data_8CBM # _model_server_result.job_id ND4wTNrjFQrAScJeZFACbg _model_server_result.datetime_utc '2025-02-28 18:37:53' _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 8cbm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":501}' # _entry.id 8CBM # _exptl.entry_id 8CBM _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 384.411 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _entity.pdbx_number_of_molecules 1 _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 8CBM _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CBM _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details heptameric _pdbx_struct_assembly.oligomeric_count 7 _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,N,O,P,Q,R _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 ? _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 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id M _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 hydrog WATSON-CRICK hydrog1 G N1 G 2 T G 2 1_555 G N3 C 67 T C 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 G N2 G 2 T G 2 1_555 G O2 C 67 T C 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 G O6 G 2 T G 2 1_555 G N4 C 67 T C 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 G N1 A 3 T A 3 1_555 G N3 U 66 T U 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 G N6 A 3 T A 3 1_555 G O4 U 66 T U 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 G N1 A 4 T A 4 1_555 G N3 U 65 T U 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 G N6 A 4 T A 4 1_555 G O4 U 65 T U 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 G N1 A 4 T A 4 1_555 G N3 U 66 T U 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 G N6 A 4 T A 4 1_555 G O4 U 66 T U 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 G N1 A 5 T A 5 1_555 G N3 U 64 T U 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 G N6 A 5 T A 5 1_555 G O4 U 64 T U 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 G N3 U 6 T U 6 1_555 G N1 A 63 T A 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 G O4 U 6 T U 6 1_555 G N6 A 63 T A 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 G N1 A 7 T A 7 1_555 G N3 U 62 T U 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 G N6 A 7 T A 7 1_555 G O4 U 62 T U 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-G MISPAIR' hydrog16 G N3 U 8 T U 8 1_555 G N7 G 13 T G 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 G N3 U 10 T U 10 1_555 G N1 A 21 T A 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 G O4 U 10 T U 10 1_555 G N6 A 21 T A 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 G N3 C 11 T C 11 1_555 G N1 G 20 T G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 G N4 C 11 T C 11 1_555 G O6 G 20 T G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 G O2 C 11 T C 11 1_555 G N2 G 20 T G 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 G N3 U 12 T U 12 1_555 G N1 A 19 T A 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 G O4 U 12 T U 12 1_555 G N6 A 19 T A 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog24 G N2 G 13 T G 13 1_555 G N7 A 18 T A 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog25 G N3 G 13 T G 13 1_555 G N6 A 18 T A 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 G N3 U 23 T U 23 1_555 G N1 A 39 T A 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 G O4 U 23 T U 23 1_555 G N6 A 39 T A 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 G N3 U 24 T U 24 1_555 G N1 A 38 T A 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 G O4 U 24 T U 24 1_555 G N6 A 38 T A 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 G N1 A 25 T A 25 1_555 G N3 U 37 T U 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 G N6 A 25 T A 25 1_555 G O4 U 37 T U 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 G N3 C 26 T C 26 1_555 G N1 G 36 T G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 G N4 C 26 T C 26 1_555 G O6 G 36 T G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 G O2 C 26 T C 26 1_555 G N2 G 36 T G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 G N3 U 27 T U 27 1_555 G N1 A 35 T A 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 G O4 U 27 T U 27 1_555 G N6 A 35 T A 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 G N1 A 43 T A 43 1_555 G N3 U 52 T U 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 G N6 A 43 T A 43 1_555 G O4 U 52 T U 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 G N1 A 45 T A 45 1_555 G N3 U 61 T U 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 G N6 A 45 T A 45 1_555 G O4 U 61 T U 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 G N1 G 46 T G 46 1_555 G N3 C 60 T C 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 G N2 G 46 T G 46 1_555 G O2 C 60 T C 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 