data_3NPN # _model_server_result.job_id ihkPutC_78QMt4CYs9sgpg _model_server_result.datetime_utc '2025-03-05 23:49:40' _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 3npn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":55}' # _entry.id 3NPN # _exptl.entry_id 3NPN _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 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 120 _cell.entry_id 3NPN _cell.length_a 105.36 _cell.length_b 105.36 _cell.length_c 107.78 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NPN _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 A N3 C 4 A C 4 1_555 A N1 G 35 A G 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 C 4 A C 4 1_555 A O6 G 35 A G 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 C 4 A C 4 1_555 A N2 G 35 A G 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-A MISPAIR' hydrog4 A N1 G 5 A G 5 1_555 A N1 A 34 A A 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N1 A 6 A A 6 1_555 A N3 U 33 A U 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N6 A 6 A A 6 1_555 A O4 U 33 A U 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 G 7 A G 7 1_555 A N3 C 32 A C 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N2 G 7 A G 7 1_555 A O2 C 32 A C 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O6 G 7 A G 7 1_555 A N4 C 32 A C 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_10_PAIR hydrog10 A N2 G 7 A G 7 1_555 A N1 A 45 A A 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_10_PAIR hydrog11 A N3 G 7 A G 7 1_555 A N6 A 45 A A 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-C PAIR' hydrog12 A N2 G 7 A G 7 1_555 A O2 C 46 A C 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-C PAIR' hydrog13 A N1 G 8 A G 8 1_555 A O2 C 53 A C 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N1 A 9 A A 9 1_555 A N3 U 52 A U 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N6 A 9 A A 9 1_555 A O4 U 52 A U 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N1 G 10 A G 10 1_555 A N3 C 51 A C 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N2 G 10 A G 10 1_555 A O2 C 51 A C 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O6 G 10 A G 10 1_555 A N4 C 51 A C 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-G PAIR' hydrog19 A O2 C 11 A C 11 1_555 A N2 G 50 A G 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N1 G 12 A G 12 1_555 A N3 C 49 A C 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N2 G 12 A G 12 1_555 A O2 C 49 A C 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A O6 G 12 A G 12 1_555 A N4 C 49 A C 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-G MISPAIR' hydrog23 A O2 U 13 A U 13 1_555 A N2 G 48 A G 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED HOOGSTEEN' hydrog24 A N3 U 14 A U 14 1_555 A N7 A 29 A A 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED HOOGSTEEN' hydrog25 A O2 U 14 A U 14 1_555 A N6 A 29 A A 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-C MISPAIR' hydrog26 A N4 C 16 A C 16 1_555 A O2 C 28 A C 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N3 C 16 A C 16 1_555 A N1 G 31 A G 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A N4 C 16 A C 16 1_555 A O6 G 31 A G 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A O2 C 16 A C 16 1_555 A N2 G 31 A G 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-C MISPAIR' hydrog30 A N6 A 17 A A 17 1_555 A O2 C 28 A C 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-C MISPAIR' hydrog31 A N6 A 18 A A 18 1_555 A O2 C 27 A C 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A N1 G 19 A G 19 1_555 A N3 C 26 A C 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 A N2 G 19 A G 19 1_555 A O2 C 26 A C 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 A O6 G 19 A G 19 1_555 A N4 C 26 A C 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 A N3 C 20 A C 20 1_555 A N1 G 25 A G 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 A N4 C 20 A C 20 1_555 A O6 G 25 A G 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 A O2 C 20 A C 20 1_555 A N2 G 25 A G 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'G-A