data_3BDC
#
_model_server_result.job_id            jMfKGNSh7XgfVsqpowPWsg 
_model_server_result.datetime_utc      '2024-10-11 10:24:26' 
_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          3bdc 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":151}' 
#
_entry.id    3BDC 
#
_exptl.entry_id    3BDC 
_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    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          94.44 
_cell.angle_gamma         90 
_cell.entry_id            3BDC 
_cell.length_a            31.097 
_cell.length_b            60.651 
_cell.length_c            36.948 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3BDC 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 A OD2 ASP 21 A ASP 21 1_555 B CA CA . A CA 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.901 ? 
metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 B CA CA . A CA 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.716 ? 
metalc ? metalc3 A O THR 41 A THR 41 1_555 B CA CA . A CA 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.836 ? 
metalc ? metalc4 A OE2 GLU 43 A GLU 43 1_555 B CA CA . A CA 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.929 ? 
metalc ? metalc5 B CA CA . A CA 150 1_555 D O HOH . A HOH 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? 
metalc ? metalc6 B CA CA . A CA 150 1_555 D O HOH . A HOH 162 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? 
#
_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                     3BDC 
_atom_sites.fract_transf_matrix[1][1]    0.032157 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002497 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016488 
_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]    0.027147 
_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
B 2 CA A 1 150 1 CA CA . 
C 3 THP A 1 151 142 THP THP . 
D 4 HOH A 1 152 1 HOH HOH . 
D 4 HOH A 2 153 2 HOH HOH . 
D 4 HOH A 3 154 3 HOH HOH . 
D 4 HOH A 4 155 4 HOH HOH . 
D 4 HOH A 5 156 5 HOH HOH . 
D 4 HOH A 6 157 6 HOH HOH . 
D 4 HOH A 7 158 7 HOH HOH . 
D 4 HOH A 8 159 8 HOH HOH . 
D 4 HOH A 9 160 9 HOH HOH . 
D 4 HOH A 10 161 10 HOH HOH . 
D 4 HOH A 11 162 11 HOH HOH . 
D 4 HOH A 12 163 12 HOH HOH . 
D 4 HOH A 13 164 13 HOH HOH . 
D 4 HOH A 14 165 14 HOH HOH . 
D 4 HOH A 15 166 15 HOH HOH . 
D 4 HOH A 16 167 16 HOH HOH . 
D 4 HOH A 17 168 17 HOH HOH . 
D 4 HOH A 18 169 18 HOH HOH . 
D 4 HOH A 19 170 19 HOH HOH . 
D 4 HOH A 20 171 20 HOH HOH . 
D 4 HOH A 21 172 21 HOH HOH . 
D 4 HOH A 22 173 22 HOH HOH . 
D 4 HOH A 23 174 23 HOH HOH . 
D 4 HOH A 24 175 24 HOH HOH . 
D 4 HOH A 25 176 25 HOH HOH . 
D 4 HOH A 26 177 26 HOH HOH . 
D 4 HOH A 27 178 27 HOH HOH . 
D 4 HOH A 28 179 28 HOH HOH . 
D 4 HOH A 29 180 29 HOH HOH . 
D 4 HOH A 30 181 30 HOH HOH . 
D 4 HOH A 31 182 31 HOH HOH . 
D 4 HOH A 32 183 32 HOH HOH . 
D 4 HOH A 33 184 33 HOH HOH . 
D 4 HOH A 34 185 34 HOH HOH . 
D 4 HOH A 35 186 35 HOH HOH . 
D 4 HOH A 36 187 36 HOH HOH . 
D 4 HOH A 37 188 37 HOH HOH . 
D 4 HOH A 38 189 38 HOH HOH . 
D 4 HOH A 39 190 39 HOH HOH . 
D 4 HOH A 40 191 40 HOH HOH . 
D 4 HOH A 41 192 41 HOH HOH . 
D 4 HOH A 42 193 42 HOH HOH . 
D 4 HOH A 43 194 43 HOH HOH . 
D 4 HOH A 44 195 44 HOH HOH . 
D 4 HOH A 45 196 45 HOH HOH . 
D 4 HOH A 46 197 46 HOH HOH . 
D 4 HOH A 47 198 47 HOH HOH . 
D 4 HOH A 48 199 48 HOH HOH . 
D 4 HOH A 49 200 49 HOH HOH . 
D 4 HOH A 50 201 50 HOH HOH . 
D 4 HOH A 51 202 51 HOH HOH . 
D 4 HOH A 52 203 52 HOH HOH . 
D 4 HOH A 53 204 53 HOH HOH . 
D 4 HOH A 54 205 54 HOH HOH . 
D 4 HOH A 55 206 55 HOH HOH . 
D 4 HOH A 56 207 56 HOH HOH . 
D 4 HOH A 57 208 57 HOH HOH . 
D 4 HOH A 58 209 58 HOH HOH . 
D 4 HOH A 59 210 59 HOH HOH . 
D 4 HOH A 60 211 60 HOH HOH . 
D 4 HOH A 61 212 61 HOH HOH . 
D 4 HOH A 62 213 62 HOH HOH . 
D 4 HOH A 63 214 63 HOH HOH . 
D 4 HOH A 64 215 64 HOH HOH . 
D 4 HOH A 65 216 65 HOH HOH . 
D 4 HOH A 66 217 66 HOH HOH . 
D 4 HOH A 67 218 67 HOH HOH . 
D 4 HOH A 68 219 68 HOH HOH . 
D 4 HOH A 69 220 69 HOH HOH . 
D 4 HOH A 70 221 70 HOH HOH . 
D 4 HOH A 71 222 71 HOH HOH . 
D 4 HOH A 72 223 72 HOH HOH . 
D 4 HOH A 73 224 73 HOH HOH . 
D 4 HOH A 74 225 74 HOH HOH . 
D 4 HOH A 75 226 75 HOH HOH . 
D 4 HOH A 76 227 76 HOH HOH . 
D 4 HOH A 77 228 77 HOH HOH . 
D 4 HOH A 78 229 78 HOH HOH . 
D 4 HOH A 79 230 79 HOH HOH . 
D 4 HOH A 80 231 80 HOH HOH . 
D 4 HOH A 81 232 81 HOH HOH . 
D 4 HOH A 82 233 82 HOH HOH . 
D 4 HOH A 83 234 83 HOH HOH . 
D 4 HOH A 84 235 84 HOH HOH . 
D 4 HOH A 85 236 85 HOH HOH . 
D 4 HOH A 86 237 86 HOH HOH . 
D 4 HOH A 87 238 87 HOH HOH . 
D 4 HOH A 88 239 88 HOH HOH . 
D 4 HOH A 89 240 89 HOH HOH . 
D 4 HOH A 90 241 90 HOH HOH . 
D 4 HOH A 91 242 91 HOH HOH . 
D 4 HOH A 92 243 92 HOH HOH . 
D 4 HOH A 93 244 93 HOH HOH . 
D 4 HOH A 94 245 94 HOH HOH . 
D 4 HOH A 95 246 95 HOH HOH . 
D 4 HOH A 96 247 96 HOH HOH . 
D 4 HOH A 97 248 97 HOH HOH . 
D 4 HOH A 98 249 98 HOH HOH . 
D 4 HOH A 99 250 99 HOH HOH . 
D 4 HOH A 100 251 100 HOH HOH . 
D 4 HOH A 101 252 101 HOH HOH . 
D 4 HOH A 102 253 102 HOH HOH . 
D 4 HOH A 103 254 103 HOH HOH . 
D 4 HOH A 104 255 104 HOH HOH . 
D 4 HOH A 105 256 105 HOH HOH . 
D 4 HOH A 106 257 106 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 . . . C 3 17.951 11.217 4.318 1 19.78 ? P2 THP 151 A 1 
HETATM 2 O O4P THP . . . C 3 16.757 11.998 4.83 1 19.47 ? O4P THP 151 A 1 
HETATM 3 O O5P THP . . . C 3 18.031 9.755 4.704 1 19.53 ? O5P THP 151 A 1 
HETATM 4 O O6P THP . . . C 3 19.218 11.933 4.649 1 19.96 ? O6P THP 151 A 1 
HETATM 5 P P1 THP . . . C 3 21.206 14.559 0.337 1 22.61 ? P1 THP 151 A 1 
HETATM 6 O O1P THP . . . C 3 22.12 15.149 -0.714 1 25.67 ? O1P THP 151 A 1 
HETATM 7 O O2P THP . . . C 3 21.951 13.495 1.086 1 24.5 ? O2P THP 151 A 1 
HETATM 8 O O3P THP . . . C 3 20.546 15.451 1.362 1 24.68 ? O3P THP 151 A 1 
HETATM 9 O O5' THP . . . C 3 17.828 11.301 2.702 1 16.52 ? O5' THP 151 A 1 
HETATM 10 C C5' THP . . . C 3 18.063 12.56 2.064 1 16.17 ? C5' THP 151 A 1 
HETATM 11 C C4' THP . . . C 3 18.947 12.356 0.846 1 18.16 ? C4' THP 151 A 1 
HETATM 12 O O4' THP . . . C 3 18.556 11.171 0.167 1 16.25 ? O4' THP 151 A 1 
HETATM 13 C C3' THP . . . C 3 18.786 13.519 -0.139 1 18.88 ? C3' THP 151 A 1 
HETATM 14 O O3' THP . . . C 3 20.084 13.941 -0.654 1 21.96 ? O3' THP 151 A 1 
HETATM 15 C C2' THP . . . C 3 17.907 12.979 -1.245 1 15.79 ? C2' THP 151 A 1 
HETATM 16 C C1' THP . . . C 3 18.092 11.462 -1.173 1 17.16 ? C1' THP 151 A 1 
HETATM 17 N N1 THP . . . C 3 16.804 10.873 -1.478 1 16.57 ? N1 THP 151 A 1 
HETATM 18 C C2 THP . . . C 3 16.485 10.622 -2.844 1 18.42 ? C2 THP 151 A 1 
HETATM 19 O O2 THP . . . C 3 17.324 10.876 -3.755 1 19.88 ? O2 THP 151 A 1 
HETATM 20 N N3 THP . . . C 3 15.305 10.095 -3.199 1 18.67 ? N3 THP 151 A 1 
HETATM 21 C C4 THP . . . C 3 14.368 9.796 -2.276 1 17.15 ? C4 THP 151 A 1 
HETATM 22 O O4 THP . . . C 3 13.322 9.299 -2.711 1 17.33 ? O4 THP 151 A 1 
HETATM 23 C C5 THP . . . C 3 14.652 10.044 -0.838 1 18.17 ? C5 THP 151 A 1 
HETATM 24 C C5M THP . . . C 3 13.634 9.762 0.244 1 15.18 ? C5M THP 151 A 1 
HETATM 25 C C6 THP . . . C 3 15.885 10.599 -0.505 1 16.71 ? C6 THP 151 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           314 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           25 
#