data_7ERX
#
_model_server_result.job_id            MQqeSlCXsjwRmqwPfjdMQA 
_model_server_result.datetime_utc      '2024-10-19 14:22:47' 
_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          7erx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":502}' 
#
_entry.id    7ERX 
#
_exptl.entry_id    7ERX 
_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    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            7ERX 
_cell.length_a            54.482 
_cell.length_b            83.173 
_cell.length_c            109.391 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7ERX 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               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 
#
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_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 471 n n 
N1 C6 UDP sing 472 n n 
N1 C1' UDP sing 473 n n 
C2 N3 UDP sing 474 n n 
C2 O2 UDP doub 475 n n 
N3 C4 UDP sing 476 n n 
N3 HN3 UDP sing 477 n n 
C4 C5 UDP sing 478 n n 
C4 O4 UDP doub 479 n n 
C5 C6 UDP doub 480 n n 
C5 H5 UDP sing 481 n n 
C6 H6 UDP sing 482 n n 
C1' C2' UDP sing 483 n n 
C1' O4' UDP sing 484 n n 
C1' H1' UDP sing 485 n n 
C2' O2' UDP sing 486 n n 
C2' C3' UDP sing 487 n n 
C2' H2' UDP sing 488 n n 
O2' HO2' UDP sing 489 n n 
C3' C4' UDP sing 490 n n 
C3' O3' UDP sing 491 n n 
C3' H3' UDP sing 492 n n 
C4' O4' UDP sing 493 n n 
C4' C5' UDP sing 494 n n 
C4' H4' UDP sing 495 n n 
O3' HO3' UDP sing 496 n n 
C5' O5' UDP sing 497 n n 
C5' "H5'1" UDP sing 498 n n 
C5' "H5'2" UDP sing 499 n n 
O5' PA UDP sing 500 n n 
PA O1A UDP doub 501 n n 
PA O2A UDP sing 502 n n 
PA O3A UDP sing 503 n n 
O2A HOA2 UDP sing 504 n n 
O3A PB UDP sing 505 n n 
PB O1B UDP doub 506 n n 
PB O2B UDP sing 507 n n 
PB O3B UDP sing 508 n n 
O2B HOB2 UDP sing 509 n n 
O3B HOB3 UDP sing 510 n n 
#
_atom_sites.entry_id                     7ERX 
_atom_sites.fract_transf_matrix[1][1]    0.018355 
_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]    0.012023 
_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]    0.009142 
_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 GOL A 1 501 501 GOL GOL . 
C 3 UDP A 1 502 601 UDP UDP . 
D 4 JC6 A 1 503 602 JC6 STB . 
E 5 HOH A 1 601 44 HOH HOH . 
E 5 HOH A 2 602 54 HOH HOH . 
E 5 HOH A 3 603 5 HOH HOH . 
E 5 HOH A 4 604 38 HOH HOH . 
E 5 HOH A 5 605 36 HOH HOH . 
E 5 HOH A 6 606 17 HOH HOH . 
E 5 HOH A 7 607 8 HOH HOH . 
E 5 HOH A 8 608 12 HOH HOH . 
E 5 HOH A 9 609 103 HOH HOH . 
E 5 HOH A 10 610 88 HOH HOH . 
E 5 HOH A 11 611 6 HOH HOH . 
E 5 HOH A 12 612 71 HOH HOH . 
E 5 HOH A 13 613 29 HOH HOH . 
E 5 HOH A 14 614 46 HOH HOH . 
E 5 HOH A 15 615 98 HOH HOH . 
E 5 HOH A 16 616 41 HOH HOH . 
E 5 HOH A 17 617 42 HOH HOH . 
E 5 HOH A 18 618 105 HOH HOH . 
E 5 HOH A 19 619 63 HOH HOH . 
E 5 HOH A 20 620 28 HOH HOH . 
E 5 HOH A 21 621 9 HOH HOH . 
E 5 HOH A 22 622 25 HOH HOH . 
E 5 HOH A 23 623 7 HOH HOH . 
E 5 HOH A 24 624 23 HOH HOH . 
E 5 HOH A 25 625 264 HOH HOH . 
E 5 HOH A 26 626 45 HOH HOH . 
E 5 HOH A 27 627 221 HOH HOH . 
E 5 HOH A 28 628 61 HOH HOH . 
E 5 HOH A 29 629 40 HOH HOH . 
E 5 HOH A 30 630 261 HOH HOH . 
E 5 HOH A 31 631 263 HOH HOH . 
E 5 HOH A 32 632 13 HOH HOH . 
E 5 HOH A 33 633 69 HOH HOH . 
E 5 HOH A 34 634 144 HOH HOH . 
E 5 HOH A 35 635 21 HOH HOH . 
E 5 HOH A 36 636 85 HOH HOH . 
E 5 HOH A 37 637 100 HOH HOH . 
E 5 HOH A 38 638 143 HOH HOH . 
E 5 HOH A 39 639 64 HOH HOH . 
E 5 HOH A 40 640 262 HOH HOH . 
E 5 HOH A 41 641 84 HOH HOH . 
E 5 HOH A 42 642 75 HOH HOH . 
E 5 HOH A 43 643 114 HOH HOH . 
E 5 HOH A 44 644 99 HOH HOH . 
E 5 HOH A 45 645 2 HOH HOH . 
E 5 HOH A 46 646 3 HOH HOH . 
E 5 HOH A 47 647 30 HOH HOH . 
E 5 HOH A 48 648 18 HOH HOH . 
E 5 HOH A 49 649 35 HOH HOH . 
E 5 HOH A 50 650 20 HOH HOH . 
E 5 HOH A 51 651 57 HOH HOH . 
