data_2RJ9 # _model_server_result.job_id 3MBiyZNQYpI9TnNu-9mOFw _model_server_result.datetime_utc '2024-11-07 12:48:24' _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 2rj9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":357}' # _entry.id 2RJ9 # _exptl.entry_id 2RJ9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-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 2RJ9 _cell.length_a 52.43 _cell.length_b 149.93 _cell.length_c 78.92 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2RJ9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA,PQS dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E 1 1 A,B,C,D,E 2 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' 3_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -39.46 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 B MN MN . A MN 1 1_555 A OD2 ASP 150 A ASP 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc2 B MN MN . A MN 1 1_555 A OD1 ASP 152 A ASP 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc3 B MN MN . A MN 1 1_555 D O2B UDP . A UDP 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc4 B MN MN . A MN 1 1_555 D O1A UDP . A UDP 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc5 B MN MN . A MN 1 1_555 E O HOH . A HOH 535 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna 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 N1 C2 UDP sing 427 n n N1 C6 UDP sing 428 n n N1 C1' UDP sing 429 n n C2 N3 UDP sing 430 n n C2 O2 UDP doub 431 n n N3 C4 UDP sing 432 n n N3 HN3 UDP sing 433 n n C4 C5 UDP sing 434 n n C4 O4 UDP doub 435 n n C5 C6 UDP doub 436 n n C5 H5 UDP sing 437 n n C6 H6 UDP sing 438 n n C1' C2' UDP sing 439 n n C1' O4' UDP sing 440 n n C1' H1' UDP sing 441 n n C2' O2' UDP sing 442 n n C2' C3' UDP sing 443 n n C2' H2' UDP sing 444 n n O2' HO2' UDP sing 445 n n C3' C4' UDP sing 446 n n C3' O3' UDP sing 447 n n C3' H3' UDP sing 448 n n C4' O4' UDP sing 449 n n C4' C5' UDP sing 450 n n C4' H4' UDP sing 451 n n O3' HO3' UDP sing 452 n n C5' O5' UDP sing 453 n n C5' "H5'1" UDP sing 454 n n C5' "H5'2" UDP sing 455 n n O5' PA UDP sing 456 n n PA O1A UDP doub 457 n n PA O2A UDP sing 458 n n PA O3A UDP sing 459 n n O2A HOA2 UDP sing 460 n n O3A PB UDP sing 461 n n PB O1B UDP doub 462 n n PB O2B UDP sing 463 n n PB O3B UDP sing 464 n n O2B HOB2 UDP sing 465 n n O3B HOB3 UDP sing 466 n n # _atom_sites.entry_id 2RJ9 _atom_sites.fract_transf_matrix[1][1] 0.019073 _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] 0.00667 _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] 0.012671 _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 MN A 1 1 1 MN MN . C 3 AD7 A 1 356 356 AD7 AD7 . D 4 UDP A 1 357 357 UDP UDP . E 5 HOH A 1 358 358 HOH HOH . E 5 HOH A 2 359 359 HOH HOH . E 5 HOH A 3 360 360 HOH HOH . E 5 HOH A 4 361 361 HOH HOH . E 5 HOH A 5 362 362 HOH HOH . E 5 HOH A 6 363 363 HOH HOH . E 5 HOH A 7 364 364 HOH HOH . E 5 HOH A 8 365 365 HOH HOH . E 5 HOH A 9 366 366 HOH HOH . E 5 HOH A 10 367 367 HOH HOH . E 5 HOH A 11 368 368 HOH HOH . E 5 HOH A 12 369 369 HOH HOH . E 5 HOH A 13 370 370 HOH HOH . E 5 HOH A 14 371 371 HOH HOH . E 5 HOH A 15 372 372 HOH HOH . E 5 HOH A 16 373 373 HOH HOH . E 5 HOH A 17 374 374 HOH HOH . E 5 HOH A 18 375 375 HOH HOH . E 5 HOH A 19 376 376 HOH HOH . E 5 HOH A 20 377 377 HOH HOH . E 5 HOH A 21 378 378 HOH HOH . E 5 HOH A 22 379 379 HOH HOH . E 5 HOH A 23 380 380 HOH HOH . E 5 HOH A 24 381 381 HOH HOH . E 5 HOH A 25 382 382 HOH HOH . E 5 HOH A 26 383 383 HOH HOH . E 5 HOH A 27 384 384 HOH HOH . E 5 HOH A 28 385 385 HOH HOH . E 5 HOH A 29 386 386 HOH HOH . E 5 HOH A 30 387 387 HOH HOH . E 5 HOH A 31 388 388 HOH HOH . E 5 HOH A 32 389 389 HOH HOH . E 5 HOH A 33 390 390 HOH HOH . E 5 HOH A 34 391 391 HOH HOH . E 5 HOH A 35 392 392 HOH HOH . E 5 HOH A 36 393 393 HOH HOH . E 5 HOH A 37 394 394 HOH HOH . E 5 HOH A 38 395 395 HOH HOH . E 5 HOH A 39 396 396 HOH HOH . E 5 HOH A 40 397 397 HOH HOH . E 5 HOH A 41 398 398 HOH HOH . E 5 HOH A 42 399 399 HOH HOH . E 5 HOH A 43 400 400 HOH HOH . E 5 HOH A 44 401 401 HOH HOH . E 5 HOH A 45 402 402 HOH HOH . E 5 HOH A 46 403 403 HOH HOH . E 5 HOH A 47 404 404 HOH HOH . E 5 HOH A 48 405 405 HOH HOH . E 5 HOH A 49 406 406 HOH HOH . E 5 HOH A 50 407 407 HOH HOH . E 5 HOH A 51 408 408 HOH HOH . E 5 HOH A 52 409 409 HOH HOH . E 5 HOH A 53 410 410 HOH HOH . E 5 HOH A 54 411 411 HOH HOH . E 5 HOH A 55 412 412 HOH HOH . E 5 HOH A 56 413 413 HOH HOH . E 5 HOH A 57 414 414 HOH HOH . E 5 HOH A 58 415 415 HOH HOH . E 5 HOH A 59 416 416 HOH HOH . E 5 HOH A 60 417 417 HOH HOH . E 5 HOH A 61 418 418 HOH HOH . E 5 HOH A 62 419 419 HOH HOH . E 5 HOH A 63 420 420 HOH HOH . E 5 HOH A 64 421 421 HOH HOH . E 5 HOH A 65 422 422 HOH HOH . E 5 HOH A 66 423 423 HOH HOH . E 5 HOH A 67 424 424 HOH HOH . E 5 HOH A 68 425 425 HOH HOH . E 5 HOH A 69 426 426 HOH HOH . E 5 HOH A 70 427 427 HOH HOH . E 5 HOH A 71 428 428 HOH HOH . E 5 HOH A 72 429 429 HOH HOH . E 5 HOH A 73 430 430 HOH HOH . E 5 HOH A 74 431 431 HOH HOH . E 5 HOH A 75 432 432 HOH HOH . E 5 HOH A 76 433 433 HOH HOH . E 5 HOH A 77 434 434 HOH HOH . E 5 HOH A 78 435 435 HOH HOH . E 5 HOH A 79 436 436 HOH HOH . E 5 HOH A 80 437 437 HOH HOH . E 5 HOH A 81 438 438 HOH HOH . E 5 HOH A 82 439 439 HOH HOH . E 5 HOH A 83 440 440 HOH HOH . E 5 HOH A 84 441 441 HOH HOH . E 5 HOH A 85 442 442 HOH HOH . E 5 HOH A 86 443 443 HOH HOH . E 5 HOH A 87 444 444 HOH HOH . E 5 HOH A 88 445 445 HOH HOH . E 5 HOH A 89 446 446 HOH HOH . E 5 HOH A 90 