MISPAIR' hydrog38 A N2 G 21 A G 21 1_555 A N7 A 24 A A 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 A N1 G 30 A G 30 1_555 A N3 C 46 A C 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 A N2 G 30 A G 30 1_555 A O2 C 46 A C 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 A O6 G 30 A G 30 1_555 A N4 C 46 A C 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-A PAIR' hydrog42 A O2 U 33 A U 33 1_555 A N6 A 44 A A 44 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 116 n n N HN1 SAH sing 117 n n N HN2 SAH sing 118 n n CA CB SAH sing 119 n n CA C SAH sing 120 n n CA HA SAH sing 121 n n CB CG SAH sing 122 n n CB HB1 SAH sing 123 n n CB HB2 SAH sing 124 n n CG SD SAH sing 125 n n CG HG1 SAH sing 126 n n CG HG2 SAH sing 127 n n SD C5' SAH sing 128 n n C O SAH doub 129 n n C OXT SAH sing 130 n n OXT HXT SAH sing 131 n n C5' C4' SAH sing 132 n n C5' "H5'1" SAH sing 133 n n C5' "H5'2" SAH sing 134 n n C4' O4' SAH sing 135 n n C4' C3' SAH sing 136 n n C4' H4' SAH sing 137 n n O4' C1' SAH sing 138 n n C3' O3' SAH sing 139 n n C3' C2' SAH sing 140 n n C3' H3' SAH sing 141 n n O3' HO3' SAH sing 142 n n C2' O2' SAH sing 143 n n C2' C1' SAH sing 144 n n C2' H2' SAH sing 145 n n O2' HO2' SAH sing 146 n n C1' N9 SAH sing 147 n n C1' H1' SAH sing 148 n n N9 C8 SAH sing 149 n y N9 C4 SAH sing 150 n y C8 N7 SAH doub 151 n y C8 H8 SAH sing 152 n n N7 C5 SAH sing 153 n y C5 C6 SAH sing 154 n y C5 C4 SAH doub 155 n y C6 N6 SAH sing 156 n n C6 N1 SAH doub 157 n y N6 HN61 SAH sing 158 n n N6 HN62 SAH sing 159 n n N1 C2 SAH sing 160 n y C2 N3 SAH doub 161 n y C2 H2 SAH sing 162 n n N3 C4 SAH sing 163 n y # _atom_sites.entry_id 3NPN _atom_sites.fract_transf_matrix[1][1] 0.009491 _atom_sites.fract_transf_matrix[1][2] 0.00548 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01096 _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] 0.009278 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id SAH _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 55 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id SAH _pdbx_nonpoly_scheme.auth_mon_id SAH _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . B 2 128.705 70.971 -2.36 1 88.47 ? N SAH 55 A 1 HETATM 2 C CA SAH . . . B 2 128.429 70.389 -3.707 1 88.48 ? CA SAH 55 A 1 HETATM 3 C CB SAH . . . B 2 128.689 68.885 -3.696 1 88.46 ? CB SAH 55 A 1 HETATM 4 C CG SAH . . . B 2 128.008 68.162 -2.538 1 88.32 ? CG SAH 55 A 1 HETATM 5 S SD SAH . . . B 2 128.162 66.418 -2.743 1 87.92 ? SD SAH 55 A 1 HETATM 6 C C SAH . . . B 2 127.008 70.651 -4.116 1 88.5 ? C SAH 55 A 1 HETATM 7 O O SAH . . . B 2 126.193 71.124 -3.325 1 88.54 ? O SAH 55 A 1 HETATM 8 O OXT SAH . . . B 2 126.622 70.388 -5.254 1 88.52 ? OXT SAH 55 A 1 HETATM 9 C C5' SAH . . . B 2 129.891 66.224 -3.033 1 88.09 ? C5' SAH 55 A 1 HETATM 10 C C4' SAH . . . B 2 130.688 66.25 -1.73 1 88.01 ? C4' SAH 55 A 1 HETATM 11 O O4' SAH . . . B 2 130.136 65.335 -0.781 1 87.97 ? O4' SAH 55 A 1 HETATM 12 C C3' SAH . . . B 2 132.126 65.827 -1.983 1 88.09 ? C3' SAH 55 A 1 HETATM 13 O O3' SAH . . . B 2 133.023 66.769 -1.387 1 88.06 ? O3' SAH 55 A 1 HETATM 14 C C2' SAH . . . B 2 132.274 64.452 -1.356 1 88.14 ? C2' SAH 55 A 1 HETATM 15 O O2' SAH . . . B 2 133.368 64.413 -0.433 1 88.3 ? O2' SAH 55 A 1 HETATM 16 C C1' SAH . . . B 2 130.966 64.178 -0.623 1 88.12 ? C1' SAH 55 A 1 HETATM 17 N N9 SAH . . . B 2 130.273 62.976 -1.174 1 88.13 ? N9 SAH 55 A 1 HETATM 18 C C8 SAH . . . B 2 129.012 62.957 -1.65 1 88.1 ? C8 SAH 55 A 1 HETATM 19 N N7 SAH . . . B 2 128.657 61.719 -2.075 1 88.11 ? N7 SAH 55 A 1 HETATM 20 C C5 SAH . . . B 2 129.711 60.91 -1.873 1 88.21 ? C5 SAH 55 A 1 HETATM 21 C C6 SAH . . . B 2 130.014 59.474 -2.099 1 88.31 ? C6 SAH 55 A 1 HETATM 22 N N6 SAH . . . B 2 129.09 58.648 -2.645 1 88.42 ? N6 SAH 55 A 1 HETATM 23 N N1 SAH . . . B 2 131.24 59.018 -1.747 1 88.32 ? N1 SAH 55 A 1 HETATM 24 C C2 SAH . . . B 2 132.169 59.831 -1.205 1 88.26 ? C2 SAH 55 A 1 HETATM 25 N N3 SAH . . . B 2 131.96 61.143 -0.971 1 88.22 ? N3 SAH 55 A 1 HETATM 26 C C4 SAH . . . B 2 130.775 61.737 -1.277 1 88.21 ? C4 SAH 55 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #