data_4RII # _model_server_result.job_id jkxCBd6JcW65GOYTrf0kkw _model_server_result.datetime_utc '2024-10-19 19:19:18' _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 4rii # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 4RII # _exptl.entry_id 4RII _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 78.78 _cell.angle_beta 70.16 _cell.angle_gamma 86.77 _cell.entry_id 4RII _cell.length_a 52.693 _cell.length_b 58.669 _cell.length_c 63.66 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RII _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _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,D,E,F,G _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N 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 150 A ASP 150 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc2 D MG MG . A MG 402 1_555 F O HOH . A HOH 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc3 D MG MG . A MG 402 1_555 F O HOH . A HOH 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc4 D MG MG . A MG 402 1_555 F O HOH . A HOH 572 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? # _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 4RII _atom_sites.fract_transf_matrix[1][1] 0.018978 _atom_sites.fract_transf_matrix[1][2] -0.001073 _atom_sites.fract_transf_matrix[1][3] -0.006767 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017072 _atom_sites.fract_transf_matrix[2][3] -0.003248 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.016999 _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 C 2 TYD A 1 401 401 TYD TYD . D 3 MG A 1 402 402 MG MG . E 2 TYD B 1 401 401 TYD TYD . F 4 HOH A 1 501 4 HOH HOH . F 4 HOH A 2 502 7 HOH HOH . F 4 HOH A 3 503 8 HOH HOH . F 4 HOH A 4 504 10 HOH HOH . F 4 HOH A 5 505 15 HOH HOH . F 4 HOH A 6 506 17 HOH HOH . F 4 HOH A 7 507 22 HOH HOH . F 4 HOH A 8 508 23 HOH HOH . F 4 HOH A 9 509 24 HOH HOH . F 4 HOH A 10 510 28 HOH HOH . F 4 HOH A 11 511 29 HOH HOH . F 4 HOH A 12 512 31 HOH HOH . F 4 HOH A 13 513 33 HOH HOH . F 4 HOH A 14 514 34 HOH HOH . F 4 HOH A 15 515 35 HOH HOH . F 4 HOH A 16 516 37 HOH HOH . F 4 HOH A 17 517 40 HOH HOH . F 4 HOH A 18 518 45 HOH HOH . F 4 HOH A 19 519 46 HOH HOH . F 4 HOH A 20 520 48 HOH HOH . F 4 HOH A 21 521 49 HOH HOH . F 4 HOH A 22 522 51 HOH HOH . F 4 HOH A 23 523 52 HOH HOH . F 4 HOH A 24 524 53 HOH HOH . F 4 HOH A 25 525 56 HOH HOH . F 4 HOH A 26 526 59 HOH HOH . F 4 HOH A 27 527 62 HOH HOH . F 4 HOH A 28 528 71 HOH HOH . F 4 HOH A 29 529 75 HOH HOH . F 4 HOH A 30 530 76 HOH HOH . F 4 HOH A 31 531 77 HOH HOH . F 4 HOH A 32 532 78 HOH HOH . F 4 HOH A 33 533 79 HOH HOH . F 4 HOH A 34 534 80 HOH HOH . F 4 HOH A 35 535 82 HOH HOH . F 4 HOH A 36 536 83 HOH HOH . F 4 HOH A 37 537 84 HOH HOH . F 4 HOH A 38 538 90 HOH HOH . F 4 HOH A 39 539 91 HOH HOH . F 4 HOH A 40 540 92 HOH HOH . F 4 HOH A 41 541 105 HOH HOH . F 4 HOH A 42 542 106 HOH HOH . F 4 HOH A 43 543 107 HOH HOH . F 4 HOH A 44 544 109 HOH HOH . F 4 HOH A 45 545 111 HOH HOH . F 4 HOH A 46 546 115 HOH HOH . F 4 HOH A 47 547 117 HOH HOH . F 4 HOH A 48 548 118 HOH HOH . F 4 HOH A 49 549 122 HOH HOH . F 4 HOH A 50 550 124 HOH HOH . F 4 HOH A 51 551 130 HOH HOH . F 4 HOH A 52 552 131 HOH HOH . F 4 HOH A 53 553 132 HOH HOH . F 4 HOH A 54 554 133 HOH HOH . F 4 HOH A 55 555 134 HOH HOH . F 4 HOH A 56 556 135 HOH HOH . F 4 HOH A 57 557 141 HOH HOH . F 4 HOH A 58 558 144 HOH HOH . F 4 HOH A 59 559 145 HOH HOH . F 4 HOH A 60 560 146 HOH HOH . F 4 HOH A 61 561 147 HOH HOH . F 4 HOH A 62 562 152 HOH HOH . F 4 HOH A 63 563 153 HOH HOH . F 4 HOH A 64 564 155 HOH HOH . F 4 HOH A 65 565 156 HOH HOH . F 4 HOH A 66 566 158 HOH HOH . F 4 HOH A 67 567 160 HOH HOH . F 4 HOH A 68 568 162 HOH HOH . F 4 HOH A 69 569 166 HOH HOH . F 4 HOH A 70 570 167 HOH HOH . F 4 HOH A 71 571 171 HOH HOH . F 4 HOH A 72 572 172 HOH HOH . F 4 HOH A 73 573 178 HOH HOH . F 4 HOH A 74 574 179 HOH HOH . F 4 HOH A 75 575 180 HOH HOH . F 4 HOH A 76 576 181 HOH HOH . F 4 HOH A 77 577 185 HOH HOH . F 4 HOH A 78 578 186 HOH HOH . F 4 HOH A 79 579 187 HOH HOH . F 4 HOH A 80 580 189 HOH HOH . F 4 HOH A 81 581 191 HOH HOH . F 4 HOH A 82 582 192 HOH HOH . F 4 HOH A 83 583 193 HOH HOH . F 4 HOH A 84 584 194 HOH HOH . F 4 HOH A 85 585 195 HOH HOH . F 4 HOH A 86 586 196 HOH HOH . F 4 HOH A 87 587 197 HOH HOH . F 4 HOH A 88 588 198 HOH HOH . F 4 HOH A 89 589 199 HOH HOH . F 4 HOH A 90 590 200 HOH HOH . F 4 HOH A 91 591 213 HOH HOH . G 4 HOH B 1 501 1 HOH HOH . G 4 HOH B 2 502 2 HOH HOH . G 4 HOH B 3 503 3 HOH HOH . G 4 HOH B 4 504 5 HOH HOH . G 4 HOH B 5 505 6 HOH HOH . G 4 HOH B 6 506 9 HOH HOH . G 4 HOH B 7 507 11 HOH HOH . G 4 HOH B 8 508 12 HOH HOH . G 4 HOH B 9 509 13 HOH HOH . G 4 HOH B 10 510 14 HOH HOH . G 4 HOH B 11 511 16 HOH HOH . G 4 HOH B 12 512 18 HOH HOH . G 4 HOH B 13 513 19 HOH HOH . G 4 HOH B 14 514 20 HOH HOH . G 4 HOH B 15 515 21 HOH HOH . G 4 HOH B 16 516 25 HOH HOH . G 4 HOH B 17 517 26 HOH HOH . G 4 HOH B 18 518 27 HOH HOH . G 4 HOH B 19 519 30 HOH HOH . G 4 HOH B 20 520 32 HOH HOH . G 4 HOH B 21 