447 447 HOH HOH . E 5 HOH A 91 448 448 HOH HOH . E 5 HOH A 92 449 449 HOH HOH . E 5 HOH A 93 450 450 HOH HOH . E 5 HOH A 94 451 451 HOH HOH . E 5 HOH A 95 452 452 HOH HOH . E 5 HOH A 96 453 453 HOH HOH . E 5 HOH A 97 454 454 HOH HOH . E 5 HOH A 98 455 455 HOH HOH . E 5 HOH A 99 456 456 HOH HOH . E 5 HOH A 100 457 457 HOH HOH . E 5 HOH A 101 458 458 HOH HOH . E 5 HOH A 102 459 459 HOH HOH . E 5 HOH A 103 460 460 HOH HOH . E 5 HOH A 104 461 461 HOH HOH . E 5 HOH A 105 462 462 HOH HOH . E 5 HOH A 106 463 463 HOH HOH . E 5 HOH A 107 464 464 HOH HOH . E 5 HOH A 108 465 465 HOH HOH . E 5 HOH A 109 466 466 HOH HOH . E 5 HOH A 110 467 467 HOH HOH . E 5 HOH A 111 468 468 HOH HOH . E 5 HOH A 112 469 469 HOH HOH . E 5 HOH A 113 470 470 HOH HOH . E 5 HOH A 114 471 471 HOH HOH . E 5 HOH A 115 472 472 HOH HOH . E 5 HOH A 116 473 473 HOH HOH . E 5 HOH A 117 474 474 HOH HOH . E 5 HOH A 118 475 475 HOH HOH . E 5 HOH A 119 476 476 HOH HOH . E 5 HOH A 120 477 477 HOH HOH . E 5 HOH A 121 478 478 HOH HOH . E 5 HOH A 122 479 479 HOH HOH . E 5 HOH A 123 480 480 HOH HOH . E 5 HOH A 124 481 481 HOH HOH . E 5 HOH A 125 482 482 HOH HOH . E 5 HOH A 126 483 483 HOH HOH . E 5 HOH A 127 484 484 HOH HOH . E 5 HOH A 128 485 485 HOH HOH . E 5 HOH A 129 486 486 HOH HOH . E 5 HOH A 130 487 487 HOH HOH . E 5 HOH A 131 488 488 HOH HOH . E 5 HOH A 132 489 489 HOH HOH . E 5 HOH A 133 490 490 HOH HOH . E 5 HOH A 134 491 491 HOH HOH . E 5 HOH A 135 492 492 HOH HOH . E 5 HOH A 136 493 493 HOH HOH . E 5 HOH A 137 494 494 HOH HOH . E 5 HOH A 138 495 495 HOH HOH . E 5 HOH A 139 496 496 HOH HOH . E 5 HOH A 140 497 497 HOH HOH . E 5 HOH A 141 498 498 HOH HOH . E 5 HOH A 142 499 499 HOH HOH . E 5 HOH A 143 500 500 HOH HOH . E 5 HOH A 144 501 501 HOH HOH . E 5 HOH A 145 502 502 HOH HOH . E 5 HOH A 146 503 503 HOH HOH . E 5 HOH A 147 504 504 HOH HOH . E 5 HOH A 148 505 505 HOH HOH . E 5 HOH A 149 506 506 HOH HOH . E 5 HOH A 150 507 507 HOH HOH . E 5 HOH A 151 508 508 HOH HOH . E 5 HOH A 152 509 509 HOH HOH . E 5 HOH A 153 510 510 HOH HOH . E 5 HOH A 154 511 511 HOH HOH . E 5 HOH A 155 512 512 HOH HOH . E 5 HOH A 156 513 513 HOH HOH . E 5 HOH A 157 514 514 HOH HOH . E 5 HOH A 158 515 515 HOH HOH . E 5 HOH A 159 516 516 HOH HOH . E 5 HOH A 160 517 517 HOH HOH . E 5 HOH A 161 518 518 HOH HOH . E 5 HOH A 162 519 519 HOH HOH . E 5 HOH A 163 520 520 HOH HOH . E 5 HOH A 164 521 521 HOH HOH . E 5 HOH A 165 522 522 HOH HOH . E 5 HOH A 166 523 523 HOH HOH . E 5 HOH A 167 524 524 HOH HOH . E 5 HOH A 168 525 525 HOH HOH . E 5 HOH A 169 526 526 HOH HOH . E 5 HOH A 170 527 527 HOH HOH . E 5 HOH A 171 528 528 HOH HOH . E 5 HOH A 172 529 529 HOH HOH . E 5 HOH A 173 530 530 HOH HOH . E 5 HOH A 174 531 531 HOH HOH . E 5 HOH A 175 532 532 HOH