data_4G2T # _model_server_result.job_id iTJ1oe-7x2mtdBBXV3PGvA _model_server_result.datetime_utc '2024-11-13 00:39:31' _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 4g2t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4G2T # _exptl.entry_id 4G2T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-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 120 _cell.entry_id 4G2T _cell.length_a 81.141 _cell.length_b 81.141 _cell.length_c 229.906 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4G2T _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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' 10_444 -y-1,-x-1,-z-1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 -40.5705 -70.270167 -38.317667 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 covale ? covale1 A C HIS 14 A HIS 0 1_555 A N MSE 15 A MSE 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C MSE 15 A MSE 1 1_555 A N ARG 16 A ARG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 A C VAL 28 A VAL 14 1_555 A N MSE 29 A MSE 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C MSE 29 A MSE 15 1_555 A N PRO 30 A PRO 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? covale ? covale5 A C ASN 52 A ASN 38 1_555 A N MSE 53 A MSE 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 A C MSE 53 A MSE 39 1_555 A N GLY 54 A GLY 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 A C ASP 72 A ASP 58 1_555 A N MSE 73 A MSE 59 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 A C ASP 72 A ASP 58 1_555 A N MSE 73 A MSE 59 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale9 A C MSE 73 A MSE 59 1_555 A N PRO 74 A PRO 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.35 ? covale ? covale10 A C THR 87 A THR 73 1_555 A N MSE 88 A MSE 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale11 A C MSE 88 A MSE 74 1_555 A N PRO 89 A PRO 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale12 A C ARG 109 A ARG 95 1_555 A N MSE 110 A MSE 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale13 A C MSE 110 A MSE 96 1_555 A N ARG 111 A ARG 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale14 A C SER 192 A SER 178 1_555 A N MSE 193 A MSE 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale15 A C MSE 193 A MSE 179 1_555 A N GLU 194 A GLU 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale16 A C LYS 203 A LYS 189 1_555 A N MSE 204 A MSE 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale17 A C MSE 204 A MSE 190 1_555 A N ARG 205 A ARG 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale18 A C ILE 296 A ILE 282 1_555 A N MSE 297 A MSE 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale19 A C MSE 297 A MSE 283 1_555 A N PRO 298 A PRO 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? covale ? covale20 A C GLU 380 A GLU 366 1_555 