521 36 HOH HOH . G 4 HOH B 22 522 38 HOH HOH . G 4 HOH B 23 523 39 HOH HOH . G 4 HOH B 24 524 41 HOH HOH . G 4 HOH B 25 525 42 HOH HOH . G 4 HOH B 26 526 43 HOH HOH . G 4 HOH B 27 527 44 HOH HOH . G 4 HOH B 28 528 47 HOH HOH . G 4 HOH B 29 529 50 HOH HOH . G 4 HOH B 30 530 54 HOH HOH . G 4 HOH B 31 531 55 HOH HOH . G 4 HOH B 32 532 57 HOH HOH . G 4 HOH B 33 533 58 HOH HOH . G 4 HOH B 34 534 60 HOH HOH . G 4 HOH B 35 535 61 HOH HOH . G 4 HOH B 36 536 63 HOH HOH . G 4 HOH B 37 537 64 HOH HOH . G 4 HOH B 38 538 65 HOH HOH . G 4 HOH B 39 539 66 HOH HOH . G 4 HOH B 40 540 67 HOH HOH . G 4 HOH B 41 541 68 HOH HOH . G 4 HOH B 42 542 69 HOH HOH . G 4 HOH B 43 543 70 HOH HOH . G 4 HOH B 44 544 72 HOH HOH . G 4 HOH B 45 545 74 HOH HOH . G 4 HOH B 46 546 81 HOH HOH . G 4 HOH B 47 547 85 HOH HOH . G 4 HOH B 48 548 86 HOH HOH . G 4 HOH B 49 549 87 HOH HOH . G 4 HOH B 50 550 88 HOH HOH . G 4 HOH B 51 551 89 HOH HOH . G 4 HOH B 52 552 93 HOH HOH . G 4 HOH B 53 553 94 HOH HOH . G 4 HOH B 54 554 95 HOH HOH . G 4 HOH B 55 555 96 HOH HOH . G 4 HOH B 56 556 97 HOH HOH . G 4 HOH B 57 557 98 HOH HOH . G 4 HOH B 58 558 99 HOH HOH . G 4 HOH B 59 559 100 HOH HOH . G 4 HOH B 60 560 101 HOH HOH . G 4 HOH B 61 561 102 HOH HOH . G 4 HOH B 62 562 103 HOH HOH . G 4 HOH B 63 563 104 HOH HOH . G 4 HOH B 64 564 108 HOH HOH . G 4 HOH B 65 565 110 HOH HOH . G 4 HOH B 66 566 112 HOH HOH . G 4 HOH B 67 567 113 HOH HOH . G 4 HOH B 68 568 116 HOH HOH . G 4 HOH B 69 569 120 HOH HOH . G 4 HOH B 70 570 121 HOH HOH . G 4 HOH B 71 571 123 HOH HOH . G 4 HOH B 72 572 125 HOH HOH . G 4 HOH B 73 573 126 HOH HOH . G 4 HOH B 74 574 127 HOH HOH . G 4 HOH B 75 575 128 HOH HOH . G 4 HOH B 76 576 129 HOH HOH . G 4 HOH B 77 577 136 HOH HOH . G 4 HOH B 78 578 137 HOH HOH . G 4 HOH B 79 579 138 HOH HOH . G 4 HOH B 80 580 139 HOH HOH . G 4 HOH B 81 581 140 HOH HOH . G 4 HOH B 82 582 142 HOH HOH . G 4 HOH B 83 583 143 HOH HOH . G 4 HOH B 84 584 148 HOH HOH . G 4 HOH B 85 585 149 HOH HOH . G 4 HOH B 86 586 151 HOH HOH . G 4 HOH B 87 587 154 HOH HOH . G 4 HOH B 88 588 157 HOH HOH . G 4 HOH B 89 589 159 HOH HOH . G 4 HOH B 90 590 161 HOH HOH . G 4 HOH B 91 591 163 HOH HOH . G 4 HOH B 92 592 164 HOH HOH . G 4 HOH B 93 593 165 HOH HOH . G 4 HOH B 94 594 168 HOH HOH . G 4 HOH B 95 595 169 HOH HOH . G 4 HOH B 96 596 170 HOH HOH . G 4 HOH B 97 597 173 HOH HOH . G 4 HOH B 98 598 174 HOH HOH . G 4 HOH B 99 599 175 HOH HOH . G 4 HOH B 100 600 176 HOH HOH . G 4 HOH B 101 601 177 HOH HOH . G 4 HOH B 102 602 182 HOH HOH . G 4 HOH B 103 603 183 HOH HOH . G 4 HOH B 104 604 184 HOH HOH . G 4 HOH B 105 605 188 HOH HOH . G 4 HOH B 106 606 201 HOH HOH . G 4 HOH B 107 607 202 HOH HOH . G 4 HOH B 108 608 203 HOH HOH . G 4 HOH B 109 609 204 HOH HOH . G 4 HOH B 110 610 205 HOH HOH . G 4 HOH B 111 611 206 HOH HOH . G 4 HOH B 112 612 207 HOH HOH . G 4 HOH B 113 613 208 HOH HOH . G 4 HOH B 114 614 209 HOH HOH . G 4 HOH B 115 615 211 HOH HOH . G 4 HOH B 116 616 212 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 . . . C 2 -12.622 8.713 -12.732 1 45.8 ? PA TYD 401 A 1 HETATM 2 O O1A TYD . . . C 2 -11.896 8.628 -14.055 1 46.59 ? O1A TYD 401 A 1 HETATM 3 O O2A TYD . . . C 2 -12.615 10.053 -12.018 1 45.34 ? O2A TYD 401 A 1 HETATM 4 O O3A TYD . . . C 2 -14.123 8.178 -13.053 1 50 ? O3A TYD 401 A 1 HETATM 5 P PB TYD . . . C 2 -15.418 8.161 -12.072 1 53.01 ? PB TYD 401 A 1 HETATM 6 O O1B TYD . . . C 2 -16.561 8.607 -12.957 1 52.21 ? O1B TYD 401 A 1 HETATM 7 O O2B TYD . . . C 2 -15.104 9.114 -10.943 1 48.24 ? O2B TYD 401 A 1 HETATM 8 O O3B TYD . . . C 2 -15.526 6.703 -11.677 1 53.56 ? O3B TYD 401 A 1 HETATM 9 O O5' TYD . . . C 2 -11.989 7.581 -11.761 1 42.83 ? O5' TYD 401 A 1 HETATM 10 C C5' TYD . . . C 2 -11.875 6.209 -12.148 1 39.97 ? C5' TYD 401 A 1 HETATM 11 C C4' TYD . . . C 2 -10.753 5.544 -11.355 1 37.27 ? C4' TYD 401 A 1 HETATM 12 O O4' TYD . . . C 2 -10.969 4.133 -11.291 1 35.57 ? O4' TYD 401 A 1 HETATM 13 C C3' TYD . . . C 2 -9.399 5.739 -12.023 1 36.53 ? C3' TYD 401 A 1 HETATM 14 O O3' TYD . . . C 2 -8.401 5.898 -11.009 1 36.64 ? O3' TYD 401 A 1 HETATM 15 C C2' TYD . . . C 2 -9.132 4.444 -12.761 1 35.3 ? C2' TYD 401 A 1 HETATM 16 C C1' TYD . . . C 2 -9.901 3.43 -11.93 1 32.96 ? C1' TYD 401 A 1 HETATM 17 N N1 TYD . . . C 2 -10.402 2.332 -12.755 1 32.13 ? N1 TYD 401 A 1 HETATM 18 C C2 TYD . . . C 2 -9.51 1.278 -13.067 1 30.15 ? C2 TYD 401 A 1 HETATM 19 O O2 TYD . . . C 2 -8.337 1.331 -12.641 1 29.1 ? O2 TYD 401 A 1 HETATM 20 N N3 TYD . . . C 2 -9.912 0.243 -13.817 1 30.03 ? N3 TYD 401 A 1 HETATM 21 C C4 TYD . . . C 2 -11.174 0.173 -14.287 1 30.29 ? C4 TYD 401 A 1 HETATM 22 O O4 TYD . . . C 2 -11.532 -0.804 -14.974 1 29.34 ? O4 TYD 401 A 1 HETATM 23 C C5 TYD . . . C 2 -12.133 1.264 -13.963 1 30.36 ? C5 TYD 401 A 1 HETATM 24 C C5M TYD . . . C 2 -13.56 1.244 -14.457 1 31.07 ? C5M TYD 401 A 1 HETATM 25 C C6 TYD . . . C 2 -11.679 2.322 -13.191 1 30.46 ? C6 TYD 401 A 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 212 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #