data_1Y1Q
#
_model_server_result.job_id            '_TpH8wEM6snZBlQrrxmSQg' 
_model_server_result.datetime_utc      '2024-11-09 01:57:32' 
_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          1y1q 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":8003}' 
#
_entry.id    1Y1Q 
#
_exptl.entry_id    1Y1Q 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              324.181 
_entity.id                          3 
_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                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            1Y1Q 
_cell.length_a            88.37 
_cell.length_b            123.73 
_cell.length_c            134.14 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1Y1Q 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_and_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             I 
_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                U5P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "URIDINE-5'-MONOPHOSPHATE" 
_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
N1 C2 U5P sing 362 n n 
N1 C6 U5P sing 363 n n 
N1 C1' U5P sing 364 n n 
C2 N3 U5P sing 365 n n 
C2 O2 U5P doub 366 n n 
N3 C4 U5P sing 367 n n 
N3 HN3 U5P sing 368 n n 
C4 C5 U5P sing 369 n n 
C4 O4 U5P doub 370 n n 
C5 C6 U5P doub 371 n n 
C5 H5 U5P sing 372 n n 
C6 H6 U5P sing 373 n n 
C1' C2' U5P sing 374 n n 
C1' O4' U5P sing 375 n n 
C1' H1' U5P sing 376 n n 
C2' O2' U5P sing 377 n n 
C2' C3' U5P sing 378 n n 
C2' H2' U5P sing 379 n n 
O2' HO2' U5P sing 380 n n 
C3' C4' U5P sing 381 n n 
C3' O3' U5P sing 382 n n 
C3' H3' U5P sing 383 n n 
C4' O4' U5P sing 384 n n 
C4' C5' U5P sing 385 n n 
C4' H4' U5P sing 386 n n 
O3' HO3' U5P sing 387 n n 
C5' O5' U5P sing 388 n n 
C5' "H5'1" U5P sing 389 n n 
C5' "H5'2" U5P sing 390 n n 
O5' P U5P sing 391 n n 
P O1P U5P doub 392 n n 
P O2P U5P sing 393 n n 
P O3P U5P sing 394 n n 
O2P HOP2 U5P sing 395 n n 
O3P HOP3 U5P sing 396 n n 
#
_atom_sites.entry_id                     1Y1Q 
_atom_sites.fract_transf_matrix[1][1]    0.011316 
_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]    0.008082 
_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]    0.007455 
_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
G 2 SO4 A 1 7003 7003 SO4 SO4 . 
H 2 SO4 A 1 7004 7004 SO4 SO4 . 
I 3 U5P C 1 8003 8003 U5P URI . 
J 2 SO4 E 1 7001 7001 SO4 SO4 . 
K 2 SO4 F 1 7005 7005 SO4 SO4 . 
L 4 HOH A 1 9005 9005 HOH HOH . 
L 4 HOH A 2 9008 9008 HOH HOH . 
L 4 HOH A 3 9010 9010 HOH HOH . 
L 4 HOH A 4 9020 9020 HOH HOH . 
L 4 HOH A 5 9024 9024 HOH HOH . 
L 4 HOH A 6 9026 9026 HOH HOH . 
L 4 HOH A 7 9031 9031 HOH HOH . 
L 4 HOH A 8 9035 9035 HOH HOH . 
L 4 HOH A 9 9038 9038 HOH HOH . 
L 4 HOH A 10 9046 9046 HOH HOH . 
L 4 HOH A 11 9050 9050 HOH HOH . 
L 4 HOH A 12 9051 9051 HOH HOH . 
L 4 HOH A 13 9052 9052 HOH HOH . 
L 4 HOH A 14 9066 9066 HOH HOH . 
L 4 HOH A 15 9076 9076 HOH HOH . 
L 4 HOH A 16 9082 9082 HOH HOH . 
L 4 HOH A 17 9085 9085 HOH HOH . 