G O6 G 46 T G 46 1_555 G N4 C 60 T C 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 G N1 G 47 T G 47 1_555 G N3 C 59 T C 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 G N2 G 47 T G 47 1_555 G O2 C 59 T C 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog46 G O6 G 47 T G 47 1_555 G N4 C 59 T C 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-C MISPAIR' hydrog47 G N6 A 48 T A 48 1_555 G N3 C 58 T C 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog48 G N1 G 49 T G 49 1_555 G N3 C 57 T C 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog49 G N2 G 49 T G 49 1_555 G O2 C 57 T C 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog50 G O6 G 49 T G 49 1_555 G N4 C 57 T C 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-C MISPAIR' hydrog51 G O2 C 50 T C 50 1_555 G N4 C 56 T C 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-A PAIR' hydrog52 G O2 U 51 T U 51 1_555 G N6 A 55 T A 55 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 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 508 n n N HN1 SAH sing 509 n n N HN2 SAH sing 510 n n CA CB SAH sing 511 n n CA C SAH sing 512 n n CA HA SAH sing 513 n n CB CG SAH sing 514 n n CB HB1 SAH sing 515 n n CB HB2 SAH sing 516 n n CG SD SAH sing 517 n n CG HG1 SAH sing 518 n n CG HG2 SAH sing 519 n n SD C5' SAH sing 520 n n C O SAH doub 521 n n C OXT SAH sing 522 n n OXT HXT SAH sing 523 n n C5' C4' SAH sing 524 n n C5' "H5'1" SAH sing 525 n n C5' "H5'2" SAH sing 526 n n C4' O4' SAH sing 527 n n C4' C3' SAH sing 528 n n C4' H4' SAH sing 529 n n O4' C1' SAH sing 530 n n C3' O3' SAH sing 531 n n C3' C2' SAH sing 532 n n C3' H3' SAH sing 533 n n O3' HO3' SAH sing 534 n n C2' O2' SAH sing 535 n n C2' C1' SAH sing 536 n n C2' H2' SAH sing 537 n n O2' HO2' SAH sing 538 n n C1' N9 SAH sing 539 n n C1' H1' SAH sing 540 n n N9 C8 SAH sing 541 n y N9 C4 SAH sing 542 n y C8 N7 SAH doub 543 n y C8 H8 SAH sing 544 n n N7 C5 SAH sing 545 n y C5 C6 SAH sing 546 n y C5 C4 SAH doub 547 n y C6 N6 SAH sing 548 n n C6 N1 SAH doub 549 n y N6 HN61 SAH sing 550 n n N6 HN62 SAH sing 551 n n N1 C2 SAH sing 552 n y C2 N3 SAH doub 553 n y C2 H2 SAH sing 554 n n N3 C4 SAH sing 555 n y # _atom_sites.entry_id 8CBM _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 H 5 NAD A 1 301 301 NAD NAD . I 5 NAD B 1 301 301 NAD NAD . J 5 NAD C 1 301 301 NAD NAD . K 5 NAD D 1 301 301 NAD NAD . L 6 CDP E 1 501 501 CDP CDP . M 7 SAH F 1 501 401 SAH SAH . N 8 HOH A 1 401 7 HOH HOH . N 8 HOH A 2 402 2 HOH HOH . O 8 HOH B 1 401 8 HOH HOH . P 8 HOH C 1 401 6 HOH HOH . Q 8 HOH D 1 401 1 HOH HOH . Q 8 HOH D 2 402 3 HOH HOH . Q 8 HOH D 3 403 5 HOH HOH . R 8 HOH F 1 601 4 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 . . . M 7 164.684 146.45 114.075 1 129.2 ? N SAH 501 F 1 HETATM 2 C CA SAH . . . M 7 164.977 147.205 115.312 1 128.94 ? CA SAH 501 F 1 HETATM 3 C CB SAH . . . M 7 163.71 147.393 116.142 1 127.8 ? CB SAH 501 F 1 HETATM 4 C CG SAH . . . M 7 163.619 148.693 116.853 1 127.68 ? CG SAH 501 F 1 HETATM 5 S SD SAH . . . M 7 162.218 148.641 117.982 1 132.4 ? SD SAH 501 F 1 HETATM 6 C C SAH . . . M 7 165.982 146.374 116.082 1 130.97 ? C SAH 501 F 1 HETATM 7 O O SAH . . . M 7 166.964 145.923 115.452 1 130.8 ? O SAH 501 F 1 HETATM 8 O OXT SAH . . . M 7 165.721 146.171 117.257 1 132.54 ? OXT SAH 501 F 1 HETATM 9 C C5' SAH . . . M 7 162.872 149.172 119.566 1 122.11 ? C5' SAH 501 F 1 HETATM 10 C C4' SAH . . . M 7 163.094 147.993 120.467 1 119.65 ? C4' SAH 501 F 1 HETATM 11 O O4' SAH . . . M 7 161.839 147.533 120.999 1 119.11 ? O4' SAH 501 F 1 HETATM 12 C C3' SAH . . . M 7 163.649 146.78 119.758 1 121.01 ? C3' SAH 501 F 1 HETATM 13 O O3' SAH . . . M 7 165.051 146.955 119.651 1 133.59 ? O3' SAH 501 F 1 HETATM 14 C C2' SAH . . . M 7 163.292 145.696 120.76 1 120.34 ? C2' SAH 501 F 1 HETATM 15 O O2' SAH . . . M 7 164.154 145.758 121.87 1 126.68 ? O2' SAH 501 F 1 HETATM 16 C C1' SAH . . . M 7 161.91 146.142 121.205 1 118.36 ? C1' SAH 501 F 1 HETATM 17 N N9 SAH . . . M 7 160.832 145.523 120.457 1 117.75 ? N9 SAH 501 F 1 HETATM 18 C C8 SAH . . . M 7 159.959 146.145 119.608 1 123.62 ? C8 SAH 501 F 1 HETATM 19 N N7 SAH . . . M 7 159.078 145.332 119.091 1 121.12 ? N7 SAH 501 F 1 HETATM 20 C C5 SAH . . . M 7 159.392 144.101 119.638 1 112.24 ? C5 SAH 501 F 1 HETATM 21 C C6 SAH . . . M 7 158.82 142.834 119.485 1 114.96 ? C6 SAH 501 F 1 HETATM 22 N N6 SAH . . . M 7 157.774 142.598 118.706 1 126.35 ? N6 SAH 501 F 1 HETATM 23 N N1 SAH . . . M 7 159.364 141.813 120.177 1 122.65 ? N1 SAH 501 F 1 HETATM 24 C C2 SAH . . . M 7 160.415 142.065 120.959 1 122.89 ? C2 SAH 501 F 1 HETATM 25 N N3 SAH . . . M 7 161.04 143.214 121.177 1 120.07 ? N3 SAH 501 F 1 HETATM 26 C C4 SAH . . . M 7 160.473 144.204 120.48 1 114.57 ? C4 SAH 501 F 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #