data_3E5S
#
_model_server_result.job_id            dQrfxNB61u-FkWUGD3ixsA 
_model_server_result.datetime_utc      '2024-10-11 10:24:56' 
_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          3e5s 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":150}' 
#
_entry.id    3E5S 
#
_exptl.entry_id    3E5S 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              402.188 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "THYMIDINE-3',5'-DIPHOSPHATE" 
_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          90.04 
_cell.angle_gamma         90 
_cell.entry_id            3E5S 
_cell.length_a            31.172 
_cell.length_b            78.514 
_cell.length_c            60.949 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3E5S 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 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,C,D,G 1 1 
B,E,F,H 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
? 2 C N N 
? 2 E N N 
#
_chem_comp.formula           'C10 H16 N2 O11 P2' 
_chem_comp.formula_weight    402.188 
_chem_comp.id                THP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "THYMIDINE-3',5'-DIPHOSPHATE" 
_chem_comp.type              'dna 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
P2 O4P THP doub 277 n n 
P2 O5P THP sing 278 n n 
P2 O6P THP sing 279 n n 
P2 O5' THP sing 280 n n 
O5P HOP5 THP sing 281 n n 
O6P HOP6 THP sing 282 n n 
P1 O1P THP doub 283 n n 
P1 O2P THP sing 284 n n 
P1 O3P THP sing 285 n n 
P1 O3' THP sing 286 n n 
O2P HOP2 THP sing 287 n n 
O3P HOP3 THP sing 288 n n 
O5' C5' THP sing 289 n n 
C5' C4' THP sing 290 n n 
C5' "H5'1" THP sing 291 n n 
C5' "H5'2" THP sing 292 n n 
C4' O4' THP sing 293 n n 
C4' C3' THP sing 294 n n 
C4' H4' THP sing 295 n n 
O4' C1' THP sing 296 n n 
C3' O3' THP sing 297 n n 
C3' C2' THP sing 298 n n 
C3' H3' THP sing 299 n n 
C2' C1' THP sing 300 n n 
C2' "H2'1" THP sing 301 n n 
C2' "H2'2" THP sing 302 n n 
C1' N1 THP sing 303 n n 
C1' H1' THP sing 304 n n 
N1 C2 THP sing 305 n n 
N1 C6 THP sing 306 n n 
C2 O2 THP doub 307 n n 
C2 N3 THP sing 308 n n 
N3 C4 THP sing 309 n n 
N3 H3 THP sing 310 n n 
C4 O4 THP doub 311 n n 
C4 C5 THP sing 312 n n 
C5 C5M THP sing 313 n n 
C5 C6 THP doub 314 n n 
C5M H51 THP sing 315 n n 
C5M H52 THP sing 316 n n 
C5M H53 THP sing 317 n n 
C6 H6 THP sing 318 n n 
#
_atom_sites.entry_id                     3E5S 
_atom_sites.fract_transf_matrix[1][1]    0.03208 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000023 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012737 
_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]    0.016407 
_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 THP A 1 150 1 THP THP . 
D 3 CA A 1 151 1 CA CA . 
E 2 THP B 1 150 1 THP THP . 
F 3 CA B 1 151 1 CA CA . 
G 4 HOH A 1 152 1 HOH HOH . 
G 4 HOH A 2 153 7 HOH HOH . 
G 4 HOH A 3 154 8 HOH HOH . 
G 4 HOH A 4 155 9 HOH HOH . 
G 4 HOH A 5 156 17 HOH HOH . 
G 4 HOH A 6 157 18 HOH HOH . 
G 4 HOH A 7 158 20 HOH HOH . 
G 4 HOH A 8 159 21 HOH HOH . 
G 4 HOH A 9 160 22 HOH HOH . 
G 4 HOH A 10 161 28 HOH HOH . 
G 4 HOH A 11 162 33 HOH HOH . 
G 4 HOH A 12 163 35 HOH HOH . 
