data_3D49
#
_model_server_result.job_id            rFLjgxkD2m3gMibKDaeSuA 
_model_server_result.datetime_utc      '2024-11-24 14:22:55' 
_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          3d49 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":1900}' 
#
_entry.id    3D49 
#
_exptl.entry_id    3D49 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              120.152 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            BENZAMIDINE 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          100.39 
_cell.angle_gamma         90 
_cell.entry_id            3D49 
_cell.length_a            70.35 
_cell.length_b            71.48 
_cell.length_c            72.47 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3D49 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             F 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 9 L CYS 1 1_555 B SG CYS 119 H CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? 
disulf ? disulf2 B SG CYS 28 H CYS 42 1_555 B SG CYS 44 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
disulf ? disulf3 B SG CYS 173 H CYS 168 1_555 B SG CYS 187 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
disulf ? disulf4 B SG CYS 201 H CYS 191 1_555 B SG CYS 231 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
covale ? covale1 C C GLU 9 I GLU 62 1_555 C N TYS 10 I TYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? 
#
_chem_comp.formula           'C7 H8 N2' 
_chem_comp.formula_weight    120.152 
_chem_comp.id                BEN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              BENZAMIDINE 
_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
C1 C2 BEN doub 70 n y 
C1 C6 BEN sing 71 n y 
C1 C BEN sing 72 n n 
C2 C3 BEN sing 73 n y 
C2 H2 BEN sing 74 n n 
C3 C4 BEN doub 75 n y 
C3 H3 BEN sing 76 n n 
C4 C5 BEN sing 77 n y 
C4 H4 BEN sing 78 n n 
C5 C6 BEN doub 79 n y 
C5 H5 BEN sing 80 n n 
C6 H6 BEN sing 81 n n 
C N1 BEN doub 82 e n 
C N2 BEN sing 83 n n 
N1 HN1 BEN sing 84 n n 
N2 HN21 BEN sing 85 n n 
N2 HN22 BEN sing 86 n n 
#
_atom_sites.entry_id                     3D49 
_atom_sites.fract_transf_matrix[1][1]    0.014216 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002607 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01399 
_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]    0.01403 
_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
D 4 NA H 1 1800 1800 NA NA . 
E 4 NA H 1 1801 1801 NA NA . 
F 5 BEN H 1 1900 1900 BEN BEN . 
G 6 HOH L 1 2007 2007 HOH HOH . 
G 6 HOH L 2 2011 2011 HOH HOH . 
G 6 HOH L 3 2012 2012 HOH HOH . 
G 6 HOH L 4 2014 2014 HOH HOH . 
G 6 HOH L 5 2029 2029 HOH HOH . 
G 6 HOH L 6 2036 2036 HOH HOH . 
G 6 HOH L 7 2040 2040 HOH HOH . 
G 6 HOH L 8 2059 2059 HOH HOH . 
G 6 HOH L 9 2074 2074 HOH HOH . 
G 6 HOH L 10 2082 2082 HOH HOH . 
G 6 HOH L 11 2088 2088 HOH HOH . 
G 6 HOH L 12 2091 2091 HOH HOH . 
G 6 HOH L 13 2106 2106 HOH HOH . 
G 6 HOH L 14 2107 2107 HOH HOH . 
G 6 HOH L 15 2127 2127 HOH HOH . 
G 6 HOH L 16 2129 2129 HOH HOH . 
G 6 HOH L 17 2139 2139 HOH HOH . 
G 6 HOH L 18 2146 2146 HOH HOH . 
G 6 HOH L 19 2149 2149 HOH HOH . 
G 6 HOH L 20 2164 2164 HOH HOH . 
G 6 HOH L 21 2166 2166 HOH HOH . 
G 6 HOH L 22 2169 2169 HOH HOH . 
G 6 HOH L 23 2173 2173 HOH HOH . 
G 6 HOH L 24 2174 2174 HOH HOH . 
G 6 HOH L 25 2181 2181 HOH HOH . 
G 6 HOH L 26 2184 2184 HOH HOH . 
G 6 HOH L 27 2186 2186 HOH HOH . 
G 6 HOH L 28 2187 2187 HOH HOH . 
G 6 HOH L 29 2188 2188 HOH HOH . 
G 6 HOH L 30 2189 2189 HOH HOH . 
H 6 HOH H 1 2000 2000 HOH HOH . 
H 6 HOH H 2 2001 2001 HOH HOH . 
H 6 HOH H 3 2002 2002 HOH HOH . 
H 6 HOH H 4 2003 2003 HOH HOH . 
H 6 HOH H 5 2004 2004 HOH HOH . 
H 6 HOH H 6 2005 2005 HOH HOH . 
H 6 HOH H 7 2006 2006 HOH HOH . 
H 6 HOH H 8 2008 2008 HOH HOH . 
H 6 HOH H 9 2009 2009 HOH HOH . 
H 6 HOH H 10 2010 2010 HOH HOH . 
H 6 HOH H 11 2013 2013 HOH HOH . 
H 6 HOH H 12 2015 2015 HOH HOH . 
H 6 HOH H 13 2016 2016 HOH HOH . 
H 6 HOH H 14 2017 2017 HOH HOH . 
H 6 HOH H 15 2018 2018 HOH HOH . 
H 6 HOH H 16 2019 2019 HOH HOH . 
H 6 HOH H 17 2020 2020 HOH HOH . 
H 6 HOH H 18 2021 2021 HOH HOH . 
H 6 HOH H 19 2022 2022 HOH HOH . 
H 6 HOH H 20 2023 2023 HOH HOH . 
H 6 HOH H 21 2024 2024 HOH HOH . 
H 6 HOH H 22 2025 2025 HOH HOH . 
H 6 HOH H 23 2026 2026 HOH HOH . 
H 6 HOH H 24 2027 2027 HOH HOH . 
H 6 HOH H 25 2028 2028 HOH HOH . 
H 6 HOH H 26 2030 2030 HOH HOH . 
H 6 HOH H 27 2031 2031 HOH HOH . 
H 6 HOH H 28 2032 2032 HOH HOH . 
H 6 HOH H 29 2033 2033 HOH HOH . 
H 6 HOH H 30 2034 2034 HOH HOH . 
H 6 HOH H 31 2035 2035 HOH HOH . 
H 6 HOH H 32 2037 2037 HOH HOH . 
H 6 HOH H 33 2038 2038 HOH HOH . 
H 6 HOH H 34 2039 2039 HOH HOH . 
H 6 HOH H 35 2042 2042 HOH HOH . 
H 6 HOH H 36 2043 2043 HOH HOH . 
H 6 HOH H 37 2044 2044 HOH HOH . 
H 6 HOH H 38 2045 2045 HOH HOH . 
H 6 HOH H 39 2046 2046 HOH HOH . 
H 6 HOH H 40 2047 2047 HOH HOH . 
H 6 HOH H 41 2048 2048 HOH HOH . 
H 6 HOH H 42 2049 2049 HOH HOH . 
H 6 HOH H 43 2050 2050 HOH HOH . 
H 6 HOH H 44 2051 2051 HOH HOH . 
H 6 HOH H 45 2052 2052 HOH HOH . 
H 6 HOH H 46 2053 2053 HOH HOH . 
H 6 HOH H 47 2054 2054 HOH HOH . 
H 6 HOH H 48 2055 2055 HOH HOH . 
H 6 HOH H 49 2056 2056 HOH HOH . 
H 6 HOH H 50 2057 2057 HOH HOH . 
H 6 HOH H 51 2058 2058 HOH HOH . 
H 6 HOH H 52 2060 2060 HOH HOH . 
H 6 HOH H 53 2061 2061 HOH HOH . 
H 6 HOH H 54 2062 2062 HOH HOH . 
H 6 HOH H 55 2063 2063 HOH HOH . 
H 6 HOH H 56 2064 2064 HOH HOH . 
H 6 HOH H 57 2065 2065 HOH HOH . 
H 6 HOH H 58 2066 2066 HOH HOH . 
H 6 HOH H 59 2067 2067 HOH HOH . 
H 6 HOH H 60 2068 2068 HOH HOH . 
H 6 HOH H 61 2069 2069 HOH HOH . 
H 6 HOH H 62 2070 2070 HOH HOH . 
H 6 HOH H 63 2071 2071 HOH HOH . 
H 6 HOH H 64 2072 2072 HOH HOH . 
H 6 HOH H 65 2073 2073 HOH HOH . 
H 6 HOH H 66 2075 2075 HOH HOH . 
H 6 HOH H 67 2076 2076 HOH HOH . 
H 6 HOH H 68 2077 2077 HOH HOH . 
H 6 HOH H 69 2078 2078 HOH HOH . 
H 6 HOH H 70 2079 2079 HOH HOH . 
H 6 HOH H 71 2080 2080 HOH HOH . 
H 6 HOH H 72 2081 2081 HOH HOH . 
H 6 HOH H 73 2083 2083 HOH HOH . 
H 6 HOH H 74 2084 2084 HOH HOH . 
H 6 HOH H 75 2085 2085 HOH HOH . 
H 6 HOH H 76 2086 2086 HOH HOH . 
H 6 HOH H 77 2087 2087 HOH HOH . 
H 6 HOH H 78 2089 2089 HOH HOH . 
H 6 HOH H 79 2090 2090 HOH HOH . 
H 6 HOH H 80 2092 2092 HOH HOH . 
H 6 HOH H 81 2093 2093 HOH HOH . 
H 6 HOH H 82 2094 2094 HOH HOH . 
H 6 HOH H 83 2095 2095 HOH HOH . 
H 6 HOH H 84 2096 2096 HOH HOH . 
H 6 HOH H 85 2097 2097 HOH HOH . 
H 6 HOH H 86 2098 2098 HOH HOH . 
H 6 HOH H 87 2099 2099 HOH HOH . 
H 6 HOH H 88 2100 2100 HOH HOH . 
H 6 HOH H 89 2101 2101 HOH HOH . 
H 6 HOH H 90 2102 2102 HOH HOH . 
H 6 HOH H 91 2103 2103 HOH HOH . 
H 6 HOH H 92 2104 2104 HOH HOH . 
H 6 HOH H 93 2105 2105 HOH HOH . 
H 6 HOH H 94 2108 2108 HOH HOH . 
H 6 HOH H 95 2109 2109 HOH HOH . 
H 6 HOH H 96 2110 2110 HOH HOH . 
H 6 HOH H 97 2111 2111 HOH HOH . 
H 6 HOH H 98 2112 2112 HOH HOH . 
H 6 HOH H 99 2113 2113 HOH HOH . 
H 6 HOH H 100 2114 2114 HOH HOH . 
H 6 HOH H 101 2115 2115 HOH HOH . 
H 6 HOH H 102 2116 2116 HOH HOH . 
H 6 HOH H 103 2117 2117 HOH HOH . 
H 6 HOH H 104 2118 2118 HOH HOH . 
H 6 HOH H 105 2119 2119 HOH HOH . 
H 6 HOH H 106 2120 2120 HOH HOH . 
H 6 HOH H 107 2121 2121 HOH HOH . 
H 6 HOH H 108 2122 2122 HOH HOH . 
H 6 HOH H 109 2123 2123 HOH HOH . 
H 6 HOH H 110 2124 2124 HOH HOH . 
H 6 HOH H 111 2125 2125 HOH HOH . 
H 6 HOH H 112 2126 2126 HOH HOH . 
H 6 HOH H 113 2128 2128 HOH HOH . 
H 6 HOH H 114 2130 2130 HOH HOH . 
H 6 HOH H 115 2131 2131 HOH HOH . 
H 6 HOH H 116 2132 2132 HOH HOH . 
H 6 HOH H 117 2133 2133 HOH HOH . 
H 6 HOH H 118 2134 2134 HOH HOH . 
H 6 HOH H 119 2135 2135 HOH HOH . 
H 6 HOH H 120 2136 2136 HOH HOH . 
H 6 HOH H 121 2137 2137 HOH HOH . 
H 6 HOH H 122 2138 2138 HOH HOH . 
H 6 HOH H 123 2140 2140 HOH HOH . 
H 6 HOH H 124 2141 2141 HOH HOH . 
H 6 HOH H 125 2142 2142 HOH HOH . 
H 6 HOH H 126 2143 2143 HOH HOH . 
H 6 HOH H 127 2144 2144 HOH HOH . 
H 6 HOH H 128 2145 2145 HOH HOH . 
H 6 HOH H 129 2147 2147 HOH HOH . 
H 6 HOH H 130 2148 2148 HOH HOH . 
H 6 HOH H 131 2150 2150 HOH HOH . 
H 6 HOH H 132 2151 2151 HOH HOH . 
H 6 HOH H 133 2152 2152 HOH HOH . 
H 6 HOH H 134 2153 2153 HOH HOH . 
H 6 HOH H 135 2154 2154 HOH HOH . 
H 6 HOH H 136 2155 2155 HOH HOH . 
H 6 HOH H 137 2156 2156 HOH HOH . 
H 6 HOH H 138 2157 2157 HOH HOH . 
H 6 HOH H 139 2158 2158 HOH HOH . 
H 6 HOH H 140 2159 2159 HOH HOH . 
H 6 HOH H 141 2160 2160 HOH HOH . 
H 6 HOH H 142 2161 2161 HOH HOH . 
H 6 HOH H 143 2162 2162 HOH HOH . 
H 6 HOH H 144 2163 2163 HOH HOH . 
H 6 HOH H 145 2165 2165 HOH HOH . 
H 6 HOH H 146 2167 2167 HOH HOH . 
H 6 HOH H 147 2168 2168 HOH HOH . 
H 6 HOH H 148 2170 2170 HOH HOH . 
H 6 HOH H 149 2171 2171 HOH HOH . 
H 6 HOH H 150 2172 2172 HOH HOH . 
H 6 HOH H 151 2175 2175 HOH HOH . 
H 6 HOH H 152 2176 2176 HOH HOH . 
H 6 HOH H 153 2177 2177 HOH HOH . 
H 6 HOH H 154 2178 2178 HOH HOH . 
H 6 HOH H 155 2182 2182 HOH HOH . 
H 6 HOH H 156 2183 2183 HOH HOH . 
H 6 HOH H 157 2185 2185 HOH HOH . 
I 6 HOH I 1 2041 2041 HOH HOH . 
I 6 HOH I 2 2179 2179 HOH HOH . 
I 6 HOH I 3 2180 2180 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 C1 BEN . A . F 5 11.986 -19.662 33.066 0.61 20.39 ? C1 BEN 1900 H 1 
HETATM 2 C C1 BEN . B . F 5 11.284 -19.649 34.726 0.39 18.73 ? C1 BEN 1900 H 1 
HETATM 3 C C2 BEN . A . F 5 11.717 -20.766 32.41 0.61 26.88 ? C2 BEN 1900 H 1 
HETATM 4 C C2 BEN . B . F 5 10.69 -18.537 35.081 0.39 14.44 ? C2 BEN 1900 H 1 
HETATM 5 C C3 BEN . A . F 5 12.359 -20.963 31.245 0.61 22.53 ? C3 BEN 1900 H 1 
HETATM 6 C C3 BEN . B . F 5 10.12 -18.492 36.292 0.39 20.17 ? C3 BEN 1900 H 1 
HETATM 7 C C4 BEN . A . F 5 13.285 -20.046 30.72 0.61 34.78 ? C4 BEN 1900 H 1 
HETATM 8 C C4 BEN . B . F 5 10.165 -19.608 37.146 0.39 12.89 ? C4 BEN 1900 H 1 
HETATM 9 C C5 BEN . A . F 5 13.539 -18.991 31.349 0.61 20.94 ? C5 BEN 1900 H 1 
HETATM 10 C C5 BEN . B . F 5 10.736 -20.656 36.787 0.39 5.91 ? C5 BEN 1900 H 1 
HETATM 11 C C6 BEN . A . F 5 12.934 -18.738 32.516 0.61 19.61 ? C6 BEN 1900 H 1 
HETATM 12 C C6 BEN . B . F 5 11.333 -20.787 35.59 0.39 11.63 ? C6 BEN 1900 H 1 
HETATM 13 C C BEN . A . F 5 11.332 -19.329 34.38 0.61 23.36 ? C BEN 1900 H 1 
HETATM 14 C C BEN . B . F 5 11.942 -19.756 33.376 0.39 19.78 ? C BEN 1900 H 1 
HETATM 15 N N1 BEN . A . F 5 10.836 -20.229 35.254 0.61 28.16 ? N1 BEN 1900 H 1 
HETATM 16 N N1 BEN . B . F 5 12.182 -18.67 32.62 0.39 13.97 ? N1 BEN 1900 H 1 
HETATM 17 N N2 BEN . A . F 5 11.214 -18.058 34.756 0.61 26.64 ? N2 BEN 1900 H 1 
HETATM 18 N N2 BEN . B . F 5 12.312 -20.917 32.878 0.39 28.63 ? N2 BEN 1900 H 1 
#
_model_server_stats.io_time_ms              50 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           222 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           18 
#