data_1R80 # _model_server_result.job_id -DxWG8PmpSRdZtnCE9tihg _model_server_result.datetime_utc '2024-11-27 14:44:09' _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 1r80 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":475}' # _entry.id 1R80 # _exptl.entry_id 1R80 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 5 _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 1R80 _cell.length_a 52.6 _cell.length_b 150.5 _cell.length_c 79.3 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1R80 _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,F,G,H 1 1 A,B,C,D,E,F,G,H 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_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 52.6 0 39.65 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 FUC _pdbx_entity_branch_link.comp_id_2 AIG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B AIG 1 B 1 AIG B 452 AIG 2 n B FUC 2 B 2 FUC B 453 FUC # 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 B O2 AIG . B AIG 1 1_555 B C1 FUC . B FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.387 ? metalc ? metalc1 A OG1 THR 57 A THR 119 1_555 E HG HG . A HG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.905 ? metalc ? metalc2 A SG CYS 147 A CYS 209 1_555 E HG HG . A HG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc3 A OD2 ASP 151 A ASP 213 1_555 F MN MN . A MN 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? metalc ? metalc4 A SG CYS 222 A CYS 284 1_555 C HG HG . A HG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? metalc ? metalc5 A N CYS 222 A CYS 284 1_555 D HG HG . A HG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.415 ? metalc ? metalc6 A SG CYS 222 A CYS 284 1_555 D HG HG . A HG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc7 A O HIS 243 A HIS 305 1_555 D HG HG . A HG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.2 ? metalc ? metalc8 E HG HG . A HG 403 1_555 H O HOH . A HOH 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc9 F MN MN . A MN 406 1_555 G O1A UDP . A UDP 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc10 F MN MN . A MN 406 1_555 G O3B UDP . A UDP 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? # _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 424 n n N1 C6 UDP sing 425 n n N1 C1' UDP sing 426 n n C2 N3 UDP sing 427 n n C2 O2 UDP doub 428 n n N3 C4 UDP sing 429 n n N3 HN3 UDP sing 430 n n C4 C5 UDP sing 431 n n C4 O4 UDP doub 432 n n C5 C6 UDP doub 433 n n C5 H5 UDP sing 434 n n C6 H6 UDP sing 435 n n C1' C2' UDP sing 436 n n C1' O4' UDP sing 437 n n C1' H1' UDP sing 438 n n C2' O2' UDP sing 439 n n C2' C3' UDP sing 440 n n C2' H2' UDP sing 441 n n O2' HO2' UDP sing 442 n n C3' C4' UDP sing 443 n n C3' O3' UDP sing 444 n n C3' H3' UDP sing 445 n n C4' O4' UDP sing 446 n n C4' C5' UDP sing 447 n n C4' H4' UDP sing 448 n n O3' HO3' UDP sing 449 n n C5' O5' UDP sing 450 n n C5' "H5'1" UDP sing 451 n n C5' "H5'2" UDP sing 452 n n O5' PA UDP sing 453 n n PA O1A UDP doub 454 n n PA O2A UDP sing 455 n n PA O3A UDP sing 456 n n O2A HOA2 UDP sing 457 n n O3A PB UDP sing 458 n n PB O1B UDP doub 459 n n PB O2B UDP sing 460 n n PB O3B UDP sing 461 n n O2B HOB2 UDP sing 462 n n O3B HOB3 UDP sing 463 n n # _atom_sites.entry_id 1R80 _atom_sites.fract_transf_matrix[1][1] 0.019011 _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] 0.006645 _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] 0.01261 _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 3 HG A 1 401 401 HG HG . D 3 HG A 1 402 402 HG HG . E 3 HG A 1 403 403 HG HG . F 4 MN A 1 406 406 MN MN . G 5 UDP A 1 475 475 UDP UDP . H 6 HOH A 1 476 2 HOH TIP . H 6 HOH A 2 477 3 HOH TIP . H 6 HOH A 3 478 4 HOH TIP . H 6 HOH A 4 479 5 HOH TIP . H 6 HOH A 5 480 6 HOH TIP . H 6 HOH A 6 481 7 HOH TIP . H 6 HOH A 7 482 8 HOH TIP . H 6 HOH A 8 483 9 HOH TIP . H 6 HOH A 9 484 10 HOH TIP . H 6 HOH A 10 485 11 HOH TIP . H 6 HOH A 11 486 12 HOH TIP . H 6 HOH A 12 487 13 HOH TIP . H 6 HOH A 13 488 14 HOH TIP . H 6 HOH A 14 489 15 HOH TIP . H 6 HOH A 15 490 16 HOH TIP . H 6 HOH A 16 491 17 HOH TIP . H 6 HOH A 17 492 18 HOH TIP . H 6 HOH A 18 493 19 HOH TIP . H 6 HOH A 19 494 20 HOH TIP . H 6 HOH A 20 495 21 HOH TIP . H 6 HOH A 21 496 22 HOH TIP . H 6 HOH A 22 497 23 HOH TIP . H 6 HOH A 23 498 24 HOH TIP . H 6 HOH A 24 499 25 HOH TIP . H 6 HOH A 25 500 26 HOH TIP . H 6 HOH A 26 501 27 HOH TIP . H 6 HOH A 27 502 28 HOH TIP . H 6 HOH A 28 503 29 HOH TIP . H 6 HOH A 29 504 30 HOH TIP . H 6 HOH A 30 505 31 HOH TIP . H 6 HOH A 31 506 32 HOH TIP . H 6 HOH A 32 507 33 HOH TIP . H 6 HOH A 33 508 34 HOH TIP . H 6 HOH A 34 509 35 HOH TIP . H 6 HOH A 35 510 36 HOH TIP . H 6 HOH A 36 511 37 HOH TIP . H 6 HOH A 37 512 38 HOH TIP . H 6 HOH A 38 513 39 HOH TIP . H 6 HOH A 39 514 40 HOH TIP . H 6 HOH A 40 515 41 HOH TIP . H 6 HOH A 41 516 42 HOH TIP . H 6 HOH A 42 517 43 HOH TIP . H 6 HOH A 43 518 44 HOH TIP . H 6 HOH A 44 519 45 HOH TIP . H 6 HOH A 45 520 46 HOH TIP . H 6 HOH A 46 521 47 HOH TIP . H 6 HOH A 47 522 48 HOH TIP . H 6 HOH A 48 523 49 HOH TIP . H 6 HOH A 49 524 50 HOH TIP . H 6 HOH A 50 525 51 HOH TIP . H 6 HOH A 51 526 52 HOH TIP . H 6 HOH A 52 527 53 HOH TIP . H 6 HOH A 53 528 54 HOH TIP . H 6 HOH A 54 529 55 HOH TIP . H 6 HOH A 55 530 56 HOH TIP . H 6 HOH A 56 531 57 HOH TIP . H 6 HOH A 57 532 58 HOH TIP . H 6 HOH A 58 533 59 HOH TIP . H 6 HOH A 59 534 60 HOH TIP . H 6 HOH A 60 535 61 HOH TIP . H 6 HOH A 61 536 62 HOH TIP . H 6 HOH A 62 537 63 HOH TIP . H 6 HOH A 63 538 64 HOH TIP . H 6 HOH A 64 539 65 HOH TIP . H 6 HOH A 65 540 66 HOH TIP . H 6 HOH A 66 541 67 HOH TIP . H 6 HOH A 67 542 68 HOH TIP . H 6 HOH A 68 543 69 HOH TIP . H 6 HOH A 69 544 70 HOH TIP . H 6 HOH A 70 545 71 HOH TIP . H 6 HOH A 71 546 72 HOH TIP . H 6 HOH A 72 547 73 HOH TIP . H 6 HOH A 73 548 74 HOH TIP . H 6 HOH A 74 549 75 HOH TIP . H 6 HOH A 75 550 76 HOH TIP . H 6 HOH A 76 551 77 HOH TIP . H 6 HOH A 77 552 78 HOH TIP . H 6 HOH A 78 553 79 HOH TIP . H 6 HOH A 79 554 80 HOH TIP . H 6 HOH A 80 555 81 HOH TIP . H 6 HOH A 81 556 82 HOH TIP . H 6 HOH A 82 557 83 HOH TIP . H 6 HOH A 83 558 84 HOH TIP . H 6 HOH A 84 559 85 HOH TIP . H 6 HOH A 85 560 86 HOH TIP . H 6 HOH A 86 561 87 HOH TIP . H 6 HOH A 87 562 88 HOH TIP . H 6 HOH A 88 563 89 HOH TIP . H 6 HOH A 89 564 90 HOH TIP . H 6 HOH A 90 565 91 HOH TIP . H 6 HOH A 91 566 92 HOH TIP . H 6 HOH A 92 567 93 HOH TIP . H 6 HOH A 93 568 94 HOH TIP . H 6 HOH A 94 569 95 HOH TIP . H 6 HOH A 95 570 96 HOH TIP . H 6 HOH A 96 571 97 HOH TIP . H 6 HOH A 97 572 98 HOH TIP . H 6 HOH A 98 573 100 HOH TIP . H 6 HOH A 99 574 101 HOH TIP . H 6 HOH A 100 575 102 HOH TIP . H 6 HOH A 101 576 103 HOH TIP . H 6 HOH A 102 577 104 HOH TIP . H 6 HOH A 103 578 105 HOH TIP . H 6 HOH A 104 579 107 HOH TIP . H 6 HOH A 105 580 109 HOH TIP . H 6 HOH A 106 581 110 HOH TIP . H 6 HOH A 107 582 111 HOH TIP . H 6 HOH A 108 583 113 HOH TIP . H 6 HOH A 109 584 115 HOH TIP . H 6 HOH A 110 585 117 HOH TIP . H 6 HOH A 111 586 120 HOH TIP . H 6 HOH A 112 587 122 HOH TIP . H 6 HOH A 113 588 123 HOH TIP . H 6 HOH A 114 589 124 HOH TIP . H 6 HOH A 115 590 126 HOH TIP . H 6 HOH A 116 591 128 HOH TIP . H 6 HOH A 117 592 129 HOH TIP . H 6 HOH A 118 593 130 HOH TIP . H 6 HOH A 119 594 131 HOH TIP . H 6 HOH A 120 595 132 HOH TIP . H 6 HOH A 121 596 135 HOH TIP . H 6 HOH A 122 597 136 HOH TIP . H 6 HOH A 123 598 138 HOH TIP . H 6 HOH A 124 599 140 HOH TIP . H 6 HOH A 125 600 141 HOH TIP . H 6 HOH A 126 601 144 HOH TIP . H 6 HOH A 127 602 146 HOH TIP . H 6 HOH A 128 603 150 HOH TIP . H 6 HOH A 129 604 151 HOH TIP . H 6 HOH A 130 605 153 HOH TIP . H 6 HOH A 131 606 154 HOH TIP . H 6 HOH A 132 607 156 HOH TIP . H 6 HOH A 133 608 157 HOH TIP . H 6 HOH A 134 609 160 HOH TIP . H 6 HOH A 135 610 163 HOH TIP . H 6 HOH A 136 611 165 HOH TIP . H 6 HOH A 137 612 166 HOH TIP . H 6 HOH A 138 613 167 HOH TIP . H 6 HOH A 139 614 168 HOH TIP . H 6 HOH A 140 615 169 HOH TIP . H 6 HOH A 141 616 170 HOH TIP . H 6 HOH A 142 617 171 HOH TIP . H 6 HOH A 143 618 172 HOH TIP . H 6 HOH A 144 619 174 HOH TIP . H 6 HOH A 145 620 175 HOH TIP . # 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 . . . G 5 9.908 51.626 47.372 1 38.42 ? N1 UDP 475 A 1 HETATM 2 C C2 UDP . . . G 5 8.842 50.751 47.644 1 39.02 ? C2 UDP 475 A 1 HETATM 3 N N3 UDP . . . G 5 8.423 50.663 48.961 1 39 ? N3 UDP 475 A 1 HETATM 4 C C4 UDP . . . G 5 8.95 51.357 50.064 1 40.68 ? C4 UDP 475 A 1 HETATM 5 C C5 UDP . . . G 5 10.149 52.335 49.722 1 40.54 ? C5 UDP 475 A 1 HETATM 6 C C6 UDP . . . G 5 10.514 52.378 48.417 1 40.31 ? C6 UDP 475 A 1 HETATM 7 O O2 UDP . . . G 5 8.291 50.081 46.759 1 33.41 ? O2 UDP 475 A 1 HETATM 8 O O4 UDP . . . G 5 8.45 51.153 51.171 1 41.64 ? O4 UDP 475 A 1 HETATM 9 C C1' UDP . . . G 5 10.394 51.75 45.96 1 40.1 ? C1' UDP 475 A 1 HETATM 10 C C2' UDP . . . G 5 9.514 52.601 45.017 1 39.51 ? C2' UDP 475 A 1 HETATM 11 O O2' UDP . . . G 5 9.403 51.989 43.752 1 40.07 ? O2' UDP 475 A 1 HETATM 12 C C3' UDP . . . G 5 10.262 53.938 44.966 1 39.87 ? C3' UDP 475 A 1 HETATM 13 C C4' UDP . . . G 5 11.699 53.49 45.011 1 40.69 ? C4' UDP 475 A 1 HETATM 14 O O4' UDP . . . G 5 11.693 52.374 45.943 1 40.2 ? O4' UDP 475 A 1 HETATM 15 O O3' UDP . . . G 5 9.963 54.565 43.717 1 39.12 ? O3' UDP 475 A 1 HETATM 16 C C5' UDP . . . G 5 12.668 54.562 45.534 1 41.62 ? C5' UDP 475 A 1 HETATM 17 O O5' UDP . . . G 5 12.171 55.08 46.759 1 44.08 ? O5' UDP 475 A 1 HETATM 18 P PA UDP . . . G 5 11.58 56.48 47.182 1 45.61 ? PA UDP 475 A 1 HETATM 19 O O1A UDP . . . G 5 10.469 56.819 46.251 1 46.97 ? O1A UDP 475 A 1 HETATM 20 O O2A UDP . . . G 5 11.232 56.387 48.64 1 46.93 ? O2A UDP 475 A 1 HETATM 21 O O3A UDP . . . G 5 12.874 57.333 46.841 1 46.4 ? O3A UDP 475 A 1 HETATM 22 P PB UDP . . . G 5 13.073 58.831 46.332 1 46.74 ? PB UDP 475 A 1 HETATM 23 O O1B UDP . . . G 5 14.624 59.142 46.654 1 46.89 ? O1B UDP 475 A 1 HETATM 24 O O2B UDP . . . G 5 12.132 59.568 47.207 1 47.43 ? O2B UDP 475 A 1 HETATM 25 O O3B UDP . . . G 5 12.983 58.989 44.858 1 47.37 ? O3B UDP 475 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 25 #