data_3D4D
#
_model_server_result.job_id            6rvhCV7xWIhVnxLAHhN4pQ 
_model_server_result.datetime_utc      '2024-10-20 03:49:29' 
_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          3d4d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":151}' 
#
_entry.id    3D4D 
#
_exptl.entry_id    3D4D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              402.188 
_entity.id                          3 
_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          90.05 
_cell.angle_gamma         90 
_cell.entry_id            3D4D 
_cell.length_a            31.022 
_cell.length_b            81.293 
_cell.length_c            60.385 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3D4D 
_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
? 3 D N N 
? 3 F 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                     3D4D 
_atom_sites.fract_transf_matrix[1][1]    0.032235 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000028 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012301 
_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]    0.01656 
_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 CA A 1 150 1 CA CA . 
D 3 THP A 1 151 142 THP PTP . 
E 2 CA B 1 150 1 CA CA . 
F 3 THP B 1 151 142 THP PTP . 
G 4 HOH A 1 152 1 HOH HOH . 
G 4 HOH A 2 153 2 HOH HOH . 
G 4 HOH A 3 154 3 HOH HOH . 
G 4 HOH A 4 155 8 HOH HOH . 
G 4 HOH A 5 156 11 HOH HOH . 
G 4 HOH A 6 157 12 HOH HOH . 
G 4 HOH A 7 158 13 HOH HOH . 
G 4 HOH A 8 159 17 HOH HOH . 
G 4 HOH A 9 160 20 HOH HOH . 
G 4 HOH A 10 161 24 HOH HOH . 
G 4 HOH A 11 162 26 HOH HOH . 
G 4 HOH A 12 163 27 HOH HOH . 
G 4 HOH A 13 164 29 HOH HOH . 
G 4 HOH A 14 165 31 HOH HOH . 
G 4 HOH A 15 166 40 HOH HOH . 
G 4 HOH A 16 167 42 HOH HOH . 
G 4 HOH A 17 168 44 HOH HOH . 
G 4 HOH A 18 169 45 HOH HOH . 
G 4 HOH A 19 170 46 HOH HOH . 
G 4 HOH A 20 171 47 HOH HOH . 
G 4 HOH A 21 172 50 HOH HOH . 
G 4 HOH A 22 173 51 HOH HOH . 
G 4 HOH A 23 174 53 HOH HOH . 
G 4 HOH A 24 175 56 HOH HOH . 
G 4 HOH A 25 176 63 HOH HOH . 
G 4 HOH A 26 177 68 HOH HOH . 
G 4 HOH A 27 178 70 HOH HOH . 
G 4 HOH A 28 179 76 HOH HOH . 
G 4 HOH A 29 180 79 HOH HOH . 
G 4 HOH A 30 181 84 HOH HOH . 
G 4 HOH A 31 182 85 HOH HOH . 
G 4 HOH A 32 183 86 HOH HOH . 
G 4 HOH A 33 184 88 HOH HOH . 
G 4 HOH A 34 185 89 HOH HOH . 
G 4 HOH A 35 186 90 HOH HOH . 
G 4 HOH A 36 187 92 HOH HOH . 
G 4 HOH A 37 188 94 HOH HOH . 
G 4 HOH A 38 189 99 HOH HOH . 
G 4 HOH A 39 190 101 HOH HOH . 
G 4 HOH A 40 191 102 HOH HOH . 
G 4 HOH A 41 192 106 HOH HOH . 
G 4 HOH A 42 193 113 HOH HOH . 
G 4 HOH A 43 194 116 HOH HOH . 
G 4 HOH A 44 195 119 HOH HOH . 
G 4 HOH A 45 196 123 HOH HOH . 
G 4 HOH A 46 197 126 HOH HOH . 
G 4 HOH A 47 198 130 HOH HOH . 
G 4 HOH A 48 199 136 HOH HOH . 
G 4 HOH A 49 200 138 HOH HOH . 
G 4 HOH A 50 201 140 HOH HOH . 
G 4 HOH A 51 202 151 HOH HOH . 
G 4 HOH A 52 203 158 HOH HOH . 
G 4 HOH A 53 204 159 HOH HOH . 
G 4 HOH A 54 205 165 HOH HOH . 
G 4 HOH A 55 206 166 HOH HOH . 
G 4 HOH A 56 207 181 HOH HOH . 
G 4 HOH A 57 208 184 HOH HOH . 
G 4 HOH A 58 209 187 HOH HOH . 
G 4 HOH A 59 210 194 HOH HOH . 
G 4 HOH A 60 211 207 HOH HOH . 
G 4 HOH A 61 212 223 HOH HOH . 
G 4 HOH A 62 213 235 HOH HOH . 
G 4 HOH A 63 214 280 HOH HOH . 
G 4 HOH A 64 215 286 HOH HOH . 
G 4 HOH A 65 216 317 HOH HOH . 
G 4 HOH A 66 217 1 HOH HOH . 
G 4 HOH A 67 218 2 HOH HOH . 
G 4 HOH A 68 219 3 HOH HOH . 
G 4 HOH A 69 220 7 HOH HOH . 
G 4 HOH A 70 221 1 HOH HOH . 
G 4 HOH A 71 222 4 HOH HOH . 
G 4 HOH A 72 223 5 HOH HOH . 
G 4 HOH A 73 224 4 HOH HOH . 
G 4 HOH A 74 225 6 HOH HOH . 
G 4 HOH A 75 226 4 HOH HOH . 
G 4 HOH A 76 227 6 HOH HOH . 
G 4 HOH A 77 228 7 HOH HOH . 
G 4 HOH A 78 229 1 HOH HOH . 
G 4 HOH A 79 230 3 HOH HOH . 
G 4 HOH A 80 231 4 HOH HOH . 
G 4 HOH A 81 232 6 HOH HOH . 
H 4 HOH B 1 152 5 HOH HOH . 
H 4 HOH B 2 153 6 HOH HOH . 
H 4 HOH B 3 154 10 HOH HOH . 
H 4 HOH B 4 155 14 HOH HOH . 
H 4 HOH B 5 156 16 HOH HOH . 
H 4 HOH B 6 157 18 HOH HOH . 
H 4 HOH B 7 158 19 HOH HOH . 
H 4 HOH B 8 159 22 HOH HOH . 
H 4 HOH B 9 160 23 HOH HOH . 
H 4 HOH B 10 161 25 HOH HOH . 
H 4 HOH B 11 162 32 HOH HOH . 
H 4 HOH B 12 163 33 HOH HOH . 
H 4 HOH B 13 164 34 HOH HOH . 
H 4 HOH B 14 165 36 HOH HOH . 
H 4 HOH B 15 166 37 HOH HOH . 
H 4 HOH B 16 167 38 HOH HOH . 
H 4 HOH B 17 168 39 HOH HOH . 
H 4 HOH B 18 169 41 HOH HOH . 
H 4 HOH B 19 170 49 HOH HOH . 
H 4 HOH B 20 171 52 HOH HOH . 
H 4 HOH B 21 172 54 HOH HOH . 
H 4 HOH B 22 173 57 HOH HOH . 
H 4 HOH B 23 174 58 HOH HOH . 
H 4 HOH B 24 175 59 HOH HOH . 
H 4 HOH B 25 176 60 HOH HOH . 
H 4 HOH B 26 177 62 HOH HOH . 
H 4 HOH B 27 178 66 HOH HOH . 
H 4 HOH B 28 179 67 HOH HOH . 
H 4 HOH B 29 180 69 HOH HOH . 
H 4 HOH B 30 181 71 HOH HOH . 
H 4 HOH B 31 182 73 HOH HOH . 
H 4 HOH B 32 183 75 HOH HOH . 
H 4 HOH B 33 184 77 HOH HOH . 
H 4 HOH B 34 185 78 HOH HOH . 
H 4 HOH B 35 186 81 HOH HOH . 
H 4 HOH B 36 187 82 HOH HOH . 
H 4 HOH B 37 188 83 HOH HOH . 
H 4 HOH B 38 189 87 HOH HOH . 
H 4 HOH B 39 190 93 HOH HOH . 
H 4 HOH B 40 191 95 HOH HOH . 
H 4 HOH B 41 192 97 HOH HOH . 
H 4 HOH B 42 193 98 HOH HOH . 
H 4 HOH B 43 194 103 HOH HOH . 
H 4 HOH B 44 195 104 HOH HOH . 
H 4 HOH B 45 196 105 HOH HOH . 
H 4 HOH B 46 197 108 HOH HOH . 
H 4 HOH B 47 198 109 HOH HOH . 
H 4 HOH B 48 199 112 HOH HOH . 
H 4 HOH B 49 200 115 HOH HOH . 
H 4 HOH B 50 201 118 HOH HOH . 
H 4 HOH B 51 202 125 HOH HOH . 
H 4 HOH B 52 203 128 HOH HOH . 
H 4 HOH B 53 204 132 HOH HOH . 
H 4 HOH B 54 205 133 HOH HOH . 
H 4 HOH B 55 206 141 HOH HOH . 
H 4 HOH B 56 207 142 HOH HOH . 
H 4 HOH B 57 208 143 HOH HOH . 
H 4 HOH B 58 209 146 HOH HOH . 
H 4 HOH B 59 210 148 HOH HOH . 
H 4 HOH B 60 211 149 HOH HOH . 
H 4 HOH B 61 212 150 HOH HOH . 
H 4 HOH B 62 213 153 HOH HOH . 
H 4 HOH B 63 214 155 HOH HOH . 
H 4 HOH B 64 215 156 HOH HOH . 
H 4 HOH B 65 216 161 HOH HOH . 
H 4 HOH B 66 217 173 HOH HOH . 
H 4 HOH B 67 218 180 HOH HOH . 
H 4 HOH B 68 219 182 HOH HOH . 
H 4 HOH B 69 220 183 HOH HOH . 
H 4 HOH B 70 221 185 HOH HOH . 
H 4 HOH B 71 222 186 HOH HOH . 
H 4 HOH B 72 223 190 HOH HOH . 
