data_4U7P # _model_server_result.job_id qCrr3qHGevSVu7mzs-e9bw _model_server_result.datetime_utc '2025-03-05 02:32:51' _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 4u7p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1004}' # _entry.id 4U7P # _exptl.entry_id 4U7P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 4 _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 4U7P _cell.length_a 252.031 _cell.length_b 252.031 _cell.length_c 75.336 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4U7P _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63 2 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 _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 4 _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 metalc ? metalc1 A SG CYS 48 A CYS 494 1_555 D ZN ZN . A ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc2 A SG CYS 51 A CYS 497 1_555 D ZN ZN . A ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc3 A SG CYS 68 A CYS 514 1_555 D ZN ZN . A ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc4 A SG CYS 71 A CYS 517 1_555 D ZN ZN . A ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc5 A SG CYS 91 A CYS 537 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc6 A SG CYS 94 A CYS 540 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc7 A SG CYS 103 A CYS 549 1_555 E ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc8 A SG CYS 108 A CYS 554 1_555 E ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc9 A SG CYS 113 A CYS 559 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc10 A SG CYS 116 A CYS 562 1_555 C ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc11 A SG CYS 137 A CYS 583 1_555 E ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc12 A SG CYS 140 A CYS 586 1_555 E ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? # _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 275 n n N HN1 SAH sing 276 n n N HN2 SAH sing 277 n n CA CB SAH sing 278 n n CA C SAH sing 279 n n CA HA SAH sing 280 n n CB CG SAH sing 281 n n CB HB1 SAH sing 282 n n CB HB2 SAH sing 283 n n CG SD SAH sing 284 n n CG HG1 SAH sing 285 n n CG HG2 SAH sing 286 n n SD C5' SAH sing 287 n n C O SAH doub 288 n n C OXT SAH sing 289 n n OXT HXT SAH sing 290 n n C5' C4' SAH sing 291 n n C5' "H5'1" SAH sing 292 n n C5' "H5'2" SAH sing 293 n n C4' O4' SAH sing 294 n n C4' C3' SAH sing 295 n n C4' H4' SAH sing 296 n n O4' C1' SAH sing 297 n n C3' O3' SAH sing 298 n n C3' C2' SAH sing 299 n n C3' H3' SAH sing 300 n n O3' HO3' SAH sing 301 n n C2' O2' SAH sing 302 n n C2' C1' SAH sing 303 n n C2' H2' SAH sing 304 n n O2' HO2' SAH sing 305 n n C1' N9 SAH sing 306 n n C1' H1' SAH sing 307 n n N9 C8 SAH sing 308 n y N9 C4 SAH sing 309 n y C8 N7 SAH doub 310 n y C8 H8 SAH sing 311 n n N7 C5 SAH sing 312 n y C5 C6 SAH sing 313 n y C5 C4 SAH doub 314 n y C6 N6 SAH sing 315 n n C6 N1 SAH doub 316 n y N6 HN61 SAH sing 317 n n N6 HN62 SAH sing 318 n n N1 C2 SAH sing 319 n y C2 N3 SAH doub 320 n y C2 H2 SAH sing 321 n n N3 C4 SAH sing 322 n y # _atom_sites.entry_id 4U7P _atom_sites.fract_transf_matrix[1][1] 0.003968 _atom_sites.fract_transf_matrix[1][2] 0.002291 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004582 _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] 0.013274 _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 3 ZN A 1 1001 1 ZN ZN . D 3 ZN A 1 1002 1 ZN ZN . E 3 ZN A 1 1003 1 ZN ZN . F 4 SAH A 1 1004 2 SAH SAH . # 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 . . . F 4 -65.067 71.282 4.422 1 35.52 ? N SAH 1004 A 1 HETATM 2 C CA SAH . . . F 4 -64.572 71.897 3.192 1 36.46 ? CA SAH 1004 A 1 HETATM 3 C CB SAH . . . F 4 -65.251 73.249 2.965 1 39.3 ? CB SAH 1004 A 1 HETATM 4 C CG SAH . . . F 4 -66.428 73.536 3.899 1 42.29 ? CG SAH 1004 A 1 HETATM 5 S SD SAH . . . F 4 -66.882 75.289 4.009 1 52.32 ? SD SAH 1004 A 1 HETATM 6 C C SAH . . . F 4 -63.042 71.993 3.168 1 32.69 ? C SAH 1004 A 1 HETATM 7 O O SAH . . . F 4 -62.451 73.025 2.851 1 29.84 ? O SAH 1004 A 1 HETATM 8 O OXT SAH . . . F 4 -62.351 71.022 3.468 1 30.73 ? OXT SAH 1004 A 1 HETATM 9 C C5' SAH . . . F 4 -68.132 75.179 2.699 1 36.71 ? C5' SAH 1004 A 1 HETATM 10 C C4' SAH . . . F 4 -67.598 75.328 1.276 1 32.52 ? C4' SAH 1004 A 1 HETATM 11 O O4' SAH . . . F 4 -68.681 75.226 0.381 1 34.95 ? O4' SAH 1004 A 1 HETATM 12 C C3' SAH . . . F 4 -66.933 76.664 0.996 1 38.3 ? C3' SAH 1004 A 1 HETATM 13 O O3' SAH . . . F 4 -65.586 76.445 0.621 1 37.38 ? O3' SAH 1004 A 1 HETATM 14 C C2' SAH . . . F 4 -67.713 77.28 -0.156 1 40.24 ? C2' SAH 1004 A 1 HETATM 15 O O2' SAH . . . F 4 -66.84 77.754 -1.158 1 40.76 ? O2' SAH 1004 A 1 HETATM 16 C C1' SAH . . . F 4 -68.556 76.137 -0.691 1 38 ? C1' SAH 1004 A 1 HETATM 17 N N9 SAH . . . F 4 -69.893 76.566 -1.157 1 37.7 ? N9 SAH 1004 A 1 HETATM 18 C C8 SAH . . . F 4 -70.632 77.617 -0.673 1 36.56 ? C8 SAH 1004 A 1 HETATM 19 N N7 SAH . . . F 4 -71.802 77.668 -1.356 1 33.79 ? N7 SAH 1004 A 1 HETATM 20 C C5 SAH . . . F 4 -71.825 76.668 -2.265 1 29.58 ? C5 SAH 1004 A 1 HETATM 21 C C6 SAH . . . F 4 -72.773 76.28 -3.2 1 26.65 ? C6 SAH 1004 A 1 HETATM 22 N N6 SAH . . . F 4 -73.911 76.957 -3.305 1 25.81 ? N6 SAH 1004 A 1 HETATM 23 N N1 SAH . . . F 4 -72.529 75.195 -4.016 1 26.26 ? N1 SAH 1004 A 1 HETATM 24 C C2 SAH . . . F 4 -71.341 74.499 -3.889 1 27.53 ? C2 SAH 1004 A 1 HETATM 25 N N3 SAH . . . F 4 -70.398 74.897 -2.96 1 29.17 ? N3 SAH 1004 A 1 HETATM 26 C C4 SAH . . . F 4 -70.633 75.964 -2.154 1 32.37 ? C4 SAH 1004 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #