data_1YAK
#
_model_server_result.job_id            L6t8tG2ChwqpE1cYRZSg1g 
_model_server_result.datetime_utc      '2024-11-15 21:24:29' 
_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          1yak 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":303}' 
#
_entry.id    1YAK 
#
_exptl.entry_id    1YAK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              139.155 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE 
_entity.pdbx_number_of_molecules    4 
_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            1YAK 
_cell.length_a            82.958 
_cell.length_b            82.928 
_cell.length_c            296.364 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1YAK 
_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,PQS tetrameric 4 author_and_software_defined_assembly 1 
PISA,PQS tetrameric 4 author_and_software_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,E,F,I,J 1 1,2 
C,D,G,H,K,L 2 1,3 
#
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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
3 'crystal symmetry operation' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 82.958 0 148.182 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
#
_chem_comp.formula           'C6 H9 N3 O' 
_chem_comp.formula_weight    139.155 
_chem_comp.id                HMH 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE 
_chem_comp.type              non-polymer 
_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
CM2 C2A HMH sing 150 n n 
CM2 HCM1 HMH sing 151 n n 
CM2 HCM2 HMH sing 152 n n 
CM2 HCM3 HMH sing 153 n n 
N1A C2A HMH doub 154 n y 
N1A C6A HMH sing 155 n y 
C2A N3A HMH sing 156 n y 
N3A C4A HMH doub 157 n y 
C4A N4A HMH sing 158 n n 
C4A C5A HMH sing 159 n y 
N4A HN41 HMH sing 160 n n 
N4A HN42 HMH sing 161 n n 
C5A C6A HMH doub 162 n y 
C5A C7A HMH sing 163 n n 
C6A HC6 HMH sing 164 n n 
C7A O1 HMH sing 165 n n 
C7A HC71 HMH sing 166 n n 
C7A HC72 HMH sing 167 n n 
O1 HO1 HMH sing 168 n n 
#
_atom_sites.entry_id                     1YAK 
_atom_sites.fract_transf_matrix[1][1]    0.012054 
_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]    0.012059 
_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]    0.003374 
_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
E 2 HMH A 1 301 301 HMH HMH . 
F 2 HMH B 1 303 303 HMH HMH . 
G 2 HMH C 1 304 304 HMH HMH . 
H 2 HMH D 1 302 302 HMH HMH . 
I 3 HOH A 1 2001 2001 HOH HOH . 
I 3 HOH A 2 2002 2002 HOH HOH . 
I 3 HOH A 3 2007 2007 HOH HOH . 
I 3 HOH A 4 2008 2008 HOH HOH . 
I 3 HOH A 5 2009 2009 HOH HOH . 
I 3 HOH A 6 2015 2015 HOH HOH . 
I 3 HOH A 7 2017 2017 HOH HOH . 
I 3 HOH A 8 2020 2020 HOH HOH . 
I 3 HOH A 9 2022 2022 HOH HOH . 
I 3 HOH A 10 2024 2024 HOH HOH . 
I 3 HOH A 11 2026 2026 HOH HOH . 
I 3 HOH A 12 2037 2037 HOH HOH . 
I 3 HOH A 13 2041 2041 HOH HOH . 
I 3 HOH A 14 2052 2052 HOH HOH . 
I 3 HOH A 15 2054 2054 HOH HOH . 
I 3 HOH A 16 2056 2056 HOH HOH . 
I 3 HOH A 17 2057 2057 HOH HOH . 
I 3 HOH A 18 2058 2058 HOH HOH . 
I 3 HOH A 19 2065 2065 HOH HOH . 
I 3 HOH A 20 2067 2067 HOH HOH . 
I 3 HOH A 21 2068 2068 HOH HOH . 
I 3 HOH A 22 2075 2075 HOH HOH . 
I 3 HOH A 23 2076 2076 HOH HOH . 
I 3 HOH A 24 2079 2079 HOH HOH . 
I 3 HOH A 25 2085 2085 HOH HOH . 
I 3 HOH A 26 2088 2088 HOH HOH . 
I 3 HOH A 27 2098 2098 HOH HOH . 
I 3 HOH A 28 2100 2100 HOH HOH . 
I 3 HOH A 29 2107 2107 HOH HOH . 
I 3 HOH A 30 2112 2112 HOH HOH . 
I 3 HOH A 31 2116 2116 HOH HOH . 
I 3 HOH A 32 2118 2118 HOH HOH . 
I 3 HOH A 33 2122 2122 HOH HOH . 
I 3 HOH A 34 2132 2132 HOH HOH . 
I 3 HOH A 35 2133 2133 HOH HOH . 
I 3 HOH A 36 2141 2141 HOH HOH . 
I 3 HOH A 37 2150 2150 HOH HOH . 
I 3 HOH A 38 2153 2153 HOH HOH . 
I 3 HOH A 39 2155 2155 HOH HOH . 
I 3 HOH A 40 2156 2156 HOH HOH . 
I 3 HOH A 41 2165 2165 HOH HOH . 
I 3 HOH A 42 2170 2170 HOH HOH . 
I 3 HOH A 43 2187 2187 HOH HOH . 
I 3 HOH A 44 2190 2190 HOH HOH . 
I 3 HOH A 45 2191 2191 HOH HOH . 
I 3 HOH A 46 2192 2192 HOH HOH . 
I 3 HOH A 47 2193 2193 HOH HOH . 
I 3 HOH A 48 2196 2196 HOH HOH . 
I 3 HOH A 49 2198 2198 HOH HOH . 
I 3 HOH A 50 2199 2199 HOH HOH . 
I 3 HOH A 51 2201 2201 HOH HOH . 
I 3 HOH A 52 2204 2204 HOH HOH . 
I 3 HOH A 53 2206 2206 HOH HOH . 
I 3 HOH A 54 2209 2209 HOH HOH . 
I 3 HOH A 55 2210 2210 HOH HOH . 
I 3 HOH A 56 2212 2212 HOH HOH . 
I 3 HOH A 57 2214 2214 HOH HOH . 
I 3 HOH A 58 2215 2215 HOH HOH . 
I 3 HOH A 59 2216 2216 HOH HOH . 
I 3 HOH A 60 2217 2217 HOH HOH . 
I 3 HOH A 61 2218 2218 HOH HOH . 
I 3 HOH A 62 2219 2219 HOH HOH . 
I 3 HOH A 63 2220 2220 HOH HOH . 
I 3 HOH A 64 2221 2221 HOH HOH . 
I 3 HOH A 65 2233 2233 HOH HOH . 
I 3 HOH A 66 2234 2234 HOH HOH . 
I 3 HOH A 67 2235 2235 HOH HOH . 
I 3 HOH A 68 2240 2240 HOH HOH . 
J 3 HOH B 1 2010 2010 HOH HOH . 
J 3 HOH B 2 2016 2016 HOH HOH . 
J 3 HOH B 3 2019 2019 HOH HOH . 
J 3 HOH B 4 2031 2031 HOH HOH . 
J 3 HOH B 5 2034 2034 HOH HOH . 
J 3 HOH B 6 2035 2035 HOH HOH . 
J 3 HOH B 7 2038 2038 HOH HOH . 
J 3 HOH B 8 2040 2040 HOH HOH . 
J 3 HOH B 9 2042 2042 HOH HOH . 
J 3 HOH B 10 2048 2048 HOH HOH . 
J 3 HOH B 11 2049 2049 HOH HOH . 
J 3 HOH B 12 2051 2051 HOH HOH . 
J 3 HOH B 13 2062 2062 HOH HOH . 
J 3 HOH B 14 2063 2063 HOH HOH . 
J 3 HOH B 15 2064 2064 HOH HOH . 
J 3 HOH B 16 2074 2074 HOH HOH . 
J 3 HOH B 17 2094 2094 HOH HOH . 
J 3 HOH B 18 2123 2123 HOH HOH . 
J 3 HOH B 19 2124 2124 HOH HOH . 
J 3 HOH B 20 2129 2129 HOH HOH . 
J 3 HOH B 21 2154 2154 HOH HOH . 
J 3 HOH B 22 2158 2158 HOH HOH . 
J 3 HOH B 23 2177 2177 HOH HOH . 
J 3 HOH B 24 2189 2189 HOH HOH . 
J 3 HOH B 25 2197 2197 HOH HOH . 
J 3 HOH B 26 2202 2202 HOH HOH . 
J 3 HOH B 27 2222 2222 HOH HOH . 
J 3 HOH B 28 2239 2239 HOH HOH . 
J 3 HOH B 29 2241 2241 HOH HOH . 
J 3 HOH B 30 2242 2242 HOH HOH . 
K 3 HOH C 1 2004 2004 HOH HOH . 
K 3 HOH C 2 2006 2006 HOH HOH . 
K 3 HOH C 3 2014 2014 HOH HOH . 
K 3 HOH C 4 2018 2018 HOH HOH . 
K 3 HOH C 5 2036 2036 HOH HOH . 
K 3 HOH C 6 2044 2044 HOH HOH . 
K 3 HOH C 7 2046 2046 HOH HOH . 
K 3 HOH C 8 2050 2050 HOH HOH . 
K 3 HOH C 9 2055 2055 HOH HOH . 
K 3 HOH C 10 2069 2069 HOH HOH . 
K 3 HOH C 11 2084 2084 HOH HOH . 
K 3 HOH C 12 2087 2087 HOH HOH . 
K 3 HOH C 13 2089 2089 HOH HOH . 
K 3 HOH C 14 2090 2090 HOH HOH . 
K 3 HOH C 15 2092 2092 HOH HOH . 
K 3 HOH C 16 2099 2099 HOH HOH . 
K 3 HOH C 17 2108 2108 HOH HOH . 
K 3 HOH C 18 2114 2114 HOH HOH . 
K 3 HOH C 19 2144 2144 HOH HOH . 
K 3 HOH C 20 2149 2149 HOH HOH . 
K 3 HOH C 21 2161 2161 HOH HOH . 
K 3 HOH C 22 2162 2162 HOH HOH . 
K 3 HOH C 23 2211 2211 HOH HOH . 
K 3 HOH C 24 2224 2224 HOH HOH . 
K 3 HOH C 25 2228 2228 HOH HOH . 
K 3 HOH C 26 2229 2229 HOH HOH . 
L 3 HOH D 1 2000 2000 HOH HOH . 
L 3 HOH D 2 2003 2003 HOH HOH . 
L 3 HOH D 3 2005 2005 HOH HOH . 
L 3 HOH D 4 2011 2011 HOH HOH . 
L 3 HOH D 5 2012 2012 HOH HOH . 
L 3 HOH D 6 2013 2013 HOH HOH . 
L 3 HOH D 7 2021 2021 HOH HOH . 
L 3 HOH D 8 2023 2023 HOH HOH . 
L 3 HOH D 9 2025 2025 HOH HOH . 
L 3 HOH D 10 2027 2027 HOH HOH . 
L 3 HOH D 11 2028 2028 HOH HOH . 
L 3 HOH D 12 2029 2029 HOH HOH . 
L 3 HOH D 13 2030 2030 HOH HOH . 
L 3 HOH D 14 2033 2033 HOH HOH . 
L 3 HOH D 15 2039 2039 HOH HOH . 
L 3 HOH D 16 2043 2043 HOH HOH . 
L 3 HOH D 17 2045 2045 HOH HOH . 
L 3 HOH D 18 2047 2047 HOH HOH . 
L 3 HOH D 19 2059 2059 HOH HOH . 
L 3 HOH D 20 2060 2060 HOH HOH . 
L 3 HOH D 21 2070 2070 HOH HOH . 
L 3 HOH D 22 2072 2072 HOH HOH . 
L 3 HOH D 23 2077 2077 HOH HOH . 
L 3 HOH D 24 2078 2078 HOH HOH . 
L 3 HOH D 25 2080 2080 HOH HOH . 
L 3 HOH D 26 2081 2081 HOH HOH . 
L 3 HOH D 27 2082 2082 HOH HOH . 
L 3 HOH D 28 2083 2083 HOH HOH . 
L 3 HOH D 29 2091 2091 HOH HOH . 
L 3 HOH D 30 2093 2093 HOH HOH . 
L 3 HOH D 31 2095 2095 HOH HOH . 
L 3 HOH D 32 2097 2097 HOH HOH . 
L 3 HOH D 33 2102 2102 HOH HOH . 
L 3 HOH D 34 2105 2105 HOH HOH . 
L 3 HOH D 35 2110 2110 HOH HOH . 
L 3 HOH D 36 2115 2115 HOH HOH . 
L 3 HOH D 37 2120 2120 HOH HOH . 
L 3 HOH D 38 2135 2135 HOH HOH . 
L 3 HOH D 39 2136 2136 HOH HOH . 
L 3 HOH D 40 2140 2140 HOH HOH . 
L 3 HOH D 41 2143 2143 HOH HOH . 
L 3 HOH D 42 2146 2146 HOH HOH . 
L 3 HOH D 43 2147 2147 HOH HOH . 
L 3 HOH D 44 2164 2164 HOH HOH . 
L 3 HOH D 45 2178 2178 HOH HOH . 
L 3 HOH D 46 2186 2186 HOH HOH . 
L 3 HOH D 47 2188 2188 HOH HOH . 
L 3 HOH D 48 2194 2194 HOH HOH . 
L 3 HOH D 49 2195 2195 HOH HOH . 
L 3 HOH D 50 2200 2200 HOH HOH . 
L 3 HOH D 51 2203 2203 HOH HOH . 
L 3 HOH D 52 2205 2205 HOH HOH . 
L 3 HOH D 53 2207 2207 HOH HOH . 
L 3 HOH D 54 2208 2208 HOH HOH . 
L 3 HOH D 55 2213 2213 HOH HOH . 
L 3 HOH D 56 2223 2223 HOH HOH . 
L 3 HOH D 57 2225 2225 HOH HOH . 
L 3 HOH D 58 2226 2226 HOH HOH . 
L 3 HOH D 59 2227 2227 HOH HOH . 
L 3 HOH D 60 2230 2230 HOH HOH . 
L 3 HOH D 61 2231 2231 HOH HOH . 
L 3 HOH D 62 2232 2232 HOH HOH . 
L 3 HOH D 63 2236 2236 HOH HOH . 
L 3 HOH D 64 2237 2237 HOH HOH . 
L 3 HOH D 65 2238 2238 HOH HOH . 
L 3 HOH D 66 2243 2243 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 C CM2 HMH . . . F 2 72.891 -21.541 11.497 1 54.55 ? CM2 HMH 303 B 1 
HETATM 2 N N1A HMH . . . F 2 74.338 -21.959 9.546 1 54.55 ? N1A HMH 303 B 1 
HETATM 3 C C2A HMH . . . F 2 73.124 -22.251 10.232 1 54.55 ? C2A HMH 303 B 1 
HETATM 4 N N3A HMH . . . F 2 72.241 -23.129 9.749 1 54.55 ? N3A HMH 303 B 1 
HETATM 5 C C4A HMH . . . F 2 72.468 -23.831 8.502 1 54.55 ? C4A HMH 303 B 1 
HETATM 6 N N4A HMH . . . F 2 71.525 -24.692 8.099 1 54.55 ? N4A HMH 303 B 1 
HETATM 7 C C5A HMH . . . F 2 73.752 -23.576 7.697 1 54.55 ? C5A HMH 303 B 1 
HETATM 8 C C6A HMH . . . F 2 74.626 -22.616 8.309 1 54.55 ? C6A HMH 303 B 1 
HETATM 9 C C7A HMH . . . F 2 73.957 -24.329 6.4 1 54.55 ? C7A HMH 303 B 1 
HETATM 10 O O1 HMH . . . F 2 73.932 -23.507 4.98 1 54.55 ? O1 HMH 303 B 1 
#
_model_server_stats.io_time_ms              74 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           10 
#