data_4O8R
#
_model_server_result.job_id            sNjF1VBR8NasY-AVfXnqug 
_model_server_result.datetime_utc      '2024-11-07 16:50:57' 
_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          4o8r 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Z","auth_seq_id":301}' 
#
_entry.id    4O8R 
#
_exptl.entry_id    4O8R 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              326.197 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE" 
_entity.pdbx_number_of_molecules    12 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          91.59 
_cell.angle_gamma         90 
_cell.entry_id            4O8R 
_cell.length_a            147.899 
_cell.length_b            101.8 
_cell.length_c            192.845 
_cell.Z_PDB               52 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4O8R 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 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 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
PISA dimeric 2 author_and_software_defined_assembly 5 
PISA dimeric 2 author_and_software_defined_assembly 6 
PISA dimeric 2 author_and_software_defined_assembly 7 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,N,O,P,AA,BA 1 1 
C,D,Q,R,CA,DA 2 1 
E,F,S,T,EA,FA 3 1 
G,H,U,V,GA,HA 4 1 
I,J,W,IA,JA 5 1 
K,L,X,Y,KA 6 1 
M,Z,LA 7 1,2 
#
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]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -147.899 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 N N N 
? 2 P N N 
? 2 Q N N 
? 2 R N N 
? 2 S N N 
? 2 T N N 
? 2 U N N 
? 2 V N N 
? 2 W N N 
? 2 X N N 
? 2 Y N N 
? 2 Z N N 
#
_chem_comp.formula           'C9 H15 N2 O9 P' 
_chem_comp.formula_weight    326.197 
_chem_comp.id                H2U 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "5,6-DIHYDROURIDINE-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
P OP1 H2U doub 129 n n 
P OP2 H2U sing 130 n n 
P OP3 H2U sing 131 n n 
P O5' H2U sing 132 n n 
OP2 HOP2 H2U sing 133 n n 
OP3 HOP3 H2U sing 134 n n 
O5' C5' H2U sing 135 n n 
C5' C4' H2U sing 136 n n 
C5' H5' H2U sing 137 n n 
C5' "H5''" H2U sing 138 n n 
C4' O4' H2U sing 139 n n 
C4' C3' H2U sing 140 n n 
C4' H4' H2U sing 141 n n 
O4' C1' H2U sing 142 n n 
C3' O3' H2U sing 143 n n 
C3' C2' H2U sing 144 n n 
C3' H3' H2U sing 145 n n 
O3' HO3' H2U sing 146 n n 
C1' C2' H2U sing 147 n n 
C1' N1 H2U sing 148 n n 
C1' H1' H2U sing 149 n n 
C2' O2' H2U sing 150 n n 
C2' H2' H2U sing 151 n n 
O2' HO2' H2U sing 152 n n 
N1 C2 H2U sing 153 n n 
N1 C6 H2U sing 154 n n 
C2 O2 H2U doub 155 n n 
C2 N3 H2U sing 156 n n 
N3 C4 H2U sing 157 n n 
N3 HN3 H2U sing 158 n n 
C4 O4 H2U doub 159 n n 
C4 C5 H2U sing 160 n n 
C5 C6 H2U sing 161 n n 
C5 H51 H2U sing 162 n n 
C5 H52 H2U sing 163 n n 
C6 H61 H2U sing 164 n n 
C6 H62 H2U sing 165 n n 
#
_atom_sites.entry_id                     4O8R 
_atom_sites.fract_transf_matrix[1][1]    0.006761 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000188 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009823 
_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]    0.005188 
_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
N 2 H2U A 1 301 229 H2U H2U . 
O 3 CL A 1 302 1 CL CL . 
P 2 H2U B 1 301 229 H2U H2U . 
Q 2 H2U C 1 301 229 H2U H2U . 
R 2 H2U D 1 301 229 H2U H2U . 
S 2 H2U E 1 301 229 H2U H2U . 
T 2 H2U F 1 301 229 H2U H2U . 
U 2 H2U G 1 301 229 H2U H2U . 