E 5 HOH A 52 652 31 HOH HOH . 
E 5 HOH A 53 653 14 HOH HOH . 
E 5 HOH A 54 654 24 HOH HOH . 
E 5 HOH A 55 655 4 HOH HOH . 
E 5 HOH A 56 656 73 HOH HOH . 
E 5 HOH A 57 657 102 HOH HOH . 
E 5 HOH A 58 658 96 HOH HOH . 
E 5 HOH A 59 659 39 HOH HOH . 
E 5 HOH A 60 660 76 HOH HOH . 
E 5 HOH A 61 661 198 HOH HOH . 
E 5 HOH A 62 662 255 HOH HOH . 
E 5 HOH A 63 663 34 HOH HOH . 
E 5 HOH A 64 664 19 HOH HOH . 
E 5 HOH A 65 665 16 HOH HOH . 
E 5 HOH A 66 666 66 HOH HOH . 
E 5 HOH A 67 667 68 HOH HOH . 
E 5 HOH A 68 668 258 HOH HOH . 
E 5 HOH A 69 669 49 HOH HOH . 
E 5 HOH A 70 670 53 HOH HOH . 
E 5 HOH A 71 671 78 HOH HOH . 
E 5 HOH A 72 672 101 HOH HOH . 
E 5 HOH A 73 673 47 HOH HOH . 
E 5 HOH A 74 674 259 HOH HOH . 
E 5 HOH A 75 675 257 HOH HOH . 
E 5 HOH A 76 676 254 HOH HOH . 
E 5 HOH A 77 677 1 HOH HOH . 
E 5 HOH A 78 678 11 HOH HOH . 
E 5 HOH A 79 679 260 HOH HOH . 
E 5 HOH A 80 680 194 HOH HOH . 
E 5 HOH A 81 681 56 HOH HOH . 
E 5 HOH A 82 682 239 HOH HOH . 
E 5 HOH A 83 683 157 HOH HOH . 
E 5 HOH A 84 684 62 HOH HOH . 
E 5 HOH A 85 685 167 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 . . . C 3 -9.937 -12.946 14.009 1 40.5 0 N1 UDP 502 A 1 
HETATM 2 C C2 UDP . . . C 3 -9.891 -13.959 13.017 1 38.46 0 C2 UDP 502 A 1 
HETATM 3 N N3 UDP . . . C 3 -10.722 -13.903 11.969 1 37.93 0 N3 UDP 502 A 1 
HETATM 4 C C4 UDP . . . C 3 -11.632 -12.927 11.839 1 41.19 0 C4 UDP 502 A 1 
HETATM 5 C C5 UDP . . . C 3 -11.718 -11.907 12.807 1 40.45 0 C5 UDP 502 A 1 
HETATM 6 C C6 UDP . . . C 3 -10.848 -11.943 13.903 1 40.56 0 C6 UDP 502 A 1 
HETATM 7 O O2 UDP . . . C 3 -9.061 -14.893 13.108 1 35.55 0 O2 UDP 502 A 1 
HETATM 8 O O4 UDP . . . C 3 -12.388 -12.953 10.839 1 40.48 0 O4 UDP 502 A 1 
HETATM 9 C C1' UDP . . . C 3 -9.057 -13.086 15.161 1 36.47 0 C1' UDP 502 A 1 
HETATM 10 C C2' UDP . . . C 3 -7.813 -12.25 15.165 1 37.24 0 C2' UDP 502 A 1 
HETATM 11 O O2' UDP . . . C 3 -6.727 -12.99 14.612 1 33.83 0 O2' UDP 502 A 1 
HETATM 12 C C3' UDP . . . C 3 -7.646 -11.931 16.65 1 37.7 0 C3' UDP 502 A 1 
HETATM 13 C C4' UDP . . . C 3 -9.061 -11.944 17.209 1 37.2 0 C4' UDP 502 A 1 
HETATM 14 O O4' UDP . . . C 3 -9.843 -12.719 16.303 1 36.86 0 O4' UDP 502 A 1 
HETATM 15 O O3' UDP . . . C 3 -6.867 -12.908 17.368 1 35.78 0 O3' UDP 502 A 1 
HETATM 16 C C5' UDP . . . C 3 -9.637 -10.537 17.348 1 37.74 0 C5' UDP 502 A 1 
HETATM 17 O O5' UDP . . . C 3 -9.124 -9.926 18.526 1 35.07 0 O5' UDP 502 A 1 
HETATM 18 P PA UDP . . . C 3 -8.839 -8.338 18.621 1 36.32 0 PA UDP 502 A 1 
HETATM 19 O O1A UDP . . . C 3 -8.003 -7.904 17.435 1 34.89 0 O1A UDP 502 A 1 
HETATM 20 O O2A UDP . . . C 3 -8.245 -8.055 19.961 1 36.43 0 O2A UDP 502 A 1 
HETATM 21 O O3A UDP . . . C 3 -10.294 -7.665 18.514 1 32.81 0 O3A UDP 502 A 1 
HETATM 22 P PB UDP . . . C 3 -11.681 -7.96 19.263 1 36.65 0 PB UDP 502 A 1 
HETATM 23 O O1B UDP . . . C 3 -12.388 -9.042 18.49 1 34.63 0 O1B UDP 502 A 1 
HETATM 24 O O2B UDP . . . C 3 -12.356 -6.608 19.143 1 37.23 0 O2B UDP 502 A 1 
HETATM 25 O O3B UDP . . . C 3 -11.353 -8.373 20.686 1 37.26 0 O3B UDP 502 A 1 
#
_model_server_stats.io_time_ms              49 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           369 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           25 
#