data_1E2N
#
_model_server_result.job_id            qGQekc2ygcP0vZyiWpAM6w 
_model_server_result.datetime_utc      '2024-12-27 04:19:42' 
_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          1e2n 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":500}' 
#
_entry.id    1E2N 
#
_exptl.entry_id    1E2N 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              296.279 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            6-{[4-(HYDROXYMETHYL)-5-METHYL-2,6-DIOXOHEXAHYDROPYRIMIDIN-5-YL]METHYL}-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE 
_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            1E2N 
_cell.length_a            113.6 
_cell.length_b            118.8 
_cell.length_c            108.5 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1E2N 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA tetrameric 4 software_defined_assembly 1 
? dimeric 2 author_defined_assembly 2 
#
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 1 1,2 
A,B,C,D,E,F,G,H 2 1 
#
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' 4_565 x,-y+1,-z 1 0 0 0 -1 0 0 0 -1 0 118.8 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 F N N 
#
_chem_comp.formula           'C12 H16 N4 O5' 
_chem_comp.formula_weight    296.279 
_chem_comp.id                RCA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              6-{[4-(HYDROXYMETHYL)-5-METHYL-2,6-DIOXOHEXAHYDROPYRIMIDIN-5-YL]METHYL}-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     HYDROXYMETHYL-HYDROTHYMYL-THYMINE;5-[THYMIN-6-YL]METHYL-6-HYDRO-6-HYDROXYMETHYL-THYMINE 
#
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
O2 C2 RCA doub 277 n n 
C3 C4 RCA sing 278 n n 
C3 C5 RCA doub 279 n y 
C3 C2 RCA sing 280 n y 
C4 H43 RCA sing 281 n n 
C4 H42 RCA sing 282 n n 
C4 H41 RCA sing 283 n n 
C5 N1 RCA sing 284 n y 
C5 C6 RCA sing 285 n n 
C1 N1 RCA sing 286 n y 
C1 N2 RCA sing 287 n y 
C1 O1 RCA doub 288 n n 
N1 H1 RCA sing 289 n n 
C2 N2 RCA sing 290 n y 
N2 H2 RCA sing 291 n n 
C11 N4 RCA sing 292 n n 
C11 C12 RCA sing 293 n n 
C11 C7 RCA sing 294 n n 
C11 H11 RCA sing 295 n n 
O4 C10 RCA doub 296 n n 
O3 C9 RCA doub 297 n n 
N4 C10 RCA sing 298 n n 
N4 H4 RCA sing 299 n n 
C10 N3 RCA sing 300 n n 
C12 O5 RCA sing 301 n n 
C12 H122 RCA sing 302 n n 
C12 H121 RCA sing 303 n n 
O5 H5 RCA sing 304 n n 
C7 C9 RCA sing 305 n n 
C7 C6 RCA sing 306 n n 
C7 C8 RCA sing 307 n n 
N3 C9 RCA sing 308 n n 
N3 H3 RCA sing 309 n n 
C6 H62 RCA sing 310 n n 
C6 H61 RCA sing 311 n n 
C8 H83 RCA sing 312 n n 
C8 H82 RCA sing 313 n n 
C8 H81 RCA sing 314 n n 
#
_atom_sites.entry_id                     1E2N 
_atom_sites.fract_transf_matrix[1][1]    0.008803 
_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]    0.008417 
_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]    0.009216 
_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 SO4 A 1 400 400 SO4 SO4 . 
D 3 RCA A 1 500 500 RCA RCA . 
E 2 SO4 B 1 400 400 SO4 SO4 . 
F 3 RCA B 1 500 500 RCA RCA . 
G 4 HOH A 1 2001 2001 HOH HOH . 
G 4 HOH A 2 2002 2002 HOH HOH . 
G 4 HOH A 3 2003 2003 HOH HOH . 
G 4 HOH A 4 2004 2004 HOH HOH . 
G 4 HOH A 5 2005 2005 HOH HOH . 
G 4 HOH A 6 2006 2006 HOH HOH . 
G 4 HOH A 7 2007 2007 HOH HOH . 
G 4 HOH A 8 2008 2008 HOH HOH . 
G 4 HOH A 9 2009 2009 HOH HOH . 
G 4 HOH A 10 2010 2010 HOH HOH . 
G 4 HOH A 11 2011 2011 HOH HOH . 
G 4 HOH A 12 2012 2012 HOH HOH . 
G 4 HOH A 13 2013 2013 HOH HOH . 
G 4 HOH A 14 2014 2014 HOH HOH . 
G 4 HOH A 15 2015 2015 HOH HOH . 
G 4 HOH A 16 2016 2016 HOH HOH . 
G 4 HOH A 17 2017 2017 HOH HOH . 
G 4 HOH A 18 2018 2018 HOH HOH . 
G 4 HOH A 19 2019 2019 HOH HOH . 
G 4 HOH A 20 2020 2020 HOH HOH . 
G 4 HOH A 21 2021 2021 HOH HOH . 
G 4 HOH A 22 2022 2022 HOH HOH . 
G 4 HOH A 23 2023 2023 HOH HOH . 
G 4 HOH A 24 2024 2024 HOH HOH . 
G 4 HOH A 25 2025 2025 HOH HOH . 
G 4 HOH A 26 2026 2026 HOH HOH . 
G 4 HOH A 27 2027 2027 HOH HOH . 
G 4 HOH A 28 2028 2028 HOH HOH . 
G 4 HOH A 29 2029 2029 HOH HOH . 
G 4 HOH A 30 2030 2030 HOH HOH . 
G 4 HOH A 31 2031 2031 HOH HOH . 
G 4 HOH A 32 2032 2032 HOH HOH . 
G 4 HOH A 33 2033 2033 HOH HOH . 
G 4 HOH A 34 2034 2034 HOH HOH . 
G 4 HOH A 35 2035 2035 HOH HOH . 
G 4 HOH A 36 2036 2036 HOH HOH . 
G 4 HOH A 37 2037 2037 HOH HOH . 
G 4 HOH A 38 2038 2038 HOH HOH . 
G 4 HOH A 39 2039 2039 HOH HOH . 
G 4 HOH A 40 2040 2040 HOH HOH . 
G 4 HOH A 41 2041 2041 HOH HOH . 
G 4 HOH A 42 2042 2042 HOH HOH . 
G 4 HOH A 43 2043 2043 HOH HOH . 
G 4 HOH A 44 2044 2044 HOH HOH . 
G 4 HOH A 45 2045 2045 HOH HOH . 
G 4 HOH A 46 2046 2046 HOH HOH . 
G 4 HOH A 47 2047 2047 HOH HOH . 
G 4 HOH A 48 2048 2048 HOH HOH . 
G 4 HOH A 49 2049 2049 HOH HOH . 
G 4 HOH A 50 2050 2050 HOH HOH . 
G 4 HOH A 51 2051 2051 HOH HOH . 
G 4 HOH A 52 2052 2052 HOH HOH . 
G 4 HOH A 53 2053 2053 HOH HOH . 
G 4 HOH A 54 2054 2054 HOH HOH . 
G 4 HOH A 55 2055 2055 HOH HOH . 
G 4 HOH A 56 2056 2056 HOH HOH . 
G 4 HOH A 57 2057 2057 HOH HOH . 
G 4 HOH A 58 2058 2058 HOH HOH . 
G 4 HOH A 59 2059 2059 HOH HOH . 
G 4 HOH A 60 2060 2060 HOH HOH . 
G 4 HOH A 61 2061 2061 HOH HOH . 
G 4 HOH A 62 2062 2062 HOH HOH . 
G 4 HOH A 63 2063 2063 HOH HOH . 
G 4 HOH A 64 2064 2064 HOH HOH . 
G 4 HOH A 65 2065 2065 HOH HOH . 
G 4 HOH A 66 2066 2066 HOH HOH . 
G 4 HOH A 67 2067 2067 HOH HOH . 
G 4 HOH A 68 2068 2068 HOH HOH . 
G 4 HOH A 69 2069 2069 HOH HOH . 
G 4 HOH A 70 2070 2070 HOH HOH . 
G 4 HOH A 71 2071 2071 HOH HOH . 
G 4 HOH A 72 2072 2072 HOH HOH . 
G 4 HOH A 73 2073 2073 HOH HOH . 
G 4 HOH A 74 2074 2074 HOH HOH . 
G 4 HOH A 75 2075 2075 HOH HOH . 
