data_1Z4K # _model_server_result.job_id eqM65urMhI_ORUGyzKcQYw _model_server_result.datetime_utc '2025-07-08 00:15:11' _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 1z4k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":4341}' # _entry.id 1Z4K # _exptl.entry_id 1Z4K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 322.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-3'-PHOSPHATE" _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 1Z4K _cell.length_a 73.18 _cell.length_b 73.18 _cell.length_c 105.92 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Z4K _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 73.18 73.18 52.96 # _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 OD1 ASN 10 A ASN 41 1_555 B MG MG . A MG 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc2 A O ASP 12 A ASP 43 1_555 B MG MG . A MG 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc3 A OD1 ASP 145 A ASP 176 1_555 B MG MG . A MG 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc4 B MG MG . A MG 229 1_555 C OP2 T3P . A T3P 4341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc5 B MG MG . A MG 229 1_555 D O HOH . A HOH 4430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc6 B MG MG . A MG 229 1_555 D O HOH . A HOH 4454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? # _chem_comp.formula 'C10 H15 N2 O8 P' _chem_comp.formula_weight 322.208 _chem_comp.id T3P _chem_comp.mon_nstd_flag n _chem_comp.name "THYMIDINE-3'-PHOSPHATE" _chem_comp.type 'dna linking' _chem_comp.pdbx_synonyms "ALPHA-ANOMERIC THYMIDINE-3'-PHOSPHATE" # 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 P OP1 T3P doub 290 n n P OP2 T3P sing 291 n n P OP3 T3P sing 292 n n P O3' T3P sing 293 n n OP2 HOP2 T3P sing 294 n n OP3 HOP3 T3P sing 295 n n O5' C5' T3P sing 296 n n O5' H5' T3P sing 297 n n C5' C4' T3P sing 298 n n C5' "H5'1" T3P sing 299 n n C5' "H5''" T3P sing 300 n n C4' O4' T3P sing 301 n n C4' C3' T3P sing 302 n n C4' H4' T3P sing 303 n n O4' C1' T3P sing 304 n n C3' O3' T3P sing 305 n n C3' C2' T3P sing 306 n n C3' H3' T3P sing 307 n n C2' C1' T3P sing 308 n n C2' H2' T3P sing 309 n n C2' "H2''" T3P sing 310 n n C1' N1 T3P sing 311 n n C1' H1' T3P sing 312 n n N1 C2 T3P sing 313 n n N1 C6 T3P sing 314 n n C2 O2 T3P doub 315 n n C2 N3 T3P sing 316 n n N3 C4 T3P sing 317 n n N3 H3 T3P sing 318 n n C4 O4 T3P doub 319 n n C4 C5 T3P sing 320 n n C5 C5M T3P sing 321 n n C5 C6 T3P doub 322 n n C5M H51 T3P sing 323 n n C5M H52 T3P sing 324 n n C5M H53 T3P sing 325 n n C6 H6 T3P sing 326 n n # _atom_sites.entry_id 1Z4K _atom_sites.fract_transf_matrix[1][1] 0.013665 _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] 0.013665 _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] 0.009441 _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 MG A 1 229 228 MG MG . C 3 T3P A 1 4341 4341 T3P T3P . D 4 HOH A 1 4342 1 HOH HOH . D 4 HOH A 2 4343 2 HOH HOH . D 4 HOH A 3 4344 3 HOH HOH . D 4 HOH A 4 4345 4 HOH HOH . D 4 HOH A 5 4346 5 HOH HOH . D 4 HOH A 6 4347 6 HOH HOH . D 4 HOH A 7 4348 7 HOH HOH . D 4 HOH A 8 4349 8 HOH HOH . D 4 HOH A 9 4350 9 HOH HOH . D 4 HOH A 10 4351 10 HOH HOH . D 4 HOH A 11 4352 11 HOH HOH . D 4 HOH A 12 4353 12 HOH HOH . D 4 HOH A 13 4354 13 HOH HOH . D 4 HOH A 14 4355 14 HOH HOH . D 4 HOH A 15 4356 15 HOH HOH . D 4 HOH A 16 4357 16 HOH HOH . D 4 HOH A 17 4358 17 HOH HOH . D 4 HOH A 18 4359 18 HOH HOH . D 4 HOH A 19 4360 19 HOH HOH . D 4 HOH A 20 4361 20 HOH HOH . D 4 HOH A 21 4362 21 HOH HOH . D 4 HOH A 22 4363 22 HOH HOH . D 4 HOH A 23 4364 23 HOH HOH . D 4 HOH A 24 4365 24 HOH HOH . D 4 HOH A 25 4366 25 HOH HOH . D 4 HOH A 26 4367 26 HOH HOH . D 4 HOH A 27 4368 27 HOH HOH . D 4 HOH A 28 4369 28 HOH HOH . D 4 HOH A 29 4370 29 HOH HOH . D 4 HOH A 30 4371 30 HOH HOH . D 4 HOH A 31 4372 31 HOH HOH . D 4 HOH A 32 4373 32 HOH HOH . D 4 HOH A 33 4374 33 HOH HOH . D 4 HOH A 34 4375 34 HOH HOH . D 4 HOH A 35 4376 35 HOH HOH . D 4 HOH A 36 4377 36 HOH HOH . D 4 HOH A 37 4378 37 HOH HOH . D 4 HOH A 38 4379 38 HOH HOH . D 4 HOH A 39 4380 39 HOH HOH . D 4 HOH A 40 4381 40 HOH HOH . D 4 HOH A 41 4382 41 HOH HOH . D 4 HOH A 42 4383 42 HOH HOH . D 4 HOH A 43 4384 43 HOH HOH . D 4 HOH A 44 4385 44 HOH HOH . D 4 HOH A 45 4386 45 HOH HOH . D 4 HOH A 46 4387 46 HOH HOH . D 4 HOH A 47 4388 47 HOH HOH . D 4 HOH A 48 4389 48 HOH HOH . D 4 HOH A 49 4390 49 HOH HOH . D 4 HOH A 50 4391 50 HOH HOH . D 4 HOH A 51 4392 51 HOH HOH . D 4 HOH A 52 4393 52 HOH HOH . D 4 HOH A 53 4394 53 HOH HOH . D 4 HOH A 54 4395 54 HOH HOH . D 4 HOH A 55 4396 55 HOH HOH . D 4 HOH A 56 4397 56 HOH HOH . D 4 HOH A 57 4398 57 HOH HOH . D 4 HOH A 58 4399 58 HOH HOH . D 4 HOH A 59 4400 59 HOH HOH . D 4 HOH A 60 4401 60 HOH HOH . D 4 HOH A 61 4402 61 HOH HOH . D 4 HOH A 62 4403 62 HOH HOH . D 4 HOH A 63 4404 63 HOH HOH . D 4 HOH A 64 4405 64 HOH HOH . D 4 HOH A 65 4406 65 HOH HOH . D 4 HOH A 66 4407 66 HOH HOH . D 4 HOH A 67 4408 67 HOH HOH . D 4 HOH A 68 4409 68 HOH HOH . D 4 HOH A 69 4410 69 HOH HOH . D 4 HOH A 70 4411 70 HOH HOH . D 4 HOH A 71 4412 71 HOH HOH . D 4 HOH A 72 4413 72 HOH HOH . D 4 HOH A 73 4414 73 HOH HOH . D 4 HOH A 74 4415 74 HOH HOH . D 4 HOH A 75 4416 75 HOH HOH . D 4 HOH A 76 4417 76 HOH HOH . D 4 HOH A 77 4418 77 HOH