L 4 HOH A 18 9098 9098 HOH HOH . 
L 4 HOH A 19 9112 9112 HOH HOH . 
L 4 HOH A 20 9117 9117 HOH HOH . 
L 4 HOH A 21 9127 9127 HOH HOH . 
L 4 HOH A 22 9130 9130 HOH HOH . 
L 4 HOH A 23 9142 9142 HOH HOH . 
L 4 HOH A 24 9148 9148 HOH HOH . 
L 4 HOH A 25 9154 9154 HOH HOH . 
L 4 HOH A 26 9193 9193 HOH HOH . 
L 4 HOH A 27 9195 9195 HOH HOH . 
L 4 HOH A 28 9196 9196 HOH HOH . 
L 4 HOH A 29 9199 9199 HOH HOH . 
L 4 HOH A 30 9202 9202 HOH HOH . 
L 4 HOH A 31 9204 9204 HOH HOH . 
L 4 HOH A 32 9207 9207 HOH HOH . 
M 4 HOH B 1 9004 9004 HOH HOH . 
M 4 HOH B 2 9011 9011 HOH HOH . 
M 4 HOH B 3 9012 9012 HOH HOH . 
M 4 HOH B 4 9019 9019 HOH HOH . 
M 4 HOH B 5 9023 9023 HOH HOH . 
M 4 HOH B 6 9025 9025 HOH HOH . 
M 4 HOH B 7 9039 9039 HOH HOH . 
M 4 HOH B 8 9043 9043 HOH HOH . 
M 4 HOH B 9 9045 9045 HOH HOH . 
M 4 HOH B 10 9048 9048 HOH HOH . 
M 4 HOH B 11 9060 9060 HOH HOH . 
M 4 HOH B 12 9070 9070 HOH HOH . 
M 4 HOH B 13 9071 9071 HOH HOH . 
M 4 HOH B 14 9075 9075 HOH HOH . 
M 4 HOH B 15 9078 9078 HOH HOH . 
M 4 HOH B 16 9088 9088 HOH HOH . 
M 4 HOH B 17 9093 9093 HOH HOH . 
M 4 HOH B 18 9097 9097 HOH HOH . 
M 4 HOH B 19 9106 9106 HOH HOH . 
M 4 HOH B 20 9108 9108 HOH HOH . 
M 4 HOH B 21 9115 9115 HOH HOH . 
M 4 HOH B 22 9133 9133 HOH HOH . 
M 4 HOH B 23 9135 9135 HOH HOH . 
M 4 HOH B 24 9138 9138 HOH HOH . 
M 4 HOH B 25 9144 9144 HOH HOH . 
M 4 HOH B 26 9152 9152 HOH HOH . 
M 4 HOH B 27 9160 9160 HOH HOH . 
M 4 HOH B 28 9167 9167 HOH HOH . 
M 4 HOH B 29 9172 9172 HOH HOH . 
M 4 HOH B 30 9185 9185 HOH HOH . 
M 4 HOH B 31 9191 9191 HOH HOH . 
M 4 HOH B 32 9198 9198 HOH HOH . 
M 4 HOH B 33 9201 9201 HOH HOH . 
M 4 HOH B 34 9203 9203 HOH HOH . 
N 4 HOH C 1 9003 9003 HOH HOH . 
N 4 HOH C 2 9017 9017 HOH HOH . 
N 4 HOH C 3 9022 9022 HOH HOH . 
N 4 HOH C 4 9033 9033 HOH HOH . 
N 4 HOH C 5 9037 9037 HOH HOH . 
N 4 HOH C 6 9042 9042 HOH HOH . 
N 4 HOH C 7 9047 9047 HOH HOH . 
N 4 HOH C 8 9049 9049 HOH HOH . 
N 4 HOH C 9 9055 9055 HOH HOH . 
N 4 HOH C 10 9063 9063 HOH HOH . 