G 4 HOH A 76 2076 2076 HOH HOH . 
G 4 HOH A 77 2077 2077 HOH HOH . 
G 4 HOH A 78 2078 2078 HOH HOH . 
G 4 HOH A 79 2079 2079 HOH HOH . 
H 4 HOH B 1 2001 2001 HOH HOH . 
H 4 HOH B 2 2002 2002 HOH HOH . 
H 4 HOH B 3 2003 2003 HOH HOH . 
H 4 HOH B 4 2004 2004 HOH HOH . 
H 4 HOH B 5 2005 2005 HOH HOH . 
H 4 HOH B 6 2006 2006 HOH HOH . 
H 4 HOH B 7 2007 2007 HOH HOH . 
H 4 HOH B 8 2008 2008 HOH HOH . 
H 4 HOH B 9 2009 2009 HOH HOH . 
H 4 HOH B 10 2010 2010 HOH HOH . 
H 4 HOH B 11 2011 2011 HOH HOH . 
H 4 HOH B 12 2012 2012 HOH HOH . 
H 4 HOH B 13 2013 2013 HOH HOH . 
H 4 HOH B 14 2014 2014 HOH HOH . 
H 4 HOH B 15 2015 2015 HOH HOH . 
H 4 HOH B 16 2016 2016 HOH HOH . 
H 4 HOH B 17 2017 2017 HOH HOH . 
H 4 HOH B 18 2018 2018 HOH HOH . 
H 4 HOH B 19 2019 2019 HOH HOH . 
H 4 HOH B 20 2020 2020 HOH HOH . 
H 4 HOH B 21 2021 2021 HOH HOH . 
H 4 HOH B 22 2022 2022 HOH HOH . 
H 4 HOH B 23 2023 2023 HOH HOH . 
H 4 HOH B 24 2024 2024 HOH HOH . 
H 4 HOH B 25 2025 2025 HOH HOH . 
H 4 HOH B 26 2026 2026 HOH HOH . 
H 4 HOH B 27 2027 2027 HOH HOH . 
H 4 HOH B 28 2028 2028 HOH HOH . 
H 4 HOH B 29 2029 2029 HOH HOH . 
H 4 HOH B 30 2030 2030 HOH HOH . 
H 4 HOH B 31 2031 2031 HOH HOH . 
H 4 HOH B 32 2032 2032 HOH HOH . 
H 4 HOH B 33 2033 2033 HOH HOH . 
H 4 HOH B 34 2034 2034 HOH HOH . 
H 4 HOH B 35 2035 2035 HOH HOH . 
H 4 HOH B 36 2036 2036 HOH HOH . 
H 4 HOH B 37 2037 2037 HOH HOH . 
H 4 HOH B 38 2038 2038 HOH HOH . 
H 4 HOH B 39 2039 2039 HOH HOH . 
H 4 HOH B 40 2040 2040 HOH HOH . 
H 4 HOH B 41 2041 2041 HOH HOH . 
H 4 HOH B 42 2042 2042 HOH HOH . 
H 4 HOH B 43 2043 2043 HOH HOH . 
H 4 HOH B 44 2044 2044 HOH HOH . 
H 4 HOH B 45 2045 2045 HOH HOH . 
H 4 HOH B 46 2046 2046 HOH HOH . 
H 4 HOH B 47 2047 2047 HOH HOH . 
H 4 HOH B 48 2048 2048 HOH HOH . 
H 4 HOH B 49 2049 2049 HOH HOH . 
H 4 HOH B 50 2050 2050 HOH HOH . 
H 4 HOH B 51 2051 2051 HOH HOH . 
H 4 HOH B 52 2052 2052 HOH HOH . 
H 4 HOH B 53 2053 2053 HOH HOH . 
H 4 HOH B 54 2054 2054 HOH HOH . 
H 4 HOH B 55 2055 2055 HOH HOH . 
H 4 HOH B 56 2056 2056 HOH HOH . 
H 4 HOH B 57 2057 2057 HOH HOH . 
H 4 HOH B 58 2058 2058 HOH HOH . 
H 4 HOH B 59 2059 2059 HOH HOH . 
H 4 HOH B 60 2060 2060 HOH HOH . 
H 4 HOH B 61 2061 2061 HOH HOH . 
H 4 HOH B 62 2062 2062 HOH HOH . 