V 2 H2U H 1 301 229 H2U H2U . 
W 2 H2U J 1 301 229 H2U H2U . 
X 2 H2U K 1 301 229 H2U H2U . 
Y 2 H2U L 1 301 229 H2U H2U . 
Z 2 H2U M 1 301 229 H2U H2U . 
AA 4 HOH A 1 401 1 HOH HOH . 
AA 4 HOH A 2 402 3 HOH HOH . 
AA 4 HOH A 3 403 8 HOH HOH . 
AA 4 HOH A 4 404 9 HOH HOH . 
AA 4 HOH A 5 405 12 HOH HOH . 
AA 4 HOH A 6 406 13 HOH HOH . 
AA 4 HOH A 7 407 14 HOH HOH . 
AA 4 HOH A 8 408 17 HOH HOH . 
AA 4 HOH A 9 409 18 HOH HOH . 
AA 4 HOH A 10 410 23 HOH HOH . 
AA 4 HOH A 11 411 24 HOH HOH . 
AA 4 HOH A 12 412 26 HOH HOH . 
AA 4 HOH A 13 413 32 HOH HOH . 
AA 4 HOH A 14 414 39 HOH HOH . 
AA 4 HOH A 15 415 42 HOH HOH . 
AA 4 HOH A 16 416 47 HOH HOH . 
AA 4 HOH A 17 417 49 HOH HOH . 
AA 4 HOH A 18 418 56 HOH HOH . 
AA 4 HOH A 19 419 59 HOH HOH . 
AA 4 HOH A 20 420 60 HOH HOH . 
AA 4 HOH A 21 421 72 HOH HOH . 
AA 4 HOH A 22 422 73 HOH HOH . 
AA 4 HOH A 23 423 74 HOH HOH . 
AA 4 HOH A 24 424 80 HOH HOH . 
AA 4 HOH A 25 425 81 HOH HOH . 
AA 4 HOH A 26 426 84 HOH HOH . 
AA 4 HOH A 27 427 111 HOH HOH . 
AA 4 HOH A 28 428 114 HOH HOH . 
AA 4 HOH A 29 429 133 HOH HOH . 
AA 4 HOH A 30 430 148 HOH HOH . 
AA 4 HOH A 31 431 158 HOH HOH . 
AA 4 HOH A 32 432 191 HOH HOH . 
AA 4 HOH A 33 433 195 HOH HOH . 
AA 4 HOH A 34 434 196 HOH HOH . 
AA 4 HOH A 35 435 197 HOH HOH . 
AA 4 HOH A 36 436 199 HOH HOH . 
BA 4 HOH B 1 401 10 HOH HOH . 
BA 4 HOH B 2 402 11 HOH HOH . 
BA 4 HOH B 3 403 15 HOH HOH . 
BA 4 HOH B 4 404 25 HOH HOH . 
BA 4 HOH B 5 405 30 HOH HOH . 
BA 4 HOH B 6 406 37 HOH HOH . 
BA 4 HOH B 7 407 61 HOH HOH . 
BA 4 HOH B 8 408 75 HOH HOH . 
BA 4 HOH B 9 409 86 HOH HOH . 
BA 4 HOH B 10 410 88 HOH HOH . 
BA 4 HOH B 11 411 104 HOH HOH . 
BA 4 HOH B 12 412 112 HOH HOH . 
BA 4 HOH B 13 413 120 HOH HOH . 
BA 4 HOH B 14 414 135 HOH HOH . 
BA 4 HOH B 15 415 144 HOH HOH . 
BA 4 HOH B 16 416 147 HOH HOH . 
BA 4 HOH B 17 417 156 HOH HOH . 
BA 4 HOH B 18 418 162 HOH HOH . 
BA 4 HOH B 19 419 163 HOH HOH . 
BA 4 HOH B 20 420 165 HOH HOH . 
BA 4 HOH B 21 421 166 HOH HOH . 
BA 4 HOH B 22 422 190 HOH HOH . 