N 4 HOH C 11 9065 9065 HOH HOH . 
N 4 HOH C 12 9072 9072 HOH HOH . 
N 4 HOH C 13 9073 9073 HOH HOH . 
N 4 HOH C 14 9095 9095 HOH HOH . 
N 4 HOH C 15 9100 9100 HOH HOH . 
N 4 HOH C 16 9103 9103 HOH HOH . 
N 4 HOH C 17 9107 9107 HOH HOH . 
N 4 HOH C 18 9113 9113 HOH HOH . 
N 4 HOH C 19 9126 9126 HOH HOH . 
N 4 HOH C 20 9134 9134 HOH HOH . 
N 4 HOH C 21 9140 9140 HOH HOH . 
N 4 HOH C 22 9147 9147 HOH HOH . 
N 4 HOH C 23 9153 9153 HOH HOH . 
N 4 HOH C 24 9161 9161 HOH HOH . 
N 4 HOH C 25 9165 9165 HOH HOH . 
N 4 HOH C 26 9166 9166 HOH HOH . 
N 4 HOH C 27 9170 9170 HOH HOH . 
N 4 HOH C 28 9180 9180 HOH HOH . 
N 4 HOH C 29 9182 9182 HOH HOH . 
N 4 HOH C 30 9206 9206 HOH HOH . 
O 4 HOH D 1 9001 9001 HOH HOH . 
O 4 HOH D 2 9009 9009 HOH HOH . 
O 4 HOH D 3 9013 9013 HOH HOH . 
O 4 HOH D 4 9014 9014 HOH HOH . 
O 4 HOH D 5 9027 9027 HOH HOH . 
O 4 HOH D 6 9034 9034 HOH HOH . 
O 4 HOH D 7 9057 9057 HOH HOH . 
O 4 HOH D 8 9058 9058 HOH HOH . 
O 4 HOH D 9 9064 9064 HOH HOH . 
O 4 HOH D 10 9074 9074 HOH HOH . 
O 4 HOH D 11 9080 9080 HOH HOH . 
O 4 HOH D 12 9089 9089 HOH HOH . 
O 4 HOH D 13 9090 9090 HOH HOH . 
O 4 HOH D 14 9091 9091 HOH HOH . 
O 4 HOH D 15 9101 9101 HOH HOH . 
O 4 HOH D 16 9120 9120 HOH HOH . 
O 4 HOH D 17 9129 9129 HOH HOH . 
O 4 HOH D 18 9136 9136 HOH HOH . 
O 4 HOH D 19 9141 9141 HOH HOH . 
O 4 HOH D 20 9145 9145 HOH HOH . 
O 4 HOH D 21 9149 9149 HOH HOH . 
O 4 HOH D 22 9157 9157 HOH HOH . 
O 4 HOH D 23 9158 9158 HOH HOH . 
O 4 HOH D 24 9162 9162 HOH HOH . 
O 4 HOH D 25 9163 9163 HOH HOH . 
O 4 HOH D 26 9164 9164 HOH HOH . 
O 4 HOH D 27 9171 9171 HOH HOH . 
O 4 HOH D 28 9173 9173 HOH HOH . 
O 4 HOH D 29 9176 9176 HOH HOH . 
O 4 HOH D 30 9177 9177 HOH HOH . 
O 4 HOH D 31 9178 9178 HOH HOH . 
O 4 HOH D 32 9179 9179 HOH HOH . 
O 4 HOH D 33 9183 9183 HOH HOH . 
O 4 HOH D 34 9188 9188 HOH HOH . 
O 4 HOH D 35 9197 9197 HOH HOH . 
P 4 HOH E 1 9002 9002 HOH HOH . 
P 4 HOH E 2 9006 9006 HOH HOH . 
P 4 HOH E 3 9016 9016 HOH HOH . 
P 4 HOH E 4 9018 9018 HOH HOH . 
P 4 HOH E 5 9040 9040 HOH HOH . 