H 4 HOH B 73 224 196 HOH HOH . 
H 4 HOH B 74 225 205 HOH HOH . 
H 4 HOH B 75 226 209 HOH HOH . 
H 4 HOH B 76 227 210 HOH HOH . 
H 4 HOH B 77 228 222 HOH HOH . 
H 4 HOH B 78 229 228 HOH HOH . 
H 4 HOH B 79 230 230 HOH HOH . 
H 4 HOH B 80 231 231 HOH HOH . 
H 4 HOH B 81 232 234 HOH HOH . 
H 4 HOH B 82 233 281 HOH HOH . 
H 4 HOH B 83 234 283 HOH HOH . 
H 4 HOH B 84 235 284 HOH HOH . 
H 4 HOH B 85 236 289 HOH HOH . 
H 4 HOH B 86 237 4 HOH HOH . 
H 4 HOH B 87 238 5 HOH HOH . 
H 4 HOH B 88 239 6 HOH HOH . 
H 4 HOH B 89 240 2 HOH HOH . 
H 4 HOH B 90 241 6 HOH HOH . 
H 4 HOH B 91 242 7 HOH HOH . 
H 4 HOH B 92 243 1 HOH HOH . 
H 4 HOH B 93 244 2 HOH HOH . 
H 4 HOH B 94 245 5 HOH HOH . 
H 4 HOH B 95 246 9 HOH HOH . 
H 4 HOH B 96 247 10 HOH HOH . 
H 4 HOH B 97 248 11 HOH HOH . 
H 4 HOH B 98 249 1 HOH HOH . 
H 4 HOH B 99 250 3 HOH HOH . 
H 4 HOH B 100 251 1 HOH HOH . 
H 4 HOH B 101 252 2 HOH HOH . 
H 4 HOH B 102 253 5 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 . . . D 3 23.488 5.514 8.114 1 6.69 ? P2 THP 151 A 1 
HETATM 2 O O4P THP . . . D 3 22.212 5.963 7.458 1 4.2 ? O4P THP 151 A 1 
HETATM 3 O O5P THP . . . D 3 23.522 5.75 9.603 1 7.2 ? O5P THP 151 A 1 
HETATM 4 O O6P THP . . . D 3 24.762 5.918 7.41 1 7.2 ? O6P THP 151 A 1 
HETATM 5 P P1 THP . . . D 3 26.87 1.843 4.633 1 9.67 ? P1 THP 151 A 1 
HETATM 6 O O1P THP . . . D 3 27.916 0.891 4.09 1 10.6 ? O1P THP 151 A 1 
HETATM 7 O O2P THP . . . D 3 27.369 2.677 5.773 1 11.82 ? O2P THP 151 A 1 
HETATM 8 O O3P THP . . . D 3 26.099 2.593 3.575 1 8.07 ? O3P THP 151 A 1 
HETATM 9 O O5' THP . . . D 3 23.425 3.906 7.983 1 7.64 ? O5' THP 151 A 1 
HETATM 10 C C5' THP . . . D 3 23.51 3.23 6.725 1 7.26 ? C5' THP 151 A 1 
HETATM 11 C C4' THP . . . D 3 24.491 2.061 6.852 1 5.69 ? C4' THP 151 A 1 
HETATM 12 O O4' THP . . . D 3 24.161 1.234 7.971 1 4.15 ? O4' THP 151 A 1 
HETATM 13 C C3' THP . . . D 3 24.496 1.149 5.636 1 6.44 ? C3' THP 151 A 1 
HETATM 14 O O3' THP . . . D 3 25.846 0.828 5.331 1 7.93 ? O3' THP 151 A 1 
HETATM 15 C C2' THP . . . D 3 23.824 -0.14 6.071 1 4.7 ? C2' THP 151 A 1 
HETATM 16 C C1' THP . . . D 3 23.848 -0.106 7.591 1 3.56 ? C1' THP 151 A 1 
HETATM 17 N N1 THP . . . D 3 22.53 -0.515 8.127 1 3.86 ? N1 THP 151 A 1 
HETATM 18 C C2 THP . . . D 3 22.242 -1.895 8.343 1 3.26 ? C2 THP 151 A 1 
HETATM 19 O O2 THP . . . D 3 23.117 -2.754 8.091 1 2.9 ? O2 THP 151 A 1 
HETATM 20 N N3 THP . . . D 3 21.042 -2.293 8.814 1 3.59 ? N3 THP 151 A 1 
HETATM 21 C C4 THP . . . D 3 20.082 -1.398 9.101 1 2.74 ? C4 THP 151 A 1 
HETATM 22 O O4 THP . . . D 3 18.978 -1.784 9.531 1 2.57 ? O4 THP 151 A 1 
HETATM 23 C C5 THP . . . D 3 20.353 0.051 8.887 1 3.25 ? C5 THP 151 A 1 
HETATM 24 C C5M THP . . . D 3 19.329 1.113 9.18 1 2.45 ? C5M THP 151 A 1 
HETATM 25 C C6 THP . . . D 3 21.599 0.419 8.394 1 3.76 ? C6 THP 151 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           289 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#