data_4XSU # _model_server_result.job_id dcmtOJ86sbdmoJJmBPbX3A _model_server_result.datetime_utc '2025-07-13 16:55:07' _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 4xsu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 4XSU # _exptl.entry_id 4XSU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-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 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 4XSU _cell.length_a 130.991 _cell.length_b 130.991 _cell.length_c 156.327 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XSU _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 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,H,I,J,K,L,M,N,O,P,Q,R _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 ? 3 D N N ? 3 K N N # _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 399 n n N1 C6 UDP sing 400 n n N1 C1' UDP sing 401 n n C2 N3 UDP sing 402 n n C2 O2 UDP doub 403 n n N3 C4 UDP sing 404 n n N3 HN3 UDP sing 405 n n C4 C5 UDP sing 406 n n C4 O4 UDP doub 407 n n C5 C6 UDP doub 408 n n C5 H5 UDP sing 409 n n C6 H6 UDP sing 410 n n C1' C2' UDP sing 411 n n C1' O4' UDP sing 412 n n C1' H1' UDP sing 413 n n C2' O2' UDP sing 414 n n C2' C3' UDP sing 415 n n C2' H2' UDP sing 416 n n O2' HO2' UDP sing 417 n n C3' C4' UDP sing 418 n n C3' O3' UDP sing 419 n n C3' H3' UDP sing 420 n n C4' O4' UDP sing 421 n n C4' C5' UDP sing 422 n n C4' H4' UDP sing 423 n n O3' HO3' UDP sing 424 n n C5' O5' UDP sing 425 n n C5' "H5'1" UDP sing 426 n n C5' "H5'2" UDP sing 427 n n O5' PA UDP sing 428 n n PA O1A UDP doub 429 n n PA O2A UDP sing 430 n n PA O3A UDP sing 431 n n O2A HOA2 UDP sing 432 n n O3A PB UDP sing 433 n n PB O1B UDP doub 434 n n PB O2B UDP sing 435 n n PB O3B UDP sing 436 n n O2B HOB2 UDP sing 437 n n O3B HOB3 UDP sing 438 n n # _atom_sites.entry_id 4XSU _atom_sites.fract_transf_matrix[1][1] 0.007634 _atom_sites.fract_transf_matrix[1][2] 0.004408 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008815 _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] 0.006397 _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 GLC B 1 401 1 GLC GLC . D 3 UDP B 1 402 402 UDP UDP . E 4 SO4 B 1 403 403 SO4 SO4 . F 4 SO4 B 1 404 404 SO4 SO4 . G 4 SO4 B 1 405 405 SO4 SO4 . H 4 SO4 B 1 406 406 SO4 SO4 . I 4 SO4 B 1 407 407 SO4 SO4 . J 2 GLC A 1 401 2 GLC GLC . K 3 UDP A 1 402 402 UDP UDP . L 4 SO4 A 1 403 403 SO4 SO4 . M 4 SO4 A 1 404 404 SO4 SO4 . N 4 SO4 A 1 405 405 SO4 SO4 . O 4 SO4 A 1 406 406 SO4 SO4 . P 5 GOL A 1 407 407 GOL GOL . Q 6 HOH B 1 501 501 HOH HOH . Q 6 HOH B 2 502 503 HOH HOH . Q 6 HOH B 3 503 502 HOH HOH . Q 6 HOH B 4 504 505 HOH HOH . Q 6 HOH B 5 505 507 HOH HOH . Q 6 HOH B 6 506 509 HOH HOH . Q 6 HOH B 7 507 506 HOH HOH . Q 6 HOH B 8 508 511 HOH HOH . Q 6 HOH B 9 509 504 HOH HOH . Q 6 HOH B 10 510 514 HOH HOH . Q 6 HOH B 11 511 508 HOH HOH . Q 6 HOH B 12 512 510 HOH HOH . Q 6 HOH B 13 513 512 HOH HOH . Q 6 HOH B 14 514 513 HOH HOH . Q 6 HOH B 15 515 515 HOH HOH . Q 6 HOH B 16 516 516 HOH HOH . Q 6 HOH B 17 517 517 HOH HOH . Q 6 HOH B 18 518 518 HOH HOH . Q 6 HOH B 19 519 519 HOH HOH . Q 6 HOH B 20 520 520 HOH HOH . Q 6 HOH B 21 521 521 HOH HOH . Q 6 HOH B 22 522 522 HOH HOH . Q 6 HOH B 23 523 523 HOH HOH . Q 6 HOH B 24 524 524 HOH HOH . Q 6 HOH B 25 525 525 HOH HOH . Q 6 HOH B 26 526 526 HOH HOH . Q 6 HOH B 27 527 527 HOH HOH . Q 6 HOH B 28 528 528 HOH HOH . Q 6 HOH B 29 529 529 HOH HOH . Q 6 HOH B 30 530 530 HOH HOH . Q 6 HOH B 31 531 531 HOH HOH . Q 6 HOH B 32 532 532 HOH HOH . Q 6 HOH B 33 533 533 HOH HOH . Q 6 HOH B 34 534 534 HOH HOH . Q 6 HOH B 35 535 535 HOH HOH . Q 6 HOH B 36 536 536 HOH HOH . Q 6 HOH B 37 537 537 HOH HOH . Q 6 HOH B 38 538 538 HOH HOH . Q 6 HOH B 39 539 539 HOH HOH . Q 6 HOH B 40 540 540 HOH HOH . Q 6 HOH B 41 541 541 HOH HOH . Q 6 HOH B 42 542 542 HOH HOH . Q 6 HOH B 43 543 543 HOH HOH . Q 6 HOH B 44 544 544 HOH HOH . Q 6 HOH B 45 545 545 HOH HOH . Q 6 HOH B 46 546 546 HOH HOH . Q 6 HOH B 47 547 547 HOH HOH . Q 6 HOH B 48 548 548 HOH HOH . Q 6 HOH B 49 549 549 HOH HOH . Q 6 HOH B 50 550 550 HOH HOH . Q 6 HOH B 51 551 551 HOH HOH . Q 6 HOH B 52 552 552 HOH HOH . Q 6 HOH B 53 553 553 HOH HOH . Q 6 HOH B 54 554 554 HOH HOH . Q 6 HOH B 55 555 555 HOH HOH . Q 6 HOH B 56 556 556 HOH HOH . Q 6 HOH B 57 557 557 HOH HOH . Q 6 HOH B 58 558 558 HOH HOH . Q 6 HOH B 59 559 559 HOH HOH . Q 6 HOH B 60 560 560 HOH HOH . Q 6 HOH B 61 561 561 HOH HOH . Q 6 HOH B 62 562 562 HOH HOH . Q 6 HOH B 63 563 563 HOH HOH . Q 6 HOH B 64 564 564 HOH HOH . Q 6 HOH B 65 565 565 HOH HOH . Q 6 HOH B 66 566 566 HOH HOH . Q 6 HOH B 67 567 567 HOH HOH . Q 6 HOH B 68 568 568 HOH HOH . Q 6 HOH B 69 569 569 HOH HOH . Q 6 HOH B 70 570 570 HOH HOH . Q 6 HOH B 71 571 571 HOH HOH . Q 6 HOH B 72 572 572 HOH HOH . Q 6 HOH B 73 573 573 HOH HOH . Q 6 HOH B 74 574 574 HOH HOH . Q 6 HOH B 75 575 575 HOH HOH . Q 6 HOH B 76 576 576 HOH HOH . Q 6 HOH B 77 577 577 HOH HOH . Q 6 HOH B 78 578 578 HOH HOH . Q 6 HOH B 79 579 579 HOH HOH . Q 6 HOH B 80 580 580 HOH HOH . Q 6 HOH B 81 581 581 HOH HOH . Q 6 HOH B 82 582 582 HOH HOH . Q 6 HOH B 83 583 583 HOH HOH . Q 6 HOH B 84 584 584 HOH HOH . Q 6 HOH B 85 585 585 HOH HOH . Q 6 HOH B 86 586 586 HOH HOH . Q 6 HOH B 87 587 587 HOH HOH . Q 6 HOH B 88 588 588 HOH HOH . Q 6 HOH B 89 589 589 HOH HOH . Q 6 HOH B 90 590 590 HOH HOH . Q 6 HOH B 91 591 591 HOH HOH . Q 6 HOH B 92 592 592 HOH HOH . Q 6 HOH B 93 593 593 HOH HOH . Q 6 HOH B 94 594 594 HOH HOH . Q 6 HOH B 95 595 595 HOH HOH . Q 6 HOH B 96 596 596 HOH HOH . Q 6 HOH B 97 597 597 HOH HOH . Q 6 HOH B 98 598 598 HOH HOH . Q 6 HOH B 99 599 599 HOH HOH . Q 6 HOH B 100 600 600 HOH HOH . Q 6 HOH B 101 601 601 HOH HOH . Q 6 HOH B 102 602 602 HOH HOH . Q 6 HOH B 103 603 603 HOH HOH . Q 6 HOH B 104 604 604 HOH HOH . Q 6 HOH B 105 605 605 HOH HOH . Q 6 HOH B 106 606 606 HOH HOH . Q 6 HOH B 107 607 607 HOH HOH . Q 6 HOH B 108 608 608 HOH HOH . Q 6 HOH B 109 609 609 HOH HOH . Q 6 HOH B 110 610 610 HOH HOH . Q 6 HOH B 111 611 611 HOH HOH . Q 6 HOH B 112 612 612 HOH HOH . R 6 HOH A 1 501 505 HOH HOH . R 6 HOH A 2 502 501 HOH HOH . R 6 HOH A 3 503 504 HOH HOH . R 6 HOH A 4 504 502 HOH HOH . R 6 HOH A 5 505 509 HOH HOH . R 6 HOH A 6 506 506 HOH HOH . R 6 HOH A 7 507 507 HOH HOH . R 6 HOH A 8 508 503 HOH HOH . R 6 HOH A 9 509 511 HOH HOH . R 6 HOH A 10 510 515 HOH HOH . R 6 HOH A 11 511 512 HOH HOH . R 6 HOH A 12 512 514 HOH HOH . R 6 HOH A 13 513 518 HOH HOH . R 6 HOH A 14 514 510 HOH HOH . R 6 HOH A 15 515 516 HOH HOH . R 6 HOH A 16 516 517 HOH HOH . R 6 HOH A 17 517 520 HOH HOH . R 6 HOH A 18 518 522 HOH HOH . R 6 HOH A 19 519 519 HOH HOH . R 6 HOH A 20 520 521 HOH HOH . R 6 HOH A 21 521 525 HOH HOH . R 6 HOH A 22 522 523 HOH HOH . R 6 HOH A 23 523 524 HOH HOH . R 6 HOH A 24 524 513 HOH HOH . R 6 HOH A 25 525 526 HOH HOH . R 6 HOH A 26 526 527 HOH HOH . R 6 HOH A 27 527 508 HOH HOH . R 6 HOH A 28 528 528 HOH HOH . R 6 HOH A 29 529 529 HOH HOH . R 6 HOH A 30 530 530 HOH HOH . R 6 HOH A 31 531 531 HOH HOH . R 6 HOH A 32 532 532 HOH HOH . R 6 HOH A 33 533 533 HOH HOH . R 6 HOH A 34 534 534 HOH HOH . R 6 HOH A 35 535 535 HOH HOH . R 6 HOH A 36 536 536 HOH HOH . R 6 HOH A 37 537 537 HOH HOH . R 6 HOH A 38 538 538 HOH HOH . R 6 HOH A 39 539 539 HOH HOH . R 6 HOH A 40 540 540 HOH HOH . R 6 HOH A 41 541 541 HOH HOH . R 6 HOH A 42 542 542 HOH HOH . R 6 HOH A 43 543 543 HOH HOH . R 6 HOH A 44 544 544 HOH HOH . R 6 HOH A 45 545 545 HOH HOH . R 6 HOH A 46 546 546 HOH HOH . R 6 HOH A 47 547 547 HOH HOH . R 6 HOH A 48 548 548 HOH HOH . R 6 HOH A 49 549 549 HOH HOH . R 6 HOH A 50 550 550 HOH HOH . R 6 HOH A 51 551 551 HOH HOH . R 6 HOH A 52 552 552 HOH HOH . R 6 HOH A 53 553 553 HOH HOH . R 6 HOH A 54 554 554 HOH HOH . R 6 HOH A 55 555 555 HOH HOH . R 6 HOH A 56 556 556 HOH HOH . R 6 HOH A 57 557 557 HOH HOH . R 6 HOH A 58 558 558 HOH HOH . R 6 HOH A 59 559 559 HOH HOH . R 6 HOH A 60 560 560 HOH HOH . R 6 HOH A 61 561 561 HOH HOH . R 6 HOH A 62 562 562 HOH HOH . R 6 HOH A 63 563 563 HOH HOH . R 6 HOH A 64 564 564 HOH HOH . R 6 HOH A 65 565 565 HOH HOH . R 6 HOH A 66 566 566 HOH HOH . R 6 HOH A 67 567 567 HOH HOH . R 6 HOH A 68 568 568 HOH HOH . R 6 HOH A 69 569 569 HOH HOH . R 6 HOH A 70 570 570 HOH HOH . R 6 HOH A 71 571 571 HOH HOH . R 6 HOH A 72 572 572 HOH HOH . R 6 HOH A 73 573 573 HOH HOH . R 6 HOH A 74 574 574 HOH HOH . R 6 HOH A 75 575 575 HOH HOH . R 6 HOH A 76 576 576 HOH HOH . R 6 HOH A 77 577 577 HOH HOH . R 6 HOH A 78 578 578 HOH HOH . R 6 HOH A 79 579 579 HOH HOH . R 6 HOH A 80 580 580 HOH HOH . R 6 HOH A 81 581 581 HOH HOH . R 6 HOH A 82 582 582 HOH HOH . R 6 HOH A 83 583 583 HOH HOH . R 6 HOH A 84 584 584 HOH HOH . R 6 HOH A 85 585 585 HOH HOH . R 6 HOH A 86 586 586 HOH HOH . R 6 HOH A 87 587 587 HOH HOH . R 6 HOH A 88 588 588 HOH HOH . R 6 HOH A 89 589 589 HOH HOH . R 6 HOH A 90 590 590 HOH HOH . R 6 HOH A 91 591 591 HOH HOH . R 6 HOH A 92 592 592 HOH HOH . R 6 HOH A 93 593 593 HOH HOH . R 6 HOH A 94 594 594 HOH HOH . R 6 HOH A 95 595 595 HOH HOH . R 6 HOH A 96 596 596 HOH HOH . R 6 HOH A 97 597 597 HOH HOH . R 6 HOH A 98 598 598 HOH HOH . R 6 HOH A 99 599 599 HOH HOH . R 6 HOH A 100 600 600 HOH HOH . R 6 HOH A 101 601 601 HOH HOH . R 6 HOH A 102 602 602 HOH HOH . R 6 HOH A 103 603 603 HOH HOH . R 6 HOH A 104 604 604 HOH HOH . R 6 HOH A 105 605 605 HOH HOH . R 6 HOH A 106 606 606 HOH HOH . R 6 HOH A 107 607 607 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 3 23.162 -42.152 6.172 1 36.06 ? N1 UDP 402 B 1 HETATM 2 C C2 UDP . . . D 3 22.881 -40.835 5.754 1 36.17 ? C2 UDP 402 B 1 HETATM 3 N N3 UDP . . . D 3 22.811 -40.541 4.45 1 38.83 ? N3 UDP 402 B 1 HETATM 4 C C4 UDP . . . D 3 23.006 -41.488 3.526 1 37.47 ? C4 UDP 402 B 1 HETATM 5 C C5 UDP . . . D 3 23.285 -42.794 3.912 1 34.17 ? C5 UDP 402 B 1 HETATM 6 C C6 UDP . . . D 3 23.36 -43.11 5.262 1 35.83 ? C6 UDP 402 B 1 HETATM 7 O O2 UDP . . . D 3 22.696 -39.938 6.605 1 39.63 ? O2 UDP 402 B 1 HETATM 8 O O4 UDP . . . D 3 22.938 -41.198 2.312 1 40.59 ? O4 UDP 402 B 1 HETATM 9 C C1' UDP . . . D 3 23.238 -42.468 7.6 1 39.94 ? C1' UDP 402 B 1 HETATM 10 C C2' UDP . . . D 3 22.097 -43.399 7.979 1 41.55 ? C2' UDP 402 B 1 HETATM 11 O O2' UDP . . . D 3 21.293 -42.799 8.999 1 39.67 ? O2' UDP 402 B 1 HETATM 12 C C3' UDP . . . D 3 22.74 -44.667 8.503 1 38.81 ? C3' UDP 402 B 1 HETATM 13 C C4' UDP . . . D 3 24.242 -44.451 8.418 1 43.05 ? C4' UDP 402 B 1 HETATM 14 O O4' UDP . . . D 3 24.466 -43.145 7.879 1 43.19 ? O4' UDP 402 B 1 HETATM 15 O O3' UDP . . . D 3 22.352 -44.888 9.862 1 32.55 ? O3' UDP 402 B 1 HETATM 16 C C5' UDP . . . D 3 24.902 -45.495 7.527 1 42.61 ? C5' UDP 402 B 1 HETATM 17 O O5' UDP . . . D 3 25.587 -46.447 8.337 1 42.59 ? O5' UDP 402 B 1 HETATM 18 P PA UDP . . . D 3 25.499 -48.02 8.003 1 42.95 ? PA UDP 402 B 1 HETATM 19 O O1A UDP . . . D 3 24.193 -48.278 7.29 1 52.73 ? O1A UDP 402 B 1 HETATM 20 O O2A UDP . . . D 3 25.838 -48.789 9.258 1 42.66 ? O2A UDP 402 B 1 HETATM 21 O O3A UDP . . . D 3 26.698 -48.223 6.948 1 51.78 ? O3A UDP 402 B 1 HETATM 22 P PB UDP . . . D 3 28.219 -47.905 7.369 1 46.49 ? PB UDP 402 B 1 HETATM 23 O O1B UDP . . . D 3 28.605 -46.742 6.485 1 52.65 ? O1B UDP 402 B 1 HETATM 24 O O2B UDP . . . D 3 28.128 -47.568 8.838 1 44.97 ? O2B UDP 402 B 1 HETATM 25 O O3B UDP . . . D 3 28.956 -49.188 7.068 1 47.04 ? O3B UDP 402 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #