data_4XVY # _model_server_result.job_id 1aCsnBmPBpfEZqs-EgfpnA _model_server_result.datetime_utc '2024-12-01 18:23:46' _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 4xvy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":302}' # _entry.id 4XVY # _exptl.entry_id 4XVY _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 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 4XVY _cell.length_a 50.057 _cell.length_b 89.892 _cell.length_c 127.655 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XVY _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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 ? 3 D N N ? 3 F 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 metalc ? metalc1 A OD1 ASP 209 A ASP 189 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc2 A OD1 ASP 211 A ASP 191 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? metalc ? metalc3 A OD2 ASP 236 A ASP 216 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc4 A OD2 ASP 237 A ASP 217 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc5 C MG MG . A MG 301 1_555 G O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc6 C MG MG . A MG 301 1_555 G O HOH . A HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc7 C MG MG . A MG 301 1_555 G O HOH . A HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc8 B OD1 ASP 209 B ASP 189 1_555 E MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc9 B OD1 ASP 211 B ASP 191 1_555 E MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc10 B OD2 ASP 236 B ASP 216 1_555 E MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc11 E MG MG . B MG 301 1_555 H O HOH . B HOH 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc12 E MG MG . B MG 301 1_555 H O HOH . B HOH 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? metalc ? metalc13 E MG MG . B MG 301 1_555 H O HOH . B HOH 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? # _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 4XVY _atom_sites.fract_transf_matrix[1][1] 0.019977 _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] 0.011124 _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] 0.007834 _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 MG A 1 301 2 MG MG . D 3 SAH A 1 302 2 SAH SAH . E 2 MG B 1 301 1 MG MG . F 3 SAH B 1 302 1 SAH SAH . G 4 HOH A 1 401 60 HOH HOH . G 4 HOH A 2 402 38 HOH HOH . G 4 HOH A 3 403 9 HOH HOH . G 4 HOH A 4 404 55 HOH HOH . G 4 HOH A 5 405 56 HOH HOH . G 4 HOH A 6 406 57 HOH HOH . G 4 HOH A 7 407 58 HOH HOH . G 4 HOH A 8 408 59 HOH HOH . G 4 HOH A 9 409 61 HOH HOH . G 4 HOH A 10 410 62 HOH HOH . G 4 HOH A 11 411 63 HOH HOH . G 4 HOH A 12 412 64 HOH HOH . H 4 HOH B 1 401 46 HOH HOH . H 4 HOH B 2 402 47 HOH HOH . H 4 HOH B 3 403 34 HOH HOH . H 4 HOH B 4 404 2 HOH HOH . H 4 HOH B 5 405 3 HOH HOH . H 4 HOH B 6 406 4 HOH HOH . H 4 HOH B 7 407 6 HOH HOH . H 4 HOH B 8 408 11 HOH HOH . H 4 HOH B 9 409 12 HOH HOH . H 4 HOH B 10 410 18 HOH HOH . H 4 HOH B 11 411 20 HOH HOH . H 4 HOH B 12 412 23 HOH HOH . H 4 HOH B 13 413 24 HOH HOH . H 4 HOH B 14 414 26 HOH HOH . H 4 HOH B 15 415 27 HOH HOH . H 4 HOH B 16 416 29 HOH HOH . H 4 HOH B 17 417 37 HOH HOH . H 4 HOH B 18 418 39 HOH HOH . H 4 HOH B 19 419 40 HOH HOH . H 4 HOH B 20 420 44 HOH HOH . H 4 HOH B 21 421 52 HOH HOH . H 4 HOH B 22 422 53 HOH HOH . H 4 HOH B 23 423 54 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 . . . F 3 -33.277 -4.52 -61.309 1 29.86 ? N SAH 302 B 1 HETATM 2 C CA SAH . . . F 3 -33.151 -5.717 -60.446 1 34.02 ? CA SAH 302 B 1 HETATM 3 C CB SAH . . . F 3 -33.032 -6.989 -61.289 1 40.07 ? CB SAH 302 B 1 HETATM 4 C CG SAH . . . F 3 -34.268 -7.269 -62.183 1 43.1 ? CG SAH 302 B 1 HETATM 5 S SD SAH . . . F 3 -34.239 -8.983 -62.654 1 50.05 ? SD SAH 302 B 1 HETATM 6 C C SAH . . . F 3 -32.016 -5.582 -59.431 1 34.97 ? C SAH 302 B 1 HETATM 7 O O SAH . . . F 3 -31.693 -4.42 -59.011 1 30.59 ? O SAH 302 B 1 HETATM 8 O OXT SAH . . . F 3 -31.454 -6.626 -58.963 1 31.74 ? OXT SAH 302 B 1 HETATM 9 C C5' SAH . . . F 3 -35.737 -9.164 -63.628 1 62.73 ? C5' SAH 302 B 1 HETATM 10 C C4' SAH . . . F 3 -37.073 -8.797 -62.952 1 63.07 ? C4' SAH 302 B 1 HETATM 11 O O4' SAH . . . F 3 -38.063 -8.417 -63.919 1 66.7 ? O4' SAH 302 B 1 HETATM 12 C C3' SAH . . . F 3 -37.705 -9.95 -62.176 1 68.35 ? C3' SAH 302 B 1 HETATM 13 O O3' SAH . . . F 3 -38.109 -9.419 -60.901 1 60.17 ? O3' SAH 302 B 1 HETATM 14 C C2' SAH . . . F 3 -38.889 -10.446 -63.028 1 72.36 ? C2' SAH 302 B 1 HETATM 15 O O2' SAH . . . F 3 -39.97 -10.982 -62.246 1 70.73 ? O2' SAH 302 B 1 HETATM 16 C C1' SAH . . . F 3 -39.31 -9.183 -63.796 1 75.91 ? C1' SAH 302 B 1 HETATM 17 N N9 SAH . . . F 3 -40.045 -9.316 -65.132 1 77.91 ? N9 SAH 302 B 1 HETATM 18 C C8 SAH . . . F 3 -39.601 -9.958 -66.238 1 77.1 ? C8 SAH 302 B 1 HETATM 19 N N7 SAH . . . F 3 -40.464 -9.853 -67.285 1 71.63 ? N7 SAH 302 B 1 HETATM 20 C C5 SAH . . . F 3 -41.505 -9.123 -66.87 1 70.68 ? C5 SAH 302 B 1 HETATM 21 C C6 SAH . . . F 3 -42.766 -8.632 -67.479 1 65.89 ? C6 SAH 302 B 1 HETATM 22 N N6 SAH . . . F 3 -43.087 -8.916 -68.75 1 65.45 ? N6 SAH 302 B 1 HETATM 23 N N1 SAH . . . F 3 -43.593 -7.88 -66.716 1 71.07 ? N1 SAH 302 B 1 HETATM 24 C C2 SAH . . . F 3 -43.29 -7.598 -65.42 1 66.7 ? C2 SAH 302 B 1 HETATM 25 N N3 SAH . . . F 3 -42.159 -8.007 -64.804 1 64.52 ? N3 SAH 302 B 1 HETATM 26 C C4 SAH . . . F 3 -41.233 -8.762 -65.458 1 70.31 ? C4 SAH 302 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #