data_3P5Y
#
_model_server_result.job_id            ScpRdakXxtDyHQG97LShfw 
_model_server_result.datetime_utc      '2024-10-13 03:25:33' 
_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          3p5y 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":229}' 
#
_entry.id    3P5Y 
#
_exptl.entry_id    3P5Y 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              340.181 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "6-HYDROXYURIDINE-5'-PHOSPHATE" 
_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            3P5Y 
_cell.length_a            52.608 
_cell.length_b            74.038 
_cell.length_c            117.503 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3P5Y 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 E N N 
#
_chem_comp.formula           'C9 H13 N2 O10 P' 
_chem_comp.formula_weight    340.181 
_chem_comp.id                BMP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "6-HYDROXYURIDINE-5'-PHOSPHATE" 
_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
P OP1 BMP doub 70 n n 
P OP2 BMP sing 71 n n 
P OP3 BMP sing 72 n n 
P O5' BMP sing 73 n n 
OP2 HOP2 BMP sing 74 n n 
OP3 HOP3 BMP sing 75 n n 
O5' C5' BMP sing 76 n n 
C5' C4' BMP sing 77 n n 
C5' H5' BMP sing 78 n n 
C5' "H5''" BMP sing 79 n n 
C4' O4' BMP sing 80 n n 
C4' C3' BMP sing 81 n n 
C4' H4' BMP sing 82 n n 
O4' C1' BMP sing 83 n n 
C3' O3' BMP sing 84 n n 
C3' C2' BMP sing 85 n n 
C3' H3' BMP sing 86 n n 
O3' HO3' BMP sing 87 n n 
C2' O2' BMP sing 88 n n 
C2' C1' BMP sing 89 n n 
C2' H2' BMP sing 90 n n 
O2' HO2' BMP sing 91 n n 
C1' N1 BMP sing 92 n n 
C1' H1' BMP sing 93 n n 
N1 C2 BMP sing 94 n n 
N1 C6 BMP sing 95 n n 
C2 O2 BMP doub 96 n n 
C2 N3 BMP sing 97 n n 
N3 C4 BMP sing 98 n n 
N3 HN3 BMP sing 99 n n 
C4 O4 BMP doub 100 n n 
C4 C5 BMP sing 101 n n 
C5 C6 BMP doub 102 n n 
C5 H51 BMP sing 103 n n 
C6 O1 BMP sing 104 n n 
O1 HO1 BMP sing 105 n n 
#
_atom_sites.entry_id                     3P5Y 
_atom_sites.fract_transf_matrix[1][1]    0.019009 
_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]    0.013507 
_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]    0.00851 
_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
C 2 BMP A 1 229 1 BMP BMP . 
D 3 GOL A 1 230 1 GOL GOL . 
E 2 BMP B 1 229 2 BMP BMP . 
F 4 HOH A 1 231 1 HOH HOH . 
F 4 HOH A 2 232 5 HOH HOH . 
F 4 HOH A 3 233 6 HOH HOH . 
F 4 HOH A 4 234 11 HOH HOH . 
F 4 HOH A 5 235 12 HOH HOH . 
F 4 HOH A 6 236 14 HOH HOH . 
F 4 HOH A 7 237 15 HOH HOH . 
F 4 HOH A 8 238 16 HOH HOH . 
F 4 HOH A 9 239 17 HOH HOH . 
F 4 HOH A 10 240 18 HOH HOH . 
F 4 HOH A 11 241 20 HOH HOH . 
F 4 HOH A 12 242 23 HOH HOH . 
F 4 HOH A 13 243 25 HOH HOH . 
F 4 HOH A 14 244 27 HOH HOH . 
F 4 HOH A 15 245 29 HOH HOH . 
F 4 HOH A 16 246 33 HOH HOH . 
F 4 HOH A 17 247 41 HOH HOH . 
F 4 HOH A 18 248 43 HOH HOH . 
F 4 HOH A 19 249 44 HOH HOH . 
F 4 HOH A 20 250 45 HOH HOH . 
F 4 HOH A 21 251 46 HOH HOH . 
F 4 HOH A 22 252 47 HOH HOH . 
F 4 HOH A 23 253 48 HOH HOH . 
F 4 HOH A 24 254 50 HOH HOH . 
F 4 HOH A 25 255 52 HOH HOH . 
F 4 HOH A 26 256 54 HOH HOH . 
F 4 HOH A 27 257 57 HOH HOH . 
F 4 HOH A 28 258 60 HOH HOH . 
F 4 HOH A 29 259 62 HOH HOH . 
F 4 HOH A 30 260 64 HOH HOH . 
F 4 HOH A 31 261 68 HOH HOH . 
F 4 HOH A 32 262 70 HOH HOH . 
F 4 HOH A 33 263 73 HOH HOH . 
F 4 HOH A 34 264 75 HOH HOH . 
F 4 HOH A 35 265 77 HOH HOH . 
F 4 HOH A 36 266 82 HOH HOH . 
F 4 HOH A 37 267 85 HOH HOH . 
F 4 HOH A 38 268 92 HOH HOH . 
F 4 HOH A 39 269 93 HOH HOH . 
F 4 HOH A 40 270 101 HOH HOH . 
F 4 HOH A 41 271 102 HOH HOH . 
F 4 HOH A 42 272 103 HOH HOH . 
F 4 HOH A 43 273 104 HOH HOH . 
F 4 HOH A 44 274 105 HOH HOH . 
F 4 HOH A 45 275 106 HOH HOH . 
F 4 HOH A 46 276 111 HOH HOH . 
F 4 HOH A 47 277 112 HOH HOH . 
F 4 HOH A 48 278 113 HOH HOH . 
F 4 HOH A 49 279 114 HOH HOH . 
F 4 HOH A 50 280 115 HOH HOH . 
F 4 HOH A 51 281 117 HOH HOH . 
F 4 HOH A 52 282 118 HOH HOH . 
F 4 HOH A 53 283 120 HOH HOH . 
F 4 HOH A 54 284 123 HOH HOH . 
F 4 HOH A 55 285 125 HOH HOH . 
F 4 HOH A 56 286 126 HOH HOH . 
F 4 HOH A 57 287 129 HOH HOH . 
F 4 HOH A 58 288 130 HOH HOH . 
F 4 HOH A 59 289 133 HOH HOH . 
F 4 HOH A 60 290 135 HOH HOH . 
F 4 HOH A 61 291 139 HOH HOH . 
F 4 HOH A 62 292 140 HOH HOH . 
F 4 HOH A 63 293 143 HOH HOH . 
F 4 HOH A 64 294 144 HOH HOH . 
F 4 HOH A 65 295 146 HOH HOH . 
F 4 HOH A 66 296 149 HOH HOH . 
F 4 HOH A 67 297 151 HOH HOH . 
F 4 HOH A 68 298 152 HOH HOH . 
F 4 HOH A 69 299 153 HOH HOH . 
F 4 HOH A 70 300 154 HOH HOH . 
F 4 HOH A 71 301 157 HOH HOH . 
F 4 HOH A 72 302 158 HOH HOH . 
F 4 HOH A 73 303 160 HOH HOH . 
F 4 HOH A 74 304 162 HOH HOH . 
F 4 HOH A 75 305 164 HOH HOH . 
F 4 HOH A 76 306 171 HOH HOH . 
F 4 HOH A 77 307 172 HOH HOH . 
F 4 HOH A 78 308 175 HOH HOH . 
G 4 HOH B 1 230 2 HOH HOH . 
G 4 HOH B 2 231 3 HOH HOH . 
G 4 HOH B 3 232 4 HOH HOH . 
G 4 HOH B 4 233 7 HOH HOH . 
G 4 HOH B 5 234 8 HOH HOH . 
G 4 HOH B 6 235 9 HOH HOH . 
G 4 HOH B 7 236 10 HOH HOH . 
G 4 HOH B 8 237 13 HOH HOH . 
G 4 HOH B 9 238 19 HOH HOH . 
