data_5MQJ
#
_model_server_result.job_id            MehRV8kDi5Of7b_0nfYAYw 
_model_server_result.datetime_utc      '2024-11-22 14:18:16' 
_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          5mqj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":302}' 
#
_entry.id    5MQJ 
#
_exptl.entry_id    5MQJ 
_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         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            5MQJ 
_cell.length_a            92.695 
_cell.length_b            92.695 
_cell.length_c            338.083 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5MQJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
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,J 1 1 
C,D,K,L,M,N,O,P 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 I N N 
? 3 L N N 
? 3 O 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 F OP1 UMP . A UMP 302 1_555 G MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
metalc ? metalc2 B OE1 GLU 74 B GLU 53 1_555 J MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.896 ? 
metalc ? metalc3 B OE2 GLU 148 B GLU 127 1_555 J MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? 
metalc ? metalc4 I OP2 UMP . B UMP 302 1_555 J MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? 
metalc ? metalc5 C OE2 GLU 148 C GLU 127 1_555 M MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.845 ? 
metalc ? metalc6 L OP2 UMP . C UMP 302 1_555 M MG MG . C MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? 
metalc ? metalc7 N O1B UDP . D UDP 301 1_555 P MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? 
metalc ? metalc8 O OP2 UMP . D UMP 302 1_555 P MG MG . D MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? 
#
_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 396 n n 
N1 C6 UMP sing 397 n n 
N1 C1' UMP sing 398 n n 
C2 N3 UMP sing 399 n n 
C2 O2 UMP doub 400 n n 
N3 C4 UMP sing 401 n n 
N3 HN3 UMP sing 402 n n 
C4 C5 UMP sing 403 n n 
C4 O4 UMP doub 404 n n 
C5 C6 UMP doub 405 n n 
C5 H5 UMP sing 406 n n 
C6 H6 UMP sing 407 n n 
C1' C2' UMP sing 408 n n 
C1' O4' UMP sing 409 n n 
C1' H1' UMP sing 410 n n 
C2' C3' UMP sing 411 n n 
C2' H2' UMP sing 412 n n 
C2' "H2''" UMP sing 413 n n 
C3' C4' UMP sing 414 n n 
C3' O3' UMP sing 415 n n 
C3' H3' UMP sing 416 n n 
C4' O4' UMP sing 417 n n 
C4' C5' UMP sing 418 n n 
C4' H4' UMP sing 419 n n 
O3' HO3' UMP sing 420 n n 
C5' O5' UMP sing 421 n n 
C5' H5' UMP sing 422 n n 
C5' "H5''" UMP sing 423 n n 
O5' P UMP sing 424 n n 
P OP1 UMP doub 425 n n 
P OP2 UMP sing 426 n n 
P OP3 UMP sing 427 n n 
OP2 HOP2 UMP sing 428 n n 
OP3 HOP3 UMP sing 429 n n 
#
_atom_sites.entry_id                     5MQJ 
_atom_sites.fract_transf_matrix[1][1]    0.010788 
_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]    0.010788 
_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]    0.002958 
_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 UDP A 1 301 500 UDP UDP . 
F 3 UMP A 1 302 510 UMP DU . 
G 4 MG A 1 303 520 MG MG . 
H 2 UDP B 1 301 500 UDP UDP . 
I 3 UMP B 1 302 510 UMP DU . 
J 4 MG B 1 303 520 MG MG . 
K 2 UDP C 1 301 500 UDP UDP . 
L 3 UMP C 1 302 510 UMP DU . 
M 4 MG C 1 303 520 MG MG . 
N 2 UDP D 1 301 500 UDP UDP . 
O 3 UMP D 1 302 510 UMP DU . 
P 4 MG D 1 303 520 MG MG . 
#
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 . . . O 3 -107.629 34.827 327.846 1 100.56 ? N1 UMP 302 D 1 
HETATM 2 C C2 UMP . . . O 3 -106.983 35.784 328.567 1 94.82 ? C2 UMP 302 D 1 
HETATM 3 N N3 UMP . . . O 3 -107.764 36.799 329.15 1 92.68 ? N3 UMP 302 D 1 
HETATM 4 C C4 UMP . . . O 3 -109.172 36.821 329.027 1 92.87 ? C4 UMP 302 D 1 
HETATM 5 C C5 UMP . . . O 3 -109.828 35.859 328.281 1 94.52 ? C5 UMP 302 D 1 
HETATM 6 C C6 UMP . . . O 3 -109.047 34.881 327.685 1 98.07 ? C6 UMP 302 D 1 
HETATM 7 O O2 UMP . . . O 3 -105.759 35.775 328.773 1 92.58 ? O2 UMP 302 D 1 
HETATM 8 O O4 UMP . . . O 3 -109.836 37.693 329.577 1 93.64 ? O4 UMP 302 D 1 
HETATM 9 C C1' UMP . . . O 3 -106.888 33.76 327.093 1 108.07 ? C1' UMP 302 D 1 
HETATM 10 C C2' UMP . . . O 3 -106.659 32.479 327.882 1 110.02 ? C2' UMP 302 D 1 
HETATM 11 C C3' UMP . . . O 3 -106.782 31.386 326.819 1 112.11 ? C3' UMP 302 D 1 
HETATM 12 C C4' UMP . . . O 3 -107.78 31.964 325.805 1 113.61 ? C4' UMP 302 D 1 
HETATM 13 O O3' UMP . . . O 3 -105.499 31.166 326.177 1 112.87 ? O3' UMP 302 D 1 
HETATM 14 O O4' UMP . . . O 3 -107.583 33.393 325.836 1 111.18 ? O4' UMP 302 D 1 
HETATM 15 C C5' UMP . . . O 3 -109.279 31.593 326.022 1 116.06 ? C5' UMP 302 D 1 
HETATM 16 O O5' UMP . . . O 3 -109.508 30.808 327.208 1 119.47 ? O5' UMP 302 D 1 
HETATM 17 P P UMP . . . O 3 -109.857 29.218 327.146 1 125.35 ? P UMP 302 D 1 
HETATM 18 O OP1 UMP . . . O 3 -108.782 28.699 326.275 1 128.78 ? OP1 UMP 302 D 1 
HETATM 19 O OP2 UMP . . . O 3 -111.229 29.207 326.561 1 125.72 ? OP2 UMP 302 D 1 
HETATM 20 O OP3 UMP . . . O 3 -109.745 28.791 328.561 1 123.9 ? OP3 UMP 302 D 1 
#
_model_server_stats.io_time_ms              28 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           296 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           20 
#