data_5F5E
#
_model_server_result.job_id            FwoJ7gjJx7TIidKVyX0MAg 
_model_server_result.datetime_utc      '2025-06-21 05:28:32' 
_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          5f5e 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":4002}' 
#
_entry.id    5F5E 
#
_exptl.entry_id    5F5E 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              384.411 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            S-ADENOSYL-L-HOMOCYSTEINE 
_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          90 
_cell.angle_gamma         120 
_cell.entry_id            5F5E 
_cell.length_a            54.574 
_cell.length_b            54.574 
_cell.length_c            104.656 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5F5E 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32 2 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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                      3 
_struct_asym.id                             C 
_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
metalc ? metalc1 A SG CYS 98 A CYS 3909 1_555 B ZN ZN . A ZN 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? 
metalc ? metalc2 A SG CYS 146 A CYS 3957 1_555 B ZN ZN . A ZN 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc3 A SG CYS 148 A CYS 3959 1_555 B ZN ZN . A ZN 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? 
metalc ? metalc4 A SG CYS 153 A CYS 3964 1_555 B ZN ZN . A ZN 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? 
metalc ? metalc5 B ZN ZN . A ZN 4001 1_555 D O HOH . A HOH 4109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? 
#
_chem_comp.formula           'C14 H20 N6 O5 S' 
_chem_comp.formula_weight    384.411 
_chem_comp.id                SAH 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              S-ADENOSYL-L-HOMOCYSTEINE 
_chem_comp.type              'l-peptide linking' 
_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 277 n n 
N HN1 SAH sing 278 n n 
N HN2 SAH sing 279 n n 
CA CB SAH sing 280 n n 
CA C SAH sing 281 n n 
CA HA SAH sing 282 n n 
CB CG SAH sing 283 n n 
CB HB1 SAH sing 284 n n 
CB HB2 SAH sing 285 n n 
CG SD SAH sing 286 n n 
CG HG1 SAH sing 287 n n 
CG HG2 SAH sing 288 n n 
SD C5' SAH sing 289 n n 
C O SAH doub 290 n n 
C OXT SAH sing 291 n n 
OXT HXT SAH sing 292 n n 
C5' C4' SAH sing 293 n n 
C5' "H5'1" SAH sing 294 n n 
C5' "H5'2" SAH sing 295 n n 
C4' O4' SAH sing 296 n n 
C4' C3' SAH sing 297 n n 
C4' H4' SAH sing 298 n n 
O4' C1' SAH sing 299 n n 
C3' O3' SAH sing 300 n n 
C3' C2' SAH sing 301 n n 
C3' H3' SAH sing 302 n n 
O3' HO3' SAH sing 303 n n 
C2' O2' SAH sing 304 n n 
C2' C1' SAH sing 305 n n 
C2' H2' SAH sing 306 n n 
O2' HO2' SAH sing 307 n n 
C1' N9 SAH sing 308 n n 
C1' H1' SAH sing 309 n n 
N9 C8 SAH sing 310 n y 
N9 C4 SAH sing 311 n y 
C8 N7 SAH doub 312 n y 
C8 H8 SAH sing 313 n n 
N7 C5 SAH sing 314 n y 
C5 C6 SAH sing 315 n y 
C5 C4 SAH doub 316 n y 
C6 N6 SAH sing 317 n n 
C6 N1 SAH doub 318 n y 
N6 HN61 SAH sing 319 n n 
N6 HN62 SAH sing 320 n n 
N1 C2 SAH sing 321 n y 
C2 N3 SAH doub 322 n y 
C2 H2 SAH sing 323 n n 
N3 C4 SAH sing 324 n y 
#
_atom_sites.entry_id                     5F5E 
_atom_sites.fract_transf_matrix[1][1]    0.018324 
_atom_sites.fract_transf_matrix[1][2]    0.010579 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.021158 
_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]    0.009555 
_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
B 2 ZN A 1 4001 4970 ZN ZN . 
C 3 SAH A 1 4002 4971 SAH SAH . 
D 4 HOH A 1 4101 94 HOH HOH . 
D 4 HOH A 2 4102 133 HOH HOH . 
