data_5MV5
#
_model_server_result.job_id            toxP9cbNNoNzWsHAOQXD6w 
_model_server_result.datetime_utc      '2024-10-20 00:40:15' 
_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          5mv5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    5MV5 
#
_exptl.entry_id    5MV5 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              324.181 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "URIDINE-5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? 240-meric 240 'complete icosahedral assembly' 1 
? tetrameric 4 'icosahedral asymmetric unit' 2 
? eicosameric 20 'icosahedral pentamer' 3 
? 24-meric 24 'icosahedral 23 hexamer' 4 
? tetrameric 4 'icosahedral asymmetric unit, std point frame' 5 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D 1 (1-60) 
A,B,C,D 2 1 
A,B,C,D 3 (1-5) 
A,B,C,D 4 (1,2,6,10,23,24) 
A,B,C,D 5 P 
#
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]
P 'transform to point frame' ? ? -0.309017 -0.809017 0.5 0.809017 -0.5 -0.309017 0.5 0.309017 0.809017 0 0 0 
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'point symmetry operation' ? ? 0.809017 -0.5 0.309017 0.5 0.309017 -0.809017 0.309017 0.809017 0.5 0 0 0 
3 'point symmetry operation' ? ? 0.5 -0.309017 0.809017 0.309017 -0.809017 -0.5 0.809017 0.5 -0.309017 0 0 0 
4 'point symmetry operation' ? ? 0.5 0.309017 0.809017 -0.309017 -0.809017 0.5 0.809017 -0.5 -0.309017 0 0 0 
5 'point symmetry operation' ? ? 0.809017 0.5 0.309017 -0.5 0.309017 0.809017 0.309017 -0.809017 0.5 0 0 0 
6 'point symmetry operation' ? ? -0.5 0.309017 0.809017 0.309017 -0.809017 0.5 0.809017 0.5 0.309017 0 0 0 
7 'point symmetry operation' ? ? 0 1 0 0 0 1 1 0 0 0 0 0 
8 'point symmetry operation' ? ? 0.5 0.309017 -0.809017 0.309017 0.809017 0.5 0.809017 -0.5 0.309017 0 0 0 
9 'point symmetry operation' ? ? 0.309017 -0.809017 -0.5 0.809017 0.5 -0.309017 0.5 -0.309017 0.809017 0 0 0 
10 'point symmetry operation' ? ? -0.309017 -0.809017 0.5 0.809017 -0.5 -0.309017 0.5 0.309017 0.809017 0 0 0 
11 'point symmetry operation' ? ? 0.309017 -0.809017 -0.5 -0.809017 -0.5 0.309017 -0.5 0.309017 -0.809017 0 0 0 
12 'point symmetry operation' ? ? -0.309017 -0.809017 0.5 -0.809017 0.5 0.309017 -0.5 -0.309017 -0.809017 0 0 0 
13 'point symmetry operation' ? ? -0.5 0.309017 0.809017 -0.309017 0.809017 -0.5 -0.809017 -0.5 -0.309017 0 0 0 
14 'point symmetry operation' ? ? 0 1 0 0 0 -1 -1 0 0 0 0 0 
15 'point symmetry operation' ? ? 0.5 0.309017 -0.809017 -0.309017 -0.809017 -0.5 -0.809017 0.5 -0.309017 0 0 0 
16 'point symmetry operation' ? ? -0.809017 0.5 -0.309017 0.5 0.309017 -0.809017 -0.309017 -0.809017 -0.5 0 0 0 
17 'point symmetry operation' ? ? -0.5 0.309017 -0.809017 0.309017 -0.809017 -0.5 -0.809017 -0.5 0.309017 0 0 0 
18 'point symmetry operation' ? ? -0.5 -0.309017 -0.809017 -0.309017 -0.809017 0.5 -0.809017 0.5 0.309017 0 0 0 
19 'point symmetry operation' ? ? -0.809017 -0.5 -0.309017 -0.5 0.309017 0.809017 -0.309017 0.809017 -0.5 0 0 0 
20 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 0 0 0 
21 'point symmetry operation' ? ? 0 -1 0 0 0 -1 1 0 0 0 0 0 
22 'point symmetry operation' ? ? -0.5 -0.309017 0.809017 -0.309017 -0.809017 -0.5 0.809017 -0.5 0.309017 0 0 0 
23 'point symmetry operation' ? ? -0.309017 0.809017 0.5 -0.809017 -0.5 0.309017 0.5 -0.309017 0.809017 0 0 0 
24 'point symmetry operation' ? ? 0.309017 0.809017 -0.5 -0.809017 0.5 0.309017 0.5 0.309017 0.809017 0 0 0 
25 'point symmetry operation' ? ? 0.5 -0.309017 -0.809017 -0.309017 0.809017 -0.5 0.809017 0.5 0.309017 0 0 0 
26 'point symmetry operation' ? ? -0.309017 0.809017 -0.5 -0.809017 -0.5 -0.309017 -0.5 0.309017 0.809017 0 0 0 
27 'point symmetry operation' ? ? 0 0 -1 -1 0 0 0 1 0 0 0 0 
28 'point symmetry operation' ? ? -0.309017 -0.809017 -0.5 -0.809017 0.5 -0.309017 0.5 0.309017 -0.809017 0 0 0 
29 'point symmetry operation' ? ? -0.809017 -0.5 0.309017 -0.5 0.309017 -0.809017 0.309017 -0.809017 -0.5 0 0 0 
30 'point symmetry operation' ? ? -0.809017 0.5 0.309017 -0.5 -0.309017 -0.809017 -0.309017 -0.809017 0.5 0 0 0 
31 'point symmetry operation' ? ? 0.809017 0.5 -0.309017 0.5 -0.309017 0.809017 0.309017 -0.809017 -0.5 0 0 0 
32 'point symmetry operation' ? ? 0.809017 -0.5 -0.309017 0.5 0.309017 0.809017 -0.309017 -0.809017 0.5 0 0 0 
33 'point symmetry operation' ? ? 0.309017 -0.809017 0.5 0.809017 0.5 0.309017 -0.5 0.309017 0.809017 0 0 0 
34 'point symmetry operation' ? ? 0 0 1 1 0 0 0 1 0 0 0 0 
35 'point symmetry operation' ? ? 0.309017 0.809017 0.5 0.809017 -0.5 0.309017 0.5 0.309017 -0.809017 0 0 0 
36 'point symmetry operation' ? ? -0.5 -0.309017 0.809017 0.309017 0.809017 0.5 -0.809017 0.5 -0.309017 0 0 0 
37 'point symmetry operation' ? ? -0.309017 0.809017 0.5 0.809017 0.5 -0.309017 -0.5 0.309017 -0.809017 0 0 0 
38 'point symmetry operation' ? ? 0.309017 0.809017 -0.5 0.809017 -0.5 -0.309017 -0.5 -0.309017 -0.809017 0 0 0 
39 'point symmetry operation' ? ? 0.5 -0.309017 -0.809017 0.309017 -0.809017 0.5 -0.809017 -0.5 -0.309017 0 0 0 
40 'point symmetry operation' ? ? 0 -1 0 0 0 1 -1 0 0 0 0 0 
41 'point symmetry operation' ? ? 0 0 1 -1 0 0 0 -1 0 0 0 0 
42 'point symmetry operation' ? ? 0.309017 0.809017 0.5 -0.809017 0.5 -0.309017 -0.5 -0.309017 0.809017 0 0 0 
43 'point symmetry operation' ? ? 0.809017 0.5 -0.309017 -0.5 0.309017 -0.809017 -0.309017 0.809017 0.5 0 0 0 
44 'point symmetry operation' ? ? 0.809017 -0.5 -0.309017 -0.5 -0.309017 -0.809017 0.309017 0.809017 -0.5 0 0 0 
45 'point symmetry operation' ? ? 0.309017 -0.809017 0.5 -0.809017 -0.5 -0.309017 0.5 -0.309017 -0.809017 0 0 0 
46 'point symmetry operation' ? ? 0.809017 0.5 0.309017 0.5 -0.309017 -0.809017 -0.309017 0.809017 -0.5 0 0 0 
47 'point symmetry operation' ? ? 1 0 0 0 -1 0 0 0 -1 0 0 0 
48 'point symmetry operation' ? ? 0.809017 -0.5 0.309017 -0.5 -0.309017 0.809017 -0.309017 -0.809017 -0.5 0 0 0 
49 'point symmetry operation' ? ? 0.5 -0.309017 0.809017 -0.309017 0.809017 0.5 -0.809017 -0.5 0.309017 0 0 0 
50 'point symmetry operation' ? ? 0.5 0.309017 0.809017 0.309017 0.809017 -0.5 -0.809017 0.5 0.309017 0 0 0 
51 'point symmetry operation' ? ? -0.5 0.309017 -0.809017 -0.309017 0.809017 0.5 0.809017 0.5 -0.309017 0 0 0 
52 'point symmetry operation' ? ? -0.5 -0.309017 -0.809017 0.309017 0.809017 -0.5 0.809017 -0.5 -0.309017 0 0 0 
53 'point symmetry operation' ? ? -0.809017 -0.5 -0.309017 0.5 -0.309017 -0.809017 0.309017 -0.809017 0.5 0 0 0 
54 'point symmetry operation' ? ? -1 0 0 0 -1 0 0 0 1 0 0 0 
55 'point symmetry operation' ? ? -0.809017 0.5 -0.309017 -0.5 -0.309017 0.809017 0.309017 0.809017 0.5 0 0 0 
56 'point symmetry operation' ? ? -0.309017 -0.809017 -0.5 0.809017 -0.5 0.309017 -0.5 -0.309017 0.809017 0 0 0 
57 'point symmetry operation' ? ? -0.809017 -0.5 0.309017 0.5 -0.309017 0.809017 -0.309017 0.809017 0.5 0 0 0 
58 'point symmetry operation' ? ? -0.809017 0.5 0.309017 0.5 0.309017 0.809017 0.309017 0.809017 -0.5 0 0 0 
59 'point symmetry operation' ? ? -0.309017 0.809017 -0.5 0.809017 0.5 0.309017 0.5 -0.309017 -0.809017 0 0 0 
60 'point symmetry operation' ? ? 0 0 -1 1 0 0 0 -1 0 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C9 H13 N2 O9 P' 
_chem_comp.formula_weight    324.181 
_chem_comp.id                U 
_chem_comp.mon_nstd_flag     y 
_chem_comp.name              "URIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type              'rna linking' 
_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
OP3 P U sing 356 n n 
OP3 HOP3 U sing 357 n n 
P OP1 U doub 358 n n 
P OP2 U sing 359 n n 
P O5' U sing 360 n n 
OP2 HOP2 U sing 361 n n 
O5' C5' U sing 362 n n 
C5' C4' U sing 363 n n 
C5' H5' U sing 364 n n 
C5' "H5''" U sing 365 n n 
C4' O4' U sing 366 n n 
C4' C3' U sing 367 n n 
C4' H4' U sing 368 n n 
O4' C1' U sing 369 n n 
C3' O3' U sing 370 n n 
C3' C2' U sing 371 n n 
C3' H3' U sing 372 n n 
O3' HO3' U sing 373 n n 
C2' O2' U sing 374 n n 
C2' C1' U sing 375 n n 
C2' H2' U sing 376 n n 
O2' HO2' U sing 377 n n 
C1' N1 U sing 378 n n 
C1' H1' U sing 379 n n 
N1 C2 U sing 380 n n 
N1 C6 U sing 381 n n 
C2 O2 U doub 382 n n 
C2 N3 U sing 383 n n 
N3 C4 U sing 384 n n 
N3 H3 U sing 385 n n 
C4 O4 U doub 386 n n 
C4 C5 U sing 387 n n 
C5 C6 U doub 388 n n 
C5 H5 U sing 389 n n 
C6 H6 U sing 390 n n 
#
_atom_sites.entry_id                     5MV5 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
_pdbx_nonpoly_scheme.asym_id          D 
_pdbx_nonpoly_scheme.entity_id        4 
_pdbx_nonpoly_scheme.mon_id           U 
_pdbx_nonpoly_scheme.pdb_strand_id    C 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      501 
_pdbx_nonpoly_scheme.auth_seq_num     1 
_pdbx_nonpoly_scheme.pdb_mon_id       U 
_pdbx_nonpoly_scheme.auth_mon_id      U 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 P P U . . . D 4 92.423 -5.224 65.982 0.94 107.99 ? P U 501 C 1 
HETATM 2 O OP1 U . . . D 4 91.589 -6.43 66.185 0.94 107.99 ? OP1 U 501 C 1 
HETATM 3 O OP2 U . . . D 4 92.474 -4.592 64.644 0.94 107.99 ? OP2 U 501 C 1 
HETATM 4 O O5' U . . . D 4 91.937 -4.119 67.018 0.94 107.99 ? O5' U 501 C 1 
HETATM 5 C C5' U . . . D 4 90.558 -3.987 67.348 0.94 107.99 ? C5' U 501 C 1 
HETATM 6 C C4' U . . . D 4 90.264 -2.707 68.098 0.94 107.99 ? C4' U 501 C 1 
HETATM 7 O O4' U . . . D 4 91.156 -2.602 69.238 0.94 107.99 ? O4' U 501 C 1 
HETATM 8 C C3' U . . . D 4 90.432 -1.413 67.304 0.94 107.99 ? C3' U 501 C 1 
HETATM 9 O O3' U . . . D 4 89.45 -0.471 67.732 0.94 107.99 ? O3' U 501 C 1 
HETATM 10 C C2' U . . . D 4 91.814 -0.931 67.732 0.94 107.99 ? C2' U 501 C 1 
HETATM 11 O O2' U . . . D 4 92.016 0.459 67.604 0.94 107.99 ? O2' U 501 C 1 
HETATM 12 C C1' U . . . D 4 91.854 -1.374 69.188 0.94 107.99 ? C1' U 501 C 1 
HETATM 13 N N1 U . . . D 4 93.204 -1.61 69.709 0.94 107.99 ? N1 U 501 C 1 
HETATM 14 C C2 U . . . D 4 93.738 -0.702 70.593 0.94 107.99 ? C2 U 501 C 1 
HETATM 15 O O2 U . . . D 4 93.148 0.299 70.952 0.94 107.99 ? O2 U 501 C 1 
HETATM 16 N N3 U . . . D 4 94.994 -1.008 71.036 0.94 107.99 ? N3 U 501 C 1 
HETATM 17 C C4 U . . . D 4 95.743 -2.108 70.698 0.94 107.99 ? C4 U 501 C 1 
HETATM 18 O O4 U . . . D 4 96.862 -2.25 71.18 0.94 107.99 ? O4 U 501 C 1 
HETATM 19 C C5 U . . . D 4 95.119 -3.001 69.784 0.94 107.99 ? C5 U 501 C 1 
HETATM 20 C C6 U . . . D 4 93.895 -2.729 69.335 0.94 107.99 ? C6 U 501 C 1 
#
_model_server_stats.io_time_ms              46 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          14 
_model_server_stats.element_count           20 
#