HOH . D 4 HOH A 78 4419 78 HOH HOH . D 4 HOH A 79 4420 79 HOH HOH . D 4 HOH A 80 4421 80 HOH HOH . D 4 HOH A 81 4422 81 HOH HOH . D 4 HOH A 82 4423 82 HOH HOH . D 4 HOH A 83 4424 83 HOH HOH . D 4 HOH A 84 4425 84 HOH HOH . D 4 HOH A 85 4426 85 HOH HOH . D 4 HOH A 86 4427 86 HOH HOH . D 4 HOH A 87 4428 87 HOH HOH . D 4 HOH A 88 4429 88 HOH HOH . D 4 HOH A 89 4430 89 HOH HOH . D 4 HOH A 90 4431 90 HOH HOH . D 4 HOH A 91 4432 91 HOH HOH . D 4 HOH A 92 4433 92 HOH HOH . D 4 HOH A 93 4434 94 HOH HOH . D 4 HOH A 94 4435 95 HOH HOH . D 4 HOH A 95 4436 96 HOH HOH . D 4 HOH A 96 4437 97 HOH HOH . D 4 HOH A 97 4438 98 HOH HOH . D 4 HOH A 98 4439 100 HOH HOH . D 4 HOH A 99 4440 101 HOH HOH . D 4 HOH A 100 4441 102 HOH HOH . D 4 HOH A 101 4442 103 HOH HOH . D 4 HOH A 102 4443 104 HOH HOH . D 4 HOH A 103 4444 105 HOH HOH . D 4 HOH A 104 4445 106 HOH HOH . D 4 HOH A 105 4446 107 HOH HOH . D 4 HOH A 106 4447 108 HOH HOH . D 4 HOH A 107 4448 109 HOH HOH . D 4 HOH A 108 4449 110 HOH HOH . D 4 HOH A 109 4450 111 HOH HOH . D 4 HOH A 110 4451 112 HOH HOH . D 4 HOH A 111 4452 113 HOH HOH . D 4 HOH A 112 4453 114 HOH HOH . D 4 HOH A 113 4454 115 HOH HOH . D 4 HOH A 114 4455 116 HOH HOH . D 4 HOH A 115 4456 117 HOH HOH . D 4 HOH A 116 4457 118 HOH HOH . D 4 HOH A 117 4458 119 HOH HOH . D 4 HOH A 118 4459 120 HOH HOH . D 4 HOH A 119 4460 121 HOH HOH . D 4 HOH A 120 4461 122 HOH HOH . D 4 HOH A 121 4462 123 HOH HOH . D 4 HOH A 122 4463 124 HOH HOH . D 4 HOH A 123 4464 125 HOH HOH . D 4 HOH A 124 4465 126 HOH HOH . D 4 HOH A 125 4466 127 HOH HOH . D 4 HOH A 126 4467 128 HOH HOH . D 4 HOH A 127 4468 129 HOH HOH . D 4 HOH A 128 4469 130 HOH HOH . D 4 HOH A 129 4470 131 HOH HOH . D 4 HOH A 130 4471 132 HOH HOH . D 4 HOH A 131 4472 133 HOH HOH . D 4 HOH A 132 4473 134 HOH HOH . D 4 HOH A 133 4474 135 HOH HOH . D 4 HOH A 134 4475 136 HOH HOH . D 4 HOH A 135 4476 137 HOH HOH . D 4 HOH A 136 4477 138 HOH HOH . D 4 HOH A 137 4478 139 HOH HOH . D 4 HOH A 138 4479 140 HOH HOH . D 4 HOH A 139 4480 141 HOH HOH . D 4 HOH A 140 4481 142 HOH HOH . D 4 HOH A 141 4482 143 HOH HOH . D 4 HOH A 142 4483 144 HOH HOH . D 4 HOH A 143 4484 145 HOH HOH . D 4 HOH A 144 4485 146 HOH HOH . D 4 HOH A 145 4486 147 HOH HOH . D 4 HOH A 146 4487 148 HOH HOH . D 4 HOH A 147 4488 149 HOH HOH . D 4 HOH A 148 4489 150 HOH HOH . D 4 HOH A 149 4490 151 HOH HOH . D 4 HOH A 150 4491 152 HOH HOH . D 4 HOH A 151 4492 153 HOH HOH . D 4 HOH A 152 4493 154 HOH HOH . D 4 HOH A 153 4494 155 HOH HOH . D 4 HOH A 154 4495 156 HOH HOH . D 4 HOH A 155 4496 157 HOH HOH . D 4 HOH A 156 4497 158 HOH HOH . D 4 HOH A 157 4498 159 HOH HOH . D 4 HOH A 158 4499 160 HOH HOH . D 4 HOH A 159 4500 161 HOH HOH . D 4 HOH A 160 4501 162 HOH HOH . D 4 HOH A 161 4502 163 HOH HOH . D 4 HOH A 162 4503 164 HOH HOH . D 4 HOH A 163 4504 165 HOH HOH . D 4 HOH A 164 4505 166 HOH HOH . D 4 HOH A 165 4506 167 HOH HOH . D 4 HOH A 166 4507 168 HOH HOH . D 4 HOH A 167 4508 169 HOH HOH . D 4 HOH A 168 4509 170 HOH HOH . D 4 HOH A 169 4510 171 HOH HOH . D 4 HOH A 170 4511 172 HOH HOH . D 4 HOH A 171 4512 173 HOH HOH . D 4 HOH A 172 4513 174 HOH HOH . D 4 HOH A 173 4514 175 HOH HOH . D 4 HOH A 174 4515 176 HOH HOH . D 4 HOH A 175 4516 177 HOH HOH . D 4 HOH A 176 4517 178 HOH HOH . D 4 HOH A 177 4518 179 HOH HOH . D 4 HOH A 178 4519 180 HOH HOH . D 4 HOH A 179 4520 181 HOH HOH . D 4 HOH A 180 4521 182 HOH HOH . D 4 HOH A 181 4522 183 HOH HOH . D 4 HOH A 182 4523 184 HOH HOH . D 4 HOH A 183 4524 185 HOH HOH . D 4 HOH A 184 4525 186 HOH HOH . D 4 HOH A 185 4526 187 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 P T3P . . . C 3 16.462 41.49 30.483 1 16.77 ? P T3P 4341 A 1 HETATM 2 O OP1 T3P . . . C 3 17.685 41.145 29.571 1 17.11 ? OP1 T3P 4341 A 1 HETATM 3 O OP2 T3P . . . C 3 15.854 40.205 31.101 1 18.47 ? OP2 T3P 4341 A 1 HETATM 4 O OP3 T3P . . . C 3 16.75 42.553 31.566 1 16.02 ? OP3 T3P 4341 A 1 HETATM 5 O O5' T3P . . . C 3 13.748 41.044 25.694 1 21.1 ? O5' T3P 4341 A 1 HETATM 6 C C5' T3P . . . C 3 14.195 42.365 26.122 1 18.44 ? C5' T3P 4341 A 1 HETATM 7 C C4' T3P . . . C 3 14.093 42.598 27.647 1 17.07 ? C4' T3P 4341 A 1 HETATM 8 O O4' T3P . . . C 3 12.737 42.462 28.033 1 18.87 ? O4' T3P 4341 A 1 HETATM 9 C C3' T3P . . . C 3 14.875 41.487 28.305 1 17.34 ? C3' T3P 4341 A 1 HETATM 10 O O3' T3P . . . C 3 15.302 42.146 29.538 1 15.67 ? O3' T3P 4341 A 1 HETATM 11 C C2' T3P . . . C 3 13.852 40.513 28.79 1 18.19 ? C2' T3P 4341 A 1 HETATM 12 C C1' T3P . . . C 3 12.526 41.281 28.798 1 19.39 ? C1' T3P 4341 A 1 HETATM 13 N N1 T3P . . . C 3 11.379 40.526 28.362 1 17.97 ? N1 T3P 4341 A 1 HETATM 14 C C2 T3P . . . C 3 10.895 39.51 29.211 1 20.37 ? C2 T3P 4341 A 1 HETATM 15 O O2 T3P . . . C 3 11.469 39.337 30.325 1 18.71 ? O2 T3P 4341 A 1 HETATM 16 N N3 T3P . . . C 3 9.844 38.802 28.8 1 20.05 ? N3 T3P 4341 A 1 HETATM 17 C C4 T3P . . . C 3 9.263 38.967 27.593 1 18.89 ? C4 T3P 4341 A 1 HETATM 18 O O4 T3P . . . C 3 8.279 38.274 27.204 1 19.75 ? O4 T3P 4341 A 1 HETATM 19 C C5 T3P . . . C 3 9.784 40.035 26.739 1 18.29 ? C5 T3P 4341 A 1 HETATM 20 C C5M T3P . . . C 3 9.169 40.328 25.468 1 11.95 ? C5M T3P 4341 A 1 HETATM 21 C C6 T3P . . . C 3 10.845 40.803 27.169 1 21.92 ? C6 T3P 4341 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #