data_4FRE
#
_model_server_result.job_id            5d_00nik7kMehQzHK48ZBQ 
_model_server_result.datetime_utc      '2024-10-13 09:14:25' 
_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          4fre 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    4FRE 
#
_exptl.entry_id    4FRE 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              404.161 
_entity.id                          2 
_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            4FRE 
_cell.length_a            52.296 
_cell.length_b            150.809 
_cell.length_c            79.532 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4FRE 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_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 
_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' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 52.296 0 39.766 
#
_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 
#
_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 398 n n 
N1 C6 UDP sing 399 n n 
N1 C1' UDP sing 400 n n 
C2 N3 UDP sing 401 n n 
C2 O2 UDP doub 402 n n 
N3 C4 UDP sing 403 n n 
N3 HN3 UDP sing 404 n n 
C4 C5 UDP sing 405 n n 
C4 O4 UDP doub 406 n n 
C5 C6 UDP doub 407 n n 
C5 H5 UDP sing 408 n n 
C6 H6 UDP sing 409 n n 
C1' C2' UDP sing 410 n n 
C1' O4' UDP sing 411 n n 
C1' H1' UDP sing 412 n n 
C2' O2' UDP sing 413 n n 
C2' C3' UDP sing 414 n n 
C2' H2' UDP sing 415 n n 
O2' HO2' UDP sing 416 n n 
C3' C4' UDP sing 417 n n 
C3' O3' UDP sing 418 n n 
C3' H3' UDP sing 419 n n 
C4' O4' UDP sing 420 n n 
C4' C5' UDP sing 421 n n 
C4' H4' UDP sing 422 n n 
O3' HO3' UDP sing 423 n n 
C5' O5' UDP sing 424 n n 
C5' "H5'1" UDP sing 425 n n 
C5' "H5'2" UDP sing 426 n n 
O5' PA UDP sing 427 n n 
PA O1A UDP doub 428 n n 
PA O2A UDP sing 429 n n 
PA O3A UDP sing 430 n n 
O2A HOA2 UDP sing 431 n n 
O3A PB UDP sing 432 n n 
PB O1B UDP doub 433 n n 
PB O2B UDP sing 434 n n 
PB O3B UDP sing 435 n n 
O2B HOB2 UDP sing 436 n n 
O3B HOB3 UDP sing 437 n n 
#
_atom_sites.entry_id                     4FRE 
_atom_sites.fract_transf_matrix[1][1]    0.019122 
_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]    0.006631 
_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]    0.012574 
_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 UDP A 1 401 1 UDP UDP . 
C 3 GAL A 1 402 2 GAL GAL . 
D 4 PEG A 1 403 3 PEG PEG . 
E 5 HOH A 1 501 1 HOH HOH . 
E 5 HOH A 2 502 2 HOH HOH . 
E 5 HOH A 3 503 3 HOH HOH . 
E 5 HOH A 4 504 4 HOH HOH . 
E 5 HOH A 5 505 5 HOH HOH . 
E 5 HOH A 6 506 6 HOH HOH . 
E 5 HOH A 7 507 7 HOH HOH . 
E 5 HOH A 8 508 8 HOH HOH . 
E 5 HOH A 9 509 9 HOH HOH . 
E 5 HOH A 10 510 10 HOH HOH . 
E 5 HOH A 11 511 11 HOH HOH . 
E 5 HOH A 12 512 12 HOH HOH . 
E 5 HOH A 13 513 13 HOH HOH . 
E 5 HOH A 14 514 14 HOH HOH . 
E 5 HOH A 15 515 15 HOH HOH . 
E 5 HOH A 16 516 16 HOH HOH . 
E 5 HOH A 17 517 17 HOH HOH . 
E 5 HOH A 18 518 18 HOH HOH . 
E 5 HOH A 19 519 19 HOH HOH . 
E 5 HOH A 20 520 20 HOH HOH . 
E 5 HOH A 21 521 21 HOH HOH . 
E 5 HOH A 22 522 22 HOH HOH . 
E 5 HOH A 23 523 23 HOH HOH . 
E 5 HOH A 24 524 24 HOH HOH . 
E 5 HOH A 25 525 25 HOH HOH . 
E 5 HOH A 26 526 26 HOH HOH . 
E 5 HOH A 27 527 27 HOH HOH . 
E 5 HOH A 28 528 28 HOH HOH . 
E 5 HOH A 29 529 29 HOH HOH . 
E 5 HOH A 30 530 30 HOH HOH . 
E 5 HOH A 31 531 31 HOH HOH . 
E 5 HOH A 32 532 32 HOH HOH . 
E 5 HOH A 33 533 33 HOH HOH . 
E 5 HOH A 34 534 34 HOH HOH . 
E 5 HOH A 35 535 35 HOH HOH . 
E 5 HOH A 36 536 36 HOH HOH . 
E 5 HOH A 37 537 37 HOH HOH . 
E 5 HOH A 38 538 38 HOH HOH . 
E 5 HOH A 39 539 39 HOH HOH . 
E 5 HOH A 40 540 40 HOH HOH . 
E 5 HOH A 41 541 41 HOH HOH . 
E 5 HOH A 42 542 42 HOH HOH . 
E 5 HOH A 43 543 43 HOH HOH . 
E 5 HOH A 44 544 44 HOH HOH . 
E 5 HOH A 45 545 45 HOH HOH . 
E 5 HOH A 46 546 46 HOH HOH . 
E 5 HOH A 47 547 47 HOH HOH . 
E 5 HOH A 48 548 48 HOH HOH . 
E 5 HOH A 49 549 49 HOH HOH . 
E 5 HOH A 50 550 50 HOH HOH . 
E 5 HOH A 51 551 51 HOH HOH . 
E 5 HOH A 52 552 52 HOH HOH . 
E 5 HOH A 53 553 53 HOH HOH . 
E 5 HOH A 54 554 54 HOH HOH . 
E 5 HOH A 55 555 55 HOH HOH . 
E 5 HOH A 56 556 56 HOH HOH . 
E 5 HOH A 57 557 57 HOH HOH . 
E 5 HOH A 58 558 58 HOH HOH . 
E 5 HOH A 59 559 59 HOH HOH . 
E 5 HOH A 60 560 60 HOH HOH . 
E 5 HOH A 61 561 61 HOH HOH . 
E 5 HOH A 62 562 62 HOH HOH . 
E 5 HOH A 63 563 63 HOH HOH . 
E 5 HOH A 64 564 64 HOH HOH . 
E 5 HOH A 65 565 65 HOH HOH . 
E 5 HOH A 66 566 66 HOH HOH . 
E 5 HOH A 67 567 67 HOH HOH . 
E 5 HOH A 68 568 68 HOH HOH . 
E 5 HOH A 69 569 69 HOH HOH . 
E 5 HOH A 70 570 70 HOH HOH . 
E 5 HOH A 71 571 71 HOH HOH . 
E 5 HOH A 72 572 72 HOH HOH . 
E 5 HOH A 73 573 73 HOH HOH . 
E 5 HOH A 74 574 74 HOH HOH . 
E 5 HOH A 75 575 75 HOH HOH . 
E 5 HOH A 76 576 76 HOH HOH . 
E 5 HOH A 77 577 77 HOH HOH . 
E 5 HOH A 78 578 78 HOH HOH . 
E 5 HOH A 79 579 79 HOH HOH . 
E 5 HOH A 80 580 80 HOH HOH . 
E 5 HOH A 81 581 81 HOH HOH . 
E 5 HOH A 82 582 82 HOH HOH . 
E 5 HOH A 83 583 83 HOH HOH . 
E 5 HOH A 84 584 84 HOH HOH . 
E 5 HOH A 85 585 85 HOH HOH . 
E 5 HOH A 86 586 86 HOH HOH . 
E 5 HOH A 87 587 87 HOH HOH . 
E 5 HOH A 88 588 88 HOH HOH . 
E 5 HOH A 89 589 89 HOH HOH . 
E 5 HOH A 90 590 90 HOH HOH . 
E 5 HOH A 91 591 91 HOH HOH . 
E 5 HOH A 92 592 92 HOH HOH . 
E 5 HOH A 93 593 93 HOH HOH . 
E 5 HOH A 94 594 94 HOH HOH . 
E 5 HOH A 95 595 95 HOH HOH . 
E 5 HOH A 96 596 96 HOH HOH . 
E 5 HOH A 97 597 97 HOH HOH . 
E 5 HOH A 98 598 98 HOH HOH . 
E 5 HOH A 99 599 99 HOH HOH . 
E 5 HOH A 100 600 100 HOH HOH . 
E 5 HOH A 101 601 101 HOH HOH . 
E 5 HOH A 102 602 102 HOH HOH . 
E 5 HOH A 103 603 103 HOH HOH . 
E 5 HOH A 104 604 104 HOH HOH . 
E 5 HOH A 105 605 105 HOH HOH . 
E 5 HOH A 106 606 106 HOH HOH . 
E 5 HOH A 107 607 107 HOH HOH . 
E 5 HOH A 108 608 108 HOH HOH . 
E 5 HOH A 109 609 109 HOH HOH . 
E 5 HOH A 110 610 110 HOH HOH . 
E 5 HOH A 111 611 111 HOH HOH . 
E 5 HOH A 112 612 112 HOH HOH . 
E 5 HOH A 113 613 113 HOH HOH . 
E 5 HOH A 114 614 114 HOH HOH . 
E 5 HOH A 115 615 115 HOH HOH . 
E 5 HOH A 116 616 116 HOH HOH . 
E 5 HOH A 117 617 117 HOH HOH . 
E 5 HOH A 118 618 118 HOH HOH . 
E 5 HOH A 119 619 119 HOH HOH . 
E 5 HOH A 120 620 120 HOH HOH . 
E 5 HOH A 121 621 121 HOH HOH . 
E 5 HOH A 122 622 122 HOH HOH . 
E 5 HOH A 123 623 123 HOH HOH . 
E 5 HOH A 124 624 124 HOH HOH . 
E 5 HOH A 125 625 125 HOH HOH . 
E 5 HOH A 126 626 126 HOH HOH . 
E 5 HOH A 127 627 127 HOH HOH . 
E 5 HOH A 128 628 128 HOH HOH . 
E 5 HOH A 129 629 129 HOH HOH . 
E 5 HOH A 130 630 130 HOH HOH . 
E 5 HOH A 131 631 131 HOH HOH . 
E 5 HOH A 132 632 132 HOH HOH . 
E 5 HOH A 133 633 133 HOH HOH . 
E 5 HOH A 134 634 134 HOH HOH . 
E 5 HOH A 135 635 135 HOH HOH . 
E 5 HOH A 136 636 136 HOH HOH . 
E 5 HOH A 137 637 137 HOH HOH . 
E 5 HOH A 138 638 138 HOH HOH . 
E 5 HOH A 139 639 139 HOH HOH . 
E 5 HOH A 140 640 140 HOH HOH . 
E 5 HOH A 141 641 141 HOH HOH . 
E 5 HOH A 142 642 142 HOH HOH . 
E 5 HOH A 143 643 143 HOH HOH . 
E 5 HOH A 144 644 144 HOH HOH . 
E 5 HOH A 145 645 145 HOH HOH . 
E 5 HOH A 146 646 146 HOH HOH . 
E 5 HOH A 147 647 147 HOH HOH . 
E 5 HOH A 148 648 148 HOH HOH . 
E 5 HOH A 149 649 149 HOH HOH . 
E 5 HOH A 150 650 150 HOH HOH . 
E 5 HOH A 151 651 151 HOH HOH . 
E 5 HOH A 152 652 152 HOH HOH . 
E 5 HOH A 153 653 153 HOH HOH . 
E 5 HOH A 154 654 154 HOH HOH . 
E 5 HOH A 155 655 155 HOH HOH . 
E 5 HOH A 156 656 156 HOH HOH . 
E 5 HOH A 157 657 157 HOH HOH . 
E 5 HOH A 158 658 158 HOH HOH . 
E 5 HOH A 159 659 159 HOH HOH . 
E 5 HOH A 160 660 160 HOH HOH . 
E 5 HOH A 161 661 161 HOH HOH . 
E 5 HOH A 162 662 162 HOH HOH . 
E 5 HOH A 163 663 163 HOH HOH . 
E 5 HOH A 164 664 164 HOH HOH . 
E 5 HOH A 165 665 165 HOH HOH . 
E 5 HOH A 166 666 166 HOH HOH . 
E 5 HOH A 167 667 167 HOH HOH . 
E 5 HOH A 168 668 168 HOH HOH . 
E 5 HOH A 169 669 169 HOH HOH . 
E 5 HOH A 170 670 170 HOH HOH . 
E 5 HOH A 171 671 171 HOH HOH . 
E 5 HOH A 172 672 172 HOH HOH . 
E 5 HOH A 173 673 173 HOH HOH . 
E 5 HOH A 174 674 174 HOH HOH . 
E 5 HOH A 175 675 175 HOH HOH . 
E 5 HOH A 176 676 176 HOH HOH . 
E 5 HOH A 177 677 177 HOH HOH . 
E 5 HOH A 178 678 178 HOH HOH . 
E 5 HOH A 179 679 179 HOH HOH . 
E 5 HOH A 180 680 181 HOH HOH . 
E 5 HOH A 181 681 182 HOH HOH . 
E 5 HOH A 182 682 183 HOH HOH . 
E 5 HOH A 183 683 184 HOH HOH . 
E 5 HOH A 184 684 185 HOH HOH . 
E 5 HOH A 185 685 186 HOH HOH . 
E 5 HOH A 186 686 187 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 . . . B 2 10.163 23.645 -7.879 1 41.49 ? N1 UDP 401 A 1 
HETATM 2 C C2 UDP . . . B 2 8.923 24.258 -8.129 1 44.88 ? C2 UDP 401 A 1 
HETATM 3 N N3 UDP . . . B 2 8.415 24.261 -9.484 1 45.12 ? N3 UDP 401 A 1 
HETATM 4 C C4 UDP . . . B 2 9.136 23.666 -10.575 1 53.4 ? C4 UDP 401 A 1 
HETATM 5 C C5 UDP . . . B 2 10.394 23.07 -10.275 1 52.19 ? C5 UDP 401 A 1 
HETATM 6 C C6 UDP . . . B 2 10.896 23.067 -8.95 1 47.31 ? C6 UDP 401 A 1 
HETATM 7 O O2 UDP . . . B 2 8.288 24.778 -7.188 1 27.28 ? O2 UDP 401 A 1 
HETATM 8 O O4 UDP . . . B 2 8.63 23.682 -11.73 1 44.81 ? O4 UDP 401 A 1 
HETATM 9 C C1' UDP . . . B 2 10.656 23.684 -6.437 1 44.74 ? C1' UDP 401 A 1 
HETATM 10 C C2' UDP . . . B 2 9.76 22.777 -5.61 1 36.19 ? C2' UDP 401 A 1 
HETATM 11 O O2' UDP . . . B 2 9.817 22.922 -4.177 1 31.52 ? O2' UDP 401 A 1 
HETATM 12 C C3' UDP . . . B 2 10.456 21.463 -5.868 1 36.14 ? C3' UDP 401 A 1 
HETATM 13 C C4' UDP . . . B 2 11.959 21.735 -5.88 1 39.7 ? C4' UDP 401 A 1 
HETATM 14 O O4' UDP . . . B 2 12.047 23.15 -6.298 1 45.07 ? O4' UDP 401 A 1 
HETATM 15 O O3' UDP . . . B 2 10.176 20.706 -4.706 1 43.48 ? O3' UDP 401 A 1 
HETATM 16 C C5' UDP . . . B 2 12.928 20.739 -6.721 1 35.08 ? C5' UDP 401 A 1 
HETATM 17 O O5' UDP . . . B 2 12.567 20.632 -8.076 0.1 31.77 ? O5' UDP 401 A 1 
HETATM 18 P PA UDP . . . B 2 12.81 19.251 -8.82 0.1 29.18 ? PA UDP 401 A 1 
HETATM 19 O O1A UDP . . . B 2 11.516 18.814 -9.382 0.1 27.41 ? O1A UDP 401 A 1 
HETATM 20 O O2A UDP . . . B 2 13.977 19.403 -9.709 0.1 28.26 ? O2A UDP 401 A 1 
HETATM 21 O O3A UDP . . . B 2 13.175 18.309 -7.611 0.1 27.65 ? O3A UDP 401 A 1 
HETATM 22 P PB UDP . . . B 2 12.053 17.44 -6.885 0.1 27.84 ? PB UDP 401 A 1 
HETATM 23 O O1B UDP . . . B 2 11.078 16.843 -8.009 0.1 26.28 ? O1B UDP 401 A 1 
HETATM 24 O O2B UDP . . . B 2 12.866 16.184 -6.277 0.1 26.61 ? O2B UDP 401 A 1 
HETATM 25 O O3B UDP . . . B 2 11.303 18.183 -5.821 0.1 26.23 ? O3B UDP 401 A 1 
HETATM 26 H HN3 UDP . . . B 2 7.528 24.675 -9.669 1 45.12 ? HN3 UDP 401 A 1 
HETATM 27 H H5 UDP . . . B 2 10.978 22.773 -11.031 1 50.63 ? H5 UDP 401 A 1 
HETATM 28 H H6 UDP . . . B 2 11.866 23.281 -9.066 1 45.43 ? H6 UDP 401 A 1 
HETATM 29 H H1' UDP . . . B 2 10.568 24.515 -5.886 1 43.82 ? H1' UDP 401 A 1 
HETATM 30 H H2' UDP . . . B 2 8.775 22.623 -5.531 1 36.17 ? H2' UDP 401 A 1 
HETATM 31 H HO2' UDP . . . B 2 10.442 23.662 -4.097 0 31.24 ? HO2' UDP 401 A 1 
HETATM 32 H H3' UDP . . . B 2 10.173 21.102 -6.757 1 37.21 ? H3' UDP 401 A 1 
HETATM 33 H H4' UDP . . . B 2 12.477 22.153 -5.134 1 38.21 ? H4' UDP 401 A 1 
HETATM 34 H HO3' UDP . . . B 2 9.666 21.309 -4.25 0 38.64 ? HO3' UDP 401 A 1 
HETATM 35 H "H5'1" UDP . . . B 2 13.845 21.131 -6.649 1 34.02 ? "H5'1" UDP 401 A 1 
HETATM 36 H "H5'2" UDP . . . B 2 12.294 20.241 -6.139 1 33.8 ? "H5'2" UDP 401 A 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           288 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           36 
#