data_6U8W # _model_server_result.job_id NbaFE6uHXL--SqThkZW6Xg _model_server_result.datetime_utc '2024-12-26 13:16:55' _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 6u8w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":901}' # _entry.id 6U8W # _exptl.entry_id 6U8W _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 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 120 _cell.entry_id 6U8W _cell.length_a 193.506 _cell.length_b 193.506 _cell.length_c 49.869 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6U8W _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall 'P 31' _symmetry.space_group_name_H-M 'P 31' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M _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 ? 4 G N N ? 4 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 E O3' DG 5 E DG 426 1_555 E P PYO 6 E PYO 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? covale ? covale2 E O3' PYO 6 E PYO 427 1_555 E P DG 7 E DG 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.613 ? covale ? covale3 F O3' DG 5 F DG 426 1_555 F P PYO 6 F PYO 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? covale ? covale4 F O3' PYO 6 F PYO 427 1_555 F P DG 7 F DG 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.611 ? hydrog WATSON-CRICK hydrog1 E N3 DC 2 E DC 423 1_555 F N1 DG 25 F DG 446 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 E N4 DC 2 E DC 423 1_555 F O6 DG 25 F DG 446 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 E O2 DC 2 E DC 423 1_555 F N2 DG 25 F DG 446 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog4 E N1 DA 3 E DA 424 1_555 F N3 DT 24 F DT 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 E N3 DT 4 E DT 425 1_555 F N1 DA 23 F DA 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 E O4 DT 4 E DT 425 1_555 F N6 DA 23 F DA 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog7 E N2 DG 5 E DG 426 1_555 F O2 DC 22 F DC 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 E N1 DG 7 E DG 428 1_555 F N3 DC 20 F DC 441 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 E N2 DG 7 E DG 428 1_555 F O2 DC 20 F DC 441 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 E O6 DG 7 E DG 428 1_555 F N4 DC 20 F DC 441 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 E N3 DT 8 E DT 429 1_555 F N1 DA 19 F DA 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 E O4 DT 8 E DT 429 1_555 F N6 DA 19 F DA 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 E N3 DT 9 E DT 430 1_555 F N1 DA 18 F DA 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 E O4 DT 9 E DT 430 1_555 F N6 DA 18 F DA 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 E N3 DC 10 E DC 431 1_555 F N1 DG 17 F DG 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 E N4 DC 10 E DC 431 1_555 F O6 DG 17 F DG 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 E O2 DC 10 E DC 431 1_555 F N2 DG 17 F DG 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 E N3 DT 11 E DT 432 1_555 F N1 DA 16 F DA 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 E O4 DT 11 E DT 432 1_555 F N6 DA 16 F DA 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 E N1 DA 12 E DA 433 1_555 F N3 DT 15 F DT 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 E N6 DA 12 E DA 433 1_555 F O4 DT 15 F DT 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 E N1 DA 13 E DA 434 1_555 F N3 DT 14 F DT 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 E N6 DA 13 E DA 434 1_555 F O4 DT 14 F DT 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 E N3 DT 14 E DT 435 1_555 F N1 DA 13 F DA 434 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 E O4 DT 14 E DT 435 1_555 F N6 DA 13 F DA 434 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 E N3 DT 15 E DT 436 1_555 F N1 DA 12 F DA 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 E O4 DT 15 E DT 436 1_555 F N6 DA 12 F DA 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 E N1 DA 16 E DA 437 1_555 F N3 DT 11 F DT 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 E N6 DA 16 E DA 437 1_555 F O4 DT 11 F DT 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 E N1 DG 17 E DG 438 1_555 F N3 DC 10 F DC 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 E N2 DG 17 E DG 438 1_555 F O2 DC 10 F DC 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 E O6 DG 17 E DG 438 1_555 F N4 DC 10 F DC 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 E N1 DA 18 E DA 439 1_555 F N3 DT 9 F DT 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 E N6 DA 18 E DA 439 1_555 F O4 DT 9 F DT 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 E N1 DA 19 E DA 440 1_555 F N3 DT 8 F DT 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 E N6 DA 19 E DA 440 1_555 F O4 DT 8 F DT 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 E N3 DC 20 E DC 441 1_555 F N1 