data_4TPU
#
_model_server_result.job_id            URTv9VKLNLFZT-0ij5YWcw 
_model_server_result.datetime_utc      '2024-12-27 00:43:16' 
_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          4tpu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":305}' 
#
_entry.id    4TPU 
#
_exptl.entry_id    4TPU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              60.055 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            UREA 
_entity.pdbx_number_of_molecules    2 
_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            4TPU 
_cell.length_a            93.181 
_cell.length_b            93.181 
_cell.length_c            93.181 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4TPU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        195 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 2 3' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
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' 8_555 -z,x,-y 0 0 -1 1 0 0 0 -1 0 0 0 0 
3 'crystal symmetry operation' 11_555 y,-z,-x 0 1 0 0 0 -1 -1 0 0 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 5 E N N 
? 5 F 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 52 A CYS 52 1_555 A SG CYS 84 A CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
metalc ? metalc1 A SG CYS 50 A CYS 50 1_555 C FE3 SF4 . A SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc2 A SG CYS 67 A CYS 67 1_555 C FE1 SF4 . A SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? 
metalc ? metalc3 A SG CYS 69 A CYS 69 1_555 C FE2 SF4 . A SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? 
metalc ? metalc4 A SG CYS 82 A CYS 82 1_555 C FE4 SF4 . A SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? 
metalc ? metalc5 A SG CYS 142 A CYS 142 1_555 D FE FE . A FE 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? 
metalc ? metalc6 A SG CYS 145 A CYS 145 1_555 D FE FE . A FE 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? 
metalc ? metalc7 A SG CYS 158 A CYS 158 1_555 D FE FE . A FE 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? 
metalc ? metalc8 A SG CYS 161 A CYS 161 1_555 D FE FE . A FE 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? 
metalc ? metalc9 A OE2 GLU 166 A GLU 166 1_555 P NA NA . A NA 315 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.043 ? 
metalc ? metalc10 I NA NA . A NA 308 1_555 R O HOH . A HOH 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.046 ? 
metalc ? metalc11 J NA NA . A NA 309 1_555 R O HOH . A HOH 413 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.901 ? 
metalc ? metalc12 P NA NA . A NA 315 1_555 R O HOH . A HOH 411 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.881 ? 
#
_chem_comp.formula           'C H4 N2 O' 
_chem_comp.formula_weight    60.055 
_chem_comp.id                URE 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              UREA 
_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
C O URE doub 374 n n 
C N1 URE sing 375 n n 
C N2 URE sing 376 n n 
N1 HN11 URE sing 377 n n 
N1 HN12 URE sing 378 n n 
N2 HN21 URE sing 379 n n 
N2 HN22 URE sing 380 n n 
#
_atom_sites.entry_id                     4TPU 
_atom_sites.fract_transf_matrix[1][1]    0.010732 
_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]    0.010732 
_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]    0.010732 
_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 SO4 A 1 301 301 SO4 SO4 . 
C 3 SF4 A 1 302 174 SF4 SF4 . 
D 4 FE A 1 303 175 FE FE . 
E 5 URE A 1 304 176 URE URE . 
F 5 URE A 1 305 177 URE URE . 
G 6 NA A 1 306 178 NA NA . 
H 7 BR A 1 307 179 BR BR . 
I 6 NA A 1 308 180 NA NA . 
J 6 NA A 1 309 181 NA NA . 
K 7 BR A 1 310 182 BR BR . 
L 7 BR A 1 311 183 BR BR . 
M 7 BR A 1 312 184 BR BR . 
N 7 BR A 1 313 185 BR BR . 
O 7 BR A 1 314 186 BR BR . 
P 6 NA A 1 315 187 NA NA . 
Q 7 BR A 1 316 188 BR BR . 
R 8 HOH A 1 401 235 HOH HOH . 
R 8 HOH A 2 402 206 HOH HOH . 
R 8 HOH A 3 403 203 HOH HOH . 
R 8 HOH A 4 404 228 HOH HOH . 
R 8 HOH A 5 405 202 HOH HOH . 
R 8 HOH A 6 406 194 HOH HOH . 
R 8 HOH A 7 407 232 HOH HOH . 
R 8 HOH A 8 408 191 HOH HOH . 
R 8 HOH A 9 409 189 HOH HOH . 
R 8 HOH A 10 410 214 HOH HOH . 
R 8 HOH A 11 411 207 HOH HOH . 
R 8 HOH A 12 412 200 HOH HOH . 
R 8 HOH A 13 413 204 HOH HOH . 
R 8 HOH A 14 414 195 HOH HOH . 
R 8 HOH A 15 415 190 HOH HOH . 
R 8 HOH A 16 416 201 HOH HOH . 
R 8 HOH A 17 417 221 HOH HOH . 
R 8 HOH A 18 418 229 HOH HOH . 
R 8 HOH A 19 419 193 HOH HOH . 
R 8 HOH A 20 420 209 HOH HOH . 
R 8 HOH A 21 421 227 HOH HOH . 
R 8 HOH A 22 422 219 HOH HOH . 
R 8 HOH A 23 423 196 HOH HOH . 
R 8 HOH A 24 424 216 HOH HOH . 
R 8 HOH A 25 425 205 HOH HOH . 
R 8 HOH A 26 426 234 HOH HOH . 
R 8 HOH A 27 427 225 HOH HOH . 
R 8 HOH A 28 428 192 HOH HOH . 
R 8 HOH A 29 429 197 HOH HOH . 
R 8 HOH A 30 430 198 HOH HOH . 
R 8 HOH A 31 431 199 HOH HOH . 
R 8 HOH A 32 432 208 HOH HOH . 
R 8 HOH A 33 433 210 HOH HOH . 
R 8 HOH A 34 434 211 HOH HOH . 
R 8 HOH A 35 435 212 HOH HOH . 
R 8 HOH A 36 436 213 HOH HOH . 
R 8 HOH A 37 437 215 HOH HOH . 
R 8 HOH A 38 438 217 HOH HOH . 
R 8 HOH A 39 439 218 HOH HOH . 
R 8 HOH A 40 440 220 HOH HOH . 
R 8 HOH A 41 441 222 HOH HOH . 
R 8 HOH A 42 442 223 HOH HOH . 
R 8 HOH A 43 443 224 HOH HOH . 
R 8 HOH A 44 444 226 HOH HOH . 
R 8 HOH A 45 445 230 HOH HOH . 
R 8 HOH A 46 446 231 HOH HOH . 
R 8 HOH A 47 447 233 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 C URE . . . F 5 46.993 12.989 8.229 1 83.83 ? C URE 305 A 1 
HETATM 2 O O URE . . . F 5 46.032 13.302 7.541 1 79.68 ? O URE 305 A 1 
HETATM 3 N N1 URE . . . F 5 47.756 11.82 7.883 1 79.73 ? N1 URE 305 A 1 
HETATM 4 N N2 URE . . . F 5 47.338 13.804 9.363 1 69.35 ? N2 URE 305 A 1 
HETATM 5 H HN11 URE . . . F 5 47.476 11.226 7.026 1 95.58 ? HN11 URE 305 A 1 
HETATM 6 H HN12 URE . . . F 5 48.608 11.534 8.483 1 95.58 ? HN12 URE 305 A 1 
HETATM 7 H HN21 URE . . . F 5 46.749 14.678 9.599 1 83.13 ? HN21 URE 305 A 1 
HETATM 8 H HN22 URE . . . F 5 48.185 13.541 9.979 1 83.13 ? HN22 URE 305 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           326 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           8 
#