data_6F57 # _model_server_result.job_id zehv_OJCQ26iO0Ld3-WkVw _model_server_result.datetime_utc '2024-11-23 20:21:57' _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 6f57 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1001}' # _entry.id 6F57 # _exptl.entry_id 6F57 _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 6F57 _cell.length_a 176.611 _cell.length_b 49.559 _cell.length_c 162.259 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6F57 _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 tetrameric 4 software_defined_assembly 1 PISA tetrameric 4 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,I 1 1 C,D,G,H,J 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 I N N ? 5 J 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 SG CYS 83 A CYS 710 1_555 F C6 Z 5 F Z 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.841 ? covale ? covale2 D SG CYS 83 D CYS 710 1_555 H C6 Z 5 H Z 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? covale ? covale3 F O3' DG 4 F DG 426 1_555 F P Z 5 F Z 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.597 ? covale ? covale4 F O3' Z 5 F Z 427 1_555 F P DG 6 F DG 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.605 ? covale ? covale5 H O3' DG 4 H DG 426 1_555 H P Z 5 H Z 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.6 ? covale ? covale6 H O3' Z 5 H Z 427 1_555 H P DG 6 H DG 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.605 ? hydrog WATSON-CRICK hydrog1 E N1 DA 1 E DA 403 1_555 F N3 DT 10 F DT 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 E N6 DA 1 E DA 403 1_555 F O4 DT 10 F DT 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 E N1 DG 2 E DG 404 1_555 F N3 DC 9 F DC 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 E N2 DG 2 E DG 404 1_555 F O2 DC 9 F DC 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 E O6 DG 2 E DG 404 1_555 F N4 DC 9 F DC 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 E N1 DA 3 E DA 405 1_555 F N3 DT 8 F DT 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 E N6 DA 3 E DA 405 1_555 F O4 DT 8 F DT 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 E N1 DG 4 E DG 406 1_555 F N3 DC 7 F DC 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 E N2 DG 4 E DG 406 1_555 F O2 DC 7 F DC 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 E O6 DG 4 E DG 406 1_555 F N4 DC 7 F DC 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 E N3 DC 5 E DC 407 1_555 F N1 DG 6 F DG 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 E N4 DC 5 E DC 407 1_555 F O6 DG 6 F DG 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 E O2 DC 5 E DC 407 1_555 F N2 DG 6 F DG 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 E N3 DC 7 E DC 409 1_555 F N1 DG 4 F DG 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 E N4 DC 7 E DC 409 1_555 F O6 DG 4 F DG 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 E O2 DC 7 E DC 409 1_555 F N2 DG 4 F DG 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 E N1 DA 8 E DA 410 1_555 F N3 DT 3 F DT 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 E N6 DA 8 E DA 410 1_555 F O4 DT 3 F DT 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 E N3 DT 9 E DT 411 1_555 F N1 DA 2 F DA 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 E O4 DT 9 E DT 411 1_555 F N6 DA 2 F DA 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 E N1 DG 10 E DG 412 1_555 F N3 DC 1 F DC 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 E N2 DG 10 E DG 412 1_555 F O2 DC 1 F DC 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 E O6 DG 10 E DG 412 1_555 F N4 DC 1 F DC 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 G N1 DA 1 G DA 403 1_555 H N3 DT 10 H DT 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 G N6 DA 1 G DA 403 1_555 H O4 DT 10 H DT 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 G N1 DG 2 G DG 404 1_555 H N3 DC 9 H DC 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 G N2 DG 2 G DG 404 1_555 H O2 DC 9 H DC 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 G O6 DG 2 G DG 404 1_555 H N4 DC 9 H DC 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 G N1 DA 3 G DA 405 1_555 H N3 DT 8 H DT 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 G N6 DA 3 G DA 405 1_555 H O4 DT 8 H DT 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 G N1 DG 4 G DG 406 1_555 H N3 DC 7 H DC 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 G N2 DG 4 G DG 406 1_555 H O2 DC 7 H DC 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 G O6 DG 4 G DG 406 1_555 H N4 DC 7 H DC 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 G N3 DC 5 G DC 407 1_555 H N1 DG 6 H DG 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 G N4 DC 5 G DC 407 1_555 H O6 DG 6 H DG 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 G O2 DC 5 G DC 407 1_555 H N2 DG 6 H DG 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 G N3 DC 7 G DC 409 1_555 H N1 DG 4 H DG 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 G N4 DC 7 G DC 409 1_555 H O6 DG 4 H DG 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 G O2 DC 7 G DC 409 1_555 H N2 DG 4 H DG 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 G N1 DA 8 G DA 410 1_555 H N3 DT 3 H DT 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 G N6 DA 8 G DA 410 1_555 H O4 DT 3 H DT 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 G N3 DT 9 G DT 411 1_555 H N1 DA 2 H DA 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 G O4 DT 9 G DT 411 1_555 H N6 DA 2 H DA 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 G N1 DG 10 G DG 412 1_555 H N3 DC 1 H DC 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 G N2 DG 10 G DG 412 1_555 H O2 DC 1 H DC 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog46 G O6 DG 10 G DG 412 1_555 H N4 DC 1 H DC 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 424 n n N HN1 SAH sing 425 n n N HN2 SAH sing 426 n n CA CB SAH sing 427 n n CA C SAH sing 428 n n CA HA SAH sing 429 n n CB CG SAH sing 430 n n CB HB1 SAH sing 431 n n CB HB2 SAH sing 432 n n CG SD SAH sing 433 n n CG HG1 SAH sing 434 n n CG HG2 SAH sing 435 n n SD C5' SAH sing 436 n n C O SAH doub 437 n n C OXT SAH sing 438 n n OXT HXT SAH sing 439 n n C5' C4' SAH sing 440 n n C5' "H5'1" SAH sing 441 n n C5' "H5'2" SAH sing 442 n n C4' O4' SAH sing 443 n n C4' C3' SAH sing 444 n n C4' H4' SAH sing 445 n n O4' C1' SAH sing 446 n n C3' O3' SAH sing 447 n n C3' C2' SAH sing 448 n n C3' H3' SAH sing 449 n n O3' HO3' SAH sing 450 n n C2' O2' SAH sing 451 n n C2' C1' SAH sing 452 n n C2' H2' SAH sing 453 n n O2' HO2' SAH sing 454 n n C1' N9 SAH sing 455 n n C1' H1' SAH sing 456 n n N9 C8 SAH sing 457 n y N9 C4 SAH sing 458 n y C8 N7 SAH doub 459 n y C8 H8 SAH sing 460 n n N7 C5 SAH sing 461 n y C5 C6 SAH sing 462 n y C5 C4 SAH doub 463 n y C6 N6 SAH sing 464 n n C6 N1 SAH doub 465 n y N6 HN61 SAH sing 466 n n N6 HN62 SAH sing 467 n n N1 C2 SAH sing 468 n y C2 N3 SAH doub 469 n y C2 H2 SAH sing 470 n n N3 C4 SAH sing 471 n y # _atom_sites.entry_id 6F57 _atom_sites.fract_transf_matrix[1][1] 0.005662 _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] 0.020178 _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] 0.006163 _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 I 5 SAH A 1 1001 1 SAH SAH . J 5 SAH D 1 1001 4 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 . . . J 5 569.02 19.643 209.923 1 71.85 ? N SAH 1001 D 1 HETATM 2 C CA SAH . . . J 5 568.716 19.659 208.494 1 63.79 ? CA SAH 1001 D 1 HETATM 3 C CB SAH . . . J 5 569.917 19.186 207.68 1 62.64 ? CB SAH 1001 D 1 HETATM 4 C CG SAH . . . J 5 571.163 18.877 208.506 1 61.64 ? CG SAH 1001 D 1 HETATM 5 S SD SAH . . . J 5 572.629 18.652 207.465 1 86.07 ? SD SAH 1001 D 1 HETATM 6 C C SAH . . . J 5 567.436 18.892 208.161 1 54.38 ? C SAH 1001 D 1 HETATM 7 O O SAH . . . J 5 567.133 18.62 206.996 1 37.98 ? O SAH 1001 D 1 HETATM 8 O OXT SAH . . . J 5 566.664 18.547 209.058 1 58.44 ? OXT SAH 1001 D 1 HETATM 9 C C5' SAH . . . J 5 573.458 20.082 208.206 1 70.63 ? C5' SAH 1001 D 1 HETATM 10 C C4' SAH . . . J 5 573.248 21.379 207.429 1 76.81 ? C4' SAH 1001 D 1 HETATM 11 O O4' SAH . . . J 5 573.941 22.442 208.057 1 78.74 ? O4' SAH 1001 D 1 HETATM 12 C C3' SAH . . . J 5 573.766 21.315 205.999 1 78.87 ? C3' SAH 1001 D 1 HETATM 13 O O3' SAH . . . J 5 572.685 21.275 205.095 1 83.39 ? O3' SAH 1001 D 1 HETATM 14 C C2' SAH . . . J 5 574.547 22.598 205.795 1 71.65 ? C2' SAH 1001 D 1 HETATM 15 O O2' SAH . . . J 5 574.021 23.325 204.71 1 63.04 ? O2' SAH 1001 D 1 HETATM 16 C C1' SAH . . . J 5 574.358 23.38 207.085 1 71.15 ? C1' SAH 1001 D 1 HETATM 17 N N9 SAH . . . J 5 575.613 24.048 207.477 1 59.9 ? N9 SAH 1001 D 1 HETATM 18 C C8 SAH . . . J 5 576.882 23.671 207.117 1 57.17 ? C8 SAH 1001 D 1 HETATM 19 N N7 SAH . . . J 5 577.761 24.539 207.668 1 45.83 ? N7 SAH 1001 D 1 HETATM 20 C C5 SAH . . . J 5 577.07 25.463 208.371 1 43.7 ? C5 SAH 1001 D 1 HETATM 21 C C6 SAH . . . J 5 577.479 26.557 209.117 1 47.53 ? C6 SAH 1001 D 1 HETATM 22 N N6 SAH . . . J 5 578.777 26.832 209.219 1 54.36 ? N6 SAH 1001 D 1 HETATM 23 N N1 SAH . . . J 5 576.535 27.348 209.742 1 44.31 ? N1 SAH 1001 D 1 HETATM 24 C C2 SAH . . . J 5 575.192 27.044 209.622 1 45.08 ? C2 SAH 1001 D 1 HETATM 25 N N3 SAH . . . J 5 574.794 25.95 208.878 1 44.5 ? N3 SAH 1001 D 1 HETATM 26 C C4 SAH . . . J 5 575.718 25.172 208.26 1 48.27 ? C4 SAH 1001 D 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 26 #