data_8RDR
#
_model_server_result.job_id            im1EpFfRVT9ighkLddLf4Q 
_model_server_result.datetime_utc      '2024-11-26 05:44:46' 
_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          8rdr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":202}' 
#
_entry.id    8RDR 
#
_exptl.entry_id    8RDR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              289.244 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (5~{S})-3-(2-nitrophenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione 
_entity.pdbx_number_of_molecules    3 
_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            8RDR 
_cell.length_a            56.663 
_cell.length_b            60.446 
_cell.length_c            88.841 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8RDR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,F,L 1 1 
B,G,H,I,M 2 1 
C,J,K,N 3 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 H N N 
? 3 K 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
metalc ? metalc1 A SG CYS 25 A CYS 24 1_555 D ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? 
metalc ? metalc2 A SG CYS 28 A CYS 27 1_555 D ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc3 A SG CYS 91 A CYS 90 1_555 D ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? 
metalc ? metalc4 A SG CYS 94 A CYS 93 1_555 D ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
metalc ? metalc5 B SG CYS 25 B CYS 24 1_555 G ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? 
metalc ? metalc6 B SG CYS 28 B CYS 27 1_555 G ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? 
metalc ? metalc7 B SG CYS 91 B CYS 90 1_555 G ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
metalc ? metalc8 B SG CYS 94 B CYS 93 1_555 G ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? 
metalc ? metalc9 C SG CYS 25 C CYS 24 1_555 J ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? 
metalc ? metalc10 C SG CYS 28 C CYS 27 1_555 J ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc11 C SG CYS 91 C CYS 90 1_555 J ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? 
metalc ? metalc12 C SG CYS 94 C CYS 93 1_555 J ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? 
#
_chem_comp.formula           'C13 H11 N3 O5' 
_chem_comp.formula_weight    289.244 
_chem_comp.id                A1HZ3 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (5~{S})-3-(2-nitrophenyl)-1-oxa-2,9-diazaspiro[4.5]dec-2-ene-8,10-dione 
_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
C9 C10 A1HZ3 doub 1 n y 
C9 C8 A1HZ3 sing 2 n y 
C10 C11 A1HZ3 sing 3 n y 
C8 C7 A1HZ3 doub 4 n y 
C11 C12 A1HZ3 doub 5 n y 
C7 C12 A1HZ3 sing 6 n y 
C7 C6 A1HZ3 sing 7 n n 
C12 N2 A1HZ3 sing 8 n n 
C6 C5 A1HZ3 sing 9 n n 
C6 N3 A1HZ3 doub 10 n n 
O5 C13 A1HZ3 doub 11 n n 
C5 C4 A1HZ3 sing 12 n n 
N2 O2 A1HZ3 sing 13 n n 
N2 O3 A1HZ3 doub 14 n n 
C13 N1 A1HZ3 sing 15 n n 
C13 C4 A1HZ3 sing 16 n n 
N3 O4 A1HZ3 sing 17 n n 
N1 C1 A1HZ3 sing 18 n n 
C4 O4 A1HZ3 sing 19 n n 
C4 C3 A1HZ3 sing 20 n n 
C1 O1 A1HZ3 doub 21 n n 
C1 C2 A1HZ3 sing 22 n n 
C2 C3 A1HZ3 sing 23 n n 
N1 H1 A1HZ3 sing 24 n n 
C3 H2 A1HZ3 sing 25 n n 
C3 H3 A1HZ3 sing 26 n n 
C2 H4 A1HZ3 sing 27 n n 
C2 H5 A1HZ3 sing 28 n n 
C5 H6 A1HZ3 sing 29 n n 
C5 H7 A1HZ3 sing 30 n n 
C11 H8 A1HZ3 sing 31 n n 
C10 H9 A1HZ3 sing 32 n n 
C9 H10 A1HZ3 sing 33 n n 
C8 H11 A1HZ3 sing 34 n n 
#
_atom_sites.entry_id                     8RDR 
_atom_sites.fract_transf_matrix[1][1]    0.017648 
_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]    0.016544 
_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]    0.011256 
_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
D 2 ZN A 1 201 150 ZN ZN . 
E 3 A1HZ3 A 1 202 201 A1HZ3 139 . 
F 4 PO4 A 1 203 2 PO4 PO4 . 
G 2 ZN B 1 201 150 ZN ZN . 
H 3 A1HZ3 B 1 202 201 A1HZ3 139 . 
I 4 PO4 B 1 203 1 PO4 PO4 . 
J 2 ZN C 1 201 150 ZN ZN . 
K 3 A1HZ3 C 1 202 201 A1HZ3 139 . 
L 5 HOH A 1 301 81 HOH HOH . 
L 5 HOH A 2 302 110 HOH HOH . 
L 5 HOH A 3 303 120 HOH HOH . 
L 5 HOH A 4 304 90 HOH HOH . 
L 5 HOH A 5 305 58 HOH HOH . 
L 5 HOH A 6 306 101 HOH HOH . 
L 5 HOH A 7 307 5 HOH HOH . 
L 5 HOH A 8 308 8 HOH HOH . 
L 5 HOH A 9 309 118 HOH HOH . 
L 5 HOH A 10 310 89 HOH HOH . 
L 5 HOH A 11 311 80 HOH HOH . 
L 5 HOH A 12 312 69 HOH HOH . 
L 5 HOH A 13 313 38 HOH HOH . 
L 5 HOH A 14 314 33 HOH HOH . 
L 5 HOH A 15 315 30 HOH HOH . 
L 5 HOH A 16 316 51 HOH HOH . 
L 5 HOH A 17 317 50 HOH HOH . 
L 5 HOH A 18 318 21 HOH HOH . 
L 5 HOH A 19 319 63 HOH HOH . 
L 5 HOH A 20 320 130 HOH HOH . 
L 5 HOH A 21 321 48 HOH HOH . 
L 5 HOH A 22 322 121 HOH HOH . 
L 5 HOH A 23 323 103 HOH HOH . 
L 5 HOH A 24 324 24 HOH HOH . 
L 5 HOH A 25 325 43 HOH HOH . 
L 5 HOH A 26 326 83 HOH HOH . 
L 5 HOH A 27 327 37 HOH HOH . 
L 5 HOH A 28 328 74 HOH HOH . 
L 5 HOH A 29 329 7 HOH HOH . 
L 5 HOH A 30 330 122 HOH HOH . 
L 5 HOH A 31 331 142 HOH HOH . 
L 5 HOH A 32 332 65 HOH HOH . 
L 5 HOH A 33 333 141 HOH HOH . 
L 5 HOH A 34 334 4 HOH HOH . 
L 5 HOH A 35 335 39 HOH HOH . 
L 5 HOH A 36 336 52 HOH HOH . 
L 5 HOH A 37 337 152 HOH HOH . 
L 5 HOH A 38 338 31 HOH HOH . 
L 5 HOH A 39 339 139 HOH HOH . 
L 5 HOH A 40 340 36 HOH HOH . 
L 5 HOH A 41 341 44 HOH HOH . 
L 5 HOH A 42 342 136 HOH HOH . 
L 5 HOH A 43 343 99 HOH HOH . 
L 5 HOH A 44 344 16 HOH HOH . 
L 5 HOH A 45 345 79 HOH HOH . 
L 5 HOH A 46 346 105 HOH HOH . 
L 5 HOH A 47 347 113 HOH HOH . 
L 5 HOH A 48 348 49 HOH HOH . 
L 5 HOH A 49 349 59 HOH HOH . 
L 5 HOH A 50 350 85 HOH HOH . 
M 5 HOH B 1 301 137 HOH HOH . 
M 5 HOH B 2 302 147 HOH HOH . 
M 5 HOH B 3 303 19 HOH HOH . 
M 5 HOH B 4 304 86 HOH HOH . 
M 5 HOH B 5 305 104 HOH HOH . 
M 5 HOH B 6 306 124 HOH HOH . 
M 5 HOH B 7 307 41 HOH HOH . 
M 5 HOH B 8 308 35 HOH HOH . 
M 5 HOH B 9 309 26 HOH HOH . 
