 134 10 HOH HOH . 
U 5 HOH C 12 135 11 HOH HOH . 
U 5 HOH C 13 136 12 HOH HOH . 
U 5 HOH C 14 137 41 HOH HOH . 
U 5 HOH C 15 138 75 HOH HOH . 
U 5 HOH C 16 139 82 HOH HOH . 
U 5 HOH C 17 140 86 HOH HOH . 
U 5 HOH C 18 141 87 HOH HOH . 
U 5 HOH C 19 142 95 HOH HOH . 
U 5 HOH C 20 143 98 HOH HOH . 
U 5 HOH C 21 144 100 HOH HOH . 
U 5 HOH C 22 145 101 HOH HOH . 
U 5 HOH C 23 146 104 HOH HOH . 
U 5 HOH C 24 147 105 HOH HOH . 
U 5 HOH C 25 148 106 HOH HOH . 
U 5 HOH C 26 149 107 HOH HOH . 
U 5 HOH C 27 150 108 HOH HOH . 
U 5 HOH C 28 151 109 HOH HOH . 
U 5 HOH C 29 152 112 HOH HOH . 
U 5 HOH C 30 153 113 HOH HOH . 
U 5 HOH C 31 154 114 HOH HOH . 
U 5 HOH C 32 155 115 HOH HOH . 
U 5 HOH C 33 156 117 HOH HOH . 
V 5 HOH D 1 124 9 HOH HOH . 
V 5 HOH D 2 125 18 HOH HOH . 
V 5 HOH D 3 126 20 HOH HOH . 
V 5 HOH D 4 127 26 HOH HOH . 
V 5 HOH D 5 128 38 HOH HOH . 
V 5 HOH D 6 129 39 HOH HOH . 
V 5 HOH D 7 130 130 HOH HOH . 
V 5 HOH D 8 131 131 HOH HOH . 
V 5 HOH D 9 132 40 HOH HOH . 
V 5 HOH D 10 133 76 HOH HOH . 
V 5 HOH D 11 134 79 HOH HOH . 
V 5 HOH D 12 135 80 HOH HOH . 
V 5 HOH D 13 136 81 HOH HOH . 
V 5 HOH D 14 137 88 HOH HOH . 
V 5 HOH D 15 138 89 HOH HOH . 
V 5 HOH D 16 139 90 HOH HOH . 
V 5 HOH D 17 140 91 HOH HOH . 
V 5 HOH D 18 141 92 HOH HOH . 
V 5 HOH D 19 142 94 HOH HOH . 
V 5 HOH D 20 143 96 HOH HOH . 
V 5 HOH D 21 144 97 HOH HOH . 
V 5 HOH D 22 145 99 HOH HOH . 
V 5 HOH D 23 146 102 HOH HOH . 
V 5 HOH D 24 147 103 HOH HOH . 
V 5 HOH D 25 148 110 HOH HOH . 
V 5 HOH D 26 149 111 HOH HOH . 
V 5 HOH D 27 150 118 HOH HOH . 
V 5 HOH D 28 151 119 HOH HOH . 
V 5 HOH D 29 152 120 HOH HOH . 
V 5 HOH D 30 153 121 HOH HOH . 
V 5 HOH D 31 154 122 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 N N1 VHH . . . L 2 8.251 -11.806 14.378 1 23.3 ? N1 VHH 1124 C 1 
HETATM 2 S S1 VHH . . . L 2 8.726 -11.086 11.055 1 28.64 ? S1 VHH 1124 C 1 
HETATM 3 C C2 VHH . . . L 2 7.025 -10.786 11.235 1 25.35 ? C2 VHH 1124 C 1 
HETATM 4 N N2 VHH . . . L 2 6.413 -12.166 13.254 1 25.54 ? N2 VHH 1124 C 1 
HETATM 5 C C3 VHH . . . L 2 7.264 -12.643 14.123 1 25.81 ? C3 VHH 1124 C 1 
HETATM 6 O O3 VHH . . . L 2 7.117 -13.778 14.784 1 26.72 ? O3 VHH 1124 C 1 
HETATM 7 C C4 VHH . . . L 2 6.817 -10.855 12.778 1 25.33 ? C4 VHH 1124 C 1 
HETATM 8 C C5 VHH . . . L 2 8.126 -10.594 13.586 1 24.13 ? C5 VHH 1124 C 1 
HETATM 9 C C6 VHH . . . L 2 9.313 -10.544 12.63 1 24.88 ? C6 VHH 1124 C 1 
HETATM 10 C C7 VHH . . . L 2 6.226 -11.693 10.287 1 28.73 ? C7 VHH 1124 C 1 
HETATM 11 C C8 VHH . . . L 2 6.344 -11.511 8.948 1 30.73 ? C8 VHH 1124 C 1 
HETATM 12 C C9 VHH . . . L 2 5.636 -12.259 7.788 1 30.58 ? C9 VHH 1124 C 1 
HETATM 13 C C10 VHH . . . L 2 6.074 -11.422 6.581 1 33.66 ? C10 VHH 1124 C 1 
HETATM 14 C C11 VHH . . . L 2 5.305 -10.442 6.061 1 34.16 ? C11 VHH 1124 C 1 
HETATM 15 O O11 VHH . . . L 2 4.16 -10.24 6.501 1 38.47 ? O11 VHH 1124 C 1 
HETATM 16 O O12 VHH . . . L 2 5.727 -9.722 5.146 1 36 ? O12 VHH 1124 C 1 
HETATM 17 C C17 VHH . . . L 2 5.126 -12.753 12.877 1 29.6 ? C17 VHH 1124 C 1 
HETATM 18 C C18 VHH . . . L 2 9.276 -12.077 15.377 1 19.85 ? C18 VHH 1124 C 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           18 
#