data_3KQM
#
_model_server_result.job_id            f6PsCap4bBn9EO5vfZXcoA 
_model_server_result.datetime_utc      '2024-11-24 18:55:10' 
_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          3kqm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":2001}' 
#
_entry.id    3KQM 
#
_exptl.entry_id    3KQM 
_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            3KQM 
_cell.length_a            93.78 
_cell.length_b            93.78 
_cell.length_c            188.661 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KQM 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf2 A SG CYS 139 A CYS 139 1_555 B SG CYS 48 B CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
#
_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 286 n n 
N HN1 SAH sing 287 n n 
N HN2 SAH sing 288 n n 
CA CB SAH sing 289 n n 
CA C SAH sing 290 n n 
CA HA SAH sing 291 n n 
CB CG SAH sing 292 n n 
CB HB1 SAH sing 293 n n 
CB HB2 SAH sing 294 n n 
CG SD SAH sing 295 n n 
CG HG1 SAH sing 296 n n 
CG HG2 SAH sing 297 n n 
SD C5' SAH sing 298 n n 
C O SAH doub 299 n n 
C OXT SAH sing 300 n n 
OXT HXT SAH sing 301 n n 
C5' C4' SAH sing 302 n n 
C5' "H5'1" SAH sing 303 n n 
C5' "H5'2" SAH sing 304 n n 
C4' O4' SAH sing 305 n n 
C4' C3' SAH sing 306 n n 
C4' H4' SAH sing 307 n n 
O4' C1' SAH sing 308 n n 
C3' O3' SAH sing 309 n n 
C3' C2' SAH sing 310 n n 
C3' H3' SAH sing 311 n n 
O3' HO3' SAH sing 312 n n 
C2' O2' SAH sing 313 n n 
C2' C1' SAH sing 314 n n 
C2' H2' SAH sing 315 n n 
O2' HO2' SAH sing 316 n n 
C1' N9 SAH sing 317 n n 
C1' H1' SAH sing 318 n n 
N9 C8 SAH sing 319 n y 
N9 C4 SAH sing 320 n y 
C8 N7 SAH doub 321 n y 
C8 H8 SAH sing 322 n n 
N7 C5 SAH sing 323 n y 
C5 C6 SAH sing 324 n y 
C5 C4 SAH doub 325 n y 
C6 N6 SAH sing 326 n n 
C6 N1 SAH doub 327 n y 
N6 HN61 SAH sing 328 n n 
N6 HN62 SAH sing 329 n n 
N1 C2 SAH sing 330 n y 
C2 N3 SAH doub 331 n y 
C2 H2 SAH sing 332 n n 
N3 C4 SAH sing 333 n y 
#
_atom_sites.entry_id                     3KQM 
_atom_sites.fract_transf_matrix[1][1]    0.010663 
_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]    0.010663 
_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]    0.005301 
_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 ES3 A 1 290 1 ES3 ES3 . 
E 2 SAH B 1 2002 2002 SAH SAH . 
F 3 ES3 B 1 290 2 ES3 ES3 . 
G 4 HOH A 1 2004 2004 HOH HOH . 
G 4 HOH A 2 2005 2005 HOH HOH . 
G 4 HOH A 3 2008 2008 HOH HOH . 
G 4 HOH A 4 2016 2016 HOH HOH . 
G 4 HOH A 5 2021 2021 HOH HOH . 
G 4 HOH A 6 2025 2025 HOH HOH . 
G 4 HOH A 7 2027 2027 HOH HOH . 
G 4 HOH A 8 2034 2034 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 2045 2045 HOH HOH . 
G 4 HOH A 12 2048 2048 HOH HOH . 
G 4 HOH A 13 2052 2052 HOH HOH . 
G 4 HOH A 14 2057 2057 HOH HOH . 
G 4 HOH A 15 2058 2058 HOH HOH . 
G 4 HOH A 16 2059 2059 HOH HOH . 
G 4 HOH A 17 2061 2061 HOH HOH . 
G 4 HOH A 18 2064 2064 HOH HOH . 
G 4 HOH A 19 2068 2068 HOH HOH . 
G 4 HOH A 20 2079 2079 HOH HOH . 
G 4 HOH A 21 2085 2085 HOH HOH . 
G 4 HOH A 22 2087 2087 HOH HOH . 
G 4 HOH A 23 2089 2089 HOH HOH . 
G 4 HOH A 24 2090 2090 HOH HOH . 
G 4 HOH A 25 2091 2091 HOH HOH . 
G 4 HOH A 26 2094 2094 HOH HOH . 
G 4 HOH A 27 2095 2095 HOH HOH . 
G 4 HOH A 28 2103 2103 HOH HOH . 
G 4 HOH A 29 2105 2105 HOH HOH . 
G 4 HOH A 30 2108 2108 HOH HOH . 
G 4 HOH A 31 2114 2114 HOH HOH . 
G 4 HOH A 32 2116 2116 HOH HOH . 
G 4 HOH A 33 2128 2128 HOH HOH . 
G 4 HOH A 34 2135 2135 HOH HOH . 
G 4 HOH A 35 2138 2138 HOH HOH . 
G 4 HOH A 36 2147 2147 HOH HOH . 
G 4 HOH A 37 2150 2150 HOH HOH . 
G 4 HOH A 38 2152 2152 HOH HOH . 
G 4 HOH A 39 2159 2159 HOH HOH . 
G 4 HOH A 40 2160 2160 HOH HOH . 
G 4 HOH A 41 2161 2161 HOH HOH . 
G 4 HOH A 42 2162 2162 HOH HOH . 
G 4 HOH A 43 2163 2163 HOH HOH . 
G 4 HOH A 44 2164 2164 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 2009 2009 HOH HOH . 
H 4 HOH B 4 2010 2010 HOH HOH . 
H 4 HOH B 5 2011 2011 HOH HOH . 
H 4 HOH B 6 2013 2013 HOH HOH . 
H 4 HOH B 7 2014 2014 HOH HOH . 
H 4 HOH B 8 2015 2015 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 2023 2023 HOH HOH . 
H 4 HOH B 12 2024 2024 HOH HOH . 
H 4 HOH B 13 2026 2026 HOH HOH . 
H 4 HOH B 14 2029 2029 HOH HOH . 
H 4 HOH B 15 2030 2030 HOH HOH . 
H 4 HOH B 16 2031 2031 HOH HOH . 
H 4 HOH B 17 2033 2033 HOH HOH . 
H 4 HOH B 18 2035 2035 HOH HOH . 
H 4 HOH B 19 2036 2036 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 2043 2043 HOH HOH . 
H 4 HOH B 25 2046 2046 HOH HOH . 
H 4 HOH B 26 2047 2047 HOH HOH . 
H 4 HOH B 27 2051 2051 HOH HOH . 
H 4 HOH B 28 2054 2054 HOH HOH . 
H 4 HOH B 29 2055 2055 HOH HOH . 
H 4 HOH B 30 2056 2056 HOH HOH . 
H 4 HOH B 31 2060 2060 HOH HOH . 
H 4 HOH B 32 2062 2062 HOH HOH . 
H 4 HOH B 33 2063 2063 HOH HOH . 
H 4 HOH B 34 2065 2065 HOH HOH . 
H 4 HOH B 35 2066 2066 HOH HOH . 
H 4 HOH B 36 2069 2069 HOH HOH . 
H 4 HOH B 37 2070 2070 HOH HOH . 
H 4 HOH B 38 2071 2071 HOH HOH . 
H 4 HOH B 39 2072 2072 HOH HOH . 
H 4 HOH B 40 2074 2074 HOH HOH . 
H 4 HOH B 41 2075 2075 HOH HOH . 
H 4 HOH B 42 2076 2076 HOH HOH . 
H 4 HOH B 43 2077 2077 HOH HOH . 
H 4 HOH B 44 2078 2078 HOH HOH . 
H 4 HOH B 45 2080 2080 HOH HOH . 
H 4 HOH B 46 2081 2081 HOH HOH . 
H 4 HOH B 47 2082 2082 HOH HOH . 
H 4 HOH B 48 2083 2083 HOH HOH . 
H 4 HOH B 49 2084 2084 HOH HOH . 
H 4 HOH B 50 2086 2086 HOH HOH . 
H 4 HOH B 51 2088 2088 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 2096 2096 HOH HOH . 
H 4 HOH B 55 2097 2097 HOH HOH . 
H 4 HOH B 56 2100 2100 HOH HOH . 
H 4 HOH B 57 2101 2101 HOH HOH . 
H 4 HOH B 58 2102 2102 HOH HOH . 
H 4 HOH B 59 2104 2104 HOH HOH . 
H 4 HOH B 60 2107 2107 HOH HOH . 
H 4 HOH B 61 2109 2109 HOH HOH . 
H 4 HOH B 62 2111 2111 HOH HOH . 
H 4 HOH B 63 2112 2112 HOH HOH . 
H 4 HOH B 64 2113 2113 HOH HOH . 
H 4 HOH B 65 2117 2117 HOH HOH . 
H 4 HOH B 66 2118 2118 HOH HOH . 
H 4 HOH B 67 2119 2119 HOH HOH . 
H 4 HOH B 68 2120 2120 HOH HOH . 
H 4 HOH B 69 2121 2121 HOH HOH . 
H 4 HOH B 70 2122 2122 HOH HOH . 
H 4 HOH B 71 2123 2123 HOH HOH . 
H 4 HOH B 72 2125 2125 HOH HOH . 
H 4 HOH B 73 2126 2126 HOH HOH . 
H 4 HOH B 74 2129 2129 HOH HOH . 
H 4 HOH B 75 2130 2130 HOH HOH . 
H 4 HOH B 76 2131 2131 HOH HOH . 
H 4 HOH B 77 2132 2132 HOH HOH . 
H 4 HOH B 78 2133 2133 HOH HOH . 
H 4 HOH B 79 2136 2136 HOH HOH . 
H 4 HOH B 80 2137 2137 HOH HOH . 
H 4 HOH B 81 2139 2139 HOH HOH . 
H 4 HOH B 82 2141 2141 HOH HOH . 
H 4 HOH B 83 2142 2142 HOH HOH . 
H 4 HOH B 84 2143 2143 HOH HOH . 
H 4 HOH B 85 2149 2149 HOH HOH . 
H 4 HOH B 86 2153 2153 HOH HOH . 
H 4 HOH B 87 2154 2154 HOH HOH . 
H 4 HOH B 88 2158 2158 HOH HOH . 
H 4 HOH B 89 2165 2165 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 26.683 53.041 17.692 1 45.58 ? N SAH 2001 A 1 
HETATM 2 C CA SAH . . . C 2 27.859 52.195 17.502 1 41.77 ? CA SAH 2001 A 1 
HETATM 3 C CB SAH . . . C 2 28.166 51.546 18.867 1 47.64 ? CB SAH 2001 A 1 
HETATM 4 C CG SAH . . . C 2 29.618 51.807 19.27 1 53.95 ? CG SAH 2001 A 1 
HETATM 5 S SD SAH . . . C 2 30.097 50.514 20.462 1 43.37 ? SD SAH 2001 A 1 
HETATM 6 C C SAH . . . C 2 27.467 51.085 16.506 1 42.81 ? C SAH 2001 A 1 
HETATM 7 O O SAH . . . C 2 26.313 50.834 16.355 1 39.89 ? O SAH 2001 A 1 
HETATM 8 O OXT SAH . . . C 2 28.421 50.141 16.104 1 41.96 ? OXT SAH 2001 A 1 
HETATM 9 C C5' SAH . . . C 2 29.742 51.096 22.151 1 54.06 ? C5' SAH 2001 A 1 
HETATM 10 C C4' SAH . . . C 2 29.912 52.622 22.235 1 54.3 ? C4' SAH 2001 A 1 
HETATM 11 O O4' SAH . . . C 2 29.543 53.115 23.562 1 55.51 ? O4' SAH 2001 A 1 
HETATM 12 C C3' SAH . . . C 2 31.361 53.077 21.998 1 53.61 ? C3' SAH 2001 A 1 
HETATM 13 O O3' SAH . . . C 2 31.378 54.078 21.013 1 45.93 ? O3' SAH 2001 A 1 
HETATM 14 C C2' SAH . . . C 2 31.734 53.671 23.332 1 50.97 ? C2' SAH 2001 A 1 
HETATM 15 O O2' SAH . . . C 2 32.789 54.6 23.305 1 46.61 ? O2' SAH 2001 A 1 
HETATM 16 C C1' SAH . . . C 2 30.416 54.259 23.811 1 50.35 ? C1' SAH 2001 A 1 
HETATM 17 N N9 SAH . . . C 2 30.502 54.487 25.242 1 52.29 ? N9 SAH 2001 A 1 
HETATM 18 C C8 SAH . . . C 2 31.539 53.929 26.163 1 57.15 ? C8 SAH 2001 A 1 
HETATM 19 N N7 SAH . . . C 2 31.216 54.366 27.519 1 56.74 ? N7 SAH 2001 A 1 
HETATM 20 C C5 SAH . . . C 2 29.99 55.172 27.444 1 49.03 ? C5 SAH 2001 A 1 
HETATM 21 C C6 SAH . . . C 2 29.203 55.875 28.507 1 51.07 ? C6 SAH 2001 A 1 
HETATM 22 N N6 SAH . . . C 2 29.649 55.795 29.892 1 53.63 ? N6 SAH 2001 A 1 
HETATM 23 N N1 SAH . . . C 2 27.999 56.622 28.139 1 51.37 ? N1 SAH 2001 A 1 
HETATM 24 C C2 SAH . . . C 2 27.552 56.688 26.703 1 45.44 ? C2 SAH 2001 A 1 
HETATM 25 N N3 SAH . . . C 2 28.348 56.001 25.643 1 43.49 ? N3 SAH 2001 A 1 
HETATM 26 C C4 SAH . . . C 2 29.554 55.243 26.027 1 47.8 ? C4 SAH 2001 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          20 
_model_server_stats.element_count           26 
#