data_3D8G
#
_model_server_result.job_id            IofcxtuVdUWDnCnTAc6vEQ 
_model_server_result.datetime_utc      '2024-10-20 03:26:01' 
_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          3d8g 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":151}' 
#
_entry.id    3D8G 
#
_exptl.entry_id    3D8G 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            3D8G 
_cell.length_a            32.181 
_cell.length_b            60.425 
_cell.length_c            73.124 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3D8G 
_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    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 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? 
metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 B CA CA . A CA 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.607 ? 
metalc ? metalc3 A O THR 41 A THR 41 1_555 B CA CA . A CA 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? 
metalc ? metalc4 B CA CA . A CA 150 1_555 C O4P THP . A THP 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.198 ? 
metalc ? metalc5 B CA CA . A CA 150 1_555 D O HOH . A HOH 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.031 ? 
metalc ? metalc6 B CA CA . A CA 150 1_555 D O HOH . A HOH 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.807 ? 
metalc ? metalc7 B CA CA . A CA 150 1_555 D O HOH . A HOH 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.059 ? 
#
_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                     3D8G 
_atom_sites.fract_transf_matrix[1][1]    0.031074 
_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]    0.016549 
_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]    0.013675 
_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 1 THP PTP . 
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 . 
#
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 -1.929 -17.401 -14.357 1 12.43 ? P2 THP 151 A 1 
HETATM 2 O O4P THP . . . C 3 -0.769 -18.313 -14.064 1 12.81 ? O4P THP 151 A 1 
HETATM 3 O O5P THP . . . C 3 -1.678 -15.948 -14.006 1 12.92 ? O5P THP 151 A 1 
HETATM 4 O O6P THP . . . C 3 -3.257 -17.921 -13.871 1 13.6 ? O6P THP 151 A 1 
HETATM 5 P P1 THP . . . C 3 -5.595 -20.383 -19.343 1 19.89 ? P1 THP 151 A 1 
HETATM 6 O O1P THP . . . C 3 -4.928 -21.703 -19.062 1 20.33 ? O1P THP 151 A 1 
HETATM 7 O O2P THP . . . C 3 -6.24 -19.71 -18.162 1 20.34 ? O2P THP 151 A 1 
HETATM 8 O O3P THP . . . C 3 -6.467 -20.361 -20.568 1 22.67 ? O3P THP 151 A 1 
HETATM 9 O O5' THP . . . C 3 -2.036 -17.354 -15.963 1 13.56 ? O5' THP 151 A 1 
HETATM 10 C C5' THP . . . C 3 -2.207 -18.52 -16.77 1 12.58 ? C5' THP 151 A 1 
HETATM 11 C C4' THP . . . C 3 -3.095 -18.191 -17.97 1 13.25 ? C4' THP 151 A 1 
HETATM 12 O O4' THP . . . C 3 -2.569 -17.063 -18.68 1 12.18 ? O4' THP 151 A 1 
HETATM 13 C C3' THP . . . C 3 -3.158 -19.339 -18.966 1 14 ? C3' THP 151 A 1 
HETATM 14 O O3' THP . . . C 3 -4.405 -19.353 -19.665 1 18.35 ? O3' THP 151 A 1 
HETATM 15 C C2' THP . . . C 3 -2.141 -18.955 -20.016 1 13.09 ? C2' THP 151 A 1 
HETATM 16 C C1' THP . . . C 3 -2.16 -17.434 -19.994 1 10.76 ? C1' THP 151 A 1 
HETATM 17 N N1 THP . . . C 3 -0.83 -16.941 -20.339 1 10.44 ? N1 THP 151 A 1 
HETATM 18 C C2 THP . . . C 3 -0.569 -16.544 -21.68 1 10.6 ? C2 THP 151 A 1 
HETATM 19 O O2 THP . . . C 3 -1.462 -16.597 -22.551 1 11.02 ? O2 THP 151 A 1 
HETATM 20 N N3 THP . . . C 3 0.636 -16.091 -22.043 1 10.3 ? N3 THP 151 A 1 
HETATM 21 C C4 THP . . . C 3 1.638 -16.014 -21.155 1 10.24 ? C4 THP 151 A 1 
HETATM 22 O O4 THP . . . C 3 2.753 -15.596 -21.521 1 10.34 ? O4 THP 151 A 1 
HETATM 23 C C5 THP . . . C 3 1.403 -16.419 -19.746 1 9.99 ? C5 THP 151 A 1 
HETATM 24 C C5M THP . . . C 3 2.505 -16.333 -18.721 1 10.58 ? C5M THP 151 A 1 
HETATM 25 C C6 THP . . . C 3 0.135 -16.875 -19.398 1 9.63 ? C6 THP 151 A 1 
#
_model_server_stats.io_time_ms              83 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           267 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           25 
#