data_4FRQ
#
_model_server_result.job_id            jbOKwnnvPQz3gzlvwCMhBw 
_model_server_result.datetime_utc      '2024-11-07 09:53:56' 
_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          4frq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    4FRQ 
#
_exptl.entry_id    4FRQ 
_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            4FRQ 
_cell.length_a            52.307 
_cell.length_b            151.386 
_cell.length_c            79.397 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4FRQ 
_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,F 
_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 52.307 0 39.6985 
#
_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 
#
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 149 A ASP 211 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? 
metalc ? metalc2 A OD1 ASP 151 A ASP 213 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc3 A OD2 ASP 151 A ASP 213 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? 
metalc ? metalc4 B O3B UDP . A UDP 401 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? 
metalc ? metalc5 B O1A UDP . A UDP 401 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? 
#
_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                     4FRQ 
_atom_sites.fract_transf_matrix[1][1]    0.019118 
_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]    0.006606 
_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]    0.012595 
_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 PEG A 1 402 1 PEG PEG . 
D 4 MN A 1 403 1 MN MN . 
E 5 GAL A 1 404 2 GAL GAL . 
F 6 HOH A 1 501 1 HOH HOH . 
F 6 HOH A 2 502 2 HOH HOH . 
F 6 HOH A 3 503 3 HOH HOH . 
F 6 HOH A 4 504 4 HOH HOH . 
F 6 HOH A 5 505 5 HOH HOH . 
F 6 HOH A 6 506 6 HOH HOH . 
F 6 HOH A 7 507 7 HOH HOH . 
F 6 HOH A 8 508 8 HOH HOH . 
F 6 HOH A 9 509 9 HOH HOH . 
F 6 HOH A 10 510 10 HOH HOH . 
F 6 HOH A 11 511 11 HOH HOH . 
F 6 HOH A 12 512 12 HOH HOH . 
F 6 HOH A 13 513 13 HOH HOH . 
F 6 HOH A 14 514 14 HOH HOH . 
F 6 HOH A 15 515 15 HOH HOH . 
F 6 HOH A 16 516 16 HOH HOH . 
F 6 HOH A 17 517 17 HOH HOH . 
F 6 HOH A 18 518 18 HOH HOH . 
F 6 HOH A 19 519 19 HOH HOH . 
F 6 HOH A 20 520 20 HOH HOH . 
F 6 HOH A 21 521 21 HOH HOH . 
F 6 HOH A 22 522 22 HOH HOH . 
F 6 HOH A 23 523 23 HOH HOH . 
F 6 HOH A 24 524 24 HOH HOH . 
F 6 HOH A 25 525 25 HOH HOH . 
F 6 HOH A 26 526 26 HOH HOH . 
F 6 HOH A 27 527 27 HOH HOH . 
F 6 HOH A 28 528 28 HOH HOH . 
F 6 HOH A 29 529 29 HOH HOH . 
F 6 HOH A 30 530 30 HOH HOH . 
F 6 HOH A 31 531 31 HOH HOH . 
F 6 HOH A 32 532 32 HOH HOH . 
F 6 HOH A 33 533 33 HOH HOH . 
F 6 HOH A 34 534 34 HOH HOH . 
F 6 HOH A 35 535 35 HOH HOH . 
F 6 HOH A 36 536 36 HOH HOH . 
F 6 HOH A 37 537 37 HOH HOH . 
F 6 HOH A 38 538 38 HOH HOH . 
F 6 HOH A 39 539 39 HOH HOH . 
F 6 HOH A 40 540 40 HOH HOH . 
F 6 HOH A 41 541 41 HOH HOH . 
F 6 HOH A 42 542 42 HOH HOH . 
F 6 HOH A 43 543 43 HOH HOH . 
F 6 HOH A 44 544 44 HOH HOH . 
F 6 HOH A 45 545 45 HOH HOH . 
F 6 HOH A 46 546 46 HOH HOH . 
F 6 HOH A 47 547 47 HOH HOH . 
F 6 HOH A 48 548 48 HOH HOH . 
F 6 HOH A 49 549 49 HOH HOH . 
F 6 HOH A 50 550 50 HOH HOH . 
F 6 HOH A 51 551 51 HOH HOH . 
F 6 HOH A 52 552 52 HOH HOH . 
F 6 HOH A 53 553 53 HOH HOH . 
F 6 HOH A 54 554 54 HOH HOH . 
F 6 HOH A 55 555 55 HOH HOH . 
F 6 HOH A 56 556 56 HOH HOH . 
F 6 HOH A 57 557 57 HOH HOH . 
F 6 HOH A 58 558 58 HOH HOH . 
F 6 HOH A 59 559 59 HOH HOH . 
F 6 HOH A 60 560 60 HOH HOH . 
F 6 HOH A 61 561 61 HOH HOH . 
F 6 HOH A 62 562 62 HOH HOH . 
F 6 HOH A 63 563 63 HOH HOH . 
F 6 HOH A 64 564 64 HOH HOH . 
F 6 HOH A 65 565 65 HOH HOH . 
F 6 HOH A 66 566 66 HOH HOH . 
F 6 HOH A 67 567 67 HOH HOH . 
F 6 HOH A 68 568 68 HOH HOH . 
F 6 HOH A 69 569 69 HOH HOH . 
F 6 HOH A 70 570 70 HOH HOH . 
F 6 HOH A 71 571 71 HOH HOH . 
F 6 HOH A 72 572 72 HOH HOH . 
F 6 HOH A 73 573 73 HOH HOH . 
F 6 HOH A 74 574 74 HOH HOH . 
F 6 HOH A 75 575 75 HOH HOH . 
F 6 HOH A 76 576 76 HOH HOH . 
F 6 HOH A 77 577 77 HOH HOH . 
F 6 HOH A 78 578 78 HOH HOH . 
F 6 HOH A 79 579 79 HOH HOH . 
F 6 HOH A 80 580 80 HOH HOH . 
F 6 HOH A 81 581 81 HOH HOH . 
F 6 HOH A 82 582 82 HOH HOH . 
F 6 HOH A 83 583 83 HOH HOH . 
F 6 HOH A 84 584 84 HOH HOH . 
F 6 HOH A 85 585 85 HOH HOH . 
F 6 HOH A 86 586 86 HOH HOH . 
F 6 HOH A 87 587 87 HOH HOH . 
F 6 HOH A 88 588 88 HOH HOH . 
F 6 HOH A 89 589 89 HOH HOH . 
F 6 HOH A 90 590 90 HOH HOH . 
F 6 HOH A 91 591 91 HOH HOH . 
F 6 HOH A 92 592 92 HOH HOH . 
F 6 HOH A 93 593 93 HOH HOH . 
F 6 HOH A 94 594 94 HOH HOH . 
F 6 HOH A 95 595 95 HOH HOH . 
F 6 HOH A 96 596 96 HOH HOH . 
F 6 HOH A 97 597 97 HOH HOH . 
F 6 HOH A 98 598 98 HOH HOH . 
F 6 HOH A 99 599 99 HOH HOH . 
F 6 HOH A 100 600 100 HOH HOH . 
F 6 HOH A 101 601 101 HOH HOH . 
F 6 HOH A 102 602 102 HOH HOH . 
F 6 HOH A 103 603 103 HOH HOH . 
F 6 HOH A 104 604 104 HOH HOH . 
F 6 HOH A 105 605 105 HOH HOH . 
F 6 HOH A 106 606 106 HOH HOH . 
F 6 HOH A 107 607 107 HOH HOH . 
F 6 HOH A 108 608 108 HOH HOH . 
F 6 HOH A 109 609 109 HOH HOH . 
F 6 HOH A 110 610 110 HOH HOH . 
F 6 HOH A 111 611 111 HOH HOH . 
F 6 HOH A 112 612 112 HOH HOH . 
F 6 HOH A 113 613 113 HOH HOH . 
F 6 HOH A 114 614 114 HOH HOH . 
F 6 HOH A 115 615 115 HOH HOH . 
F 6 HOH A 116 616 116 HOH HOH . 
F 6 HOH A 117 617 117 HOH HOH . 
F 6 HOH A 118 618 118 HOH HOH . 
F 6 HOH A 119 619 119 HOH HOH . 
F 6 HOH A 120 620 120 HOH HOH . 
F 6 HOH A 121 621 121 HOH HOH . 
F 6 HOH A 122 622 122 HOH HOH . 
F 6 HOH A 123 623 123 HOH HOH . 
F 6 HOH A 124 624 124 HOH HOH . 
F 6 HOH A 125 625 125 HOH HOH . 
F 6 HOH A 126 626 126 HOH HOH . 
F 6 HOH A 127 627 127 HOH HOH . 
F 6 HOH A 128 628 128 HOH HOH . 
F 6 HOH A 129 629 129 HOH HOH . 
F 6 HOH A 130 630 130 HOH HOH . 
F 6 HOH A 131 631 131 HOH HOH . 
F 6 HOH A 132 632 132 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 10.293 23.866 -8.005 1 26.51 ? N1 UDP 401 A 1 
HETATM 2 C C2 UDP . . . B 2 9.25 24.696 -8.286 1 28.58 ? C2 UDP 401 A 1 
HETATM 3 N N3 UDP . . . B 2 8.746 24.725 -9.599 1 30.35 ? N3 UDP 401 A 1 
HETATM 4 C C4 UDP . . . B 2 9.298 23.917 -10.63 1 30.46 ? C4 UDP 401 A 1 
HETATM 5 C C5 UDP . . . B 2 10.39 23.075 -10.331 1 28.32 ? C5 UDP 401 A 1 
HETATM 6 C C6 UDP . . . B 2 10.886 23.059 -9.026 1 27.07 ? C6 UDP 401 A 1 
HETATM 7 O O2 UDP . . . B 2 8.725 25.395 -7.407 1 25.23 ? O2 UDP 401 A 1 
HETATM 8 O O4 UDP . . . B 2 8.793 23.971 -11.763 1 29.09 ? O4 UDP 401 A 1 
HETATM 9 C C1' UDP . . . B 2 10.827 23.915 -6.618 1 22.55 ? C1' UDP 401 A 1 
HETATM 10 C C2' UDP . . . B 2 9.951 23.183 -5.609 1 20.01 ? C2' UDP 401 A 1 
HETATM 11 O O2' UDP . . . B 2 10.113 23.814 -4.284 1 18.09 ? O2' UDP 401 A 1 
HETATM 12 C C3' UDP . . . B 2 10.629 21.883 -5.722 1 19.07 ? C3' UDP 401 A 1 
HETATM 13 C C4' UDP . . . B 2 12.103 22.265 -5.69 1 18.53 ? C4' UDP 401 A 1 
HETATM 14 O O4' UDP . . . B 2 12.189 23.408 -6.593 1 20.19 ? O4' UDP 401 A 1 
HETATM 15 O O3' UDP . . . B 2 10.279 21.105 -4.64 1 19.04 ? O3' UDP 401 A 1 
HETATM 16 C C5' UDP . . . B 2 13.069 21.116 -6.086 1 17.66 ? C5' UDP 401 A 1 
HETATM 17 O O5' UDP . . . B 2 12.813 20.516 -7.374 1 16.64 ? O5' UDP 401 A 1 
HETATM 18 P PA UDP . . . B 2 12.241 19.071 -7.559 0.6 14.86 ? PA UDP 401 A 1 
HETATM 19 O O1A UDP . . . B 2 11.377 18.757 -6.383 0.6 15.15 ? O1A UDP 401 A 1 
HETATM 20 O O2A UDP . . . B 2 11.745 19.021 -8.91 0.6 14.85 ? O2A UDP 401 A 1 
HETATM 21 O O3A UDP . . . B 2 13.661 18.291 -7.541 0.6 15.21 ? O3A UDP 401 A 1 
HETATM 22 P PB UDP . . . B 2 13.781 16.765 -7.033 0.6 15.91 ? PB UDP 401 A 1 
HETATM 23 O O1B UDP . . . B 2 12.757 15.965 -7.89 0.6 15.89 ? O1B UDP 401 A 1 
HETATM 24 O O2B UDP . . . B 2 15.158 16.38 -7.428 0.6 15.49 ? O2B UDP 401 A 1 
HETATM 25 O O3B UDP . . . B 2 13.263 16.595 -5.678 0.6 14.58 ? O3B UDP 401 A 1 
HETATM 26 H HN3 UDP . . . B 2 7.96 25.299 -9.811 1 29.28 ? HN3 UDP 401 A 1 
HETATM 27 H H5 UDP . . . B 2 10.838 22.451 -11.104 1 28.36 ? H5 UDP 401 A 1 
HETATM 28 H H6 UDP . . . B 2 11.736 22.421 -8.796 1 26.91 ? H6 UDP 401 A 1 
HETATM 29 H H1' UDP . . . B 2 10.898 24.96 -6.314 1 22.32 ? H1' UDP 401 A 1 
HETATM 30 H H2' UDP . . . B 2 8.915 23.127 -5.937 1 20.34 ? H2' UDP 401 A 1 
HETATM 31 H HO2' UDP . . . B 2 10.742 24.507 -4.386 0 17.49 ? HO2' UDP 401 A 1 
HETATM 32 H H3' UDP . . . B 2 10.385 21.4 -6.665 1 19.38 ? H3' UDP 401 A 1 
HETATM 33 H H4' UDP . . . B 2 12.358 22.598 -4.687 1 18.85 ? H4' UDP 401 A 1 
HETATM 34 H HO3' UDP . . . B 2 9.624 21.627 -4.017 0 18.26 ? HO3' UDP 401 A 1 
HETATM 35 H "H5'1" UDP . . . B 2 14.079 21.522 -6.1 1 17.57 ? "H5'1" UDP 401 A 1 
HETATM 36 H "H5'2" UDP . . . B 2 13.026 20.351 -5.324 1 17.39 ? "H5'2" UDP 401 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           304 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           36 
#