data_1JU6
#
_model_server_result.job_id            RSQ4ptWx-uoaa4AzyJ3lAw 
_model_server_result.datetime_utc      '2025-03-31 03:20:39' 
_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          1ju6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":314}' 
#
_entry.id    1JU6 
#
_exptl.entry_id    1JU6 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              308.182 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         71.67 
_cell.angle_beta          85.72 
_cell.angle_gamma         75.11 
_cell.entry_id            1JU6 
_cell.length_a            68.138 
_cell.length_b            69.633 
_cell.length_c            73.958 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1JU6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,G,H,I,N,O 1 1 
C,D,J,K,L,M,P,Q 2 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 F N N 
? 3 H N N 
? 3 J N N 
? 3 L 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 SG CYS 195 A CYS 195 1_555 F C6 UMP . A UMP 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.823 ? 
covale ? covale2 B SG CYS 195 B CYS 195 1_555 H C6 UMP . B UMP 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.832 ? 
covale ? covale3 C SG CYS 195 C CYS 195 1_555 J C6 UMP . C UMP 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.84 ? 
covale ? covale4 D SG CYS 195 D CYS 195 1_555 L C6 UMP . D UMP 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.811 ? 
#
_chem_comp.formula           'C9 H13 N2 O8 P' 
_chem_comp.formula_weight    308.182 
_chem_comp.id                UMP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     DUMP 
#
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 C2 UMP sing 416 n n 
N1 C6 UMP sing 417 n n 
N1 C1' UMP sing 418 n n 
C2 N3 UMP sing 419 n n 
C2 O2 UMP doub 420 n n 
N3 C4 UMP sing 421 n n 
N3 HN3 UMP sing 422 n n 
C4 C5 UMP sing 423 n n 
C4 O4 UMP doub 424 n n 
C5 C6 UMP doub 425 n n 
C5 H5 UMP sing 426 n n 
C6 H6 UMP sing 427 n n 
C1' C2' UMP sing 428 n n 
C1' O4' UMP sing 429 n n 
C1' H1' UMP sing 430 n n 
C2' C3' UMP sing 431 n n 
C2' H2' UMP sing 432 n n 
C2' "H2''" UMP sing 433 n n 
C3' C4' UMP sing 434 n n 
C3' O3' UMP sing 435 n n 
C3' H3' UMP sing 436 n n 
C4' O4' UMP sing 437 n n 
C4' C5' UMP sing 438 n n 
C4' H4' UMP sing 439 n n 
O3' HO3' UMP sing 440 n n 
C5' O5' UMP sing 441 n n 
C5' H5' UMP sing 442 n n 
C5' "H5''" UMP sing 443 n n 
O5' P UMP sing 444 n n 
P OP1 UMP doub 445 n n 
P OP2 UMP sing 446 n n 
P OP3 UMP sing 447 n n 
OP2 HOP2 UMP sing 448 n n 
OP3 HOP3 UMP sing 449 n n 
#
_atom_sites.entry_id                     1JU6 
_atom_sites.fract_transf_matrix[1][1]    0.014676 
_atom_sites.fract_transf_matrix[1][2]    -0.003901 
_atom_sites.fract_transf_matrix[1][3]    0.000102 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01486 
_atom_sites.fract_transf_matrix[2][3]    -0.004783 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.014244 
_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 PO4 A 1 316 316 PO4 PO4 . 
F 3 UMP A 1 314 314 UMP DUM . 
G 4 LYA A 1 317 315 LYA LYA . 
H 3 UMP B 1 314 314 UMP DUM . 
I 4 LYA B 1 315 315 LYA LYA . 
J 3 UMP C 1 314 314 UMP DUM . 
K 4 LYA C 1 315 315 LYA LYA . 
L 3 UMP D 1 314 314 UMP DUM . 
M 4 LYA D 1 315 315 LYA LYA . 
N 5 HOH A 1 401 318 HOH WAT . 
N 5 HOH A 2 402 319 HOH WAT . 
N 5 HOH A 3 403 320 HOH WAT . 
N 5 HOH A 4 404 321 HOH WAT . 
N 5 HOH A 5 405 322 HOH WAT . 
N 5 HOH A 6 406 324 HOH WAT . 
N 5 HOH A 7 407 325 HOH WAT . 
N 5 HOH A 8 408 326 HOH WAT . 
N 5 HOH A 9 409 328 HOH WAT . 
N 5 HOH A 10 410 329 HOH WAT . 
N 5 HOH A 11 411 330 HOH WAT . 
N 5 HOH A 12 412 331 HOH WAT . 
O 5 HOH B 1 413 318 HOH WAT . 
O 5 HOH B 2 414 319 HOH WAT . 
O 5 HOH B 3 415 320 HOH WAT . 
O 5 HOH B 4 416 321 HOH WAT . 
