data_5C8S # _model_server_result.job_id K1mGildh5J1NqA5AuEKksg _model_server_result.datetime_utc '2024-12-18 01:43:10' _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 5c8s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":605}' # _entry.id 5C8S # _exptl.entry_id 5C8S _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 5 _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 5C8S _cell.length_a 188.797 _cell.length_b 196.84 _cell.length_c 180.1 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5C8S _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,B,E,F,G,H,I,J,K,L 1 1 C,D,M,N,O,P,Q,R,S,T 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 ? 5 K N N ? 5 S 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 B SG CYS 226 B CYS 226 1_555 B CD2 HIS 229 B HIS 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.836 ? metalc ? metalc1 A SG CYS 79 A CYS 74 1_555 E ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc2 A SG CYS 82 A CYS 77 1_555 E ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc3 A NE2 HIS 88 A HIS 83 1_555 E ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc4 A SG CYS 95 A CYS 90 1_555 E ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc5 A SG CYS 122 A CYS 117 1_555 F ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc6 A SG CYS 125 A CYS 120 1_555 F ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc7 A SG CYS 133 A CYS 128 1_555 F ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc8 A SG CYS 135 A CYS 130 1_555 F ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc9 B OD1 ASP 90 B ASP 90 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc10 B OE1 GLU 191 B GLU 191 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc11 B OE2 GLU 191 B GLU 191 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? metalc ? metalc12 B SG CYS 207 B CYS 207 1_555 G ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc13 B SG CYS 210 B CYS 210 1_555 G ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc14 B SG CYS 226 B CYS 226 1_555 G ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc15 B NE2 HIS 229 B HIS 229 1_555 G ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.929 ? metalc ? metalc16 B NE2 HIS 257 B HIS 257 1_555 H ZN ZN . B ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc17 B SG CYS 261 B CYS 261 1_555 H ZN ZN . B ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc18 B ND1 HIS 264 B HIS 264 1_555 H ZN ZN . B ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc19 B SG CYS 279 B CYS 279 1_555 H ZN ZN . B ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc20 B SG CYS 452 B CYS 452 1_555 I ZN ZN . B ZN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc21 B SG CYS 477 B CYS 477 1_555 I ZN ZN . B ZN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc22 B SG CYS 484 B CYS 484 1_555 I ZN ZN . B ZN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc23 B ND1 HIS 487 B HIS 487 1_555 I ZN ZN . B ZN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc24 B NE2 HIS 487 B HIS 487 1_555 I ZN ZN . B ZN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc25 C SG CYS 79 C CYS 74 1_555 M ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc26 C SG CYS 82 C CYS 77 1_555 M ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc27 C NE2 HIS 88 C HIS 83 1_555 M ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc28 C SG CYS 95 C CYS 90 1_555 M ZN ZN . C ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc29 C SG CYS 122 C CYS 117 1_555 N ZN ZN . C ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc30 C SG CYS 125 C CYS 120 1_555 N ZN ZN . C ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc31 C SG CYS 133 C CYS 128 1_555 N ZN ZN . C ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc32 C SG CYS 135 C CYS 130 1_555 N ZN ZN . C ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc33 D OD1 ASP 90 D ASP 90 1_555 R MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc34 D OE1 GLU 191 D GLU 191 1_555 R MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc35 D OE2 GLU 191 D GLU 191 1_555 R MG MG . D MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.951 ? metalc ? metalc36 D SG CYS 207 D CYS 207 1_555 O ZN ZN . D ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc37 D SG CYS 210 D CYS 210 1_555 O ZN ZN . D ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc38 D SG CYS 226 D CYS 226 1_555 O ZN ZN . D ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc39 D NE2 HIS 229 D HIS 229 1_555 O ZN ZN . D ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc40 D NE2 HIS 257 D HIS 257 1_555 P ZN ZN . D ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc41 D SG CYS 261 D CYS 261 1_555 P ZN ZN . D ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc42 D SG CYS 279 D CYS 279 1_555 P ZN ZN . D ZN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc43 D SG CYS 452 D CYS 452 1_555 Q ZN ZN . D ZN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc44 D SG CYS 477 D CYS 477 1_555 Q ZN ZN . D ZN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc45 D SG CYS 484 D CYS 484 1_555 Q ZN ZN . D ZN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc46 D ND1 HIS 487 D HIS 487 1_555 Q ZN ZN . D ZN 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _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 N CA SAH sing 357 n n N HN1 SAH sing 358 n n N HN2 SAH sing 359 n n CA CB SAH sing 360 n n CA C SAH sing 361 n n CA HA SAH sing 362 n n CB CG SAH sing 363 n n CB HB1 SAH sing 364 n n CB HB2 SAH sing 365 n n CG SD SAH sing 366 n n CG HG1 SAH sing 367 n n CG HG2 SAH sing 368 n n SD C5' SAH sing 369 n n C O SAH doub 370 n n C OXT SAH sing 371 n n OXT HXT SAH sing 372 n n C5' C4' SAH sing 373 n n C5' "H5'1" SAH sing 374 n n C5' "H5'2" SAH sing 375 n n C4' O4' SAH sing 376 n n C4' C3' SAH sing 377 n n C4' H4' SAH sing 378 n n O4' C1' SAH sing 379 n n C3' O3' SAH sing 380 n n C3' C2' SAH sing 381 n n C3' H3' SAH sing 382 n n O3' HO3' SAH sing 383 n n C2' O2' SAH sing 384 n n C2' C1' SAH sing 385 n n C2' H2' SAH sing 386 n n O2' HO2' SAH sing 387 n n C1' N9 SAH sing 388 n n C1' H1' SAH sing 389 n n N9 C8 SAH sing 390 n y N9 C4 SAH sing 391 n y C8 N7 SAH doub 392 n y C8 H8 SAH sing 393 n n N7 C5 SAH sing 394 n y C5 C6 SAH sing 395 n y C5 C4 SAH doub 396 n y C6 N6 SAH sing 397 n n C6 N1 SAH doub 398 n y N6 HN61 SAH sing 399 n n N6 HN62 SAH sing 400 n n N1 C2 SAH sing 401 n y C2 N3 SAH doub 402 n y C2 H2 SAH sing 403 n n N3 C4 SAH sing 404 n y # _atom_sites.entry_id 5C8S _atom_sites.fract_transf_matrix[1][1] 0.005297 _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] 0.00508 _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] 0.005552 _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 E 3 ZN A 1 201 150 ZN ZN . F 3 ZN A 1 202 151 ZN ZN . G 3 ZN B 1 601 530 ZN ZN . H 3 ZN B 1 602 531 ZN ZN . I 3 ZN B 1 603 532 ZN ZN . J 4 MG B 1 604 533 MG MG . K 5 SAH B 1 605 540 SAH SAH . L 6 G3A B 1 606 541 G3A G3A . M 3 ZN C 1 201 150 ZN ZN . N 3 ZN C 1 202 151 ZN ZN . O 3 ZN D 1 601 530 ZN ZN . P 3 ZN D 1 602 531 ZN ZN . Q 3 ZN D 1 603 532 ZN ZN . R 4 MG D 1 604 533 MG MG . S 5 SAH D 1 605 540 SAH SAH . T 6 G3A D 1 606 541 G3A G3A . # 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 . . . S 5 9.968 -33.385 8.832 1 129.83 ? N SAH 605 D 1 HETATM 2 C CA SAH . . . S 5 8.575 -33.792 9.137 1 151.54 ? CA SAH 605 D 1 HETATM 3 C CB SAH . . . S 5 7.669 -32.682 9.719 1 154.5 ? CB SAH 605 D 1 HETATM 4 C CG SAH . . . S 5 8.22 -31.75 10.788 1 156.21 ? CG SAH 605 D 1 HETATM 5 S SD SAH . . . S 5 6.954 -31.163 11.949 1 128.55 ? SD SAH 605 D 1 HETATM 6 C C SAH . . . S 5 7.835 -34.411 7.947 1 152.79 ? C SAH 605 D 1 HETATM 7 O O SAH . . . S 5 8.4 -35.174 7.172 1 150.15 ? O SAH 605 D 1 HETATM 8 O OXT SAH . . . S 5 6.641 -34.178 7.726 1 142.11 ? OXT SAH 605 D 1 HETATM 9 C C5' SAH . . . S 5 7.838 -31.382 13.535 1 135.27 ? C5' SAH 605 D 1 HETATM 10 C C4' SAH . . . S 5 7.743 -32.817 14.03 1 142.73 ? C4' SAH 605 D 1 HETATM 11 O O4' SAH . . . S 5 8.943 -33.174 14.698 1 143.08 ? O4' SAH 605 D 1 HETATM 12 C C3' SAH . . . S 5 6.618 -33.001 15.027 1 154.35 ? C3' SAH 605 D 1 HETATM 13 O O3' SAH . . . S 5 6.03 -34.29 14.907 1 151.27 ? O3' SAH 605 D 1 HETATM 14 C C2' SAH . . . S 5 7.313 -32.881 16.372 1 160.18 ? C2' SAH 605 D 1 HETATM 15 O O2' SAH . . . S 5 6.665 -33.682 17.332 1 161.75 ? O2' SAH 605 D 1 HETATM 16 C C1' SAH . . . S 5 8.711 -33.414 16.085 1 143.37 ? C1' SAH 605 D 1 HETATM 17 N N9 SAH . . . S 5 9.802 -32.779 16.843 1 136.25 ? N9 SAH 605 D 1 HETATM 18 C C8 SAH . . . S 5 10.102 -31.457 16.934 1 140.09 ? C8 SAH 605 D 1 HETATM 19 N N7 SAH . . . S 5 11.19 -31.302 17.709 1 134.1 ? N7 SAH 605 D 1 HETATM 20 C C5 SAH . . . S 5 11.591 -32.527 18.097 1 139.18 ? C5 SAH 605 D 1 HETATM 21 C C6 SAH . . . S 5 12.646 -32.935 18.89 1 140.12 ? C6 SAH 605 D 1 HETATM 22 N N6 SAH . . . S 5 13.48 -32.028 19.412 1 125.77 ? N6 SAH 605 D 1 HETATM 23 N N1 SAH . . . S 5 12.801 -34.297 19.119 1 142.02 ? N1 SAH 605 D 1 HETATM 24 C C2 SAH . . . S 5 11.929 -35.22 18.569 1 131 ? C2 SAH 605 D 1 HETATM 25 N N3 SAH . . . S 5 10.872 -34.794 17.77 1 118.11 ? N3 SAH 605 D 1 HETATM 26 C C4 SAH . . . S 5 10.729 -33.465 17.553 1 132.02 ? C4 SAH 605 D 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 26 #