P 4 HOH E 6 9041 9041 HOH HOH . 
P 4 HOH E 7 9061 9061 HOH HOH . 
P 4 HOH E 8 9067 9067 HOH HOH . 
P 4 HOH E 9 9083 9083 HOH HOH . 
P 4 HOH E 10 9084 9084 HOH HOH . 
P 4 HOH E 11 9086 9086 HOH HOH . 
P 4 HOH E 12 9087 9087 HOH HOH . 
P 4 HOH E 13 9096 9096 HOH HOH . 
P 4 HOH E 14 9099 9099 HOH HOH . 
P 4 HOH E 15 9102 9102 HOH HOH . 
P 4 HOH E 16 9104 9104 HOH HOH . 
P 4 HOH E 17 9121 9121 HOH HOH . 
P 4 HOH E 18 9122 9122 HOH HOH . 
P 4 HOH E 19 9125 9125 HOH HOH . 
P 4 HOH E 20 9128 9128 HOH HOH . 
P 4 HOH E 21 9132 9132 HOH HOH . 
P 4 HOH E 22 9139 9139 HOH HOH . 
P 4 HOH E 23 9143 9143 HOH HOH . 
P 4 HOH E 24 9146 9146 HOH HOH . 
P 4 HOH E 25 9155 9155 HOH HOH . 
P 4 HOH E 26 9156 9156 HOH HOH . 
P 4 HOH E 27 9169 9169 HOH HOH . 
P 4 HOH E 28 9174 9174 HOH HOH . 
P 4 HOH E 29 9181 9181 HOH HOH . 
P 4 HOH E 30 9186 9186 HOH HOH . 
P 4 HOH E 31 9189 9189 HOH HOH . 
P 4 HOH E 32 9190 9190 HOH HOH . 
P 4 HOH E 33 9192 9192 HOH HOH . 
P 4 HOH E 34 9194 9194 HOH HOH . 
P 4 HOH E 35 9200 9200 HOH HOH . 
Q 4 HOH F 1 9007 9007 HOH HOH . 
Q 4 HOH F 2 9015 9015 HOH HOH . 
Q 4 HOH F 3 9021 9021 HOH HOH . 
Q 4 HOH F 4 9028 9028 HOH HOH . 
Q 4 HOH F 5 9029 9029 HOH HOH . 
Q 4 HOH F 6 9030 9030 HOH HOH . 
Q 4 HOH F 7 9032 9032 HOH HOH . 
Q 4 HOH F 8 9036 9036 HOH HOH . 
Q 4 HOH F 9 9044 9044 HOH HOH . 
Q 4 HOH F 10 9053 9053 HOH HOH . 
Q 4 HOH F 11 9054 9054 HOH HOH . 
Q 4 HOH F 12 9056 9056 HOH HOH . 
Q 4 HOH F 13 9059 9059 HOH HOH . 
Q 4 HOH F 14 9062 9062 HOH HOH . 
Q 4 HOH F 15 9068 9068 HOH HOH . 
Q 4 HOH F 16 9069 9069 HOH HOH . 
Q 4 HOH F 17 9077 9077 HOH HOH . 
Q 4 HOH F 18 9079 9079 HOH HOH . 
Q 4 HOH F 19 9081 9081 HOH HOH . 
Q 4 HOH F 20 9092 9092 HOH HOH . 
Q 4 HOH F 21 9094 9094 HOH HOH . 
Q 4 HOH F 22 9105 9105 HOH HOH . 
Q 4 HOH F 23 9109 9109 HOH HOH . 
Q 4 HOH F 24 9110 9110 HOH HOH . 
Q 4 HOH F 25 9111 9111 HOH HOH . 
Q 4 HOH F 26 9114 9114 HOH HOH . 
Q 4 HOH F 27 9116 9116 HOH HOH . 
Q 4 HOH F 28 9118 9118 HOH HOH . 
Q 4 HOH F 29 9119 9119 HOH HOH . 
Q 4 HOH F 30 9123 9123 HOH HOH . 
Q 4 HOH F 31 9124 9124 HOH HOH . 
Q 4 HOH F 32 9131 9131 HOH HOH . 
Q 4 HOH F 33 9137 9137 HOH HOH . 
Q 4 HOH F 34 9150 9150 HOH HOH . 
Q 4 HOH F 35 9151 9151 HOH HOH . 
Q 4 HOH F 36 9159 9159 HOH HOH . 
Q 4 HOH F 37 9168 9168 HOH HOH . 
Q 4 HOH F 38 9175 9175 HOH HOH . 
Q 4 HOH F 39 9184 9184 HOH HOH . 
Q 4 HOH F 40 9187 9187 HOH HOH . 
Q 4 HOH F 41 9205 9205 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 N N1 U5P . . . I 3 -6.851 47.049 87.348 1 58.36 ? N1 U5P 8003 C 1 
HETATM 2 C C2 U5P . . . I 3 -7.837 48.018 87.207 1 53.29 ? C2 U5P 8003 C 1 
HETATM 3 N N3 U5P . . . I 3 -9.098 47.533 86.934 1 35.89 ? N3 U5P 8003 C 1 
HETATM 4 C C4 U5P . . . I 3 -9.466 46.205 86.787 1 38.65 ? C4 U5P 8003 C 1 
HETATM 5 C C5 U5P . . . I 3 -8.391 45.269 86.944 1 47.44 ? C5 U5P 8003 C 1 
HETATM 6 C C6 U5P . . . I 3 -7.153 45.71 87.214 1 58.2 ? C6 U5P 8003 C 1 
HETATM 7 O O2 U5P . . . I 3 -7.607 49.215 87.317 1 63.47 ? O2 U5P 8003 C 1 
HETATM 8 O O4 U5P . . . I 3 -10.646 45.921 86.543 1 39.02 ? O4 U5P 8003 C 1 
HETATM 9 C C1' U5P . . . I 3 -5.485 47.512 87.647 1 71.82 ? C1' U5P 8003 C 1 
HETATM 10 C C2' U5P . . . I 3 -5.329 48.063 89.066 1 71.82 ? C2' U5P 8003 C 1 
HETATM 11 O O2' U5P . . . I 3 -4.407 49.137 89.064 1 71.82 ? O2' U5P 8003 C 1 
HETATM 12 C C3' U5P . . . I 3 -4.814 46.834 89.808 1 71.82 ? C3' U5P 8003 C 1 
HETATM 13 C C4' U5P . . . I 3 -3.886 46.205 88.775 1 71.82 ? C4' U5P 8003 C 1 
HETATM 14 O O3' U5P . . . I 3 -4.113 47.196 90.998 1 71.82 ? O3' U5P 8003 C 1 
HETATM 15 O O4' U5P . . . I 3 -4.586 46.417 87.516 1 71.82 ? O4' U5P 8003 C 1 
HETATM 16 C C5' U5P . . . I 3 -3.615 44.724 88.938 1 71.82 ? C5' U5P 8003 C 1 
HETATM 17 O O5' U5P . . . I 3 -3.563 44.373 90.338 1 71.82 ? O5' U5P 8003 C 1 
HETATM 18 P P U5P . . . I 3 -2.206 44.583 91.222 1 56.94 ? P U5P 8003 C 1 
HETATM 19 O O1P U5P . . . I 3 -1.229 43.518 90.739 1 38.75 ? O1P U5P 8003 C 1 
HETATM 20 O O2P U5P . . . I 3 -1.724 46.01 90.969 1 42.84 ? O2P U5P 8003 C 1 
HETATM 21 O O3P U5P . . . I 3 -2.625 44.366 92.67 1 56.94 ? O3P U5P 8003 C 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           308 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           21 
#