H 4 HOH B 63 2063 2063 HOH HOH . 
H 4 HOH B 64 2064 2064 HOH HOH . 
H 4 HOH B 65 2065 2065 HOH HOH . 
H 4 HOH B 66 2066 2066 HOH HOH . 
H 4 HOH B 67 2067 2067 HOH HOH . 
H 4 HOH B 68 2068 2068 HOH HOH . 
H 4 HOH B 69 2069 2069 HOH HOH . 
H 4 HOH B 70 2070 2070 HOH HOH . 
H 4 HOH B 71 2071 2071 HOH HOH . 
H 4 HOH B 72 2072 2072 HOH HOH . 
H 4 HOH B 73 2073 2073 HOH HOH . 
H 4 HOH B 74 2074 2074 HOH HOH . 
H 4 HOH B 75 2075 2075 HOH HOH . 
H 4 HOH B 76 2076 2076 HOH HOH . 
H 4 HOH B 77 2077 2077 HOH HOH . 
H 4 HOH B 78 2078 2078 HOH HOH . 
H 4 HOH B 79 2079 2079 HOH HOH . 
H 4 HOH B 80 2080 2080 HOH HOH . 
H 4 HOH B 81 2081 2081 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 O2 RCA . . . D 3 42.934 35.023 1.953 0.9 30.4 ? O2 RCA 500 A 1 
HETATM 2 C C3 RCA . . . D 3 45.278 35.549 1.5 0.9 32.22 ? C3 RCA 500 A 1 
HETATM 3 C C4 RCA . . . D 3 45.34 36.685 2.457 0.9 27.5 ? C4 RCA 500 A 1 
HETATM 4 C C5 RCA . . . D 3 46.369 35.185 0.761 0.9 34.44 ? C5 RCA 500 A 1 
HETATM 5 C C1 RCA . . . D 3 45.099 33.361 -0.309 0.9 30.82 ? C1 RCA 500 A 1 
HETATM 6 N N1 RCA . . . D 3 46.296 34.107 -0.138 0.9 30.43 ? N1 RCA 500 A 1 
HETATM 7 C C2 RCA . . . D 3 44.004 34.827 1.377 0.9 30.64 ? C2 RCA 500 A 1 
HETATM 8 N N2 RCA . . . D 3 43.964 33.731 0.449 0.9 30.47 ? N2 RCA 500 A 1 
HETATM 9 O O1 RCA . . . D 3 45.079 32.427 -1.103 0.9 29.96 ? O1 RCA 500 A 1 
HETATM 10 C C11 RCA . . . D 3 50.094 35.838 1.75 0.9 47.11 ? C11 RCA 500 A 1 
HETATM 11 O O4 RCA . . . D 3 52.317 32.959 1.719 0.9 55.15 ? O4 RCA 500 A 1 
HETATM 12 O O3 RCA . . . D 3 48.724 33.612 -0.821 0.9 44.33 ? O3 RCA 500 A 1 
HETATM 13 N N4 RCA . . . D 3 51.155 34.887 2.222 0.9 50.71 ? N4 RCA 500 A 1 
HETATM 14 C C10 RCA . . . D 3 51.457 33.772 1.401 0.9 51.38 ? C10 RCA 500 A 1 
HETATM 15 C C12 RCA . . . D 3 50.71 36.752 0.648 0.9 47.34 ? C12 RCA 500 A 1 
HETATM 16 O O5 RCA . . . D 3 50.66 38.072 1.132 0.9 51.55 ? O5 RCA 500 A 1 
HETATM 17 C C7 RCA . . . D 3 48.896 34.979 1.22 0.9 43.68 ? C7 RCA 500 A 1 
HETATM 18 N N3 RCA . . . D 3 50.696 33.557 0.205 0.9 47.67 ? N3 RCA 500 A 1 
HETATM 19 C C9 RCA . . . D 3 49.424 34.159 0.024 0.9 45.52 ? C9 RCA 500 A 1 
HETATM 20 C C6 RCA . . . D 3 47.709 35.884 0.852 0.9 37.98 ? C6 RCA 500 A 1 
HETATM 21 C C8 RCA . . . D 3 48.508 33.995 2.321 0.9 41.55 ? C8 RCA 500 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           300 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           21 
#