M 5 HOH B 10 310 106 HOH HOH . 
M 5 HOH B 11 311 138 HOH HOH . 
M 5 HOH B 12 312 95 HOH HOH . 
M 5 HOH B 13 313 12 HOH HOH . 
M 5 HOH B 14 314 29 HOH HOH . 
M 5 HOH B 15 315 22 HOH HOH . 
M 5 HOH B 16 316 9 HOH HOH . 
M 5 HOH B 17 317 17 HOH HOH . 
M 5 HOH B 18 318 93 HOH HOH . 
M 5 HOH B 19 319 128 HOH HOH . 
M 5 HOH B 20 320 71 HOH HOH . 
M 5 HOH B 21 321 115 HOH HOH . 
M 5 HOH B 22 322 146 HOH HOH . 
M 5 HOH B 23 323 126 HOH HOH . 
M 5 HOH B 24 324 34 HOH HOH . 
M 5 HOH B 25 325 148 HOH HOH . 
M 5 HOH B 26 326 60 HOH HOH . 
M 5 HOH B 27 327 15 HOH HOH . 
M 5 HOH B 28 328 150 HOH HOH . 
M 5 HOH B 29 329 14 HOH HOH . 
M 5 HOH B 30 330 116 HOH HOH . 
M 5 HOH B 31 331 144 HOH HOH . 
M 5 HOH B 32 332 40 HOH HOH . 
M 5 HOH B 33 333 6 HOH HOH . 
M 5 HOH B 34 334 117 HOH HOH . 
M 5 HOH B 35 335 10 HOH HOH . 
M 5 HOH B 36 336 55 HOH HOH . 
M 5 HOH B 37 337 98 HOH HOH . 
M 5 HOH B 38 338 68 HOH HOH . 
M 5 HOH B 39 339 42 HOH HOH . 
M 5 HOH B 40 340 76 HOH HOH . 
M 5 HOH B 41 341 145 HOH HOH . 
M 5 HOH B 42 342 56 HOH HOH . 
M 5 HOH B 43 343 54 HOH HOH . 
M 5 HOH B 44 344 87 HOH HOH . 
M 5 HOH B 45 345 23 HOH HOH . 
M 5 HOH B 46 346 92 HOH HOH . 
M 5 HOH B 47 347 82 HOH HOH . 
M 5 HOH B 48 348 11 HOH HOH . 
M 5 HOH B 49 349 75 HOH HOH . 
M 5 HOH B 50 350 45 HOH HOH . 
M 5 HOH B 51 351 3 HOH HOH . 
M 5 HOH B 52 352 132 HOH HOH . 
M 5 HOH B 53 353 133 HOH HOH . 
M 5 HOH B 54 354 140 HOH HOH . 
M 5 HOH B 55 355 27 HOH HOH . 
M 5 HOH B 56 356 77 HOH HOH . 
M 5 HOH B 57 357 119 HOH HOH . 
N 5 HOH C 1 301 134 HOH HOH . 
N 5 HOH C 2 302 70 HOH HOH . 
N 5 HOH C 3 303 64 HOH HOH . 
N 5 HOH C 4 304 111 HOH HOH . 
N 5 HOH C 5 305 61 HOH HOH . 
N 5 HOH C 6 306 127 HOH HOH . 
N 5 HOH C 7 307 47 HOH HOH . 
N 5 HOH C 8 308 112 HOH HOH . 
N 5 HOH C 9 309 91 HOH HOH . 
N 5 HOH C 10 310 62 HOH HOH . 
N 5 HOH C 11 311 94 HOH HOH . 
N 5 HOH C 12 312 107 HOH HOH . 
N 5 HOH C 13 313 88 HOH HOH . 
N 5 HOH C 14 314 151 HOH HOH . 
N 5 HOH C 15 315 108 HOH HOH . 
N 5 HOH C 16 316 149 HOH HOH . 
N 5 HOH C 17 317 72 HOH HOH . 
N 5 HOH C 18 318 28 HOH HOH . 
N 5 HOH C 19 319 131 HOH HOH . 
N 5 HOH C 20 320 20 HOH HOH . 
N 5 HOH C 21 321 100 HOH HOH . 
N 5 HOH C 22 322 32 HOH HOH . 
N 5 HOH C 23 323 46 HOH HOH . 
N 5 HOH C 24 324 129 HOH HOH . 
N 5 HOH C 25 325 67 HOH HOH . 
N 5 HOH C 26 326 125 HOH HOH . 
N 5 HOH C 27 327 109 HOH HOH . 
N 5 HOH C 28 328 84 HOH HOH . 
N 5 HOH C 29 329 73 HOH HOH . 
N 5 HOH C 30 330 53 HOH HOH . 
N 5 HOH C 31 331 102 HOH HOH . 
N 5 HOH C 32 332 96 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 O O5 A1HZ3 . . . E 3 26.039 16.894 -9.191 1 31.55 ? O5 A1HZ3 202 A 1 
HETATM 2 C C13 A1HZ3 . . . E 3 25.122 17.418 -8.548 1 31.63 ? C13 A1HZ3 202 A 1 
HETATM 3 N N1 A1HZ3 . . . E 3 23.874 16.836 -8.449 1 29.69 ? N1 A1HZ3 202 A 1 
HETATM 4 C C4 A1HZ3 . . . E 3 25.296 18.777 -7.96 1 32.36 ? C4 A1HZ3 202 A 1 
HETATM 5 C C3 A1HZ3 . . . E 3 24.435 18.924 -6.709 1 29.55 ? C3 A1HZ3 202 A 1 
HETATM 6 C C2 A1HZ3 . . . E 3 22.963 18.598 -7 1 28.5 ? C2 A1HZ3 202 A 1 
HETATM 7 C C1 A1HZ3 . . . E 3 22.789 17.308 -7.733 1 27.9 ? C1 A1HZ3 202 A 1 
HETATM 8 O O1 A1HZ3 . . . E 3 21.778 16.642 -7.654 1 26.96 ? O1 A1HZ3 202 A 1 
HETATM 9 O O4 A1HZ3 . . . E 3 26.731 19.036 -7.652 1 35.32 ? O4 A1HZ3 202 A 1 
HETATM 10 N N3 A1HZ3 . . . E 3 27.233 20.035 -8.525 1 40.56 ? N3 A1HZ3 202 A 1 
HETATM 11 C C6 A1HZ3 . . . E 3 26.286 20.443 -9.293 1 41.61 ? C6 A1HZ3 202 A 1 
HETATM 12 C C5 A1HZ3 . . . E 3 24.949 19.821 -9.009 1 36.67 ? C5 A1HZ3 202 A 1 
HETATM 13 C C7 A1HZ3 . . . E 3 26.481 21.451 -10.344 1 48.67 ? C7 A1HZ3 202 A 1 
HETATM 14 C C12 A1HZ3 . . . E 3 26.605 22.81 -10.023 1 53.66 ? C12 A1HZ3 202 A 1 
HETATM 15 N N2 A1HZ3 . . . E 3 26.62 23.302 -8.654 1 55.93 ? N2 A1HZ3 202 A 1 
HETATM 16 O O3 A1HZ3 . . . E 3 26.14 22.601 -7.773 1 59.28 ? O3 A1HZ3 202 A 1 
HETATM 17 O O2 A1HZ3 . . . E 3 27.059 24.422 -8.45 1 62.1 ? O2 A1HZ3 202 A 1 
HETATM 18 C C11 A1HZ3 . . . E 3 26.749 23.75 -11.037 1 54.67 ? C11 A1HZ3 202 A 1 
HETATM 19 C C10 A1HZ3 . . . E 3 26.717 23.34 -12.356 1 56.34 ? C10 A1HZ3 202 A 1 
HETATM 20 C C9 A1HZ3 . . . E 3 26.557 22.009 -12.679 1 56.62 ? C9 A1HZ3 202 A 1 
HETATM 21 C C8 A1HZ3 . . . E 3 26.426 21.062 -11.682 1 51.14 ? C8 A1HZ3 202 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           237 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           21 
#