data_1F8Y
#
_model_server_result.job_id            0VD8gy_6RLg6zOxaCO6Muw 
_model_server_result.datetime_utc      '2024-10-12 02:28:18' 
_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          1f8y 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":2}' 
#
_entry.id    1F8Y 
#
_exptl.entry_id    1F8Y 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              242.229 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2'-deoxy-1-methyl-pseudouridine" 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            1F8Y 
_cell.length_a            149.6 
_cell.length_b            149.6 
_cell.length_c            149.6 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1F8Y 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        199 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 21 3' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_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    1,2,3 
#
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' 6_555 z+1/2,-x+1/2,-y 0 0 1 -1 0 0 0 -1 0 74.8 74.8 0 
3 'crystal symmetry operation' 12_554 -y+1/2,-z,x-1/2 0 -1 0 0 0 -1 1 0 0 74.8 0 -74.8 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D N N 
#
_chem_comp.formula           'C10 H14 N2 O5' 
_chem_comp.formula_weight    242.229 
_chem_comp.id                5MD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2'-deoxy-1-methyl-pseudouridine" 
_chem_comp.type              'dna linking' 
_chem_comp.pdbx_synonyms     "5-METHYL-2'-DEOXYPSEUDOURIDINE" 
#
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
O5' C5' 5MD sing 1 n n 
O5' H5' 5MD sing 2 n n 
C5' C4' 5MD sing 3 n n 
C5' "H5'1" 5MD sing 4 n n 
C5' "H5'2" 5MD sing 5 n n 
C4' O4' 5MD sing 6 n n 
C4' C3' 5MD sing 7 n n 
C4' H4' 5MD sing 8 n n 
O4' C1' 5MD sing 9 n n 
C1' C1 5MD sing 10 n n 
C1' C2' 5MD sing 11 n n 
C1' H1' 5MD sing 12 n n 
C1 C6 5MD doub 13 n n 
C1 C2 5MD sing 14 n n 
C6 N5 5MD sing 15 n n 
C6 H6 5MD sing 16 n n 
C2 O2 5MD doub 17 n n 
C2 N3 5MD sing 18 n n 
N3 C4 5MD sing 19 n n 
N3 HN3 5MD sing 20 n n 
C4 O4 5MD doub 21 n n 
C4 N5 5MD sing 22 n n 
N5 C5 5MD sing 23 n n 
C5 H51 5MD sing 24 n n 
C5 H52 5MD sing 25 n n 
C5 H53 5MD sing 26 n n 
C3' O3' 5MD sing 27 n n 
C3' C2' 5MD sing 28 n n 
C3' H3' 5MD sing 29 n n 
O3' "H3'A" 5MD sing 30 n n 
C2' "H2'1" 5MD sing 31 n n 
C2' "H2'2" 5MD sing 32 n n 
#
_atom_sites.entry_id                     1F8Y 
_atom_sites.fract_transf_matrix[1][1]    0.006684 
_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]    0.006684 
_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]    0.006684 
_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 5MD A 1 158 1 5MD 5MD . 
D 2 5MD B 1 2 2 5MD 5MD . 
E 3 HOH A 1 801 801 HOH HOH . 
E 3 HOH A 2 803 803 HOH HOH . 
E 3 HOH A 3 804 804 HOH HOH . 
E 3 HOH A 4 806 806 HOH HOH . 
E 3 HOH A 5 807 807 HOH HOH . 
E 3 HOH A 6 808 808 HOH HOH . 
E 3 HOH A 7 809 809 HOH HOH . 
E 3 HOH A 8 810 810 HOH HOH . 
E 3 HOH A 9 811 811 HOH HOH . 
E 3 HOH A 10 812 812 HOH HOH . 
E 3 HOH A 11 813 813 HOH HOH . 
E 3 HOH A 12 814 814 HOH HOH . 
E 3 HOH A 13 816 816 HOH HOH . 
E 3 HOH A 14 817 817 HOH HOH . 
E 3 HOH A 15 818 818 HOH HOH . 
E 3 HOH A 16 819 819 HOH HOH . 
E 3 HOH A 17 820 820 HOH HOH . 
E 3 HOH A 18 821 821 HOH HOH . 
E 3 HOH A 19 822 822 HOH HOH . 
E 3 HOH A 20 823 823 HOH HOH . 
E 3 HOH A 21 824 824 HOH HOH . 
E 3 HOH A 22 825 825 HOH HOH . 
E 3 HOH A 23 827 827 HOH HOH . 
E 3 HOH A 24 836 836 HOH HOH . 
E 3 HOH A 25 839 839 HOH HOH . 
E 3 HOH A 26 841 841 HOH HOH . 
E 3 HOH A 27 842 842 HOH HOH . 
E 3 HOH A 28 843 843 HOH HOH . 
E 3 HOH A 29 844 844 HOH HOH . 
E 3 HOH A 30 848 848 HOH HOH . 
E 3 HOH A 31 849 849 HOH HOH . 
E 3 HOH A 32 850 850 HOH HOH . 
E 3 HOH A 33 852 852 HOH HOH . 
E 3 HOH A 34 853 853 HOH HOH . 
E 3 HOH A 35 855 855 HOH HOH . 
E 3 HOH A 36 856 856 HOH HOH . 
E 3 HOH A 37 857 857 HOH HOH . 
E 3 HOH A 38 858 858 HOH HOH . 
E 3 HOH A 39 859 859 HOH HOH . 
E 3 HOH A 40 860 860 HOH HOH . 
E 3 HOH A 41 867 867 HOH HOH . 
E 3 HOH A 42 868 868 HOH HOH . 
E 3 HOH A 43 869 869 HOH HOH . 
E 3 HOH A 44 870 870 HOH HOH . 
E 3 HOH A 45 874 874 HOH HOH . 
E 3 HOH A 46 875 875 HOH HOH . 
E 3 HOH A 47 876 876 HOH HOH . 
F 3 HOH B 1 802 802 HOH HOH . 
F 3 HOH B 2 805 805 HOH HOH . 
F 3 HOH B 3 815 815 HOH HOH . 
F 3 HOH B 4 826 826 HOH HOH . 
F 3 HOH B 5 828 828 HOH HOH . 
F 3 HOH B 6 829 829 HOH HOH . 
F 3 HOH B 7 830 830 HOH HOH . 
F 3 HOH B 8 831 831 HOH HOH . 
F 3 HOH B 9 832 832 HOH HOH . 
F 3 HOH B 10 833 833 HOH HOH . 
F 3 HOH B 11 834 834 HOH HOH . 
F 3 HOH B 12 835 835 HOH HOH . 
F 3 HOH B 13 837 837 HOH HOH . 
F 3 HOH B 14 838 838 HOH HOH . 
F 3 HOH B 15 840 840 HOH HOH . 
F 3 HOH B 16 845 845 HOH HOH . 
F 3 HOH B 17 846 846 HOH HOH . 
F 3 HOH B 18 847 847 HOH HOH . 
F 3 HOH B 19 851 851 HOH HOH . 
F 3 HOH B 20 854 854 HOH HOH . 
F 3 HOH B 21 861 861 HOH HOH . 
F 3 HOH B 22 862 862 HOH HOH . 
F 3 HOH B 23 863 863 HOH HOH . 
F 3 HOH B 24 864 864 HOH HOH . 
F 3 HOH B 25 865 865 HOH HOH . 
F 3 HOH B 26 866 866 HOH HOH . 
F 3 HOH B 27 871 871 HOH HOH . 
F 3 HOH B 28 872 872 HOH HOH . 
F 3 HOH B 29 873 873 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 O O5' 5MD . . . D 2 55.671 -13.204 -6.913 1 16.16 ? O5' 5MD 2 B 1 
HETATM 2 C C5' 5MD . . . D 2 56.71 -13.714 -6.033 1 14.74 ? C5' 5MD 2 B 1 
HETATM 3 C C4' 5MD . . . D 2 57.688 -12.631 -5.636 1 14.46 ? C4' 5MD 2 B 1 
HETATM 4 O O4' 5MD . . . D 2 56.915 -11.515 -5.162 1 10.59 ? O4' 5MD 2 B 1 
HETATM 5 C C1' 5MD . . . D 2 56.799 -11.482 -3.72 1 11.47 ? C1' 5MD 2 B 1 
HETATM 6 C C1 5MD . . . D 2 55.421 -11.953 -3.262 1 10.16 ? C1 5MD 2 B 1 
HETATM 7 C C6 5MD . . . D 2 54.461 -12.306 -4.147 1 11.89 ? C6 5MD 2 B 1 
HETATM 8 C C2 5MD . . . D 2 55.195 -12.075 -1.859 1 10.76 ? C2 5MD 2 B 1 
HETATM 9 O O2 5MD . . . D 2 55.984 -11.872 -0.961 1 13.26 ? O2 5MD 2 B 1 
HETATM 10 N N3 5MD . . . D 2 53.943 -12.586 -1.56 1 11.77 ? N3 5MD 2 B 1 
HETATM 11 C C4 5MD . . . D 2 52.934 -12.951 -2.434 1 14.15 ? C4 5MD 2 B 1 
HETATM 12 O O4 5MD . . . D 2 51.838 -13.264 -2.009 1 18.66 ? O4 5MD 2 B 1 
HETATM 13 N N5 5MD . . . D 2 53.238 -12.785 -3.768 1 16.61 ? N5 5MD 2 B 1 
HETATM 14 C C5 5MD . . . D 2 52.242 -13.014 -4.793 1 10.81 ? C5 5MD 2 B 1 
HETATM 15 C C3' 5MD . . . D 2 58.547 -13.091 -4.467 1 13.67 ? C3' 5MD 2 B 1 
HETATM 16 O O3' 5MD . . . D 2 59.935 -12.735 -4.593 1 14.4 ? O3' 5MD 2 B 1 
HETATM 17 C C2' 5MD . . . D 2 57.911 -12.44 -3.263 1 10.42 ? C2' 5MD 2 B 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           325 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           17 
#