data_1JI5 # _model_server_result.job_id DefouKE14ODnj-asyBg2aw _model_server_result.datetime_utc '2024-10-19 15:48:20' _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 1ji5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":2001}' # _entry.id 1JI5 # _exptl.entry_id 1JI5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-2-METHYL-2,4-PENTANEDIOL _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 1JI5 _cell.length_a 89.224 _cell.length_b 89.224 _cell.length_c 210.165 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1JI5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details author_and_software_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 1,2,3 # 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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id G _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 metalc ? metalc1 A NE2 HIS 24 A HIS 27 1_555 F FE FE . B FE 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc2 A OD1 ASP 51 A ASP 54 1_555 E FE FE . A FE 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? metalc ? metalc3 A OD2 ASP 51 A ASP 54 1_555 E FE FE . A FE 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc4 A OE2 GLU 55 A GLU 58 1_555 E FE FE . A FE 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc5 E FE FE . A FE 152 1_555 B NE2 HIS 24 B HIS 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.882 ? metalc ? metalc6 E FE FE . A FE 152 1_555 K O HOH . B HOH 2028 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc7 J O HOH . A HOH 198 1_555 F FE FE . B FE 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc8 B OD1 ASP 51 B ASP 54 1_555 F FE FE . B FE 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.716 ? metalc ? metalc9 B OD2 ASP 51 B ASP 54 1_555 F FE FE . B FE 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc10 B OE2 GLU 55 B GLU 58 1_555 F FE FE . B FE 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc11 C NE2 HIS 24 C HIS 27 1_555 I FE FE . D FE 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc12 C OD1 ASP 51 C ASP 54 1_555 H FE FE . C FE 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.69 ? metalc ? metalc13 C OD2 ASP 51 C ASP 54 1_555 H FE FE . C FE 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc14 C OE2 GLU 55 C GLU 58 1_555 H FE FE . C FE 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc15 H FE FE . C FE 154 1_555 D NE2 HIS 24 D HIS 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc16 H FE FE . C FE 154 1_555 M O HOH . D HOH 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.843 ? metalc ? metalc17 L O HOH . C HOH 191 1_555 I FE FE . D FE 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.713 ? metalc ? metalc18 D OD2 ASP 51 D ASP 54 1_555 I FE FE . D FE 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.884 ? metalc ? metalc19 D OD1 ASP 51 D ASP 54 1_555 I FE FE . D FE 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.588 ? metalc ? metalc20 D OE2 GLU 55 D GLU 58 1_555 I FE FE . D FE 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? # _chem_comp.formula 'C6 H14 O2' _chem_comp.formula_weight 118.174 _chem_comp.id MPD _chem_comp.mon_nstd_flag . _chem_comp.name (4S)-2-METHYL-2,4-PENTANEDIOL _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 C1 C2 MPD sing 224 n n C1 H11 MPD sing 225 n n C1 H12 MPD sing 226 n n C1 H13 MPD sing 227 n n C2 O2 MPD sing 228 n n C2 CM MPD sing 229 n n C2 C3 MPD sing 230 n n O2 HO2 MPD sing 231 n n CM HM1 MPD sing 232 n n CM HM2 MPD sing 233 n n CM HM3 MPD sing 234 n n C3 C4 MPD sing 235 n n C3 H31 MPD sing 236 n n C3 H32 MPD sing 237 n n C4 O4 MPD sing 238 n n C4 C5 MPD sing 239 n n C4 H4 MPD sing 240 n n O4 HO4 MPD sing 241 n n C5 H51 MPD sing 242 n n C5 H52 MPD sing 243 n n C5 H53 MPD sing 244 n n # _atom_sites.entry_id 1JI5 _atom_sites.fract_transf_matrix[1][1] 0.011208 _atom_sites.fract_transf_matrix[1][2] 0.006471 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012942 _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] 0.004758 _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 E 2 FE A 1 152 152 FE OF3 . F 2 FE B 1 151 151 FE OF3 . G 3 MPD B 1 2001 2001 MPD MPD . H 2 FE C 1 154 154 FE OF3 . I 2 FE D 1 153 153 FE OF3 . J 4 HOH A 1 153 2 HOH HOH . J 4 HOH A 2 154 3 HOH HOH . J 4 HOH A 3 155 12 HOH HOH . J 4 HOH A 4 156 13 HOH HOH . J 4 HOH A 5 157 14 HOH HOH . J 4 HOH A 6 158 15 HOH HOH . J 4 HOH A 7 159 21 HOH HOH . J 4 HOH A 8 160 31 HOH HOH . J 4 HOH A 9 161 35 HOH HOH . J 4 HOH A 10 162 37 HOH HOH . J 4 HOH A 11 163 38 HOH HOH . J 4 HOH A 12 164 42 HOH HOH . J 4 HOH A 13 165 46 HOH HOH . J 4 HOH A 14 166 49 HOH HOH . J 4 HOH A 15 167 52 HOH HOH . J 4 HOH A 16 168 55 HOH HOH . J 4 HOH A 17 169 57 HOH HOH . J 4 HOH A 18 170 58 HOH HOH . J 4 HOH A 19 171 61 HOH HOH . J 4 HOH A 20 172 62 HOH HOH . J 4 HOH A 21 173 67 HOH HOH . J 4 HOH A 22 174 68 HOH HOH . J 4 HOH A 23 175 69 HOH HOH . J 4 HOH A 24 176 78 HOH HOH . J 4 HOH A 25 177 80 HOH HOH . J 4 HOH A 26 178 81 HOH HOH . J 4 HOH A 27 179 82 HOH HOH . J 4 HOH A 28 180 89 HOH HOH . J 4 HOH A 29 181 91 HOH HOH . J 4 HOH A 30 182 93 HOH HOH . J 4 HOH A 31 183 95 HOH HOH . J 4 HOH A 32 184 97 HOH HOH . J 4 HOH A 33 185 104 HOH HOH . J 4 HOH A 34 186 110 HOH HOH . J 4 HOH A 35 187 116 HOH HOH . J 4 HOH A 36 188 118 HOH HOH . J 4 HOH A 37 189 125 HOH HOH . J 4 HOH A 38 190 128 HOH HOH . J 4 HOH A 39 191 138 HOH HOH . J 4 HOH A 40 192 139 HOH HOH . J 4 HOH A 41 193 142 HOH HOH . J 4 HOH A 42 194 143 HOH HOH . J 4 HOH A 43 195 145 HOH HOH . J 4 HOH A 44 196 147 HOH HOH . J 4 HOH A 45 197 148 HOH HOH . J 4 HOH A 46 198 151 HOH OF3 . K 4 HOH B 1 2002 1 HOH HOH . K 4 HOH B 2 2003 10 HOH HOH . K 4 HOH B 3 2004 17 HOH HOH . K 4 HOH B 4 2005 18 HOH HOH . K 4 HOH B 5 2006 27 HOH HOH . K 4 HOH B 6 2007 56 HOH HOH . K 4 HOH B 7 2008 66 HOH HOH . K 4 HOH B 8 2009 76 HOH HOH . K 4 HOH B 9 2010 84 HOH HOH . K 4 HOH B 10 2011 92 HOH HOH . K 4 HOH B 11 2012 102 HOH HOH . K 4 HOH B 12 2013 111 HOH HOH . K 4 HOH B 13 2014 121 HOH HOH . K 4 HOH B 14 2015 124 HOH HOH . K 4 HOH B 15 2016 127 HOH HOH . K 4 HOH B 16 2017 129 HOH HOH . K 4 HOH B 17 2018 130 HOH HOH . K 4 HOH B 18 2019 131 HOH HOH . K 4 HOH B 19 2020 132 HOH HOH . K 4 HOH B 20 2021 133 HOH HOH . K 4 HOH B 21 2022 135 HOH HOH . K 4 HOH B 22 2023 137 HOH HOH . K 4 HOH B 23 2024 140 HOH HOH . K 4 HOH B 24 2025 144 HOH HOH . K 4 HOH B 25 2026 146 HOH HOH . K 4 HOH B 26 2027 149 HOH HOH . K 4 HOH B 27 2028 152 HOH OF3 . L 4 HOH C 1 155 4 HOH HOH . L 4 HOH C 2 156 5 HOH HOH . L 4 HOH C 3 157 6 HOH HOH . L 4 HOH C 4 158 9 HOH HOH . L 4 HOH C 5 159 16 HOH HOH . L 4 HOH C 6 160 19 HOH HOH . L 4 HOH C 7 161 22 HOH HOH . L 4 HOH C 8 162 23 HOH HOH . L 4 HOH C 9 163 28 HOH HOH . L 4 HOH C 10 164 29 HOH HOH . L 4 HOH C 11 165 40 HOH HOH . L 4 HOH C 12 166 41 HOH HOH . L 4 HOH C 13 167 43 HOH HOH . L 4 HOH C 14 168 44 HOH HOH . L 4 HOH C 15 169 47 HOH HOH . L 4 HOH C 16 170 50 HOH HOH . L 4 HOH C 17 171 51 HOH HOH . L 4 HOH C 18 172 54 HOH HOH . L 4 HOH C 19 173 65 HOH HOH . L 4 HOH C 20 174 70 HOH HOH . L 4 HOH C 21 175 72 HOH HOH . L 4 HOH C 22 176 74 HOH HOH . L 4 HOH C 23 177 77 HOH HOH . L 4 HOH C 24 178 79 HOH HOH . L 4 HOH C 25 179 83 HOH HOH . L 4 HOH C 26 180 88 HOH HOH . L 4 HOH C 27 181 96 HOH HOH . L 4 HOH C 28 182 103 HOH HOH . L 4 HOH C 29 183 105 HOH HOH . L 4 HOH C 30 184 106 HOH HOH . L 4 HOH C 31 185 107 HOH HOH . L 4 HOH C 32 186 113 HOH HOH . L 4 HOH C 33 187 117 HOH HOH . L 4 HOH C 34 188 119 HOH HOH . L 4 HOH C 35 189 122 HOH HOH . L 4 HOH C 36 190 136 HOH HOH . L 4 HOH C 37 191 153 HOH OF3 . M 4 HOH D 1 154 7 HOH HOH . M 4 HOH D 2 155 8 HOH HOH . M 4 HOH D 3 156 11 HOH HOH . M 4 HOH D 4 157 20 HOH HOH . M 4 HOH D 5 158 24 HOH HOH . M 4 HOH D 6 159 25 HOH HOH . M 4 HOH D 7 160 26 HOH HOH . M 4 HOH D 8 161 30 HOH HOH . M 4 HOH D 9 162 32 HOH HOH . M 4 HOH D 10 163 33 HOH HOH . M 4 HOH D 11 164 34 HOH HOH . M 4 HOH D 12 165 36 HOH HOH . M 4 HOH D 13 166 39 HOH HOH . M 4 HOH D 14 167 45 HOH HOH . M 4 HOH D 15 168 48 HOH HOH . M 4 HOH D 16 169 53 HOH HOH . M 4 HOH D 17 170 59 HOH HOH . M 4 HOH D 18 171 60 HOH HOH . M 4 HOH D 19 172 63 HOH HOH . M 4 HOH D 20 173 64 HOH HOH . M 4 HOH D 21 174 71 HOH HOH . M 4 HOH D 22 175 73 HOH HOH . M 4 HOH D 23 176 75 HOH HOH . M 4 HOH D 24 177 85 HOH HOH . M 4 HOH D 25 178 86 HOH HOH . M 4 HOH D 26 179 87 HOH HOH . M 4 HOH D 27 180 90 HOH HOH . M 4 HOH D 28 181 94 HOH HOH . M 4 HOH D 29 182 108 HOH HOH . M 4 HOH D 30 183 109 HOH HOH . M 4 HOH D 31 184 112 HOH HOH . M 4 HOH D 32 185 114 HOH HOH . M 4 HOH D 33 186 115 HOH HOH . M 4 HOH D 34 187 120 HOH HOH . M 4 HOH D 35 188 123 HOH HOH . M 4 HOH D 36 189 126 HOH HOH . M 4 HOH D 37 190 134 HOH HOH . M 4 HOH D 38 191 141 HOH HOH . M 4 HOH D 39 192 154 HOH OF3 . # 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 C C1 MPD . . . G 3 -6.628 -27.378 -17.675 1 75.98 ? C1 MPD 2001 B 1 HETATM 2 C C2 MPD . . . G 3 -6.438 -25.895 -17.527 1 72.98 ? C2 MPD 2001 B 1 HETATM 3 O O2 MPD . . . G 3 -6.8 -25.326 -18.801 1 69.74 ? O2 MPD 2001 B 1 HETATM 4 C CM MPD . . . G 3 -7.338 -25.364 -16.465 1 70.16 ? CM MPD 2001 B 1 HETATM 5 C C3 MPD . . . G 3 -4.949 -25.489 -17.185 1 71.49 ? C3 MPD 2001 B 1 HETATM 6 C C4 MPD . . . G 3 -3.843 -25.507 -18.284 1 71.21 ? C4 MPD 2001 B 1 HETATM 7 O O4 MPD . . . G 3 -4.105 -24.589 -19.308 1 70.59 ? O4 MPD 2001 B 1 HETATM 8 C C5 MPD . . . G 3 -2.498 -25.096 -17.735 1 68.61 ? C5 MPD 2001 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 370 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 8 #