HOH . E 5 HOH A 176 533 533 HOH HOH . E 5 HOH A 177 534 534 HOH HOH . E 5 HOH A 178 535 535 HOH HOH . E 5 HOH A 179 536 536 HOH HOH . E 5 HOH A 180 537 537 HOH HOH . E 5 HOH A 181 538 538 HOH HOH . E 5 HOH A 182 539 539 HOH HOH . E 5 HOH A 183 540 540 HOH HOH . E 5 HOH A 184 541 541 HOH HOH . E 5 HOH A 185 542 542 HOH HOH . E 5 HOH A 186 543 543 HOH HOH . E 5 HOH A 187 544 544 HOH HOH . E 5 HOH A 188 545 545 HOH HOH . E 5 HOH A 189 546 546 HOH HOH . E 5 HOH A 190 547 547 HOH HOH . E 5 HOH A 191 548 548 HOH HOH . E 5 HOH A 192 549 549 HOH HOH . E 5 HOH A 193 550 550 HOH HOH . E 5 HOH A 194 551 551 HOH HOH . E 5 HOH A 195 552 552 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 N N1 UDP . . . D 4 -16.465 -23.261 7.824 1 23.69 ? N1 UDP 357 A 1 HETATM 2 C C2 UDP . . . D 4 -17.592 -23.977 8.102 1 23.64 ? C2 UDP 357 A 1 HETATM 3 N N3 UDP . . . D 4 -18.164 -23.924 9.403 1 26.21 ? N3 UDP 357 A 1 HETATM 4 C C4 UDP . . . D 4 -17.556 -23.127 10.403 1 27.01 ? C4 UDP 357 A 1 HETATM 5 C C5 UDP . . . D 4 -16.406 -22.387 10.102 1 25.54 ? C5 UDP 357 A 1 HETATM 6 C C6 UDP . . . D 4 -15.859 -22.441 8.825 1 25.56 ? C6 UDP 357 A 1 HETATM 7 O O2 UDP . . . D 4 -18.124 -24.679 7.236 1 22.56 ? O2 UDP 357 A 1 HETATM 8 O O4 UDP . . . D 4 -18.031 -23.069 11.534 1 26.3 ? O4 UDP 357 A 1 HETATM 9 C C1' UDP . . . D 4 -15.89 -23.331 6.463 1 23.49 ? C1' UDP 357 A 1 HETATM 10 C C2' UDP . . . D 4 -16.759 -22.535 5.49 1 19.87 ? C2' UDP 357 A 1 HETATM 11 O O2' UDP . . . D 4 -16.685 -23.121 4.16 1 20.92 ? O2' UDP 357 A 1 HETATM 12 C C3' UDP . . . D 4 -16.079 -21.213 5.509 1 19.12 ? C3' UDP 357 A 1 HETATM 13 C C4' UDP . . . D 4 -14.585 -21.637 5.499 1 19.16 ? C4' UDP 357 A 1 HETATM 14 O O4' UDP . . . D 4 -14.538 -22.783 6.401 1 21.68 ? O4' UDP 357 A 1 HETATM 15 O O3' UDP . . . D 4 -16.408 -20.52 4.289 1 19.52 ? O3' UDP 357 A 1 HETATM 16 C C5' UDP . . . D 4 -13.669 -20.535 6.013 1 17.41 ? C5' UDP 357 A 1 HETATM 17 O O5' UDP . . . D 4 -14.158 -19.989 7.253 0.5 10.92 ? O5' UDP 357 A 1 HETATM 18 P PA UDP . . . D 4 -14.711 -18.5 7.389 0.5 13.39 ? PA UDP 357 A 1 HETATM 19 O O1A UDP . . . D 4 -15.092 -18.134 6.069 0.5 10.87 ? O1A UDP 357 A 1 HETATM 20 O O2A UDP . . . D 4 -15.285 -18.444 8.68 0.5 12.54 ? O2A UDP 357 A 1 HETATM 21 O O3A UDP . . . D 4 -13.647 -17.712 6.741 0.5 14.28 ? O3A UDP 357 A 1 HETATM 22 P PB UDP . . . D 4 -13.278 -16.094 6.785 0.5 14.76 ? PB UDP 357 A 1 HETATM 23 O O1B UDP . . . D 4 -13.954 -15.322 7.858 1 23.85 ? O1B UDP 357 A 1 HETATM 24 O O2B UDP . . . D 4 -13.591 -15.672 5.32 0.5 16.51 ? O2B UDP 357 A 1 HETATM 25 O O3B UDP . . . D 4 -11.734 -15.886 6.96 0.5 16.32 ? O3B UDP 357 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 345 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #