data_5NEX # _model_server_result.job_id OukXPJ5iv5l2Hxr-3D51_g _model_server_result.datetime_utc '2024-11-29 20:13:17' _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 5nex # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":109}' # _entry.id 5NEX # _exptl.entry_id 5NEX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 130.191 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description AGMATINE _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 5NEX _cell.length_a 55.639 _cell.length_b 55.639 _cell.length_c 135.927 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NEX _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K 1 1 A,B,C,D,E,F,G,H,I,J,K 1 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 10_455 y-1/3,x+1/3,-z+1/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 -27.8195 16.061596 45.309 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id J _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 covale ? covale1 A O3' A 16 A A 16 1_555 A P CBV 17 A CBV 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.625 ? covale ? covale2 A O3' CBV 17 A CBV 17 1_555 A P C 18 A C 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.605 ? metalc ? metalc1 A O2' G 5 A G 5 1_555 F NA NA . A NA 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.842 ? metalc ? metalc2 A O2' G 5 A G 5 1_555 F NA NA . A NA 105 2_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.842 ? metalc ? metalc3 A O2' G 5 A G 5 1_555 I NA NA . A NA 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.1 ? metalc ? metalc4 A OP1 G 6 A G 6 1_555 C NA NA . A NA 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? metalc ? metalc5 A OP1 G 6 A G 6 1_555 C NA NA . A NA 102 2_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.81 ? metalc ? metalc6 A O2' G 6 A G 6 1_555 H NA NA . A NA 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? metalc ? metalc7 A OP2 G 6 A G 6 1_555 H NA NA . A NA 107 2_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.908 ? metalc ? metalc8 A O2' A 16 A A 16 1_555 B NA NA . A NA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.892 ? metalc ? metalc9 A O2' A 16 A A 16 1_555 G NA NA . A NA 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.934 ? metalc ? metalc10 A O2' A 16 A A 16 1_555 G NA NA . A NA 106 2_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.935 ? metalc ? metalc11 A O2P CBV 17 A CBV 17 1_555 D NA NA . A NA 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.851 ? metalc ? metalc12 A O2P CBV 17 A CBV 17 1_555 D NA NA . A NA 103 2_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? metalc ? metalc13 A O2' CBV 17 A CBV 17 1_555 E NA NA . A NA 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.78 ? metalc ? metalc14 A O1P CBV 17 A CBV 17 1_555 E NA NA . A NA 104 3_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.944 ? metalc ? metalc15 E NA NA . A NA 104 1_555 K O HOH . A HOH 215 2_565 ? ? ? ? ? ? ? ? ? ? ? ? 3.028 ? metalc ? metalc16 I NA NA . A NA 108 1_555 K O HOH . A HOH 214 3_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.835 ? hydrog WATSON-CRICK hydrog1 A N1 G 1 A G 1 1_555 A N3 C 18 A C 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 G 1 A G 1 1_555 A O2 C 18 A C 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 G 1 A G 1 1_555 A N4 C 18 A C 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 G 2 A G 2 1_555 A N3 CBV 17 A CBV 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 G 2 A G 2 1_555 A O2 CBV 17 A CBV 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 G 2 A G 2 1_555 A N4 CBV 17 A CBV 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 U 3 A U 3 1_555 A N1 A 16 A A 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A O4 U 3 A U 3 1_555 A N6 A 16 A A 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N1 G 4 A G 4 1_555 A N3 C 15 A C 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N2 G 4 A G 4 1_555 A O2 C 15 A C 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O6 G 4 A G 4 1_555 A N4 C 15 A C 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N1 G 5 A G 5 1_555 A N3 C 14 A C 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N2 G 5 A G 5 1_555 A O2 C 14 A C 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O6 G 5 A G 5 1_555 A N4 C 14 A C 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N1 G 6 A G 6 1_555 A N3 C 13 A C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N2 G 6 A G 6 1_555 A O2 C 13 A C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A O6 G 6 A G 6 1_555 A N4 C 13 A C 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N1 G 7 A G 7 1_555 A N3 C 12 A C 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N2 G 7 A G 7 1_555 A O2 C 12 A C 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A O6 G 7 A G 7 1_555 A N4 C 12 A C 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C5 H14 N4' _chem_comp.formula_weight 130.191 _chem_comp.id AG2 _chem_comp.mon_nstd_flag . _chem_comp.name AGMATINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms (4-AMINOBUTYL)GUANIDINE # 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 AG2 sing 40 n n N HN1 AG2 sing 41 n n N HN2 AG2 sing 42 n n CA CB AG2 sing 43 n n CA HA1 AG2 sing 44 n n CA HA2 AG2 sing 45 n n CB CG AG2 sing 46 n n CB HB1 AG2 sing 47 n n CB HB2 AG2 sing 48 n n CG CD AG2 sing 49 n n CG HG1 AG2 sing 50 n n CG HG2 AG2 sing 51 n n CD NE AG2 sing 52 n n CD HD1 AG2 sing 53 n n CD HD2 AG2 sing 54 n n NE CZ AG2 sing 55 n n NE HE1 AG2 sing 56 n n CZ NH1 AG2 doub 57 n n CZ NH2 AG2 sing 58 n n NH1 HH11 AG2 sing 59 n n NH2 HH21 AG2 sing 60 n n NH2 HH22 AG2 sing 61 n n # _atom_sites.entry_id 5NEX _atom_sites.fract_transf_matrix[1][1] 0.017973 _atom_sites.fract_transf_matrix[1][2] 0.010377 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020753 _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] 0.007357 _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 B 2 NA A 1 101 1 NA NA . C 2 NA A 1 102 2 NA NA . D 2 NA A 1 103 3 NA NA . E 2 NA A 1 104 4 NA NA . F 2 NA A 1 105 5 NA NA . G 2 NA A 1 106 6 NA NA . H 2 NA A 1 107 7 NA NA . I 2 NA A 1 108 8 NA NA . J 3 AG2 A 1 109 1 AG2 AG2 . K 4 HOH A 1 201 9 HOH HOH . K 4 HOH A 2 202 8 HOH HOH . K 4 HOH A 3 203 3 HOH HOH . K 4 HOH A 4 204 12 HOH HOH . K 4 HOH A 5 205 1 HOH HOH . K 4 HOH A 6 206 4 HOH HOH . K 4 HOH A 7 207 10 HOH HOH . K 4 HOH A 8 208 14 HOH HOH . K 4 HOH A 9 209 7 HOH HOH . K 4 HOH A 10 210 6 HOH HOH . K 4 HOH A 11 211 11 HOH HOH . K 4 HOH A 12 212 2 HOH HOH . K 4 HOH A 13 213 5 HOH HOH . K 4 HOH A 14 214 13 HOH HOH . K 4 HOH A 15 215 15 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 AG2 . A . J 3 -10.377 10.519 19.99 0.45 48.52 ? N AG2 109 A 1 HETATM 2 N N AG2 . B . J 3 -11.979 11.124 17.861 0.55 48.58 ? N AG2 109 A 1 HETATM 3 C CA AG2 . A . J 3 -11.388 10.457 21.032 0.45 65.64 ? CA AG2 109 A 1 HETATM 4 C CA AG2 . B . J 3 -11.661 10.877 19.267 0.55 67.32 ? CA AG2 109 A 1 HETATM 5 C CB AG2 . A . J 3 -12.533 11.426 20.732 0.45 71.27 ? CB AG2 109 A 1 HETATM 6 C CB AG2 . B . J 3 -12.687 11.509 20.217 0.55 72.77 ? CB AG2 109 A 1 HETATM 7 C CG AG2 . A . J 3 -12.119 12.861 21.08 0.45 65.72 ? CG AG2 109 A 1 HETATM 8 C CG AG2 . B . J 3 -12.067 12.724 20.919 0.55 67.21 ? CG AG2 109 A 1 HETATM 9 C CD AG2 . A . J 3 -13.113 13.479 22.059 0.45 51.99 ? CD AG2 109 A 1 HETATM 10 C CD AG2 . B . J 3 -13.044 13.328 21.929 0.55 53.21 ? CD AG2 109 A 1 HETATM 11 N NE AG2 . A . J 3 -13.209 14.916 21.855 0.45 59.71 ? NE AG2 109 A 1 HETATM 12 N NE AG2 . B . J 3 -13.15 14.767 21.74 0.55 51.75 ? NE AG2 109 A 1 HETATM 13 C CZ AG2 . A . J 3 -14.492 15.569 22.044 0.45 74.63 ? CZ AG2 109 A 1 HETATM 14 C CZ AG2 . B . J 3 -14.405 15.448 22.024 0.55 74.41 ? CZ AG2 109 A 1 HETATM 15 N NH1 AG2 . A . J 3 -15.481 14.873 22.381 0.45 93.12 ? NH1 AG2 109 A 1 HETATM 16 N NH1 AG2 . B . J 3 -15.393 14.791 22.433 0.55 94.65 ? NH1 AG2 109 A 1 HETATM 17 N NH2 AG2 . A . J 3 -14.622 17.005 21.853 0.45 60 ? NH2 AG2 109 A 1 HETATM 18 N NH2 AG2 . B . J 3 -14.511 16.886 21.838 0.55 61.88 ? NH2 AG2 109 A 1 HETATM 19 H HN1 AG2 . A . J 3 -9.595 10.747 20.347 0.45 58.22 ? HN1 AG2 109 A 1 HETATM 20 H HN1 AG2 . B . J 3 -11.302 11.553 17.475 0.55 58.29 ? HN1 AG2 109 A 1 HETATM 21 H HN2 AG2 . A . J 3 -10.614 11.126 19.383 0.45 58.22 ? HN2 AG2 109 A 1 HETATM 22 H HN2 AG2 . B . J 3 -12.716 11.62 17.806 0.55 58.29 ? HN2 AG2 109 A 1 HETATM 23 H HA1 AG2 . A . J 3 -11.739 9.555 21.084 0.45 78.77 ? HA1 AG2 109 A 1 HETATM 24 H HA1 AG2 . B . J 3 -11.639 9.919 19.421 0.55 80.79 ? HA1 AG2 109 A 1 HETATM 25 H HA2 AG2 . A . J 3 -10.984 10.693 21.882 0.45 78.77 ? HA2 AG2 109 A 1 HETATM 26 H HA2 AG2 . B . J 3 -10.785 11.246 19.46 0.55 80.79 ? HA2 AG2 109 A 1 HETATM 27 H HB1 AG2 . A . J 3 -12.756 11.377 19.79 0.45 85.53 ? HB1 AG2 109 A 1 HETATM 28 H HB1 AG2 . B . J 3 -13.464 11.793 19.709 0.55 87.33 ? HB1 AG2 109 A 1 HETATM 29 H HB2 AG2 . A . J 3 -13.308 11.179 21.259 0.45 85.53 ? HB2 AG2 109 A 1 HETATM 30 H HB2 AG2 . B . J 3 -12.957 10.856 20.881 0.55 87.33 ? HB2 AG2 109 A 1 HETATM 31 H HG1 AG2 . A . J 3 -11.237 12.851 21.484 0.45 78.87 ? HG1 AG2 109 A 1 HETATM 32 H HG1 AG2 . B . J 3 -11.261 12.447 21.383 0.55 80.66 ? HG1 AG2 109 A 1 HETATM 33 H HG2 AG2 . A . J 3 -12.094 13.393 20.27 0.45 78.87 ? HG2 AG2 109 A 1 HETATM 34 H HG2 AG2 . B . J 3 -11.839 13.394 20.256 0.55 80.66 ? HG2 AG2 109 A 1 HETATM 35 H HD1 AG2 . A . J 3 -13.986 13.078 21.924 0.45 62.38 ? HD1 AG2 109 A 1 HETATM 36 H HD1 AG2 . B . J 3 -13.918 12.925 21.809 0.55 63.85 ? HD1 AG2 109 A 1 HETATM 37 H HD2 AG2 . A . J 3 -12.818 13.305 22.967 0.45 62.38 ? HD2 AG2 109 A 1 HETATM 38 H HD2 AG2 . B . J 3 -12.728 13.147 22.828 0.55 63.85 ? HD2 AG2 109 A 1 HETATM 39 H HE1 AG2 . A . J 3 -12.516 15.371 21.626 0.45 71.65 ? HE1 AG2 109 A 1 HETATM 40 H HE1 AG2 . B . J 3 -12.471 15.215 21.461 0.55 62.1 ? HE1 AG2 109 A 1 HETATM 41 H HH11 AG2 . A . J 3 -16.275 15.257 22.502 0.45 111.75 ? HH11 AG2 109 A 1 HETATM 42 H HH11 AG2 . B . J 3 -16.161 15.205 22.607 0.55 113.59 ? HH11 AG2 109 A 1 HETATM 43 H HH21 AG2 . A . J 3 -15.384 17.387 21.966 0.45 72 ? HH21 AG2 109 A 1 HETATM 44 H HH21 AG2 . B . J 3 -15.253 17.288 22.006 0.55 74.26 ? HH21 AG2 109 A 1 HETATM 45 H HH22 AG2 . A . J 3 -13.937 17.472 21.622 0.45 72 ? HH22 AG2 109 A 1 HETATM 46 H HH22 AG2 . B . J 3 -13.833 17.335 21.558 0.55 74.26 ? HH22 AG2 109 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 46 #