A N MSE 381 A MSE 367 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale21 A C MSE 381 A MSE 367 1_555 A N ALA 382 A ALA 368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _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 PA O1A TYD doub 334 n n PA O2A TYD sing 335 n n PA O3A TYD sing 336 n n PA O5' TYD sing 337 n n O2A HOA2 TYD sing 338 n n O3A PB TYD sing 339 n n PB O1B TYD doub 340 n n PB O2B TYD sing 341 n n PB O3B TYD sing 342 n n O2B HOB2 TYD sing 343 n n O3B HOB3 TYD sing 344 n n O5' C5' TYD sing 345 n n C5' C4' TYD sing 346 n n C5' "H5'1" TYD sing 347 n n C5' "H5'2" TYD sing 348 n n C4' O4' TYD sing 349 n n C4' C3' TYD sing 350 n n C4' H4' TYD sing 351 n n O4' C1' TYD sing 352 n n C3' O3' TYD sing 353 n n C3' C2' TYD sing 354 n n C3' H3' TYD sing 355 n n O3' HO3' TYD sing 356 n n C2' C1' TYD sing 357 n n C2' "H2'1" TYD sing 358 n n C2' "H2'2" TYD sing 359 n n C1' N1 TYD sing 360 n n C1' H1' TYD sing 361 n n N1 C2 TYD sing 362 n y N1 C6 TYD sing 363 n y C2 O2 TYD doub 364 n n C2 N3 TYD sing 365 n y N3 C4 TYD sing 366 n y N3 HN3 TYD sing 367 n n C4 O4 TYD doub 368 n n C4 C5 TYD sing 369 n y C5 C5M TYD sing 370 n n C5 C6 TYD doub 371 n y C5M H51 TYD sing 372 n n C5M H52 TYD sing 373 n n C5M H53 TYD sing 374 n n C6 H6 TYD sing 375 n n # _atom_sites.entry_id 4G2T _atom_sites.fract_transf_matrix[1][1] 0.012324 _atom_sites.fract_transf_matrix[1][2] 0.007115 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014231 _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] 0.00435 _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 TYD A 1 401 1 TYD TYD . C 3 HOH A 1 501 1 HOH HOH . C 3 HOH A 2 502 2 HOH HOH . C 3 HOH A 3 503 3 HOH HOH . C 3 HOH A 4 504 4 HOH HOH . C 3 HOH A 5 505 5 HOH HOH . C 3 HOH A 6 506 6 HOH HOH . C 3 HOH A 7 507 7 HOH HOH . C 3 HOH A 8 508 8 HOH HOH . C 3 HOH A 9 509 9 HOH HOH . C 3 HOH A 10 510 10 HOH HOH . C 3 HOH A 11 511 11 HOH HOH . C 3 HOH A 12 512 12 HOH HOH . C 3 HOH A 13 513 13 HOH HOH . C 3 HOH A 14 514 14 HOH HOH . C 3 HOH A 15 515 15 HOH HOH . C 3 HOH A 16 516 17 HOH HOH . C 3 HOH A 17 517 18 HOH HOH . C 3 HOH A 18 518 19 HOH HOH . C 3 HOH A 19 519 21 HOH HOH . C 3 HOH A 20 520 22 HOH HOH . C 3 HOH A 21 521 23 HOH HOH . C 3 HOH A 22 522 24 HOH HOH . C 3 HOH A 23 523 25 HOH HOH . C 3 HOH A 24 524 26 HOH HOH . C 3 HOH A 25 525 27 HOH HOH . C 3 HOH A 26 526 28 HOH HOH . C 3 HOH A 27 527 29 HOH HOH . C 3 HOH A 28 528 30 HOH HOH . C 3 HOH A 29 529 31 HOH HOH . C 3 HOH A 30 530 32 HOH HOH . C 3 HOH A 31 531 33 HOH HOH . C 3 HOH A 32 532 35 HOH HOH . C 3 HOH A 33 533 36 HOH HOH . C 3 HOH A 34 534 37 HOH HOH . C 3 HOH A 35 535 38 HOH HOH . C 3 HOH A 36 536 39 HOH HOH . C 3 HOH A 37 537 41 HOH HOH . C 3 HOH A 38 538 42 HOH HOH . C 3 HOH A 39 539 43 HOH HOH . C 3 HOH A 40 540 44 HOH HOH . C 3 HOH A 41 