data_3KQP
#
_model_server_result.job_id            IIDvB87TKLf0V3lbFtrMSQ 
_model_server_result.datetime_utc      '2024-11-06 15:27:23' 
_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          3kqp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":2001}' 
#
_entry.id    3KQP 
#
_exptl.entry_id    3KQP 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              384.411 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            S-ADENOSYL-L-HOMOCYSTEINE 
_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            3KQP 
_cell.length_a            93.568 
_cell.length_b            93.568 
_cell.length_c            188.745 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KQP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 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,G,H 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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
? 2 C N N 
? 2 E 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
disulf ? disulf1 A SG CYS 48 A CYS 48 1_555 B SG CYS 139 B CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf2 A SG CYS 139 A CYS 139 1_555 B SG CYS 48 B CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
#
_chem_comp.formula           'C14 H20 N6 O5 S' 
_chem_comp.formula_weight    384.411 
_chem_comp.id                SAH 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              S-ADENOSYL-L-HOMOCYSTEINE 
_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
N CA SAH sing 297 n n 
N HN1 SAH sing 298 n n 
N HN2 SAH sing 299 n n 
CA CB SAH sing 300 n n 
CA C SAH sing 301 n n 
CA HA SAH sing 302 n n 
CB CG SAH sing 303 n n 
CB HB1 SAH sing 304 n n 
CB HB2 SAH sing 305 n n 
CG SD SAH sing 306 n n 
CG HG1 SAH sing 307 n n 
CG HG2 SAH sing 308 n n 
SD C5' SAH sing 309 n n 
C O SAH doub 310 n n 
C OXT SAH sing 311 n n 
OXT HXT SAH sing 312 n n 
C5' C4' SAH sing 313 n n 
C5' "H5'1" SAH sing 314 n n 
C5' "H5'2" SAH sing 315 n n 
C4' O4' SAH sing 316 n n 
C4' C3' SAH sing 317 n n 
C4' H4' SAH sing 318 n n 
O4' C1' SAH sing 319 n n 
C3' O3' SAH sing 320 n n 
C3' C2' SAH sing 321 n n 
C3' H3' SAH sing 322 n n 
O3' HO3' SAH sing 323 n n 
C2' O2' SAH sing 324 n n 
C2' C1' SAH sing 325 n n 
C2' H2' SAH sing 326 n n 
O2' HO2' SAH sing 327 n n 
C1' N9 SAH sing 328 n n 
C1' H1' SAH sing 329 n n 
N9 C8 SAH sing 330 n y 
N9 C4 SAH sing 331 n y 
C8 N7 SAH doub 332 n y 
C8 H8 SAH sing 333 n n 
N7 C5 SAH sing 334 n y 
C5 C6 SAH sing 335 n y 
C5 C4 SAH doub 336 n y 
C6 N6 SAH sing 337 n n 
C6 N1 SAH doub 338 n y 
N6 HN61 SAH sing 339 n n 
N6 HN62 SAH sing 340 n n 
N1 C2 SAH sing 341 n y 
C2 N3 SAH doub 342 n y 
C2 H2 SAH sing 343 n n 
N3 C4 SAH sing 344 n y 
#
_atom_sites.entry_id                     3KQP 
_atom_sites.fract_transf_matrix[1][1]    0.010687 
_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]    0.010687 
_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]    0.005298 
_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 SAH A 1 2001 2001 SAH SAH . 
D 3 ES5 A 1 290 1 ES5 ES5 . 
E 2 SAH B 1 2002 2002 SAH SAH . 
F 3 ES5 B 1 290 2 ES5 ES5 . 
G 4 HOH A 1 2003 2003 HOH HOH . 
G 4 HOH A 2 2010 2010 HOH HOH . 
G 4 HOH A 3 2014 2014 HOH HOH . 
G 4 HOH A 4 2022 2022 HOH HOH . 
G 4 HOH A 5 2023 2023 HOH HOH . 
G 4 HOH A 6 2024 2024 HOH HOH . 
G 4 HOH A 7 2027 2027 HOH HOH . 
G 4 HOH A 8 2036 2036 HOH HOH . 
G 4 HOH A 9 2040 2040 HOH HOH . 
G 4 HOH A 10 2044 2044 HOH HOH . 
G 4 HOH A 11 2053 2053 HOH HOH . 
G 4 HOH A 12 2055 2055 HOH HOH . 
G 4 HOH A 13 2057 2057 HOH HOH . 
G 4 HOH A 14 2064 2064 HOH HOH . 
G 4 HOH A 15 2071 2071 HOH HOH . 
G 4 HOH A 16 2072 2072 HOH HOH . 
G 4 HOH A 17 2075 2075 HOH HOH . 
G 4 HOH A 18 2076 2076 HOH HOH . 
G 4 HOH A 19 2078 2078 HOH HOH . 
G 4 HOH A 20 2080 2080 HOH HOH . 
G 4 HOH A 21 2081 2081 HOH HOH . 
G 4 HOH A 22 2084 2084 HOH HOH . 
G 4 HOH A 23 2088 2088 HOH HOH . 
G 4 HOH A 24 2090 2090 HOH HOH . 
G 4 HOH A 25 2095 2095 HOH HOH . 
G 4 HOH A 26 2096 2096 HOH HOH . 
G 4 HOH A 27 2098 2098 HOH HOH . 
G 4 HOH A 28 2105 2105 HOH HOH . 
G 4 HOH A 29 2107 2107 HOH HOH . 
G 4 HOH A 30 2109 2109 HOH HOH . 
G 4 HOH A 31 2111 2111 HOH HOH . 
G 4 HOH A 32 2112 2112 HOH HOH . 
G 4 HOH A 33 2113 2113 HOH HOH . 
G 4 HOH A 34 2115 2115 HOH HOH . 
G 4 HOH A 35 2119 2119 HOH HOH . 
G 4 HOH A 36 2121 2121 HOH HOH . 
G 4 HOH A 37 2122 2122 HOH HOH . 
G 4 HOH A 38 2125 2125 HOH HOH . 
G 4 HOH A 39 2126 2126 HOH HOH . 
G 4 HOH A 40 2132 2132 HOH HOH . 
G 4 HOH A 41 2133 2133 HOH HOH . 
G 4 HOH A 42 2135 2135 HOH HOH . 
G 4 HOH A 43 2139 2139 HOH HOH . 
G 4 HOH A 44 2145 2145 HOH HOH . 
G 4 HOH A 45 2146 2146 HOH HOH . 
G 4 HOH A 46 2147 2147 HOH HOH . 
G 4 HOH A 47 2149 2149 HOH HOH . 
G 4 HOH A 48 2150 2150 HOH HOH . 
G 4 HOH A 49 2151 2151 HOH HOH . 
G 4 HOH A 50 2153 2153 HOH HOH . 
G 4 HOH A 51 2157 2157 HOH HOH . 
G 4 HOH A 52 2161 2161 HOH HOH . 
G 4 HOH A 53 2165 2165 HOH HOH . 
G 4 HOH A 54 2168 2168 HOH HOH . 
G 4 HOH A 55 2169 2169 HOH HOH . 
G 4 HOH A 56 2173 2173 HOH HOH . 
G 4 HOH A 57 2175 2175 HOH HOH . 
G 4 HOH A 58 2177 2177 HOH HOH . 
G 4 HOH A 59 2181 2181 HOH HOH . 
G 4 HOH A 60 2182 2182 HOH HOH . 
G 4 HOH A 61 2185 2185 HOH HOH . 
G 4 HOH A 62 2186 2186 HOH HOH . 
G 4 HOH A 63 2187 2187 HOH HOH . 
G 4 HOH A 64 2188 2188 HOH HOH . 
G 4 HOH A 65 2189 2189 HOH HOH . 
G 4 HOH A 66 2190 2190 HOH HOH . 
G 4 HOH A 67 2191 2191 HOH HOH . 
G 4 HOH A 68 2192 2192 HOH HOH . 
G 4 HOH A 69 2193 2193 HOH HOH . 
G 4 HOH A 70 2194 2194 HOH HOH . 
G 4 HOH A 71 2195 2195 HOH HOH . 
H 4 HOH B 1 2006 2006 HOH HOH . 
H 4 HOH B 2 2007 2007 HOH HOH . 
H 4 HOH B 3 2008 2008 HOH HOH . 
H 4 HOH B 4 2009 2009 HOH HOH . 
H 4 HOH B 5 2012 2012 HOH HOH . 
H 4 HOH B 6 2013 2013 HOH HOH . 
H 4 HOH B 7 2015 2015 HOH HOH . 
H 4 HOH B 8 2016 2016 HOH HOH . 
H 4 HOH B 9 2017 2017 HOH HOH . 
H 4 HOH B 10 2018 2018 HOH HOH . 
H 4 HOH B 11 2020 2020 HOH HOH . 
H 4 HOH B 12 2021 2021 HOH HOH . 
H 4 HOH B 13 2025 2025 HOH HOH . 
H 4 HOH B 14 2028 2028 HOH HOH . 
H 4 HOH B 15 2029 2029 HOH HOH . 
H 4 HOH B 16 2030 2030 HOH HOH . 
H 4 HOH B 17 2031 2031 HOH HOH . 
H 4 HOH B 18 2032 2032 HOH HOH . 
H 4 HOH B 19 2034 2034 HOH HOH . 
H 4 HOH B 20 2037 2037 HOH HOH . 
H 4 HOH B 21 2038 2038 HOH HOH . 
H 4 HOH B 22 2039 2039 HOH HOH . 
H 4 HOH B 23 2041 2041 HOH HOH . 
H 4 HOH B 24 2042 2042 HOH HOH . 
H 4 HOH B 25 2043 2043 HOH HOH . 
H 4 HOH B 26 2045 2045 HOH HOH . 
H 4 HOH B 27 2046 2046 HOH HOH . 
H 4 HOH B 28 2047 2047 HOH HOH . 
H 4 HOH B 29 2050 2050 HOH HOH . 
H 4 HOH B 30 2054 2054 HOH HOH . 
H 4 HOH B 31 2056 2056 HOH HOH . 
H 4 HOH B 32 2058 2058 HOH HOH . 
H 4 HOH B 33 2059 2059 HOH HOH . 
H 4 HOH B 34 2060 2060 HOH HOH . 
H 4 HOH B 35 2061 2061 HOH HOH . 
H 4 HOH B 36 2062 2062 HOH HOH . 
H 4 HOH B 37 2063 2063 HOH HOH . 
H 4 HOH B 38 2065 2065 HOH HOH . 
H 4 HOH B 39 2066 2066 HOH HOH . 
H 4 HOH B 40 2067 2067 HOH HOH . 
H 4 HOH B 41 2068 2068 HOH HOH . 
H 4 HOH B 42 2069 2069 HOH HOH . 
H 4 HOH B 43 2070 2070 HOH HOH . 
H 4 HOH B 44 2073 2073 HOH HOH . 
H 4 HOH B 45 2074 2074 HOH HOH . 
H 4 HOH B 46 2077 2077 HOH HOH . 
H 4 HOH B 47 2079 2079 HOH HOH . 
H 4 HOH B 48 2083 2083 HOH HOH . 
H 4 HOH B 49 2086 2086 HOH HOH . 
H 4 HOH B 50 2087 2087 HOH HOH . 
H 4 HOH B 51 2091 2091 HOH HOH . 
H 4 HOH B 52 2092 2092 HOH HOH . 
H 4 HOH B 53 2093 2093 HOH HOH . 
H 4 HOH B 54 2094 2094 HOH HOH . 
H 4 HOH B 55 2099 2099 HOH HOH . 
H 4 HOH B 56 2101 2101 HOH HOH . 
H 4 HOH B 57 2102 2102 HOH HOH . 
H 4 HOH B 58 2103 2103 HOH HOH . 
H 4 HOH B 59 2110 2110 HOH HOH . 
H 4 HOH B 60 2116 2116 HOH HOH . 
H 4 HOH B 61 2117 2117 HOH HOH . 
H 4 HOH B 62 2118 2118 HOH HOH . 
H 4 HOH B 63 2120 2120 HOH HOH . 
H 4 HOH B 64 2124 2124 HOH HOH . 
H 4 HOH B 65 2128 2128 HOH HOH . 
H 4 HOH B 66 2129 2129 HOH HOH . 
H 4 HOH B 67 2131 2131 HOH HOH . 
H 4 HOH B 68 2134 2134 HOH HOH . 
H 4 HOH B 69 2137 2137 HOH HOH . 
H 4 HOH B 70 2138 2138 HOH HOH . 
H 4 HOH B 71 2142 2142 HOH HOH . 
H 4 HOH B 72 2143 2143 HOH HOH . 
H 4 HOH B 73 2144 2144 HOH HOH . 
H 4 HOH B 74 2154 2154 HOH HOH . 
H 4 HOH B 75 2155 2155 HOH HOH . 
H 4 HOH B 76 2156 2156 HOH HOH . 
H 4 HOH B 77 2159 2159 HOH HOH . 
H 4 HOH B 78 2160 2160 HOH HOH . 
H 4 HOH B 79 2162 2162 HOH HOH . 
H 4 HOH B 80 2163 2163 HOH HOH . 
H 4 HOH B 81 2170 2170 HOH HOH . 
H 4 HOH B 82 2171 2171 HOH HOH . 
H 4 HOH B 83 2172 2172 HOH HOH . 
H 4 HOH B 84 2174 2174 HOH HOH . 
H 4 HOH B 85 2176 2176 HOH HOH . 
H 4 HOH B 86 2178 2178 HOH HOH . 
H 4 HOH B 87 2179 2179 HOH HOH . 
H 4 HOH B 88 2180 2180 HOH HOH . 
H 4 HOH B 89 2183 2183 HOH HOH . 
H 4 HOH B 90 2184 2184 HOH HOH . 
H 4 HOH B 91 2196 2196 HOH HOH . 
H 4 HOH B 92 2197 2197 HOH HOH . 
H 4 HOH B 93 2198 2198 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 N SAH . . . C 2 26.746 53.216 17.863 1 43.77 ? N SAH 2001 A 1 
HETATM 2 C CA SAH . . . C 2 27.88 52.382 17.479 1 45.49 ? CA SAH 2001 A 1 
HETATM 3 C CB SAH . . . C 2 28.314 51.601 18.733 1 49.63 ? CB SAH 2001 A 1 
HETATM 4 C CG SAH . . . C 2 29.716 52.039 19.155 1 56.93 ? CG SAH 2001 A 1 
HETATM 5 S SD SAH . . . C 2 30.299 50.807 20.359 1 42.59 ? SD SAH 2001 A 1 
HETATM 6 C C SAH . . . C 2 27.424 51.362 16.42 1 45.21 ? C SAH 2001 A 1 
HETATM 7 O O SAH . . . C 2 26.264 51.205 16.219 1 47.1 ? O SAH 2001 A 1 
HETATM 8 O OXT SAH . . . C 2 28.309 50.34 16.067 1 30.85 ? OXT SAH 2001 A 1 
HETATM 9 C C5' SAH . . . C 2 29.838 51.333 22.037 1 50.36 ? C5' SAH 2001 A 1 
HETATM 10 C C4' SAH . . . C 2 30.032 52.85 22.177 1 53.25 ? C4' SAH 2001 A 1 
HETATM 11 O O4' SAH . . . C 2 29.658 53.288 23.521 1 52.1 ? O4' SAH 2001 A 1 
HETATM 12 C C3' SAH . . . C 2 31.497 53.277 21.963 1 54.51 ? C3' SAH 2001 A 1 
HETATM 13 O O3' SAH . . . C 2 31.558 54.301 21.001 1 48.78 ? O3' SAH 2001 A 1 
HETATM 14 C C2' SAH . . . C 2 31.883 53.805 23.319 1 48.04 ? C2' SAH 2001 A 1 
HETATM 15 O O2' SAH . . . C 2 32.948 54.722 23.335 1 42.81 ? O2' SAH 2001 A 1 
HETATM 16 C C1' SAH . . . C 2 30.571 54.387 23.82 1 48.72 ? C1' SAH 2001 A 1 
HETATM 17 N N9 SAH . . . C 2 30.651 54.569 25.253 1 47.38 ? N9 SAH 2001 A 1 
HETATM 18 C C8 SAH . . . C 2 31.671 53.961 26.155 1 48.12 ? C8 SAH 2001 A 1 
HETATM 19 N N7 SAH . . . C 2 31.36 54.382 27.513 1 52.57 ? N7 SAH 2001 A 1 
HETATM 20 C C5 SAH . . . C 2 30.162 55.231 27.465 1 46.18 ? C5 SAH 2001 A 1 
HETATM 21 C C6 SAH . . . C 2 29.398 55.93 28.548 1 49.01 ? C6 SAH 2001 A 1 
HETATM 22 N N6 SAH . . . C 2 29.837 55.792 29.933 1 50.81 ? N6 SAH 2001 A 1 
HETATM 23 N N1 SAH . . . C 2 28.22 56.721 28.2 1 52.1 ? N1 SAH 2001 A 1 
HETATM 24 C C2 SAH . . . C 2 27.771 56.84 26.767 1 50.6 ? C2 SAH 2001 A 1 
HETATM 25 N N3 SAH . . . C 2 28.537 56.148 25.692 1 44.94 ? N3 SAH 2001 A 1 
HETATM 26 C C4 SAH . . . C 2 29.724 55.346 26.052 1 45.92 ? C4 SAH 2001 A 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           26 
#