data_6XFI
#
_model_server_result.job_id            m49Pm9DYnaW5Kk8mmGPHhA 
_model_server_result.datetime_utc      '2024-10-13 12:21:26' 
_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          6xfi 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":601}' 
#
_entry.id    6XFI 
#
_exptl.entry_id    6XFI 
_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            6XFI 
_cell.length_a            129.84 
_cell.length_b            129.84 
_cell.length_c            81.56 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6XFI 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        90 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 4 21 2' 
#
_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' 8_665 -y+1,-x+1,-z 0 -1 0 -1 0 0 0 0 -1 129.84 129.84 0 
#
_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
disulf ? disulf1 A SG CYS 18 A CYS 69 1_555 A SG CYS 28 A CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf2 A SG CYS 34 A CYS 85 1_555 A SG CYS 177 A CYS 228 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.065 ? 
disulf ? disulf3 A SG CYS 34 A CYS 85 1_555 A SG CYS 177 A CYS 228 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.059 ? 
disulf ? disulf4 A SG CYS 385 A CYS 436 1_555 A SG CYS 386 A CYS 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf5 A SG CYS 439 A CYS 490 1_555 A SG CYS 527 A CYS 578 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
covale ? covale1 A ND2 ASN 48 A ASN 99 1_555 C C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
#
_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     ? 
#
_atom_sites.entry_id                     6XFI 
_atom_sites.fract_transf_matrix[1][1]    0.007702 
_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]    0.007702 
_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]    0.012261 
_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 1 601 600 UDP UDP . 
C 3 NAG A 1 602 701 NAG NAG . 
D 4 PO4 A 1 603 1 PO4 PO4 . 
E 4 PO4 A 1 604 2 PO4 PO4 . 
F 5 HOH A 1 701 57 HOH HOH . 
F 5 HOH A 2 702 74 HOH HOH . 
F 5 HOH A 3 703 157 HOH HOH . 
F 5 HOH A 4 704 168 HOH HOH . 
F 5 HOH A 5 705 64 HOH HOH . 
F 5 HOH A 6 706 84 HOH HOH . 
F 5 HOH A 7 707 108 HOH HOH . 
F 5 HOH A 8 708 163 HOH HOH . 
F 5 HOH A 9 709 155 HOH HOH . 
F 5 HOH A 10 710 29 HOH HOH . 
F 5 HOH A 11 711 137 HOH HOH . 
F 5 HOH A 12 712 129 HOH HOH . 
F 5 HOH A 13 713 67 HOH HOH . 
F 5 HOH A 14 714 131 HOH HOH . 
F 5 HOH A 15 715 139 HOH HOH . 
F 5 HOH A 16 716 135 HOH HOH . 
F 5 HOH A 17 717 58 HOH HOH . 
F 5 HOH A 18 718 104 HOH HOH . 
F 5 HOH A 19 719 27 HOH HOH . 
F 5 HOH A 20 720 45 HOH HOH . 
F 5 HOH A 21 721 44 HOH HOH . 
F 5 HOH A 22 722 100 HOH HOH . 
F 5 HOH A 23 723 51 HOH HOH . 
F 5 HOH A 24 724 133 HOH HOH . 
F 5 HOH A 25 725 162 HOH HOH . 
F 5 HOH A 26 726 10 HOH HOH . 
F 5 HOH A 27 727 128 HOH HOH . 
F 5 HOH A 28 728 16 HOH HOH . 
F 5 HOH A 29 729 122 HOH HOH . 
F 5 HOH A 30 730 143 HOH HOH . 
F 5 HOH A 31 731 23 HOH HOH . 
F 5 HOH A 32 732 50 HOH HOH . 
F 5 HOH A 33 733 111 HOH HOH . 
F 5 HOH A 34 734 146 HOH HOH . 
F 5 HOH A 35 735 36 HOH HOH . 
F 5 HOH A 36 736 178 HOH HOH . 
F 5 HOH A 37 737 106 HOH HOH . 
F 5 HOH A 38 738 151 HOH HOH . 
F 5 HOH A 39 739 22 HOH HOH . 
F 5 HOH A 40 740 31 HOH HOH . 
F 5 HOH A 41 741 43 HOH HOH . 