DG 7 F DG 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 E N4 DC 20 E DC 441 1_555 F O6 DG 7 F DG 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 E O2 DC 20 E DC 441 1_555 F N2 DG 7 F DG 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog40 E O2 DC 22 E DC 443 1_555 F N2 DG 5 F DG 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 E N1 DA 23 E DA 444 1_555 F N3 DT 4 F DT 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 E N6 DA 23 E DA 444 1_555 F O4 DT 4 F DT 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog43 E N3 DT 24 E DT 445 1_555 F N1 DA 3 F DA 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 E N1 DG 25 E DG 446 1_555 F N3 DC 2 F DC 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 E N2 DG 25 E DG 446 1_555 F O2 DC 2 F DC 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog46 E O6 DG 25 E DG 446 1_555 F N4 DC 2 F 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 460 n n N HN1 SAH sing 461 n n N HN2 SAH sing 462 n n CA CB SAH sing 463 n n CA C SAH sing 464 n n CA HA SAH sing 465 n n CB CG SAH sing 466 n n CB HB1 SAH sing 467 n n CB HB2 SAH sing 468 n n CG SD SAH sing 469 n n CG HG1 SAH sing 470 n n CG HG2 SAH sing 471 n n SD C5' SAH sing 472 n n C O SAH doub 473 n n C OXT SAH sing 474 n n OXT HXT SAH sing 475 n n C5' C4' SAH sing 476 n n C5' "H5'1" SAH sing 477 n n C5' "H5'2" SAH sing 478 n n C4' O4' SAH sing 479 n n C4' C3' SAH sing 480 n n C4' H4' SAH sing 481 n n O4' C1' SAH sing 482 n n C3' O3' SAH sing 483 n n C3' C2' SAH sing 484 n n C3' H3' SAH sing 485 n n O3' HO3' SAH sing 486 n n C2' O2' SAH sing 487 n n C2' C1' SAH sing 488 n n C2' H2' SAH sing 489 n n O2' HO2' SAH sing 490 n n C1' N9 SAH sing 491 n n C1' H1' SAH sing 492 n n N9 C8 SAH sing 493 n y N9 C4 SAH sing 494 n y C8 N7 SAH doub 495 n y C8 H8 SAH sing 496 n n N7 C5 SAH sing 497 n y C5 C6 SAH sing 498 n y C5 C4 SAH doub 499 n y C6 N6 SAH sing 500 n n C6 N1 SAH doub 501 n y N6 HN61 SAH sing 502 n n N6 HN62 SAH sing 503 n n N1 C2 SAH sing 504 n y C2 N3 SAH doub 505 n y C2 H2 SAH sing 506 n n N3 C4 SAH sing 507 n y # _atom_sites.entry_id 6U8W _atom_sites.fract_transf_matrix[1][1] 0.005168 _atom_sites.fract_transf_matrix[1][2] 0.002984 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005967 _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] 0.020053 _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 G 4 SAH A 1 901 1 SAH SAH . H 5 MG A 1 902 1 MG MG . I 4 SAH D 1 901 2 SAH SAH . J 5 MG D 1 902 2 MG MG . K 6 HOH A 1 1001 15 HOH HOH . K 6 HOH A 2 1002 5 HOH HOH . K 6 HOH A 3 1003 8 HOH HOH . K 6 HOH A 4 1004 7 HOH HOH . K 6 HOH A 5 1005 9 HOH HOH . K 6 HOH A 6 1006 11 HOH HOH . L 6 HOH D 1 1001 6 HOH HOH . L 6 HOH D 2 1002 4 HOH HOH . L 6 HOH D 3 1003 16 HOH HOH . L 6 HOH D 4 1004 3 HOH HOH . M 6 HOH F 1 501 14 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 . . . I 4 54.857 52.581 6.231 1 59.43 ? N SAH 901 D 1 HETATM 2 C CA SAH . . . I 4 53.607 52.913 5.55 1 56.17 ? CA SAH 901 D 1 HETATM 3 C CB SAH . . . I 4 52.639 51.731 5.573 1 48.5 ? CB SAH 901 D 1 HETATM 4 C CG SAH . . . I 4 53.234 50.375 5.947 1 51.61 ? CG SAH 901 D 1 HETATM 5 S SD SAH . . . I 4 51.971 49.076 5.867 1 59.64 ? SD SAH 901 D 1 HETATM 6 C C SAH . . . I 4 52.93 54.147 6.147 1 51.67 ? C SAH 901 D 1 HETATM 7 O O SAH . . . I 4 53.58 54.993 6.766 1 47.22 ? O SAH 901 D 1 HETATM 8 O OXT SAH . . . I 4 51.718 54.34 6.008 1 48.94 ? OXT SAH 901 D 1 HETATM 9 C C5' SAH . . . I 4 52.83 48.238 4.511 1 61.04 ? C5' SAH 901 D 1 HETATM 10 C C4' SAH . . . I 4 52.236 48.55 3.137 1 58.66 ? C4' SAH 901 D 1 HETATM 11 O O4' SAH . . . I 4 52.774 47.702 2.133 1 67.88 ? O4' SAH 901 D 1 HETATM 12 C C3' SAH . . . I 4 50.725 48.357 3.085 1 53.97 ? C3' SAH 901 D 1 HETATM 13 O O3' SAH . . . I 4 50.101 49.587 2.779 1 43.59 ? O3' SAH 901 D 1 HETATM 14 C C2' SAH . . . I 4 50.476 47.385 1.945 1 47.83 ? C2' SAH 901 D 1 HETATM 15 O O2' SAH . . . I 4 49.389 47.808 1.151 1 50.75 ? O2' SAH 901 D 1 HETATM 16 C C1' SAH . . . I 4 51.775 47.442 1.163 1 55.55 ? C1' SAH 901 D 1 HETATM 17 N N9 SAH . . . I 4 52.016 46.207 0.39 1 51.18 ? N9 SAH 901 D 1 HETATM 18 C C8 SAH . . . I 4 51.556 44.937 0.645 1 49.22 ? C8 SAH 901 D 1 HETATM 19 N N7 SAH . . . I 4 52.012 44.111 -0.329 1 47.89 ? N7 SAH 901 D 1 HETATM 20 C C5 SAH . . . I 4 52.75 44.839 -1.2 1 61.07 ? C5 SAH 901 D 1 HETATM 21 C C6 SAH . . . I 4 53.439 44.505 -2.362 1 56.69 ? C6 SAH 901 D 1 HETATM 22 N N6 SAH . . . I 4 53.441 43.247 -2.794 1 56.78 ? N6 SAH 901 D 1 HETATM 23 N N1 SAH . . . I 4 54.12 45.482 -3.06 1 51.21 ? N1 SAH 901 D 1 HETATM 24 C C2 SAH . . . I 4 54.112 46.784 -2.604 1 58.59 ? C2 SAH 901 D 1 HETATM 25 N N3 SAH . . . I 4 53.428 47.111 -1.452 1 57.51 ? N3 SAH 901 D 1 HETATM 26 C C4 SAH . . . I 4 52.756 46.156 -0.762 1 54.33 ? C4 SAH 901 D 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 26 #