CA 4 HOH C 1 401 4 HOH HOH . 
CA 4 HOH C 2 402 19 HOH HOH . 
CA 4 HOH C 3 403 29 HOH HOH . 
CA 4 HOH C 4 404 31 HOH HOH . 
CA 4 HOH C 5 405 34 HOH HOH . 
CA 4 HOH C 6 406 38 HOH HOH . 
CA 4 HOH C 7 407 40 HOH HOH . 
CA 4 HOH C 8 408 43 HOH HOH . 
CA 4 HOH C 9 409 44 HOH HOH . 
CA 4 HOH C 10 410 48 HOH HOH . 
CA 4 HOH C 11 411 50 HOH HOH . 
CA 4 HOH C 12 412 51 HOH HOH . 
CA 4 HOH C 13 413 53 HOH HOH . 
CA 4 HOH C 14 414 62 HOH HOH . 
CA 4 HOH C 15 415 67 HOH HOH . 
CA 4 HOH C 16 416 78 HOH HOH . 
CA 4 HOH C 17 417 79 HOH HOH . 
CA 4 HOH C 18 418 85 HOH HOH . 
CA 4 HOH C 19 419 96 HOH HOH . 
CA 4 HOH C 20 420 100 HOH HOH . 
CA 4 HOH C 21 421 101 HOH HOH . 
CA 4 HOH C 22 422 102 HOH HOH . 
CA 4 HOH C 23 423 105 HOH HOH . 
CA 4 HOH C 24 424 108 HOH HOH . 
CA 4 HOH C 25 425 117 HOH HOH . 
CA 4 HOH C 26 426 121 HOH HOH . 
CA 4 HOH C 27 427 122 HOH HOH . 
CA 4 HOH C 28 428 123 HOH HOH . 
CA 4 HOH C 29 429 126 HOH HOH . 
CA 4 HOH C 30 430 140 HOH HOH . 
CA 4 HOH C 31 431 143 HOH HOH . 
CA 4 HOH C 32 432 149 HOH HOH . 
CA 4 HOH C 33 433 150 HOH HOH . 
CA 4 HOH C 34 434 167 HOH HOH . 
DA 4 HOH D 1 401 2 HOH HOH . 
DA 4 HOH D 2 402 5 HOH HOH . 
DA 4 HOH D 3 403 6 HOH HOH . 
DA 4 HOH D 4 404 33 HOH HOH . 
DA 4 HOH D 5 405 52 HOH HOH . 
DA 4 HOH D 6 406 77 HOH HOH . 
DA 4 HOH D 7 407 90 HOH HOH . 
DA 4 HOH D 8 408 94 HOH HOH . 
DA 4 HOH D 9 409 98 HOH HOH . 
DA 4 HOH D 10 410 103 HOH HOH . 
DA 4 HOH D 11 411 110 HOH HOH . 
DA 4 HOH D 12 412 115 HOH HOH . 
DA 4 HOH D 13 413 116 HOH HOH . 
DA 4 HOH D 14 414 127 HOH HOH . 
DA 4 HOH D 15 415 132 HOH HOH . 
DA 4 HOH D 16 416 153 HOH HOH . 
DA 4 HOH D 17 417 160 HOH HOH . 
DA 4 HOH D 18 418 168 HOH HOH . 
DA 4 HOH D 19 419 194 HOH HOH . 
EA 4 HOH E 1 401 93 HOH HOH . 
EA 4 HOH E 2 402 134 HOH HOH . 
EA 4 HOH E 3 403 159 HOH HOH . 
EA 4 HOH E 4 404 169 HOH HOH . 
EA 4 HOH E 5 405 170 HOH HOH . 
EA 4 HOH E 6 406 171 HOH HOH . 
EA 4 HOH E 7 407 172 HOH HOH . 
FA 4 HOH F 1 401 20 HOH HOH . 
FA 4 HOH F 2 402 28 HOH HOH . 
FA 4 HOH F 3 403 113 HOH HOH . 
FA 4 HOH F 4 404 119 HOH HOH . 
FA 4 HOH F 5 405 124 HOH HOH . 
FA 4 HOH F 6 406 130 HOH HOH . 
FA 4 HOH F 7 407 141 HOH HOH . 
FA 4 HOH F 8 408 146 HOH HOH . 
FA 4 HOH F 9 409 173 HOH HOH . 
FA 4 HOH F 10 410 174 HOH HOH . 
FA 4 HOH F 11 411 186 HOH HOH . 
GA 4 HOH G 1 401 118 HOH HOH . 
GA 4 HOH G 2 402 138 HOH HOH . 
GA 4 HOH G 3 403 175 HOH HOH . 
GA 4 HOH G 4 404 176 HOH HOH . 
GA 4 HOH G 5 405 177 HOH HOH . 
GA 4 HOH G 6 406 193 HOH HOH . 
HA 4 HOH H 1 401 54 HOH HOH . 
HA 4 HOH H 2 402 137 HOH HOH . 
HA 4 HOH H 3 403 161 HOH HOH . 
HA 4 HOH H 4 404 178 HOH HOH . 
HA 4 HOH H 5 405 179 HOH HOH . 
HA 4 HOH H 6 406 187 HOH HOH . 
IA 4 HOH I 1 301 22 HOH HOH . 
IA 4 HOH I 2 302 45 HOH HOH . 
IA 4 HOH I 3 303 46 HOH HOH . 
IA 4 HOH I 4 304 58 HOH HOH . 
IA 4 HOH I 5 305 82 HOH HOH . 
IA 4 HOH I 6 306 83 HOH HOH . 
IA 4 HOH I 7 307 106 HOH HOH . 
IA 4 HOH I 8 308 107 HOH HOH . 
IA 4 HOH I 9 309 109 HOH HOH . 
IA 4 HOH I 10 310 192 HOH HOH . 
IA 4 HOH I 11 311 198 HOH HOH . 
JA 4 HOH J 1 401 27 HOH HOH . 
JA 4 HOH J 2 402 36 HOH HOH . 
JA 4 HOH J 3 403 55 HOH HOH . 
JA 4 HOH J 4 404 63 HOH HOH . 
JA 4 HOH J 5 405 64 HOH HOH . 
JA 4 HOH J 6 406 66 HOH HOH . 
JA 4 HOH J 7 407 69 HOH HOH . 
JA 4 HOH J 8 408 87 HOH HOH . 
JA 4 HOH J 9 409 91 HOH HOH . 
JA 4 HOH J 10 410 92 HOH HOH . 
JA 4 HOH J 11 411 95 HOH HOH . 
JA 4 HOH J 12 412 99 HOH HOH . 
JA 4 HOH J 13 413 131 HOH HOH . 
JA 4 HOH J 14 414 139 HOH HOH . 
JA 4 HOH J 15 415 142 HOH HOH . 
JA 4 HOH J 16 416 152 HOH HOH . 
JA 4 HOH J 17 417 154 HOH HOH . 
JA 4 HOH J 18 418 164 HOH HOH . 
JA 4 HOH J 19 419 180 HOH HOH . 
JA 4 HOH J 20 420 181 HOH HOH . 
KA 4 HOH K 1 401 157 HOH HOH . 
KA 4 HOH K 2 402 182 HOH HOH . 
KA 4 HOH K 3 403 183 HOH HOH . 
KA 4 HOH K 4 404 188 HOH HOH . 
LA 4 HOH M 1 401 7 HOH HOH . 
LA 4 HOH M 2 402 16 HOH HOH . 
LA 4 HOH M 3 403 21 HOH HOH . 
LA 4 HOH M 4 404 35 HOH HOH . 
LA 4 HOH M 5 405 41 HOH HOH . 
LA 4 HOH M 6 406 57 HOH HOH . 
LA 4 HOH M 7 407 65 HOH HOH . 
LA 4 HOH M 8 408 68 HOH HOH . 
LA 4 HOH M 9 409 70 HOH HOH . 
LA 4 HOH M 10 410 71 HOH HOH . 
LA 4 HOH M 11 411 76 HOH HOH . 
LA 4 HOH M 12 412 89 HOH HOH . 
LA 4 HOH M 13 413 97 HOH HOH . 
LA 4 HOH M 14 414 125 HOH HOH . 
LA 4 HOH M 15 415 128 HOH HOH . 
LA 4 HOH M 16 416 129 HOH HOH . 
LA 4 HOH M 17 417 136 HOH HOH . 
LA 4 HOH M 18 418 145 HOH HOH . 
LA 4 HOH M 19 419 151 HOH HOH . 
LA 4 HOH M 20 420 155 HOH HOH . 
LA 4 HOH M 21 421 184 HOH HOH . 
LA 4 HOH M 22 422 185 HOH HOH . 
LA 4 HOH M 23 423 189 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 H2U . . . Z 2 -66.531 51.308 -15.756 1 77.6 ? P H2U 301 M 1 
HETATM 2 O OP1 H2U . . . Z 2 -65.888 50.049 -15.166 1 78.28 ? OP1 H2U 301 M 1 
HETATM 3 O OP2 H2U . . . Z 2 -65.915 52.672 -15.451 1 78.06 ? OP2 H2U 301 M 1 
HETATM 4 O OP3 H2U . . . Z 2 -66.554 51.14 -17.275 1 79.07 ? OP3 H2U 301 M 1 
HETATM 5 O O5' H2U . . . Z 2 -68.035 51.331 -15.233 1 69.31 ? O5' H2U 301 M 1 
HETATM 6 C C5' H2U . . . Z 2 -68.435 50.501 -14.147 1 67.65 ? C5' H2U 301 M 1 
HETATM 7 C C4' H2U . . . Z 2 -69.476 51.16 -13.275 1 64.88 ? C4' H2U 301 M 1 
HETATM 8 O O4' H2U . . . Z 2 -70.462 50.16 -12.89 1 64.27 ? O4' H2U 301 M 1 
HETATM 9 C C3' H2U . . . Z 2 -68.947 51.741 -11.968 1 63.53 ? C3' H2U 301 M 1 
HETATM 10 O O3' H2U . . . Z 2 -69.8 52.803 -11.542 1 59.64 ? O3' H2U 301 M 1 
HETATM 11 C C1' H2U . . . Z 2 -70.427 49.973 -11.484 1 63.3 ? C1' H2U 301 M 1 
HETATM 12 C C2' H2U . . . Z 2 -69.096 50.562 -11.015 1 64.04 ? C2' H2U 301 M 1 
HETATM 13 O O2' H2U . . . Z 2 -69.119 50.9 -9.643 1 63.09 ? O2' H2U 301 M 1 
HETATM 14 N N1 H2U . . . Z 2 -70.594 48.542 -11.186 1 63 ? N1 H2U 301 M 1 
HETATM 15 C C2 H2U . . . Z 2 -69.698 47.62 -11.602 1 64.56 ? C2 H2U 301 M 1 
HETATM 16 O O2 H2U . . . Z 2 -68.737 47.988 -12.258 1 66.45 ? O2 H2U 301 M 1 
HETATM 17 N N3 H2U . . . Z 2 -69.836 46.312 -11.323 1 64.35 ? N3 H2U 301 M 1 
HETATM 18 C C4 H2U . . . Z 2 -70.887 45.861 -10.614 1 63 ? C4 H2U 301 M 1 
HETATM 19 O O4 H2U . . . Z 2 -70.972 44.678 -10.378 1 63.1 ? O4 H2U 301 M 1 
HETATM 20 C C5 H2U . . . Z 2 -72.145 46.688 -10.621 1 61.97 ? C5 H2U 301 M 1 
HETATM 21 C C6 H2U . . . Z 2 -71.771 48.156 -10.409 1 61.68 ? C6 H2U 301 M 1 
#
_model_server_stats.io_time_ms              46 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           340 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           21 
#