D 4 HOH A 3 4103 128 HOH HOH . 
D 4 HOH A 4 4104 111 HOH HOH . 
D 4 HOH A 5 4105 136 HOH HOH . 
D 4 HOH A 6 4106 53 HOH HOH . 
D 4 HOH A 7 4107 90 HOH HOH . 
D 4 HOH A 8 4108 75 HOH HOH . 
D 4 HOH A 9 4109 109 HOH HOH . 
D 4 HOH A 10 4110 118 HOH HOH . 
D 4 HOH A 11 4111 112 HOH HOH . 
D 4 HOH A 12 4112 88 HOH HOH . 
D 4 HOH A 13 4113 1 HOH HOH . 
D 4 HOH A 14 4114 115 HOH HOH . 
D 4 HOH A 15 4115 63 HOH HOH . 
D 4 HOH A 16 4116 51 HOH HOH . 
D 4 HOH A 17 4117 36 HOH HOH . 
D 4 HOH A 18 4118 66 HOH HOH . 
D 4 HOH A 19 4119 103 HOH HOH . 
D 4 HOH A 20 4120 13 HOH HOH . 
D 4 HOH A 21 4121 16 HOH HOH . 
D 4 HOH A 22 4122 14 HOH HOH . 
D 4 HOH A 23 4123 69 HOH HOH . 
D 4 HOH A 24 4124 104 HOH HOH . 
D 4 HOH A 25 4125 77 HOH HOH . 
D 4 HOH A 26 4126 34 HOH HOH . 
D 4 HOH A 27 4127 70 HOH HOH . 
D 4 HOH A 28 4128 30 HOH HOH . 
D 4 HOH A 29 4129 89 HOH HOH . 
D 4 HOH A 30 4130 87 HOH HOH . 
D 4 HOH A 31 4131 8 HOH HOH . 
D 4 HOH A 32 4132 59 HOH HOH . 
D 4 HOH A 33 4133 6 HOH HOH . 
D 4 HOH A 34 4134 85 HOH HOH . 
D 4 HOH A 35 4135 49 HOH HOH . 
D 4 HOH A 36 4136 44 HOH HOH . 
D 4 HOH A 37 4137 72 HOH HOH . 
D 4 HOH A 38 4138 2 HOH HOH . 
D 4 HOH A 39 4139 60 HOH HOH . 
D 4 HOH A 40 4140 45 HOH HOH . 
D 4 HOH A 41 4141 41 HOH HOH . 
D 4 HOH A 42 4142 9 HOH HOH . 
D 4 HOH A 43 4143 50 HOH HOH . 
D 4 HOH A 44 4144 23 HOH HOH . 
D 4 HOH A 45 4145 43 HOH HOH . 
D 4 HOH A 46 4146 20 HOH HOH . 
D 4 HOH A 47 4147 54 HOH HOH . 
D 4 HOH A 48 4148 102 HOH HOH . 
D 4 HOH A 49 4149 138 HOH HOH . 
D 4 HOH A 50 4150 25 HOH HOH . 
D 4 HOH A 51 4151 22 HOH HOH . 
D 4 HOH A 52 4152 24 HOH HOH . 
D 4 HOH A 53 4153 7 HOH HOH . 
D 4 HOH A 54 4154 116 HOH HOH . 
D 4 HOH A 55 4155 76 HOH HOH . 
D 4 HOH A 56 4156 26 HOH HOH . 
D 4 HOH A 57 4157 110 HOH HOH . 
D 4 HOH A 58 4158 108 HOH HOH . 
D 4 HOH A 59 4159 11 HOH HOH . 
D 4 HOH A 60 4160 19 HOH HOH . 
D 4 HOH A 61 4161 4 HOH HOH . 
D 4 HOH A 62 4162 56 HOH HOH . 
D 4 HOH A 63 4163 140 HOH HOH . 
D 4 HOH A 64 4164 3 HOH HOH . 
D 4 HOH A 65 4165 28 HOH HOH . 
D 4 HOH A 66 4166 117 HOH HOH . 
D 4 HOH A 67 4167 47 HOH HOH . 
D 4 HOH A 68 4168 84 HOH HOH . 
D 4 HOH A 69 4169 5 HOH HOH . 
D 4 HOH A 70 4170 52 HOH HOH . 
D 4 HOH A 71 4171 18 HOH HOH . 
D 4 HOH A 72 4172 62 HOH HOH . 
D 4 HOH A 73 4173 21 HOH HOH . 
D 4 HOH A 74 4174 73 HOH HOH . 
D 4 HOH A 75 4175 74 HOH HOH . 
D 4 HOH A 76 4176 92 HOH HOH . 
D 4 HOH A 77 4177 78 HOH HOH . 
D 4 HOH A 78 4178 29 HOH HOH . 
D 4 HOH A 79 4179 113 HOH HOH . 
D 4 HOH A 80 4180 100 HOH HOH . 
D 4 HOH A 81 4181 126 HOH HOH . 
D 4 HOH A 82 4182 130 HOH HOH . 
D 4 HOH A 83 4183 105 HOH HOH . 
D 4 HOH A 84 4184 10 HOH HOH . 
D 4 HOH A 85 4185 80 HOH HOH . 
D 4 HOH A 86 4186 27 HOH HOH . 
D 4 HOH A 87 4187 135 HOH HOH . 
D 4 HOH A 88 4188 12 HOH HOH . 
D 4 HOH A 89 4189 39 HOH HOH . 
D 4 HOH A 90 4190 91 HOH HOH . 
D 4 HOH A 91 4191 32 HOH HOH . 
D 4 HOH A 92 4192 35 HOH HOH . 
D 4 HOH A 93 4193 42 HOH HOH . 
D 4 HOH A 94 4194 58 HOH HOH . 
D 4 HOH A 95 4195 99 HOH HOH . 
D 4 HOH A 96 4196 17 HOH HOH . 
D 4 HOH A 97 4197 79 HOH HOH . 
D 4 HOH A 98 4198 107 HOH HOH . 
D 4 HOH A 99 4199 81 HOH HOH . 
D 4 HOH A 100 4200 46 HOH HOH . 
D 4 HOH A 101 4201 48 HOH HOH . 
D 4 HOH A 102 4202 114 HOH HOH . 
D 4 HOH A 103 4203 141 HOH HOH . 
D 4 HOH A 104 4204 132 HOH HOH . 
D 4 HOH A 105 4205 86 HOH HOH . 
D 4 HOH A 106 4206 71 HOH HOH . 
D 4 HOH A 107 4207 64 HOH HOH . 
D 4 HOH A 108 4208 38 HOH HOH . 
D 4 HOH A 109 4209 97 HOH HOH . 
D 4 HOH A 110 4210 33 HOH HOH . 
D 4 HOH A 111 4211 127 HOH HOH . 
D 4 HOH A 112 4212 83 HOH HOH . 
D 4 HOH A 113 4213 121 HOH HOH . 
D 4 HOH A 114 4214 124 HOH HOH . 
D 4 HOH A 115 4215 67 HOH HOH . 
D 4 HOH A 116 4216 40 HOH HOH . 
D 4 HOH A 117 4217 106 HOH HOH . 
D 4 HOH A 118 4218 15 HOH HOH . 
D 4 HOH A 119 4219 31 HOH HOH . 
D 4 HOH A 120 4220 123 HOH HOH . 
D 4 HOH A 121 4221 82 HOH HOH . 
D 4 HOH A 122 4222 57 HOH HOH . 
D 4 HOH A 123 4223 55 HOH HOH . 
D 4 HOH A 124 4224 101 HOH HOH . 
D 4 HOH A 125 4225 61 HOH HOH . 
D 4 HOH A 126 4226 65 HOH HOH . 
D 4 HOH A 127 4227 134 HOH HOH . 
D 4 HOH A 128 4228 142 HOH HOH . 
D 4 HOH A 129 4229 125 HOH HOH . 
D 4 HOH A 130 4230 137 HOH HOH . 
D 4 HOH A 131 4231 68 HOH HOH . 
D 4 HOH A 132 4232 131 HOH HOH . 
D 4 HOH A 133 4233 37 HOH HOH . 
D 4 HOH A 134 4234 98 HOH HOH . 
D 4 HOH A 135 4235 129 HOH HOH . 
D 4 HOH A 136 4236 95 HOH HOH . 
D 4 HOH A 137 4237 122 HOH HOH . 
D 4 HOH A 138 4238 93 HOH HOH . 
D 4 HOH A 139 4239 96 HOH HOH . 
D 4 HOH A 140 4240 120 HOH HOH . 
D 4 HOH A 141 4241 139 HOH HOH . 
D 4 HOH A 142 4242 119 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 3 -4.329 305.086 221.895 1 25.98 ? N SAH 4002 A 1 
HETATM 2 C CA SAH . . . C 3 -4.106 306.117 222.912 1 30.08 ? CA SAH 4002 A 1 
HETATM 3 C CB SAH . . . C 3 -4.632 307.471 222.427 1 23.45 ? CB SAH 4002 A 1 
HETATM 4 C CG SAH . . . C 3 -3.55 308.283 221.687 1 24.95 ? CG SAH 4002 A 1 
HETATM 5 S SD SAH . . . C 3 -2.362 308.913 222.891 1 28.59 ? SD SAH 4002 A 1 
HETATM 6 C C SAH . . . C 3 -4.731 305.699 224.235 1 31.16 ? C SAH 4002 A 1 
HETATM 7 O O SAH . . . C 3 -5.642 304.855 224.284 1 32.19 ? O SAH 4002 A 1 
HETATM 8 O OXT SAH . . . C 3 -4.318 306.19 225.286 1 27.57 ? OXT SAH 4002 A 1 
HETATM 9 C C5' SAH . . . C 3 -0.843 308.575 221.942 1 31.87 ? C5' SAH 4002 A 1 
HETATM 10 C C4' SAH . . . C 3 -0.183 307.263 222.347 1 34.75 ? C4' SAH 4002 A 1 
HETATM 11 O O4' SAH . . . C 3 -0.96 306.203 221.819 1 33.22 ? O4' SAH 4002 A 1 
HETATM 12 C C3' SAH . . . C 3 1.227 307.062 221.801 1 34.97 ? C3' SAH 4002 A 1 
HETATM 13 O O3' SAH . . . C 3 2.198 307.456 222.74 1 35.87 ? O3' SAH 4002 A 1 
HETATM 14 C C2' SAH . . . C 3 1.289 305.566 221.632 1 32.76 ? C2' SAH 4002 A 1 
HETATM 15 O O2' SAH . . . C 3 1.566 305.008 222.888 1 36.81 ? O2' SAH 4002 A 1 
HETATM 16 C C1' SAH . . . C 3 -0.129 305.185 221.278 1 34.89 ? C1' SAH 4002 A 1 
HETATM 17 N N9 SAH . . . C 3 -0.235 305.193 219.811 1 32.93 ? N9 SAH 4002 A 1 
HETATM 18 C C8 SAH . . . C 3 -0.812 306.151 219.033 1 26.7 ? C8 SAH 4002 A 1 
HETATM 19 N N7 SAH . . . C 3 -0.688 305.803 217.729 1 35.61 ? N7 SAH 4002 A 1 
HETATM 20 C C5 SAH . . . C 3 -0.026 304.631 217.661 1 35.24 ? C5 SAH 4002 A 1 
HETATM 21 C C6 SAH . . . C 3 0.366 303.843 216.579 1 33.87 ? C6 SAH 4002 A 1 
HETATM 22 N N6 SAH . . . C 3 0.095 304.188 215.32 1 38.42 ? N6 SAH 4002 A 1 
HETATM 23 N N1 SAH . . . C 3 1.031 302.68 216.843 1 32.7 ? N1 SAH 4002 A 1 
HETATM 24 C C2 SAH . . . C 3 1.32 302.298 218.133 1 31.83 ? C2 SAH 4002 A 1 
HETATM 25 N N3 SAH . . . C 3 0.927 303.083 219.201 1 38.62 ? N3 SAH 4002 A 1 
HETATM 26 C C4 SAH . . . C 3 0.268 304.234 218.957 1 37.49 ? C4 SAH 4002 A 1 
#
_model_server_stats.io_time_ms              59 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           277 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           26 
#