541 45 HOH HOH . C 3 HOH A 42 542 46 HOH HOH . C 3 HOH A 43 543 47 HOH HOH . C 3 HOH A 44 544 48 HOH HOH . C 3 HOH A 45 545 49 HOH HOH . C 3 HOH A 46 546 50 HOH HOH . C 3 HOH A 47 547 51 HOH HOH . C 3 HOH A 48 548 52 HOH HOH . C 3 HOH A 49 549 53 HOH HOH . C 3 HOH A 50 550 54 HOH HOH . C 3 HOH A 51 551 55 HOH HOH . C 3 HOH A 52 552 56 HOH HOH . C 3 HOH A 53 553 57 HOH HOH . C 3 HOH A 54 554 58 HOH HOH . C 3 HOH A 55 555 59 HOH HOH . C 3 HOH A 56 556 60 HOH HOH . C 3 HOH A 57 557 61 HOH HOH . C 3 HOH A 58 558 62 HOH HOH . C 3 HOH A 59 559 63 HOH HOH . C 3 HOH A 60 560 64 HOH HOH . C 3 HOH A 61 561 65 HOH HOH . C 3 HOH A 62 562 66 HOH HOH . C 3 HOH A 63 563 67 HOH HOH . C 3 HOH A 64 564 68 HOH HOH . C 3 HOH A 65 565 69 HOH HOH . C 3 HOH A 66 566 70 HOH HOH . C 3 HOH A 67 567 71 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 PA TYD . . . B 2 -5.597 -36.763 -1.72 1 18.44 ? PA TYD 401 A 1 HETATM 2 O O1A TYD . . . B 2 -6.756 -37.475 -1.067 1 15.25 ? O1A TYD 401 A 1 HETATM 3 O O2A TYD . . . B 2 -5.876 -35.278 -1.776 1 13.27 ? O2A TYD 401 A 1 HETATM 4 O O3A TYD . . . B 2 -4.307 -37.05 -0.887 1 26.11 ? O3A TYD 401 A 1 HETATM 5 P PB TYD . . . B 2 -2.925 -36.496 -1.359 1 24.24 ? PB TYD 401 A 1 HETATM 6 O O1B TYD . . . B 2 -3.107 -35.181 -2.078 1 21.47 ? O1B TYD 401 A 1 HETATM 7 O O2B TYD . . . B 2 -2.056 -36.291 -0.141 1 32.85 ? O2B TYD 401 A 1 HETATM 8 O O3B TYD . . . B 2 -2.266 -37.487 -2.29 1 22.46 ? O3B TYD 401 A 1 HETATM 9 O O5' TYD . . . B 2 -5.383 -37.308 -3.165 1 25.31 ? O5' TYD 401 A 1 HETATM 10 C C5' TYD . . . B 2 -5.221 -38.661 -3.372 1 15.58 ? C5' TYD 401 A 1 HETATM 11 C C4' TYD . . . B 2 -5.997 -39.058 -4.578 1 11.13 ? C4' TYD 401 A 1 HETATM 12 O O4' TYD . . . B 2 -5.446 -40.199 -5.144 1 19.05 ? O4' TYD 401 A 1 HETATM 13 C C3' TYD . . . B 2 -7.41 -39.397 -4.185 1 19.35 ? C3' TYD 401 A 1 HETATM 14 O O3' TYD . . . B 2 -8.272 -39.054 -5.202 1 21.32 ? O3' TYD 401 A 1 HETATM 15 C C2' TYD . . . B 2 -7.44 -40.868 -3.93 1 13.13 ? C2' TYD 401 A 1 HETATM 16 C C1' TYD . . . B 2 -6.34 -41.349 -4.947 1 16.83 ? C1' TYD 401 A 1 HETATM 17 N N1 TYD . . . B 2 -5.706 -42.735 -4.702 1 11.9 ? N1 TYD 401 A 1 HETATM 18 C C2 TYD . . . B 2 -6.452 -43.967 -4.858 1 12.75 ? C2 TYD 401 A 1 HETATM 19 O O2 TYD . . . B 2 -7.623 -43.938 -5.19 1 16.46 ? O2 TYD 401 A 1 HETATM 20 N N3 TYD . . . B 2 -5.854 -45.228 -4.627 1 15.06 ? N3 TYD 401 A 1 HETATM 21 C C4 TYD . . . B 2 -4.507 -45.305 -4.242 1 14.93 ? C4 TYD 401 A 1 HETATM 22 O O4 TYD . . . B 2 -3.983 -46.404 -4.042 1 22.46 ? O4 TYD 401 A 1 HETATM 23 C C5 TYD . . . B 2 -3.729 -44.042 -4.083 1 19.33 ? C5 TYD 401 A 1 HETATM 24 C C5M TYD . . . B 2 -2.297 -44.121 -3.675 1 21.34 ? C5M TYD 401 A 1 HETATM 25 C C6 TYD . . . B 2 -4.307 -42.811 -4.306 1 13.12 ? C6 TYD 401 A 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 25 #