data_3K04 # _model_server_result.job_id LZTzphcZ9wAt00pe5wvDjQ _model_server_result.datetime_utc '2025-07-13 21:21:34' _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 3k04 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 3K04 # _exptl.entry_id 3K04 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-2-METHYL-2,4-PENTANEDIOL _entity.pdbx_number_of_molecules 6 _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 3K04 _cell.length_a 67.84 _cell.length_b 67.84 _cell.length_c 89.38 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3K04 _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,J,K,L,Q 1 1,2,3,4 B,M,N,O,P,R 2 1,2,3,4 # 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 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 M N N ? 2 N 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 metalc ? metalc1 Q O HOH . A HOH 1 1_555 H NA NA . A NA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? metalc ? metalc2 G NA NA . A NA 2 1_555 A O THR 46 A THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc3 H NA NA . A NA 4 1_555 A OG1 THR 46 A THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc4 I NA NA . A NA 5 1_555 A O VAL 47 A VAL 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.823 ? metalc ? metalc5 J NA NA . A NA 6 1_555 Q O HOH . A HOH 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc6 K NA NA . A NA 7 1_555 A O GLY 48 A GLY 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.784 ? metalc ? metalc7 L NA NA . A NA 8 1_555 Q O HOH . A HOH 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.959 ? metalc ? metalc8 O NA NA . B NA 1 1_555 B O THR 46 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc9 P NA NA . B NA 3 1_555 B OG1 THR 46 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc10 P NA NA . B NA 3 1_555 R O HOH . B HOH 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? # _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 3K04 _atom_sites.fract_transf_matrix[1][1] 0.014741 _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] 0.014741 _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] 0.011188 _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 C 2 MPD A 1 502 502 MPD MPD . D 2 MPD A 1 504 504 MPD MPD . E 2 MPD A 1 505 505 MPD MPD . F 2 MPD A 1 506 506 MPD MPD . G 3 NA A 1 2 2 NA NA . H 3 NA A 1 4 4 NA NA . I 3 NA A 1 5 5 NA NA . J 3 NA A 1 6 6 NA NA . K 3 NA A 1 7 7 NA NA . L 3 NA A 1 8 8 NA NA . M 2 MPD B 1 501 501 MPD MPD . N 2 MPD B 1 503 503 MPD MPD . O 3 NA B 1 1 1 NA NA . P 3 NA B 1 3 3 NA NA . Q 4 HOH A 1 1 1 HOH HOH . Q 4 HOH A 2 9 9 HOH HOH . Q 4 HOH A 3 10 10 HOH HOH . Q 4 HOH A 4 11 11 HOH HOH . Q 4 HOH A 5 13 13 HOH HOH . Q 4 HOH A 6 14 14 HOH HOH . Q 4 HOH A 7 15 15 HOH HOH . Q 4 HOH A 8 114 2 HOH HOH . Q 4 HOH A 9 115 5 HOH HOH . Q 4 HOH A 10 116 6 HOH HOH . Q 4 HOH A 11 117 117 HOH HOH . Q 4 HOH A 12 118 118 HOH HOH . Q 4 HOH A 13 119 119 HOH HOH . Q 4 HOH A 14 120 120 HOH HOH . Q 4 HOH A 15 121 121 HOH HOH . Q 4 HOH A 16 122 7 HOH HOH . Q 4 HOH A 17 123 20 HOH HOH . Q 4 HOH A 18 124 24 HOH HOH . Q 4 HOH A 19 125 125 HOH HOH . Q 4 HOH A 20 126 26 HOH HOH . Q 4 HOH A 21 127 27 HOH HOH . Q 4 HOH A 22 128 29 HOH HOH . Q 4 HOH A 23 129 32 HOH HOH . Q 4 HOH A 24 130 36 HOH HOH . Q 4 HOH A 25 131 131 HOH HOH . Q 4 HOH A 26 132 37 HOH HOH . Q 4 HOH A 27 133 38 HOH HOH . Q 4 HOH A 28 134 39 HOH HOH . Q 4 HOH A 29 135 135 HOH HOH . Q 4 HOH A 30 136 41 HOH HOH . Q 4 HOH A 31 137 137 HOH HOH . Q 4 HOH A 32 138 138 HOH HOH . Q 4 HOH A 33 139 42 HOH HOH . Q 4 HOH A 34 140 43 HOH HOH . Q 4 HOH A 35 141 141 HOH HOH . Q 4 HOH A 36 142 44 HOH HOH . Q 4 HOH A 37 143 45 HOH HOH . Q 4 HOH A 38 144 144 HOH HOH . Q 4 HOH A 39 145 145 HOH HOH . Q 4 HOH A 40 146 47 HOH HOH . Q 4 HOH A 41 147 147 HOH HOH . Q 4 HOH A 42 148 51 HOH HOH . Q 4 HOH A 43 149 52 HOH HOH . Q 4 HOH A 44 150 54 HOH HOH . Q 4 HOH A 45 151 59 HOH HOH . Q 4 HOH A 46 152 60 HOH HOH . Q 4 HOH A 47 153 61 HOH HOH . Q 4 HOH A 48 154 62 HOH HOH . Q 4 HOH A 49 155 63 HOH HOH . Q 4 HOH A 50 156 64 HOH HOH . Q 4 HOH A 51 157 65 HOH HOH . Q 4 HOH A 52 158 68 HOH HOH . Q 4 HOH A 53 159 70 HOH HOH . Q 4 HOH A 54 160 72 HOH HOH . Q 4 HOH A 55 161 75 HOH HOH . Q 4 HOH A 56 162 77 HOH HOH . Q 4 HOH A 57 163 79 HOH HOH . Q 4 HOH A 58 164 80 HOH HOH . Q 4 HOH A 59 165 83 HOH HOH . Q 4 HOH A 60 166 85 HOH HOH . Q 4 HOH A 61 167 86 HOH HOH . Q 4 HOH A 62 168 87 HOH HOH . Q 4 HOH A 63 169 88 HOH HOH . Q 4 HOH A 64 170 89 HOH HOH . Q 4 HOH A 65 171 90 HOH HOH . Q 4 HOH A 66 172 91 HOH HOH . Q 4 HOH A 67 173 94 HOH HOH . Q 4 HOH A 68 174 100 HOH HOH . Q 4 HOH A 69 175 105 HOH HOH . Q 4 HOH A 70 176 106 HOH HOH . Q 4 HOH A 71 177 107 HOH HOH . Q 4 HOH A 72 178 108 HOH HOH . Q 4 HOH A 73 179 109 HOH HOH . Q 4 HOH A 74 180 112 HOH HOH . Q 4 HOH A 75 181 55 HOH HOH . R 4 HOH B 1 4 4 HOH HOH . R 4 HOH B 2 8 8 HOH HOH . R 4 HOH B 3 12 12 HOH HOH . R 4 HOH B 4 16 16 HOH HOH . R 4 HOH B 5 17 17 HOH HOH . R 4 HOH B 6 114 114 HOH HOH . R 4 HOH B 7 115 115 HOH HOH . R 4 HOH B 8 116 116 HOH HOH . R 4 HOH B 9 117 3 HOH HOH . R 4 HOH B 10 118 18 HOH HOH . R 4 HOH B 11 119 19 HOH HOH . R 4 HOH B 12 120 21 HOH HOH . R 4 HOH B 13 121 22 HOH HOH . R 4 HOH B 14 122 122 HOH HOH . R 4 HOH B 15 123 123 HOH HOH . R 4 HOH B 16 124 124 HOH HOH . R 4 HOH B 17 125 23 HOH HOH . R 4 HOH B 18 126 126 HOH HOH . R 4 HOH B 19 127 127 HOH HOH . R 4 HOH B 20 128 128 HOH HOH . R 4 HOH B 21 129 129 HOH HOH . R 4 HOH B 22 130 130 HOH HOH . R 4 HOH B 23 131 25 HOH HOH . R 4 HOH B 24 132 132 HOH HOH . R 4 HOH B 25 133 133 HOH HOH . R 4 HOH B 26 134 134 HOH HOH . R 4 HOH B 27 135 28 HOH HOH . R 4 HOH B 28 136 136 HOH HOH . R 4 HOH B 29 137 30 HOH HOH . R 4 HOH B 30 138 31 HOH HOH . R 4 HOH B 31 139 139 HOH HOH . R 4 HOH B 32 140 140 HOH HOH . R 4 HOH B 33 141 33 HOH HOH . R 4 HOH B 34 142 142 HOH HOH . R 4 HOH B 35 143 143 HOH HOH . R 4 HOH B 36 144 34 HOH HOH . R 4 HOH B 37 145 35 HOH HOH . R 4 HOH B 38 146 146 HOH HOH . R 4 HOH B 39 147 40 HOH HOH . R 4 HOH B 40 148 46 HOH HOH . R 4 HOH B 41 149 48 HOH HOH . R 4 HOH B 42 150 49 HOH HOH . R 4 HOH B 43 151 50 HOH HOH . R 4 HOH B 44 152 53 HOH HOH . R 4 HOH B 45 154 56 HOH HOH . R 4 HOH B 46 155 57 HOH HOH . R 4 HOH B 47 156 58 HOH HOH . R 4 HOH B 48 157 66 HOH HOH . R 4 HOH B 49 158 67 HOH HOH . R 4 HOH B 50 159 69 HOH HOH . R 4 HOH B 51 160 71 HOH HOH . R 4 HOH B 52 161 73 HOH HOH . R 4 HOH B 53 162 74 HOH HOH . R 4 HOH B 54 163 76 HOH HOH . R 4 HOH B 55 164 78 HOH HOH . R 4 HOH B 56 165 81 HOH HOH . R 4 HOH B 57 166 82 HOH HOH . R 4 HOH B 58 167 84 HOH HOH . R 4 HOH B 59 168 92 HOH HOH . R 4 HOH B 60 169 93 HOH HOH . R 4 HOH B 61 170 95 HOH HOH . R 4 HOH B 62 171 96 HOH HOH . R 4 HOH B 63 172 97 HOH HOH . R 4 HOH B 64 173 98 HOH HOH . R 4 HOH B 65 174 99 HOH HOH . R 4 HOH B 66 175 101 HOH HOH . R 4 HOH B 67 176 102 HOH HOH . R 4 HOH B 68 177 103 HOH HOH . R 4 HOH B 69 178 104 HOH HOH . R 4 HOH B 70 179 110 HOH HOH . R 4 HOH B 71 180 111 HOH HOH . R 4 HOH B 72 181 113 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 C C1 MPD . . . C 2 3.81 -19.5 27.191 1 61.89 ? C1 MPD 502 A 1 HETATM 2 C C2 MPD . . . C 2 4.326 -18.254 26.465 1 63.56 ? C2 MPD 502 A 1 HETATM 3 O O2 MPD . . . C 2 4.293 -17.132 27.35 1 63.8 ? O2 MPD 502 A 1 HETATM 4 C CM MPD . . . C 2 5.759 -18.496 25.995 1 62.48 ? CM MPD 502 A 1 HETATM 5 C C3 MPD . . . C 2 3.442 -17.959 25.25 1 59.45 ? C3 MPD 502 A 1 HETATM 6 C C4 MPD . . . C 2 3.564 -18.583 23.857 1 61.24 ? C4 MPD 502 A 1 HETATM 7 O O4 MPD . . . C 2 3.887 -17.57 22.901 1 60.53 ? O4 MPD 502 A 1 HETATM 8 C C5 MPD . . . C 2 4.655 -19.654 23.867 1 55.49 ? C5 MPD 502 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 8 #