G 4 HOH B 10 239 21 HOH HOH . 
G 4 HOH B 11 240 22 HOH HOH . 
G 4 HOH B 12 241 24 HOH HOH . 
G 4 HOH B 13 242 26 HOH HOH . 
G 4 HOH B 14 243 28 HOH HOH . 
G 4 HOH B 15 244 30 HOH HOH . 
G 4 HOH B 16 245 31 HOH HOH . 
G 4 HOH B 17 246 32 HOH HOH . 
G 4 HOH B 18 247 34 HOH HOH . 
G 4 HOH B 19 248 35 HOH HOH . 
G 4 HOH B 20 249 36 HOH HOH . 
G 4 HOH B 21 250 37 HOH HOH . 
G 4 HOH B 22 251 38 HOH HOH . 
G 4 HOH B 23 252 39 HOH HOH . 
G 4 HOH B 24 253 40 HOH HOH . 
G 4 HOH B 25 254 42 HOH HOH . 
G 4 HOH B 26 255 49 HOH HOH . 
G 4 HOH B 27 256 51 HOH HOH . 
G 4 HOH B 28 257 53 HOH HOH . 
G 4 HOH B 29 258 55 HOH HOH . 
G 4 HOH B 30 259 56 HOH HOH . 
G 4 HOH B 31 260 58 HOH HOH . 
G 4 HOH B 32 261 59 HOH HOH . 
G 4 HOH B 33 262 61 HOH HOH . 
G 4 HOH B 34 263 63 HOH HOH . 
G 4 HOH B 35 264 65 HOH HOH . 
G 4 HOH B 36 265 67 HOH HOH . 
G 4 HOH B 37 266 69 HOH HOH . 
G 4 HOH B 38 267 71 HOH HOH . 
G 4 HOH B 39 268 72 HOH HOH . 
G 4 HOH B 40 269 74 HOH HOH . 
G 4 HOH B 41 270 76 HOH HOH . 
G 4 HOH B 42 271 78 HOH HOH . 
G 4 HOH B 43 272 79 HOH HOH . 
G 4 HOH B 44 273 80 HOH HOH . 
G 4 HOH B 45 274 81 HOH HOH . 
G 4 HOH B 46 275 83 HOH HOH . 
G 4 HOH B 47 276 84 HOH HOH . 
G 4 HOH B 48 277 86 HOH HOH . 
G 4 HOH B 49 278 87 HOH HOH . 
G 4 HOH B 50 279 88 HOH HOH . 
G 4 HOH B 51 280 89 HOH HOH . 
G 4 HOH B 52 281 90 HOH HOH . 
G 4 HOH B 53 282 91 HOH HOH . 
G 4 HOH B 54 283 94 HOH HOH . 
G 4 HOH B 55 284 95 HOH HOH . 
G 4 HOH B 56 285 96 HOH HOH . 
G 4 HOH B 57 286 97 HOH HOH . 
G 4 HOH B 58 287 98 HOH HOH . 
G 4 HOH B 59 288 99 HOH HOH . 
G 4 HOH B 60 289 100 HOH HOH . 
G 4 HOH B 61 290 107 HOH HOH . 
G 4 HOH B 62 291 108 HOH HOH . 
G 4 HOH B 63 292 110 HOH HOH . 
G 4 HOH B 64 293 116 HOH HOH . 
G 4 HOH B 65 294 119 HOH HOH . 
G 4 HOH B 66 295 121 HOH HOH . 
G 4 HOH B 67 296 122 HOH HOH . 
G 4 HOH B 68 297 124 HOH HOH . 
G 4 HOH B 69 298 127 HOH HOH . 
G 4 HOH B 70 299 128 HOH HOH . 
G 4 HOH B 71 300 131 HOH HOH . 
G 4 HOH B 72 301 132 HOH HOH . 
G 4 HOH B 73 302 134 HOH HOH . 
G 4 HOH B 74 303 136 HOH HOH . 
G 4 HOH B 75 304 137 HOH HOH . 
G 4 HOH B 76 305 138 HOH HOH . 
G 4 HOH B 77 306 141 HOH HOH . 
G 4 HOH B 78 307 142 HOH HOH . 
G 4 HOH B 79 308 145 HOH HOH . 
G 4 HOH B 80 309 147 HOH HOH . 
G 4 HOH B 81 310 148 HOH HOH . 
G 4 HOH B 82 311 150 HOH HOH . 
G 4 HOH B 83 312 155 HOH HOH . 
G 4 HOH B 84 313 156 HOH HOH . 
G 4 HOH B 85 314 159 HOH HOH . 
G 4 HOH B 86 315 161 HOH HOH . 
G 4 HOH B 87 316 163 HOH HOH . 
G 4 HOH B 88 317 165 HOH HOH . 
G 4 HOH B 89 318 166 HOH HOH . 
G 4 HOH B 90 319 173 HOH HOH . 
G 4 HOH B 91 320 174 HOH HOH . 
G 4 HOH B 92 321 176 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 P P BMP . . . E 2 18.067 9.605 37.996 1 21.91 ? P BMP 229 B 1 
HETATM 2 O OP1 BMP . . . E 2 19.031 8.894 37.146 1 22.13 ? OP1 BMP 229 B 1 
HETATM 3 O OP2 BMP . . . E 2 17.138 8.627 38.82 1 21.23 ? OP2 BMP 229 B 1 
HETATM 4 O OP3 BMP . . . E 2 18.853 10.559 38.998 1 21.27 ? OP3 BMP 229 B 1 
HETATM 5 O O5' BMP . . . E 2 16.971 10.458 37.124 1 20.21 ? O5' BMP 229 B 1 
HETATM 6 C C5' BMP . . . E 2 17.527 11.053 35.958 1 20.96 ? C5' BMP 229 B 1 
HETATM 7 C C4' BMP . . . E 2 16.365 11.842 35.326 1 18.84 ? C4' BMP 229 B 1 
HETATM 8 O O4' BMP . . . E 2 16.823 12.675 34.238 1 19.42 ? O4' BMP 229 B 1 
HETATM 9 C C3' BMP . . . E 2 15.298 10.899 34.738 1 21.02 ? C3' BMP 229 B 1 
HETATM 10 O O3' BMP . . . E 2 14.001 11.497 34.896 1 21.02 ? O3' BMP 229 B 1 
HETATM 11 C C2' BMP . . . E 2 15.731 10.771 33.257 1 17.42 ? C2' BMP 229 B 1 
HETATM 12 O O2' BMP . . . E 2 14.611 10.52 32.418 1 19.57 ? O2' BMP 229 B 1 
HETATM 13 C C1' BMP . . . E 2 16.296 12.185 32.984 1 17.77 ? C1' BMP 229 B 1 
HETATM 14 N N1 BMP . . . E 2 17.374 12.29 31.992 1 19.98 ? N1 BMP 229 B 1 
HETATM 15 C C2 BMP . . . E 2 18.515 11.587 32.102 1 19.12 ? C2 BMP 229 B 1 
HETATM 16 O O2 BMP . . . E 2 18.645 10.78 33.009 1 20.35 ? O2 BMP 229 B 1 
HETATM 17 N N3 BMP . . . E 2 19.502 11.725 31.203 1 19.4 ? N3 BMP 229 B 1 
HETATM 18 C C4 BMP . . . E 2 19.404 12.611 30.189 1 19.92 ? C4 BMP 229 B 1 
HETATM 19 O O4 BMP . . . E 2 20.312 12.733 29.386 1 20.57 ? O4 BMP 229 B 1 
HETATM 20 C C5 BMP . . . E 2 18.248 13.39 30.068 1 20.74 ? C5 BMP 229 B 1 
HETATM 21 C C6 BMP . . . E 2 17.253 13.223 30.986 1 19.27 ? C6 BMP 229 B 1 
HETATM 22 O O1 BMP . . . E 2 16.138 13.956 30.898 1 19.32 ? O1 BMP 229 B 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           270 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           22 
#