O 5 HOH B 5 417 322 HOH WAT . 
O 5 HOH B 6 418 324 HOH WAT . 
O 5 HOH B 7 419 325 HOH WAT . 
O 5 HOH B 8 420 326 HOH WAT . 
O 5 HOH B 9 421 328 HOH WAT . 
O 5 HOH B 10 422 329 HOH WAT . 
O 5 HOH B 11 423 330 HOH WAT . 
O 5 HOH B 12 424 331 HOH WAT . 
P 5 HOH C 1 425 318 HOH WAT . 
P 5 HOH C 2 426 319 HOH WAT . 
P 5 HOH C 3 427 320 HOH WAT . 
P 5 HOH C 4 428 321 HOH WAT . 
P 5 HOH C 5 429 322 HOH WAT . 
P 5 HOH C 6 430 324 HOH WAT . 
P 5 HOH C 7 431 325 HOH WAT . 
P 5 HOH C 8 432 326 HOH WAT . 
P 5 HOH C 9 433 328 HOH WAT . 
P 5 HOH C 10 434 329 HOH WAT . 
P 5 HOH C 11 435 330 HOH WAT . 
P 5 HOH C 12 436 331 HOH WAT . 
P 5 HOH C 13 440 321 HOH WAT . 
Q 5 HOH D 1 437 318 HOH WAT . 
Q 5 HOH D 2 438 319 HOH WAT . 
Q 5 HOH D 3 439 320 HOH WAT . 
Q 5 HOH D 4 441 322 HOH WAT . 
Q 5 HOH D 5 442 324 HOH WAT . 
Q 5 HOH D 6 443 325 HOH WAT . 
Q 5 HOH D 7 444 326 HOH WAT . 
Q 5 HOH D 8 445 328 HOH WAT . 
Q 5 HOH D 9 446 329 HOH WAT . 
Q 5 HOH D 10 447 330 HOH WAT . 
Q 5 HOH D 11 448 331 HOH WAT . 
#
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 UMP . . . H 3 -13.852 -1.245 5.898 1 14.69 ? N1 UMP 314 B 1 
HETATM 2 C C2 UMP . . . H 3 -13.178 -2.304 6.474 1 15.99 ? C2 UMP 314 B 1 
HETATM 3 N N3 UMP . . . H 3 -12.761 -3.273 5.62 1 16.99 ? N3 UMP 314 B 1 
HETATM 4 C C4 UMP . . . H 3 -13.365 -3.558 4.425 1 15.27 ? C4 UMP 314 B 1 
HETATM 5 C C5 UMP . . . H 3 -14.14 -2.486 3.68 1 14.58 ? C5 UMP 314 B 1 
HETATM 6 C C6 UMP . . . H 3 -14.142 -1.136 4.414 1 15.16 ? C6 UMP 314 B 1 
HETATM 7 O O2 UMP . . . H 3 -12.957 -2.389 7.681 1 16.61 ? O2 UMP 314 B 1 
HETATM 8 O O4 UMP . . . H 3 -13.271 -4.699 3.973 1 15.58 ? O4 UMP 314 B 1 
HETATM 9 C C1' UMP . . . H 3 -14.324 -0.179 6.779 1 13.14 ? C1' UMP 314 B 1 
HETATM 10 C C2' UMP . . . H 3 -13.327 0.973 6.86 1 13.02 ? C2' UMP 314 B 1 
HETATM 11 C C3' UMP . . . H 3 -14.23 2.119 7.278 1 11.34 ? C3' UMP 314 B 1 
HETATM 12 C C4' UMP . . . H 3 -15.514 1.971 6.448 1 11.58 ? C4' UMP 314 B 1 
HETATM 13 O O3' UMP . . . H 3 -14.563 1.772 8.572 1 13.44 ? O3' UMP 314 B 1 
HETATM 14 O O4' UMP . . . H 3 -15.545 0.498 6.283 1 11.49 ? O4' UMP 314 B 1 
HETATM 15 C C5' UMP . . . H 3 -15.379 2.631 5.072 1 11.76 ? C5' UMP 314 B 1 
HETATM 16 O O5' UMP . . . H 3 -15.488 4.074 5.284 1 14.15 ? O5' UMP 314 B 1 
HETATM 17 P P UMP . . . H 3 -14.786 5.216 4.381 1 15.2 ? P UMP 314 B 1 
HETATM 18 O OP1 UMP . . . H 3 -15.402 6.55 4.647 1 13.63 ? OP1 UMP 314 B 1 
HETATM 19 O OP2 UMP . . . H 3 -13.351 5.168 4.757 1 15.4 ? OP2 UMP 314 B 1 
HETATM 20 O OP3 UMP . . . H 3 -14.919 4.939 2.945 1 15.14 ? OP3 UMP 314 B 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    25 
_model_server_stats.query_time_ms           331 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           20 
#