data_2Z87
#
_model_server_result.job_id            5OKYvGx3NY9vqEJ8gCfICQ 
_model_server_result.datetime_utc      '2024-11-26 01:35:04' 
_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          2z87 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":684}' 
#
_entry.id    2Z87 
#
_exptl.entry_id    2Z87 
_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          103.47 
_cell.angle_gamma         90 
_cell.entry_id            2Z87 
_cell.length_a            82.371 
_cell.length_b            109.285 
_cell.length_c            85.575 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2Z87 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? dimeric 2 author_defined_assembly 1 
PISA monomeric 1 software_defined_assembly 2 
PISA monomeric 1 software_defined_assembly 3 
#
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,I,J,K,L 1 1 
A,C,D,E,F,K 2 1 
B,G,H,I,J,L 3 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 H N 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 E MN MN . A MN 1 1_555 A OD2 ASP 183 A ASP 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
metalc ? metalc2 E MN MN . A MN 1 1_555 C O1A UD2 . A UD2 683 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.83 ? 
metalc ? metalc3 E MN MN . A MN 1 1_555 K O HOH . A HOH 690 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc4 F MN MN . A MN 2 1_555 A OD2 ASP 463 A ASP 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? 
metalc ? metalc5 H O1B UDP . B UDP 1 1_555 J MN MN . B MN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
metalc ? metalc6 I MN MN . B MN 3 1_555 G O1B UD2 . B UD2 683 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.868 ? 
metalc ? metalc7 I MN MN . B MN 3 1_555 G O1A UD2 . B UD2 683 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? 
metalc ? metalc8 I MN MN . B MN 3 1_555 L O HOH . B HOH 712 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
metalc ? metalc9 I MN MN . B MN 3 1_555 L O HOH . B HOH 746 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? 
metalc ? metalc10 J MN MN . B MN 4 1_555 B OD2 ASP 463 B ASP 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
#
_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 426 n n 
N1 C6 UDP sing 427 n n 
N1 C1' UDP sing 428 n n 
C2 N3 UDP sing 429 n n 
C2 O2 UDP doub 430 n n 
N3 C4 UDP sing 431 n n 
N3 HN3 UDP sing 432 n n 
C4 C5 UDP sing 433 n n 
C4 O4 UDP doub 434 n n 
C5 C6 UDP doub 435 n n 
C5 H5 UDP sing 436 n n 
C6 H6 UDP sing 437 n n 
C1' C2' UDP sing 438 n n 
C1' O4' UDP sing 439 n n 
C1' H1' UDP sing 440 n n 
C2' O2' UDP sing 441 n n 
C2' C3' UDP sing 442 n n 
C2' H2' UDP sing 443 n n 
O2' HO2' UDP sing 444 n n 
C3' C4' UDP sing 445 n n 
C3' O3' UDP sing 446 n n 
C3' H3' UDP sing 447 n n 
C4' O4' UDP sing 448 n n 
C4' C5' UDP sing 449 n n 
C4' H4' UDP sing 450 n n 
O3' HO3' UDP sing 451 n n 
C5' O5' UDP sing 452 n n 
C5' "H5'1" UDP sing 453 n n 
C5' "H5'2" UDP sing 454 n n 
O5' PA UDP sing 455 n n 
PA O1A UDP doub 456 n n 
PA O2A UDP sing 457 n n 
PA O3A UDP sing 458 n n 
O2A HOA2 UDP sing 459 n n 
O3A PB UDP sing 460 n n 
PB O1B UDP doub 461 n n 
PB O2B UDP sing 462 n n 
PB O3B UDP sing 463 n n 
O2B HOB2 UDP sing 464 n n 
O3B HOB3 UDP sing 465 n n 
#
_atom_sites.entry_id                     2Z87 
_atom_sites.fract_transf_matrix[1][1]    0.01214 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002908 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00915 
_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]    0.012016 
_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 UD2 A 1 683 404 UD2 UD2 . 
D 3 UDP A 1 684 1 UDP UDP . 
E 4 MN A 1 1 1 MN MN . 
F 4 MN A 1 2 2 MN MN . 
G 2 UD2 B 1 683 404 UD2 UD2 . 
H 3 UDP B 1 1 1 UDP UDP . 
I 4 MN B 1 3 3 MN MN . 
J 4 MN B 1 4 4 MN MN . 
K 5 HOH A 1 685 2 HOH HOH . 
K 5 HOH A 2 686 3 HOH HOH . 
K 5 HOH A 3 687 4 HOH HOH . 
K 5 HOH A 4 688 5 HOH HOH . 
K 5 HOH A 5 689 6 HOH HOH . 
K 5 HOH A 6 690 9 HOH HOH . 
K 5 HOH A 7 691 11 HOH HOH . 
K 5 HOH A 8 692 12 HOH HOH . 
K 5 HOH A 9 693 14 HOH HOH . 
K 5 HOH A 10 694 15 HOH HOH . 
K 5 HOH A 11 695 18 HOH HOH . 
K 5 HOH A 12 696 20 HOH HOH . 
K 5 HOH A 13 697 22 HOH HOH . 
K 5 HOH A 14 698 27 HOH HOH . 
K 5 HOH A 15 699 28 HOH HOH . 
K 5 HOH A 16 700 30 HOH HOH . 
K 5 HOH A 17 701 31 HOH HOH . 
K 5 HOH A 18 702 33 HOH HOH . 
K 5 HOH A 19 703 34 HOH HOH . 
K 5 HOH A 20 704 35 HOH HOH . 
K 5 HOH A 21 705 36 HOH HOH . 
K 5 HOH A 22 706 37 HOH HOH . 
K 5 HOH A 23 707 41 HOH HOH . 
K 5 HOH A 24 708 42 HOH HOH . 
K 5 HOH A 25 709 44 HOH HOH . 
K 5 HOH A 26 710 45 HOH HOH . 
K 5 HOH A 27 711 47 HOH HOH . 
K 5 HOH A 28 712 48 HOH HOH . 
K 5 HOH A 29 713 49 HOH HOH . 
K 5 HOH A 30 714 51 HOH HOH . 
K 5 HOH A 31 715 52 HOH HOH . 
K 5 HOH A 32 716 55 HOH HOH . 
K 5 HOH A 33 717 57 HOH HOH . 
K 5 HOH A 34 718 58 HOH HOH . 
K 5 HOH A 35 719 61 HOH HOH . 
K 5 HOH A 36 720 62 HOH HOH . 
K 5 HOH A 37 721 64 HOH HOH . 
K 5 HOH A 38 722 65 HOH HOH . 
K 5 HOH A 39 723 66 HOH HOH . 
K 5 HOH A 40 724 67 HOH HOH . 
K 5 HOH A 41 725 68 HOH HOH . 
K 5 HOH A 42 726 69 HOH HOH . 
K 5 HOH A 43 727 70 HOH HOH . 
K 5 HOH A 44 728 71 HOH HOH . 
K 5 HOH A 45 729 72 HOH HOH . 
K 5 HOH A 46 730 73 HOH HOH . 
K 5 HOH A 47 731 75 HOH HOH . 
K 5 HOH A 48 732 76 HOH HOH . 
K 5 HOH A 49 733 77 HOH HOH . 
K 5 HOH A 50 734 80 HOH HOH . 
K 5 HOH A 51 735 81 HOH HOH . 
K 5 HOH A 52 736 83 HOH HOH . 
K 5 HOH A 53 737 84 HOH HOH . 
K 5 HOH A 54 738 85 HOH HOH . 
K 5 HOH A 55 739 86 HOH HOH . 
K 5 HOH A 56 740 87 HOH HOH . 
K 5 HOH A 57 741 93 HOH HOH . 
K 5 HOH A 58 742 94 HOH HOH . 
K 5 HOH A 59 743 98 HOH HOH . 
K 5 HOH A 60 744 99 HOH HOH . 
K 5 HOH A 61 745 101 HOH HOH . 
K 5 HOH A 62 746 102 HOH HOH . 
K 5 HOH A 63 747 106 HOH HOH . 
K 5 HOH A 64 748 108 HOH HOH . 
K 5 HOH A 65 749 112 HOH HOH . 
K 5 HOH A 66 750 113 HOH HOH . 
K 5 HOH A 67 751 115 HOH HOH . 
K 5 HOH A 68 752 118 HOH HOH . 
K 5 HOH A 69 753 123 HOH HOH . 
K 5 HOH A 70 754 124 HOH HOH . 
K 5 HOH A 71 755 126 HOH HOH . 
K 5 HOH A 72 756 129 HOH HOH . 
K 5 HOH A 73 757 132 HOH HOH . 
K 5 HOH A 74 758 134 HOH HOH . 
K 5 HOH A 75 759 135 HOH HOH . 
K 5 HOH A 76 760 136 HOH HOH . 
K 5 HOH A 77 761 138 HOH HOH . 
K 5 HOH A 78 762 39 HOH HOH . 
L 5 HOH B 1 684 1 HOH HOH . 
L 5 HOH B 2 685 7 HOH HOH . 
L 5 HOH B 3 686 8 HOH HOH . 
L 5 HOH B 4 687 10 HOH HOH . 
L 5 HOH B 5 688 13 HOH HOH . 
L 5 HOH B 6 689 16 HOH HOH . 
L 5 HOH B 7 690 17 HOH HOH . 
L 5 HOH B 8 691 19 HOH HOH . 
L 5 HOH B 9 692 21 HOH HOH . 
L 5 HOH B 10 693 23 HOH HOH . 
L 5 HOH B 11 694 24 HOH HOH . 
L 5 HOH B 12 695 25 HOH HOH . 
L 5 HOH B 13 696 26 HOH HOH . 
L 5 HOH B 14 697 29 HOH HOH . 
L 5 HOH B 15 698 32 HOH HOH . 
L 5 HOH B 16 699 38 HOH HOH . 
L 5 HOH B 17 700 40 HOH HOH . 
L 5 HOH B 18 701 43 HOH HOH . 
L 5 HOH B 19 702 46 HOH HOH . 
L 5 HOH B 20 703 50 HOH HOH . 
L 5 HOH B 21 704 53 HOH HOH . 
L 5 HOH B 22 705 54 HOH HOH . 
L 5 HOH B 23 706 56 HOH HOH . 
L 5 HOH B 24 707 59 HOH HOH . 
L 5 HOH B 25 708 60 HOH HOH . 
L 5 HOH B 26 709 63 HOH HOH . 
L 5 HOH B 27 710 74 HOH HOH . 
L 5 HOH B 28 711 78 HOH HOH . 
L 5 HOH B 29 712 79 HOH HOH . 
L 5 HOH B 30 713 82 HOH HOH . 
L 5 HOH B 31 714 88 HOH HOH . 
L 5 HOH B 32 715 89 HOH HOH . 
L 5 HOH B 33 716 90 HOH HOH . 
L 5 HOH B 34 717 91 HOH HOH . 
L 5 HOH B 35 718 92 HOH HOH . 
L 5 HOH B 36 719 95 HOH HOH . 
L 5 HOH B 37 720 96 HOH HOH . 
L 5 HOH B 38 721 97 HOH HOH . 
L 5 HOH B 39 722 100 HOH HOH . 
L 5 HOH B 40 723 103 HOH HOH . 
L 5 HOH B 41 724 104 HOH HOH . 
L 5 HOH B 42 725 105 HOH HOH . 
L 5 HOH B 43 726 107 HOH HOH . 
L 5 HOH B 44 727 109 HOH HOH . 
L 5 HOH B 45 728 110 HOH HOH . 
L 5 HOH B 46 729 111 HOH HOH . 
L 5 HOH B 47 730 114 HOH HOH . 
L 5 HOH B 48 731 116 HOH HOH . 
L 5 HOH B 49 732 117 HOH HOH . 
L 5 HOH B 50 733 119 HOH HOH . 
L 5 HOH B 51 734 120 HOH HOH . 
L 5 HOH B 52 735 121 HOH HOH . 
L 5 HOH B 53 736 122 HOH HOH . 
L 5 HOH B 54 737 125 HOH HOH . 
L 5 HOH B 55 738 127 HOH HOH . 
L 5 HOH B 56 739 128 HOH HOH . 
L 5 HOH B 57 740 130 HOH HOH . 
L 5 HOH B 58 741 131 HOH HOH . 
L 5 HOH B 59 742 133 HOH HOH . 
L 5 HOH B 60 743 137 HOH HOH . 
L 5 HOH B 61 744 139 HOH HOH . 
L 5 HOH B 62 745 140 HOH HOH . 
L 5 HOH B 63 746 141 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 7.111 11.809 32.973 1 77.74 ? N1 UDP 684 A 1 
HETATM 2 C C2 UDP . . . D 3 6.391 11.71 31.803 1 76.25 ? C2 UDP 684 A 1 
HETATM 3 N N3 UDP . . . D 3 5.1 11.436 31.747 1 83.11 ? N3 UDP 684 A 1 
HETATM 4 C C4 UDP . . . D 3 4.462 11.236 32.879 1 85.7 ? C4 UDP 684 A 1 
HETATM 5 C C5 UDP . . . D 3 5.144 11.318 34.069 1 80.96 ? C5 UDP 684 A 1 
HETATM 6 C C6 UDP . . . D 3 6.486 11.614 34.106 1 81.6 ? C6 UDP 684 A 1 
HETATM 7 O O2 UDP . . . D 3 6.945 11.879 30.715 1 59.77 ? O2 UDP 684 A 1 
HETATM 8 O O4 UDP . . . D 3 3.262 10.982 32.838 1 90.2 ? O4 UDP 684 A 1 
HETATM 9 C C1' UDP . . . D 3 8.537 12.094 32.892 1 73.42 ? C1' UDP 684 A 1 
HETATM 10 C C2' UDP . . . D 3 9.01 13.054 33.926 1 69.29 ? C2' UDP 684 A 1 
HETATM 11 O O2' UDP . . . D 3 9.045 14.356 33.41 1 62.68 ? O2' UDP 684 A 1 
HETATM 12 C C3' UDP . . . D 3 10.436 12.672 34.004 1 64.2 ? C3' UDP 684 A 1 
HETATM 13 C C4' UDP . . . D 3 10.446 11.196 33.91 1 67.12 ? C4' UDP 684 A 1 
HETATM 14 O O4' UDP . . . D 3 9.265 10.921 33.194 1 73.7 ? O4' UDP 684 A 1 
HETATM 15 O O3' UDP . . . D 3 10.844 13.087 32.751 1 52.96 ? O3' UDP 684 A 1 
HETATM 16 C C5' UDP . . . D 3 10.51 10.584 35.305 1 79.52 ? C5' UDP 684 A 1 
HETATM 17 O O5' UDP . . . D 3 9.435 10.963 36.179 1 98.25 ? O5' UDP 684 A 1 
HETATM 18 P PA UDP . . . D 3 9.396 12.003 37.387 1 99.93 ? PA UDP 684 A 1 
HETATM 19 O O1A UDP . . . D 3 8.031 12.504 37.628 1 86.45 ? O1A UDP 684 A 1 
HETATM 20 O O2A UDP . . . D 3 10.449 13.032 37.339 1 95.05 ? O2A UDP 684 A 1 
HETATM 21 O O3A UDP . . . D 3 9.806 10.946 38.446 1 103.74 ? O3A UDP 684 A 1 
HETATM 22 P PB UDP . . . D 3 10.984 10.073 37.896 1 109.87 ? PB UDP 684 A 1 
HETATM 23 O O1B UDP . . . D 3 11.718 11.128 37.18 1 106.99 ? O1B UDP 684 A 1 
HETATM 24 O O2B UDP . . . D 3 10.273 9.046 37.12 1 102.17 ? O2B UDP 684 A 1 
HETATM 25 O O3B UDP . . . D 3 11.757 9.55 39.045 1 110.43 ? O3B UDP 684 A 1 
#
_model_server_stats.io_time_ms              57 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#