F 5 HOH A 42 742 76 HOH HOH . 
F 5 HOH A 43 743 126 HOH HOH . 
F 5 HOH A 44 744 32 HOH HOH . 
F 5 HOH A 45 745 42 HOH HOH . 
F 5 HOH A 46 746 72 HOH HOH . 
F 5 HOH A 47 747 101 HOH HOH . 
F 5 HOH A 48 748 53 HOH HOH . 
F 5 HOH A 49 749 136 HOH HOH . 
F 5 HOH A 50 750 39 HOH HOH . 
F 5 HOH A 51 751 20 HOH HOH . 
F 5 HOH A 52 752 26 HOH HOH . 
F 5 HOH A 53 753 40 HOH HOH . 
F 5 HOH A 54 754 158 HOH HOH . 
F 5 HOH A 55 755 6 HOH HOH . 
F 5 HOH A 56 756 112 HOH HOH . 
F 5 HOH A 57 757 99 HOH HOH . 
F 5 HOH A 58 758 164 HOH HOH . 
F 5 HOH A 59 759 60 HOH HOH . 
F 5 HOH A 60 760 11 HOH HOH . 
F 5 HOH A 61 761 35 HOH HOH . 
F 5 HOH A 62 762 2 HOH HOH . 
F 5 HOH A 63 763 18 HOH HOH . 
F 5 HOH A 64 764 41 HOH HOH . 
F 5 HOH A 65 765 65 HOH HOH . 
F 5 HOH A 66 766 69 HOH HOH . 
F 5 HOH A 67 767 17 HOH HOH . 
F 5 HOH A 68 768 7 HOH HOH . 
F 5 HOH A 69 769 145 HOH HOH . 
F 5 HOH A 70 770 172 HOH HOH . 
F 5 HOH A 71 771 150 HOH HOH . 
F 5 HOH A 72 772 1 HOH HOH . 
F 5 HOH A 73 773 171 HOH HOH . 
F 5 HOH A 74 774 169 HOH HOH . 
F 5 HOH A 75 775 33 HOH HOH . 
F 5 HOH A 76 776 61 HOH HOH . 
F 5 HOH A 77 777 174 HOH HOH . 
F 5 HOH A 78 778 4 HOH HOH . 
F 5 HOH A 79 779 15 HOH HOH . 
F 5 HOH A 80 780 94 HOH HOH . 
F 5 HOH A 81 781 34 HOH HOH . 
F 5 HOH A 82 782 186 HOH HOH . 
F 5 HOH A 83 783 75 HOH HOH . 
F 5 HOH A 84 784 81 HOH HOH . 
F 5 HOH A 85 785 25 HOH HOH . 
F 5 HOH A 86 786 120 HOH HOH . 
F 5 HOH A 87 787 13 HOH HOH . 
F 5 HOH A 88 788 102 HOH HOH . 
F 5 HOH A 89 789 121 HOH HOH . 
F 5 HOH A 90 790 9 HOH HOH . 
F 5 HOH A 91 791 192 HOH HOH . 
F 5 HOH A 92 792 98 HOH HOH . 
F 5 HOH A 93 793 21 HOH HOH . 
F 5 HOH A 94 794 124 HOH HOH . 
F 5 HOH A 95 795 177 HOH HOH . 
F 5 HOH A 96 796 144 HOH HOH . 
F 5 HOH A 97 797 52 HOH HOH . 
F 5 HOH A 98 798 138 HOH HOH . 
F 5 HOH A 99 799 12 HOH HOH . 
F 5 HOH A 100 800 66 HOH HOH . 
F 5 HOH A 101 801 181 HOH HOH . 
F 5 HOH A 102 802 91 HOH HOH . 
F 5 HOH A 103 803 48 HOH HOH . 
F 5 HOH A 104 804 28 HOH HOH . 
F 5 HOH A 105 805 153 HOH HOH . 
F 5 HOH A 106 806 110 HOH HOH . 
F 5 HOH A 107 807 37 HOH HOH . 
F 5 HOH A 108 808 49 HOH HOH . 
F 5 HOH A 109 809 107 HOH HOH . 
F 5 HOH A 110 810 19 HOH HOH . 
F 5 HOH A 111 811 185 HOH HOH . 
F 5 HOH A 112 812 30 HOH HOH . 
F 5 HOH A 113 813 14 HOH HOH . 
F 5 HOH A 114 814 55 HOH HOH . 
F 5 HOH A 115 815 5 HOH HOH . 
F 5 HOH A 116 816 152 HOH HOH . 
F 5 HOH A 117 817 73 HOH HOH . 
F 5 HOH A 118 818 130 HOH HOH . 
F 5 HOH A 119 819 70 HOH HOH . 
F 5 HOH A 120 820 46 HOH HOH . 
F 5 HOH A 121 821 68 HOH HOH . 
F 5 HOH A 122 822 114 HOH HOH . 
F 5 HOH A 123 823 59 HOH HOH . 
F 5 HOH A 124 824 24 HOH HOH . 
F 5 HOH A 125 825 180 HOH HOH . 
F 5 HOH A 126 826 127 HOH HOH . 
F 5 HOH A 127 827 92 HOH HOH . 
F 5 HOH A 128 828 119 HOH HOH . 
F 5 HOH A 129 829 147 HOH HOH . 
F 5 HOH A 130 830 3 HOH HOH . 
F 5 HOH A 131 831 77 HOH HOH . 
F 5 HOH A 132 832 86 HOH HOH . 
F 5 HOH A 133 833 176 HOH HOH . 
F 5 HOH A 134 834 148 HOH HOH . 
F 5 HOH A 135 835 56 HOH HOH . 
F 5 HOH A 136 836 113 HOH HOH . 
F 5 HOH A 137 837 193 HOH HOH . 
F 5 HOH A 138 838 173 HOH HOH . 
F 5 HOH A 139 839 85 HOH HOH . 
F 5 HOH A 140 840 117 HOH HOH . 
F 5 HOH A 141 841 8 HOH HOH . 
F 5 HOH A 142 842 82 HOH HOH . 
F 5 HOH A 143 843 115 HOH HOH . 
F 5 HOH A 144 844 140 HOH HOH . 
F 5 HOH A 145 845 105 HOH HOH . 
F 5 HOH A 146 846 62 HOH HOH . 
F 5 HOH A 147 847 167 HOH HOH . 
F 5 HOH A 148 848 179 HOH HOH . 
F 5 HOH A 149 849 184 HOH HOH . 
F 5 HOH A 150 850 93 HOH HOH . 
F 5 HOH A 151 851 118 HOH HOH . 
F 5 HOH A 152 852 38 HOH HOH . 
F 5 HOH A 153 853 141 HOH HOH . 
F 5 HOH A 154 854 96 HOH HOH . 
F 5 HOH A 155 855 187 HOH HOH . 
F 5 HOH A 156 856 87 HOH HOH . 
F 5 HOH A 157 857 195 HOH HOH . 
F 5 HOH A 158 858 194 HOH HOH . 
F 5 HOH A 159 859 183 HOH HOH . 
F 5 HOH A 160 860 189 HOH HOH . 
F 5 HOH A 161 861 149 HOH HOH . 
F 5 HOH A 162 862 63 HOH HOH . 
F 5 HOH A 163 863 190 HOH HOH . 
F 5 HOH A 164 864 156 HOH HOH . 
F 5 HOH A 165 865 123 HOH HOH . 
F 5 HOH A 166 866 97 HOH HOH . 
F 5 HOH A 167 867 132 HOH HOH . 
F 5 HOH A 168 868 83 HOH HOH . 
F 5 HOH A 169 869 175 HOH HOH . 
F 5 HOH A 170 870 88 HOH HOH . 
F 5 HOH A 171 871 161 HOH HOH . 
F 5 HOH A 172 872 191 HOH HOH . 
F 5 HOH A 173 873 47 HOH HOH . 
F 5 HOH A 174 874 154 HOH HOH . 
F 5 HOH A 175 875 159 HOH HOH . 
F 5 HOH A 176 876 80 HOH HOH . 
F 5 HOH A 177 877 109 HOH HOH . 
F 5 HOH A 178 878 95 HOH HOH . 
F 5 HOH A 179 879 116 HOH HOH . 
F 5 HOH A 180 880 89 HOH HOH . 
F 5 HOH A 181 881 103 HOH HOH . 
F 5 HOH A 182 882 90 HOH HOH . 
F 5 HOH A 183 883 125 HOH HOH . 
F 5 HOH A 184 884 54 HOH HOH . 
F 5 HOH A 185 885 160 HOH HOH . 
F 5 HOH A 186 886 78 HOH HOH . 
F 5 HOH A 187 887 165 HOH HOH . 
F 5 HOH A 188 888 196 HOH HOH . 
F 5 HOH A 189 889 182 HOH HOH . 
F 5 HOH A 190 890 71 HOH HOH . 
F 5 HOH A 191 891 79 HOH HOH . 
F 5 HOH A 192 892 166 HOH HOH . 
F 5 HOH A 193 893 170 HOH HOH . 
F 5 HOH A 194 894 188 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 94.775 53.618 33.392 1 32.5 ? N1 UDP 601 A 1 
HETATM 2 C C2 UDP . . . B 2 94.749 54.911 33.87 1 34.66 ? C2 UDP 601 A 1 
HETATM 3 N N3 UDP . . . B 2 95.521 55.13 34.988 1 29.42 ? N3 UDP 601 A 1 
HETATM 4 C C4 UDP . . . B 2 96.291 54.198 35.658 1 34.88 ? C4 UDP 601 A 1 
HETATM 5 C C5 UDP . . . B 2 96.26 52.883 35.102 1 41.24 ? C5 UDP 601 A 1 
HETATM 6 C C6 UDP . . . B 2 95.518 52.639 34.009 1 37.18 ? C6 UDP 601 A 1 
HETATM 7 O O2 UDP . . . B 2 94.099 55.804 33.344 1 34.85 ? O2 UDP 601 A 1 
HETATM 8 O O4 UDP . . . B 2 96.938 54.54 36.66 1 45.46 ? O4 UDP 601 A 1 
HETATM 9 C C1' UDP . . . B 2 93.986 53.291 32.19 1 40.26 ? C1' UDP 601 A 1 
HETATM 10 C C2' UDP . . . B 2 94.883 52.916 31.004 1 33.21 ? C2' UDP 601 A 1 
HETATM 11 O O2' UDP . . . B 2 95.16 54.116 30.29 1 30.25 ? O2' UDP 601 A 1 
HETATM 12 C C3' UDP . . . B 2 93.985 51.949 30.22 1 34.13 ? C3' UDP 601 A 1 
HETATM 13 C C4' UDP . . . B 2 93.178 51.26 31.325 1 35.09 ? C4' UDP 601 A 1 
HETATM 14 O O4' UDP . . . B 2 93.214 52.141 32.477 1 34.23 ? O4' UDP 601 A 1 
HETATM 15 O O3' UDP . . . B 2 93.139 52.656 29.309 1 30.43 ? O3' UDP 601 A 1 
HETATM 16 C C5' UDP . . . B 2 93.645 49.883 31.723 1 37.52 ? C5' UDP 601 A 1 
HETATM 17 O O5' UDP . . . B 2 95.05 49.921 32.064 1 32.74 ? O5' UDP 601 A 1 
HETATM 18 P PA UDP . . . B 2 95.959 48.653 31.884 1 36.39 ? PA UDP 601 A 1 
HETATM 19 O O1A UDP . . . B 2 95.117 47.452 32.105 1 32.91 ? O1A UDP 601 A 1 
HETATM 20 O O2A UDP . . . B 2 97.218 48.743 32.75 1 38.9 ? O2A UDP 601 A 1 
HETATM 21 O O3A UDP . . . B 2 96.439 48.707 30.343 1 45.1 ? O3A UDP 601 A 1 
HETATM 22 P PB UDP . . . B 2 97.826 49.238 29.784 1 35.2 ? PB UDP 601 A 1 
HETATM 23 O O1B UDP . . . B 2 97.679 49.043 28.269 1 29.03 ? O1B UDP 601 A 1 
HETATM 24 O O2B UDP . . . B 2 98.816 48.216 30.306 1 32.99 ? O2B UDP 601 A 1 
HETATM 25 O O3B UDP . . . B 2 98.077 50.645 30.184 1 33.72 ? O3B UDP 601 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           25 
#