G 4 HOH A 13 164 38 HOH HOH . 
G 4 HOH A 14 165 39 HOH HOH . 
G 4 HOH A 15 166 41 HOH HOH . 
G 4 HOH A 16 167 42 HOH HOH . 
G 4 HOH A 17 168 43 HOH HOH . 
G 4 HOH A 18 169 44 HOH HOH . 
G 4 HOH A 19 170 45 HOH HOH . 
G 4 HOH A 20 171 48 HOH HOH . 
G 4 HOH A 21 172 49 HOH HOH . 
G 4 HOH A 22 173 50 HOH HOH . 
G 4 HOH A 23 174 51 HOH HOH . 
G 4 HOH A 24 175 55 HOH HOH . 
G 4 HOH A 25 176 56 HOH HOH . 
G 4 HOH A 26 177 57 HOH HOH . 
G 4 HOH A 27 178 59 HOH HOH . 
G 4 HOH A 28 179 60 HOH HOH . 
G 4 HOH A 29 180 61 HOH HOH . 
G 4 HOH A 30 181 64 HOH HOH . 
G 4 HOH A 31 182 65 HOH HOH . 
G 4 HOH A 32 183 68 HOH HOH . 
G 4 HOH A 33 184 69 HOH HOH . 
G 4 HOH A 34 185 70 HOH HOH . 
G 4 HOH A 35 186 72 HOH HOH . 
G 4 HOH A 36 187 73 HOH HOH . 
G 4 HOH A 37 188 74 HOH HOH . 
G 4 HOH A 38 189 75 HOH HOH . 
G 4 HOH A 39 190 78 HOH HOH . 
G 4 HOH A 40 191 80 HOH HOH . 
G 4 HOH A 41 192 83 HOH HOH . 
G 4 HOH A 42 193 85 HOH HOH . 
G 4 HOH A 43 194 86 HOH HOH . 
G 4 HOH A 44 195 87 HOH HOH . 
G 4 HOH A 45 196 88 HOH HOH . 
G 4 HOH A 46 197 90 HOH HOH . 
G 4 HOH A 47 198 93 HOH HOH . 
G 4 HOH A 48 199 95 HOH HOH . 
G 4 HOH A 49 200 97 HOH HOH . 
G 4 HOH A 50 201 99 HOH HOH . 
G 4 HOH A 51 202 100 HOH HOH . 
G 4 HOH A 52 203 101 HOH HOH . 
G 4 HOH A 53 204 102 HOH HOH . 
G 4 HOH A 54 205 103 HOH HOH . 
G 4 HOH A 55 206 104 HOH HOH . 
G 4 HOH A 56 207 105 HOH HOH . 
G 4 HOH A 57 208 106 HOH HOH . 
G 4 HOH A 58 209 107 HOH HOH . 
G 4 HOH A 59 210 108 HOH HOH . 
G 4 HOH A 60 211 122 HOH HOH . 
G 4 HOH A 61 212 123 HOH HOH . 
G 4 HOH A 62 213 124 HOH HOH . 
G 4 HOH A 63 214 125 HOH HOH . 
G 4 HOH A 64 215 126 HOH HOH . 
G 4 HOH A 65 216 127 HOH HOH . 
G 4 HOH A 66 217 128 HOH HOH . 
G 4 HOH A 67 218 129 HOH HOH . 
G 4 HOH A 68 219 130 HOH HOH . 
G 4 HOH A 69 220 131 HOH HOH . 
G 4 HOH A 70 221 132 HOH HOH . 
G 4 HOH A 71 222 133 HOH HOH . 
G 4 HOH A 72 223 134 HOH HOH . 
G 4 HOH A 73 224 135 HOH HOH . 
G 4 HOH A 74 225 136 HOH HOH . 
G 4 HOH A 75 226 137 HOH HOH . 
G 4 HOH A 76 227 138 HOH HOH . 
H 4 HOH B 1 152 2 HOH HOH . 
H 4 HOH B 2 153 3 HOH HOH . 
H 4 HOH B 3 154 4 HOH HOH . 
H 4 HOH B 4 155 5 HOH HOH . 
H 4 HOH B 5 156 6 HOH HOH . 
H 4 HOH B 6 157 10 HOH HOH . 
H 4 HOH B 7 158 11 HOH HOH . 
H 4 HOH B 8 159 12 HOH HOH . 
H 4 HOH B 9 160 13 HOH HOH . 
H 4 HOH B 10 161 14 HOH HOH . 
H 4 HOH B 11 162 15 HOH HOH . 
H 4 HOH B 12 163 16 HOH HOH . 
H 4 HOH B 13 164 19 HOH HOH . 
H 4 HOH B 14 165 23 HOH HOH . 
H 4 HOH B 15 166 24 HOH HOH . 
H 4 HOH B 16 167 25 HOH HOH . 
H 4 HOH B 17 168 26 HOH HOH . 
H 4 HOH B 18 169 27 HOH HOH . 
H 4 HOH B 19 170 29 HOH HOH . 
H 4 HOH B 20 171 30 HOH HOH . 
H 4 HOH B 21 172 31 HOH HOH . 
H 4 HOH B 22 173 32 HOH HOH . 
H 4 HOH B 23 174 34 HOH HOH . 
H 4 HOH B 24 175 36 HOH HOH . 
H 4 HOH B 25 176 37 HOH HOH . 
H 4 HOH B 26 177 40 HOH HOH . 
H 4 HOH B 27 178 46 HOH HOH . 
H 4 HOH B 28 179 47 HOH HOH . 
H 4 HOH B 29 180 52 HOH HOH . 
H 4 HOH B 30 181 53 HOH HOH . 
H 4 HOH B 31 182 54 HOH HOH . 
H 4 HOH B 32 183 58 HOH HOH . 
H 4 HOH B 33 184 62 HOH HOH . 
H 4 HOH B 34 185 63 HOH HOH . 
H 4 HOH B 35 186 66 HOH HOH . 
H 4 HOH B 36 187 67 HOH HOH . 
H 4 HOH B 37 188 71 HOH HOH . 
H 4 HOH B 38 189 76 HOH HOH . 
H 4 HOH B 39 190 77 HOH HOH . 
H 4 HOH B 40 191 79 HOH HOH . 
H 4 HOH B 41 192 81 HOH HOH . 
H 4 HOH B 42 193 82 HOH HOH . 
H 4 HOH B 43 194 84 HOH HOH . 
H 4 HOH B 44 195 89 HOH HOH . 
H 4 HOH B 45 196 91 HOH HOH . 
H 4 HOH B 46 197 92 HOH HOH . 
H 4 HOH B 47 198 94 HOH HOH . 
H 4 HOH B 48 199 96 HOH HOH . 
H 4 HOH B 49 200 98 HOH HOH . 
H 4 HOH B 50 201 109 HOH HOH . 
H 4 HOH B 51 202 110 HOH HOH . 
H 4 HOH B 52 203 111 HOH HOH . 
H 4 HOH B 53 204 112 HOH HOH . 
H 4 HOH B 54 205 113 HOH HOH . 
H 4 HOH B 55 206 114 HOH HOH . 
H 4 HOH B 56 207 115 HOH HOH . 
H 4 HOH B 57 208 116 HOH HOH . 
H 4 HOH B 58 209 117 HOH HOH . 
H 4 HOH B 59 210 118 HOH HOH . 
H 4 HOH B 60 211 119 HOH HOH . 
H 4 HOH B 61 212 120 HOH HOH . 
H 4 HOH B 62 213 121 HOH HOH . 
H 4 HOH B 63 214 139 HOH HOH . 
H 4 HOH B 64 215 140 HOH HOH . 
H 4 HOH B 65 216 141 HOH HOH . 
H 4 HOH B 66 217 142 HOH HOH . 
H 4 HOH B 67 218 143 HOH HOH . 
H 4 HOH B 68 219 144 HOH HOH . 
H 4 HOH B 69 220 145 HOH HOH . 
H 4 HOH B 70 221 146 HOH HOH . 
H 4 HOH B 71 222 147 HOH HOH . 
H 4 HOH B 72 223 148 HOH HOH . 
H 4 HOH B 73 224 149 HOH HOH . 
H 4 HOH B 74 225 150 HOH HOH . 
H 4 HOH B 75 226 151 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 P2 THP . . . E 2 -9.028 37.638 10.389 1 9.9 ? P2 THP 150 B 1 
HETATM 2 O O4P THP . . . E 2 -10.267 37.062 9.805 1 8.65 ? O4P THP 150 B 1 
HETATM 3 O O5P THP . . . E 2 -8.833 37.139 11.902 1 10.17 ? O5P THP 150 B 1 
HETATM 4 O O6P THP . . . E 2 -7.781 37.205 9.476 1 9.91 ? O6P THP 150 B 1 
HETATM 5 P P1 THP . . . E 2 -12.205 41.625 6.92 1 13.2 ? P1 THP 150 B 1 
HETATM 6 O O1P THP . . . E 2 -11.588 40.872 5.818 1 14.77 ? O1P THP 150 B 1 
HETATM 7 O O2P THP . . . E 2 -12.98 40.615 7.904 1 21.05 ? O2P THP 150 B 1 
HETATM 8 O O3P THP . . . E 2 -13.192 42.667 6.198 1 17.66 ? O3P THP 150 B 1 
HETATM 9 O O5' THP . . . E 2 -8.99 39.245 10.457 1 13.18 ? O5' THP 150 B 1 
HETATM 10 C C5' THP . . . E 2 -8.982 39.847 9.161 1 6.38 ? C5' THP 150 B 1 
HETATM 11 C C4' THP . . . E 2 -9.937 41.046 9.249 1 4.65 ? C4' THP 150 B 1 
HETATM 12 O O4' THP . . . E 2 -9.633 41.868 10.397 1 8.65 ? O4' THP 150 B 1 
HETATM 13 C C3' THP . . . E 2 -9.905 41.961 8.003 1 2.95 ? C3' THP 150 B 1 
HETATM 14 O O3' THP . . . E 2 -11.185 42.564 7.776 1 9.42 ? O3' THP 150 B 1 
HETATM 15 C C2' THP . . . E 2 -8.876 43.027 8.44 1 10.39 ? C2' THP 150 B 1 
HETATM 16 C C1' THP . . . E 2 -9.146 43.143 9.959 1 13.01 ? C1' THP 150 B 1 
HETATM 17 N N1 THP . . . E 2 -7.875 43.488 10.584 1 12.39 ? N1 THP 150 B 1 
HETATM 18 C C2 THP . . . E 2 -7.622 44.794 10.817 1 10.67 ? C2 THP 150 B 1 
HETATM 19 O O2 THP . . . E 2 -8.443 45.651 10.549 1 9.25 ? O2 THP 150 B 1 
HETATM 20 N N3 THP . . . E 2 -6.459 45.186 11.366 1 14.42 ? N3 THP 150 B 1 
HETATM 21 C C4 THP . . . E 2 -5.503 44.282 11.656 1 14.93 ? C4 THP 150 B 1 
HETATM 22 O O4 THP . . . E 2 -4.45 44.667 12.142 1 9.18 ? O4 THP 150 B 1 
HETATM 23 C C5 THP . . . E 2 -5.746 42.904 11.413 1 17.45 ? C5 THP 150 B 1 
HETATM 24 C C5M THP . . . E 2 -4.68 41.895 11.772 1 7.24 ? C5M THP 150 B 1 
HETATM 25 C C6 THP . . . E 2 -6.931 42.524 10.873 1 12.22 ? C6 THP 150 B 1 
#
_model_server_stats.io_time_ms              53 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           299 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#