data_5U0B # _model_server_result.job_id N8Kd20Rim4wA27T518kWEA _model_server_result.datetime_utc '2024-11-17 06:27:37' _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 5u0b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1001}' # _entry.id 5U0B # _exptl.entry_id 5U0B _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 5U0B _cell.length_a 136.5 _cell.length_b 197 _cell.length_c 95.28 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5U0B _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H 1 1 B,I,J,K,L,M,N 2 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 I 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 covale ? covale1 A NZ LYS 691 A LYS 691 1_555 G O3 SO4 . A SO4 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.298 ? covale ? covale2 B NZ LYS 691 B LYS 691 1_555 M O1 SO4 . B SO4 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.298 ? metalc ? metalc1 A OE1 GLU 439 A GLU 439 1_555 D ZN ZN . A ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc2 A NE2 HIS 443 A HIS 443 1_555 D ZN ZN . A ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc3 A SG CYS 448 A CYS 448 1_555 D ZN ZN . A ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc4 A SG CYS 451 A CYS 451 1_555 D ZN ZN . A ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc5 A NE2 HIS 714 A HIS 714 1_555 E ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc6 A SG CYS 730 A CYS 730 1_555 E ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc7 A SG CYS 849 A CYS 849 1_555 E ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc8 B OE1 GLU 439 B GLU 439 1_555 J ZN ZN . B ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc9 B NE2 HIS 443 B HIS 443 1_555 J ZN ZN . B ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc10 B SG CYS 448 B CYS 448 1_555 J ZN ZN . B ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc11 B SG CYS 451 B CYS 451 1_555 J ZN ZN . B ZN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc12 B NE2 HIS 714 B HIS 714 1_555 K ZN ZN . B ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc13 B SG CYS 730 B CYS 730 1_555 K ZN ZN . B ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc14 B SG CYS 849 B CYS 849 1_555 K ZN ZN . B ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? # _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 5U0B _atom_sites.fract_transf_matrix[1][1] 0.007326 _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] 0.005076 _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] 0.010495 _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 1001 1 SAH SAH . D 3 ZN A 1 1002 1 ZN ZN . E 3 ZN A 1 1003 2 ZN ZN . F 4 SO4 A 1 1004 1 SO4 SO4 . G 4 SO4 A 1 1005 2 SO4 SO4 . H 4 SO4 A 1 1006 3 SO4 SO4 . I 2 SAH B 1 1001 2 SAH SAH . J 3 ZN B 1 1002 3 ZN ZN . K 3 ZN B 1 1003 4 ZN ZN . L 4 SO4 B 1 1004 4 SO4 SO4 . M 4 SO4 B 1 1005 5 SO4 SO4 . N 4 SO4 B 1 1006 6 SO4 SO4 . # 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 . . . I 2 31.139 63.303 11.396 1 45.53 ? N SAH 1001 B 1 HETATM 2 C CA SAH . . . I 2 31.008 62.104 12.22 1 40.2 ? CA SAH 1001 B 1 HETATM 3 C CB SAH . . . I 2 29.618 61.479 12.1 1 39.35 ? CB SAH 1001 B 1 HETATM 4 C CG SAH . . . I 2 28.622 62.243 11.232 1 38.49 ? CG SAH 1001 B 1 HETATM 5 S SD SAH . . . I 2 27.33 61.17 10.549 1 36.42 ? SD SAH 1001 B 1 HETATM 6 C C SAH . . . I 2 32.099 61.08 11.916 1 30.78 ? C SAH 1001 B 1 HETATM 7 O O SAH . . . I 2 33.208 61.433 11.513 1 39.48 ? O SAH 1001 B 1 HETATM 8 O OXT SAH . . . I 2 31.901 59.875 12.078 1 27.28 ? OXT SAH 1001 B 1 HETATM 9 C C5' SAH . . . I 2 26.048 61.984 11.539 1 23.83 ? C5' SAH 1001 B 1 HETATM 10 C C4' SAH . . . I 2 25.408 61.092 12.597 1 32.27 ? C4' SAH 1001 B 1 HETATM 11 O O4' SAH . . . I 2 24.423 61.819 13.307 1 37.91 ? O4' SAH 1001 B 1 HETATM 12 C C3' SAH . . . I 2 24.708 59.889 11.986 1 41.3 ? C3' SAH 1001 B 1 HETATM 13 O O3' SAH . . . I 2 25.275 58.705 12.496 1 58.72 ? O3' SAH 1001 B 1 HETATM 14 C C2' SAH . . . I 2 23.262 59.984 12.428 1 29.75 ? C2' SAH 1001 B 1 HETATM 15 O O2' SAH . . . I 2 22.796 58.73 12.869 1 27.79 ? O2' SAH 1001 B 1 HETATM 16 C C1' SAH . . . I 2 23.302 60.995 13.562 1 31.16 ? C1' SAH 1001 B 1 HETATM 17 N N9 SAH . . . I 2 22.06 61.787 13.647 1 32.78 ? N9 SAH 1001 B 1 HETATM 18 C C8 SAH . . . I 2 21.211 62.139 12.63 1 44.43 ? C8 SAH 1001 B 1 HETATM 19 N N7 SAH . . . I 2 20.194 62.863 13.156 1 51.26 ? N7 SAH 1001 B 1 HETATM 20 C C5 SAH . . . I 2 20.385 62.975 14.49 1 49.59 ? C5 SAH 1001 B 1 HETATM 21 C C6 SAH . . . I 2 19.662 63.6 15.5 1 57.51 ? C6 SAH 1001 B 1 HETATM 22 N N6 SAH . . . I 2 18.539 64.25 15.212 1 60.46 ? N6 SAH 1001 B 1 HETATM 23 N N1 SAH . . . I 2 20.116 63.541 16.802 1 52.43 ? N1 SAH 1001 B 1 HETATM 24 C C2 SAH . . . I 2 21.283 62.866 17.094 1 39.23 ? C2 SAH 1001 B 1 HETATM 25 N N3 SAH . . . I 2 21.995 62.249 16.087 1 34.07 ? N3 SAH 1001 B 1 HETATM 26 C C4 SAH . . . I 2 21.553 62.301 14.809 1 38.72 ? C4 SAH 1001 B 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 51 _model_server_stats.query_time_ms 381 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 26 #