data_3TP6
#
_model_server_result.job_id            gtlDDiDao0_OCzzO98Xgyg 
_model_server_result.datetime_utc      '2024-10-11 10:26:41' 
_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          3tp6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":151}' 
#
_entry.id    3TP6 
#
_exptl.entry_id    3TP6 
_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          93.85 
_cell.angle_gamma         90 
_cell.entry_id            3TP6 
_cell.length_a            31.178 
_cell.length_b            60.472 
_cell.length_c            38.063 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3TP6 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? 
metalc ? metalc2 A OD1 ASP 40 A ASP 40 1_555 B CA CA . A CA 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.943 ? 
metalc ? metalc3 B CA CA . A CA 150 1_555 C O5P THP . A THP 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.922 ? 
metalc ? metalc4 B CA CA . A CA 150 1_555 D O HOH . A HOH 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.925 ? 
metalc ? metalc5 B CA CA . A CA 150 1_555 D O HOH . A HOH 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? 
metalc ? metalc6 B CA CA . A CA 150 1_555 D O HOH . A HOH 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.928 ? 
metalc ? metalc7 B CA CA . A CA 150 1_555 D O HOH . A HOH 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.849 ? 
#
_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                     3TP6 
_atom_sites.fract_transf_matrix[1][1]    0.032074 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002158 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016537 
_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]    0.026332 
_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 44 HOH HOH . 
D 4 HOH A 2 153 45 HOH HOH . 
D 4 HOH A 3 154 46 HOH HOH . 
D 4 HOH A 4 156 48 HOH HOH . 
D 4 HOH A 5 157 49 HOH HOH . 
D 4 HOH A 6 158 1 HOH HOH . 
D 4 HOH A 7 159 2 HOH HOH . 
D 4 HOH A 8 160 3 HOH HOH . 
D 4 HOH A 9 161 4 HOH HOH . 
D 4 HOH A 10 162 1 HOH HOH . 
D 4 HOH A 11 163 2 HOH HOH . 
D 4 HOH A 12 164 3 HOH HOH . 
D 4 HOH A 13 165 4 HOH HOH . 
D 4 HOH A 14 166 5 HOH HOH . 
D 4 HOH A 15 167 6 HOH HOH . 
D 4 HOH A 16 168 7 HOH HOH . 
D 4 HOH A 17 169 8 HOH HOH . 
D 4 HOH A 18 170 9 HOH HOH . 
D 4 HOH A 19 171 10 HOH HOH . 
D 4 HOH A 20 172 11 HOH HOH . 
D 4 HOH A 21 173 12 HOH HOH . 
D 4 HOH A 22 174 13 HOH HOH . 
D 4 HOH A 23 175 14 HOH HOH . 
D 4 HOH A 24 176 15 HOH HOH . 
D 4 HOH A 25 177 16 HOH HOH . 
D 4 HOH A 26 178 19 HOH HOH . 
D 4 HOH A 27 179 20 HOH HOH . 
D 4 HOH A 28 180 21 HOH HOH . 
D 4 HOH A 29 181 22 HOH HOH . 
D 4 HOH A 30 182 23 HOH HOH . 
D 4 HOH A 31 183 24 HOH HOH . 
D 4 HOH A 32 184 25 HOH HOH . 
D 4 HOH A 33 185 27 HOH HOH . 
D 4 HOH A 34 186 28 HOH HOH . 
D 4 HOH A 35 187 29 HOH HOH . 
D 4 HOH A 36 188 30 HOH HOH . 
D 4 HOH A 37 189 31 HOH HOH . 
D 4 HOH A 38 190 33 HOH HOH . 
D 4 HOH A 39 191 34 HOH HOH . 
D 4 HOH A 40 192 35 HOH HOH . 
D 4 HOH A 41 193 36 HOH HOH . 
D 4 HOH A 42 194 37 HOH HOH . 
D 4 HOH A 43 195 38 HOH HOH . 
D 4 HOH A 44 196 39 HOH HOH . 
D 4 HOH A 45 197 40 HOH HOH . 
D 4 HOH A 46 198 41 HOH HOH . 
D 4 HOH A 47 199 42 HOH HOH . 
D 4 HOH A 48 200 43 HOH HOH . 
D 4 HOH A 49 201 50 HOH HOH . 
D 4 HOH A 50 202 53 HOH HOH . 
D 4 HOH A 51 203 55 HOH HOH . 
D 4 HOH A 52 204 56 HOH HOH . 
D 4 HOH A 53 205 58 HOH HOH . 
D 4 HOH A 54 206 60 HOH HOH . 
D 4 HOH A 55 207 61 HOH HOH . 
D 4 HOH A 56 208 65 HOH HOH . 
D 4 HOH A 57 209 69 HOH HOH . 
D 4 HOH A 58 210 70 HOH HOH . 
D 4 HOH A 59 211 72 HOH HOH . 
D 4 HOH A 60 212 73 HOH HOH . 
D 4 HOH A 61 213 74 HOH HOH . 
D 4 HOH A 62 214 77 HOH HOH . 
D 4 HOH A 63 215 78 HOH HOH . 
D 4 HOH A 64 216 98 HOH HOH . 
D 4 HOH A 65 217 99 HOH HOH . 
D 4 HOH A 66 218 100 HOH HOH . 
D 4 HOH A 67 219 101 HOH HOH . 
D 4 HOH A 68 220 103 HOH HOH . 
D 4 HOH A 69 221 104 HOH HOH . 
D 4 HOH A 70 222 105 HOH HOH . 
D 4 HOH A 71 223 106 HOH HOH . 
D 4 HOH A 72 224 109 HOH HOH . 
D 4 HOH A 73 225 110 HOH HOH . 
D 4 HOH A 74 226 111 HOH HOH . 
D 4 HOH A 75 227 112 HOH HOH . 
D 4 HOH A 76 228 114 HOH HOH . 
D 4 HOH A 77 229 115 HOH HOH . 
D 4 HOH A 78 230 116 HOH HOH . 
D 4 HOH A 79 231 117 HOH HOH . 
D 4 HOH A 80 232 119 HOH HOH . 
D 4 HOH A 81 233 122 HOH HOH . 
D 4 HOH A 82 234 126 HOH HOH . 
D 4 HOH A 83 235 127 HOH HOH . 
D 4 HOH A 84 236 132 HOH HOH . 
D 4 HOH A 85 237 134 HOH HOH . 
D 4 HOH A 86 238 1 HOH HOH . 
D 4 HOH A 87 239 2 HOH HOH . 
D 4 HOH A 88 240 3 HOH HOH . 
D 4 HOH A 89 241 4 HOH HOH . 
D 4 HOH A 90 242 5 HOH HOH . 
D 4 HOH A 91 243 6 HOH HOH . 
D 4 HOH A 92 244 7 HOH HOH . 
D 4 HOH A 93 245 8 HOH HOH . 
D 4 HOH A 94 246 9 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 17.954 10.877 4.675 1 14.18 ? P2 THP 151 A 1 
HETATM 2 O O4P THP . . . C 3 18.022 9.442 5.051 1 15.31 ? O4P THP 151 A 1 
HETATM 3 O O5P THP . . . C 3 16.698 11.638 5.305 1 12.84 ? O5P THP 151 A 1 
HETATM 4 O O6P THP . . . C 3 19.195 11.657 5.269 1 14.88 ? O6P THP 151 A 1 
HETATM 5 P P1 THP . . . C 3 21.218 14.313 0.889 1 16.62 ? P1 THP 151 A 1 
HETATM 6 O O1P THP . . . C 3 22.155 14.957 -0.06 1 17.72 ? O1P THP 151 A 1 
HETATM 7 O O2P THP . . . C 3 21.959 13.164 1.69 1 18.68 ? O2P THP 151 A 1 
HETATM 8 O O3P THP . . . C 3 20.554 15.322 1.919 1 14.93 ? O3P THP 151 A 1 
HETATM 9 O O5' THP . . . C 3 17.88 11.001 3.071 1 12.32 ? O5' THP 151 A 1 
HETATM 10 C C5' THP . . . C 3 17.995 12.33 2.56 1 14.16 ? C5' THP 151 A 1 
HETATM 11 C C4' THP . . . C 3 18.925 12.185 1.34 1 11.8 ? C4' THP 151 A 1 
HETATM 12 O O4' THP . . . C 3 18.483 11.042 0.605 1 13.61 ? O4' THP 151 A 1 
HETATM 13 C C3' THP . . . C 3 18.831 13.425 0.389 1 12.16 ? C3' THP 151 A 1 
HETATM 14 O O3' THP . . . C 3 20.131 13.72 -0.175 1 13.76 ? O3' THP 151 A 1 
HETATM 15 C C2' THP . . . C 3 17.938 12.898 -0.745 1 10.34 ? C2' THP 151 A 1 
HETATM 16 C C1' THP . . . C 3 18.239 11.371 -0.778 1 9.81 ? C1' THP 151 A 1 
HETATM 17 N N1 THP . . . C 3 16.962 10.746 -1.186 1 10.58 ? N1 THP 151 A 1 
HETATM 18 C C2 THP . . . C 3 16.69 10.522 -2.511 1 12.73 ? C2 THP 151 A 1 
HETATM 19 O O2 THP . . . C 3 17.509 10.814 -3.396 1 15.18 ? O2 THP 151 A 1 
HETATM 20 N N3 THP . . . C 3 15.49 10.036 -2.92 1 11.77 ? N3 THP 151 A 1 
HETATM 21 C C4 THP . . . C 3 14.537 9.706 -2.003 1 10.5 ? C4 THP 151 A 1 
HETATM 22 O O4 THP . . . C 3 13.445 9.307 -2.408 1 12.63 ? O4 THP 151 A 1 
HETATM 23 C C5 THP . . . C 3 14.785 9.977 -0.618 1 10.87 ? C5 THP 151 A 1 
HETATM 24 C C5M THP . . . C 3 13.756 9.585 0.43 1 12.14 ? C5M THP 151 A 1 
HETATM 25 C C6 THP . . . C 3 16.013 10.449 -0.232 1 8.33 ? C6 THP 151 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    18 
_model_server_stats.query_time_ms           316 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           25 
#