data_6D72 # _model_server_result.job_id jwSYfdiz1RJ-ssNHX7-vqQ _model_server_result.datetime_utc '2024-12-26 17:46:08' _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 6d72 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":202}' # _entry.id 6D72 # _exptl.entry_id 6D72 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 102.046 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MALONATE ION' _entity.pdbx_number_of_molecules 7 _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 6D72 _cell.length_a 101.761 _cell.length_b 120.804 _cell.length_c 123.33 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6D72 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _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,N,O,P,Q,R _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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_575 -x,-y+2,z -1 0 0 0 -1 0 0 0 1 0 241.608 0 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_575 x,-y+2,-z 1 0 0 0 -1 0 0 0 -1 0 241.608 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 G N N ? 4 I N N ? 4 K N N ? 4 L N N ? 4 M N N ? 4 N N N ? 4 O 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 covale ? covale1 K C1 MLI . C MLI 202 1_555 L C1 MLI . C MLI 203 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.31 ? covale ? covale2 K C1 MLI . C MLI 202 1_555 L C2 MLI . C MLI 203 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.073 ? covale ? covale3 K C1 MLI . C MLI 202 1_555 L O7 MLI . C MLI 203 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.525 ? covale ? covale4 K C3 MLI . C MLI 202 1_555 L C3 MLI . C MLI 203 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? covale ? covale5 K O8 MLI . C MLI 202 1_555 L C1 MLI . C MLI 203 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale6 K O9 MLI . C MLI 202 1_555 L C1 MLI . C MLI 203 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? metalc ? metalc1 A OE1 GLU 38 A GLU 35 1_555 D CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc2 A OE2 GLU 38 A GLU 35 1_555 D CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.155 ? metalc ? metalc3 A OE2 GLU 38 A GLU 35 1_555 E CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc4 A OE1 GLU 79 A GLU 76 1_555 D CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc5 A OE2 GLU 79 A GLU 76 1_555 D CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.101 ? metalc ? metalc6 D CA CA . A CA 201 1_555 P O HOH . A HOH 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc7 D CA CA . A CA 201 1_555 B OE2 GLU 38 B GLU 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc8 D CA CA . A CA 201 1_555 Q O HOH . B HOH 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc9 E CA CA . A CA 202 1_555 B OE1 GLU 38 B GLU 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc10 E CA CA . A CA 202 1_555 B OE2 GLU 38 B GLU 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.155 ? metalc ? metalc11 E CA CA . A CA 202 1_555 B OE1 GLU 79 B GLU 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc12 E CA CA . A CA 202 1_555 Q O HOH . B HOH 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc13 E CA CA . A CA 202 1_555 Q O HOH . B HOH 351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc14 C OE2 GLU 38 C GLU 35 1_555 J CA CA . C CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc15 C OE1 GLU 38 C GLU 35 1_555 J CA CA . C CA 201 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc16 C OE1 GLU 79 C GLU 76 1_555 J CA CA . C CA 201 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc17 J CA CA . C CA 201 1_555 R O HOH . C HOH 339 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc18 J CA CA . C CA 201 1_555 R O HOH . C HOH 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? # _chem_comp.formula 'C3 H2 O4 -2' _chem_comp.formula_weight 102.046 _chem_comp.id MLI _chem_comp.mon_nstd_flag . _chem_comp.name 'MALONATE ION' _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 MLI sing 237 n n C1 C3 MLI sing 238 n n C1 H11 MLI sing 239 n n C1 H12 MLI sing 240 n n C2 O6 MLI doub 241 n n C2 O7 MLI sing 242 n n C3 O8 MLI doub 243 n n C3 O9 MLI sing 244 n n # _atom_sites.entry_id 6D72 _atom_sites.fract_transf_matrix[1][1] 0.009827 _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] 0.008278 _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] 0.008108 _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 D 2 CA A 1 201 1 CA CA . E 2 CA A 1 202 2 CA CA . F 3 PEG A 1 203 1 PEG PEG . G 4 MLI A 1 204 4 MLI MLI . H 3 PEG B 1 201 2 PEG PEG . I 4 MLI B 1 202 1 MLI MLI . J 2 CA C 1 201 3 CA CA . K 4 MLI C 1 202 2 MLI MLI . L 4 MLI C 1 203 3 MLI MLI . M 4 MLI C 1 204 7 MLI MLI . N 4 MLI C 1 205 8 MLI MLI . O 4 MLI C 1 206 9 MLI MLI . P 5 HOH A 1 301 88 HOH HOH . P 5 HOH A 2 302 87 HOH HOH . P 5 HOH A 3 303 120 HOH HOH . P 5 HOH A 4 304 73 HOH HOH . P 5 HOH A 5 305 85 HOH HOH . P 5 HOH A 6 306 68 HOH HOH . P 5 HOH A 7 307 2 HOH HOH . P 5 HOH A 8 308 84 HOH HOH . P 5 HOH A 9 309 18 HOH HOH . P 5 HOH A 10 310 67 HOH HOH . P 5 HOH A 11 311 70 HOH HOH . P 5 HOH A 12 312 7 HOH HOH . P 5 HOH A 13 313 69 HOH HOH . P 5 HOH A 14 314 11 HOH HOH . P 5 HOH A 15 315 170 HOH HOH . P 5 HOH A 16 316 146 HOH HOH . P 5 HOH A 17 317 4 HOH HOH . P 5 HOH A 18 318 44 HOH HOH . P 5 HOH A 19 319 46 HOH HOH . P 5 HOH A 20 320 20 HOH HOH . P 5 HOH A 21 321 113 HOH HOH . P 5 HOH A 22 322 77 HOH HOH . P 5 HOH A 23 323 61 HOH HOH . P 5 HOH A 24 324 127 HOH HOH . P 5 HOH A 25 325 76 HOH HOH . P 5 HOH A 26 326 27 HOH HOH . P 5 HOH A 27 327 177 HOH HOH . P 5 HOH A 28 328 125 HOH HOH . P 5 HOH A 29 329 58 HOH HOH . P 5 HOH A 30 330 13 HOH HOH . P 5 HOH A 31 331 38 HOH HOH . P 5 HOH A 32 332 153 HOH HOH . P 5 HOH A 33 333 43 HOH HOH . P 5 HOH A 34 334 104 HOH HOH . P 5 HOH A 35 335 119 HOH HOH . P 5 HOH A 36 336 117 HOH HOH . P 5 HOH A 37 337 121 HOH HOH . P 5 HOH A 38 338 169 HOH HOH . P 5 HOH A 39 339 144 HOH HOH . P 5 HOH A 40 340 164 HOH HOH . P 5 HOH A 41 341 71 HOH HOH . P 5 HOH A 42 342 159 HOH HOH . P 5 HOH A 43 343 63 HOH HOH . P 5 HOH A 44 344 166 HOH HOH . P 5 HOH A 45 345 174 HOH HOH . P 5 HOH A 46 346 83 HOH HOH . P 5 HOH A 47 347 118 HOH HOH . P 5 HOH A 48 348 143 HOH HOH . P 5 HOH A 49 349 158 HOH HOH . P 5 HOH A 50 350 173 HOH HOH . P 5 HOH A 51 351 157 HOH HOH . P 5 HOH A 52 352 128 HOH HOH . P 5 HOH A 53 353 131 HOH HOH . P 5 HOH A 54 354 129 HOH HOH . P 5 HOH A 55 355 168 HOH HOH . P 5 HOH A 56 356 62 HOH HOH . P 5 HOH A 57 357 167 HOH HOH . P 5 HOH A 58 358 138 HOH HOH . P 5 HOH A 59 359 182 HOH HOH . P 5 HOH A 60 360 156 HOH HOH . Q 5 HOH B 1 301 126 HOH HOH . Q 5 HOH B 2 302 103 HOH HOH . Q 5 HOH B 3 303 80 HOH HOH . Q 5 HOH B 4 304 141 HOH HOH . Q 5 HOH B 5 305 140 HOH HOH . Q 5 HOH B 6 306 86 HOH HOH . Q 5 HOH B 7 307 8 HOH HOH . Q 5 HOH B 8 308 33 HOH HOH . Q 5 HOH B 9 309 90 HOH HOH . Q 5 HOH B 10 310 31 HOH HOH . Q 5 HOH B 11 311 99 HOH HOH . Q 5 HOH B 12 312 91 HOH HOH . Q 5 HOH B 13 313 34 HOH HOH . Q 5 HOH B 14 314 112 HOH HOH . Q 5 HOH B 15 315 114 HOH HOH . Q 5 HOH B 16 316 17 HOH HOH . Q 5 HOH B 17 317 42 HOH HOH . Q 5 HOH B 18 318 155 HOH HOH . Q 5 HOH B 19 319 130 HOH HOH . Q 5 HOH B 20 320 36 HOH HOH . Q 5 HOH B 21 321 3 HOH HOH . Q 5 HOH B 22 322 39 HOH HOH . Q 5 HOH B 23 323 96 HOH HOH . Q 5 HOH B 24 324 172 HOH HOH . Q 5 HOH B 25 325 28 HOH HOH . Q 5 HOH B 26 326 47 HOH HOH . Q 5 HOH B 27 327 37 HOH HOH . Q 5 HOH B 28 328 1 HOH HOH . Q 5 HOH B 29 329 95 HOH HOH . Q 5 HOH B 30 330 15 HOH HOH . Q 5 HOH B 31 331 29 HOH HOH . Q 5 HOH B 32 332 35 HOH HOH . Q 5 HOH B 33 333 181 HOH HOH . Q 5 HOH B 34 334 97 HOH HOH . Q 5 HOH B 35 335 92 HOH HOH . Q 5 HOH B 36 336 161 HOH HOH . Q 5 HOH B 37 337 22 HOH HOH . Q 5 HOH B 38 338 93 HOH HOH . Q 5 HOH B 39 339 106 HOH HOH . Q 5 HOH B 40 340 65 HOH HOH . Q 5 HOH B 41 341 124 HOH HOH . Q 5 HOH B 42 342 81 HOH HOH . Q 5 HOH B 43 343 116 HOH HOH . Q 5 HOH B 44 344 52 HOH HOH . Q 5 HOH B 45 345 160 HOH HOH . Q 5 HOH B 46 346 26 HOH HOH . Q 5 HOH B 47 347 145 HOH HOH . Q 5 HOH B 48 348 175 HOH HOH . Q 5 HOH B 49 349 21 HOH HOH . Q 5 HOH B 50 350 142 HOH HOH . Q 5 HOH B 51 351 115 HOH HOH . Q 5 HOH B 52 352 94 HOH HOH . Q 5 HOH B 53 353 32 HOH HOH . Q 5 HOH B 54 354 122 HOH HOH . Q 5 HOH B 55 355 171 HOH HOH . Q 5 HOH B 56 356 180 HOH HOH . Q 5 HOH B 57 357 178 HOH HOH . Q 5 HOH B 58 358 14 HOH HOH . Q 5 HOH B 59 359 98 HOH HOH . Q 5 HOH B 60 360 176 HOH HOH . Q 5 HOH B 61 361 79 HOH HOH . Q 5 HOH B 62 362 137 HOH HOH . Q 5 HOH B 63 363 78 HOH HOH . Q 5 HOH B 64 364 135 HOH HOH . Q 5 HOH B 65 365 162 HOH HOH . Q 5 HOH B 66 366 139 HOH HOH . Q 5 HOH B 67 367 148 HOH HOH . R 5 HOH C 1 301 110 HOH HOH . R 5 HOH C 2 302 53 HOH HOH . R 5 HOH C 3 303 50 HOH HOH . R 5 HOH C 4 304 59 HOH HOH . R 5 HOH C 5 305 133 HOH HOH . R 5 HOH C 6 306 30 HOH HOH . R 5 HOH C 7 307 149 HOH HOH . R 5 HOH C 8 308 72 HOH HOH . R 5 HOH C 9 309 51 HOH HOH . R 5 HOH C 10 310 40 HOH HOH . R 5 HOH C 11 311 66 HOH HOH . R 5 HOH C 12 312 56 HOH HOH . R 5 HOH C 13 313 24 HOH HOH . R 5 HOH C 14 314 107 HOH HOH . R 5 HOH C 15 315 6 HOH HOH . R 5 HOH C 16 316 185 HOH HOH . R 5 HOH C 17 317 179 HOH HOH . R 5 HOH C 18 318 147 HOH HOH . R 5 HOH C 19 319 25 HOH HOH . R 5 HOH C 20 320 109 HOH HOH . R 5 HOH C 21 321 108 HOH HOH . R 5 HOH C 22 322 16 HOH HOH . R 5 HOH C 23 323 23 HOH HOH . R 5 HOH C 24 324 183 HOH HOH . R 5 HOH C 25 325 188 HOH HOH . R 5 HOH C 26 326 48 HOH HOH . R 5 HOH C 27 327 19 HOH HOH . R 5 HOH C 28 328 105 HOH HOH . R 5 HOH C 29 329 45 HOH HOH . R 5 HOH C 30 330 12 HOH HOH . R 5 HOH C 31 331 74 HOH HOH . R 5 HOH C 32 332 5 HOH HOH . R 5 HOH C 33 333 9 HOH HOH . R 5 HOH C 34 334 60 HOH HOH . R 5 HOH C 35 335 163 HOH HOH . R 5 HOH C 36 336 184 HOH HOH . R 5 HOH C 37 337 136 HOH HOH . R 5 HOH C 38 338 54 HOH HOH . R 5 HOH C 39 339 151 HOH HOH . R 5 HOH C 40 340 75 HOH HOH . R 5 HOH C 41 341 64 HOH HOH . R 5 HOH C 42 342 10 HOH HOH . R 5 HOH C 43 343 100 HOH HOH . R 5 HOH C 44 344 49 HOH HOH . R 5 HOH C 45 345 134 HOH HOH . R 5 HOH C 46 346 150 HOH HOH . R 5 HOH C 47 347 186 HOH HOH . R 5 HOH C 48 348 101 HOH HOH . R 5 HOH C 49 349 111 HOH HOH . R 5 HOH C 50 350 57 HOH HOH . R 5 HOH C 51 351 132 HOH HOH . R 5 HOH C 52 352 154 HOH HOH . R 5 HOH C 53 353 89 HOH HOH . R 5 HOH C 54 354 187 HOH HOH . R 5 HOH C 55 355 55 HOH HOH . R 5 HOH C 56 356 123 HOH HOH . R 5 HOH C 57 357 152 HOH HOH . R 5 HOH C 58 358 165 HOH HOH . R 5 HOH C 59 359 102 HOH HOH . R 5 HOH C 60 360 82 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 MLI . . . I 4 1.548 136.3 33.012 1 91.46 ? C1 MLI 202 B 1 HETATM 2 C C2 MLI . . . I 4 1.292 136.634 31.554 1 94.59 ? C2 MLI 202 B 1 HETATM 3 C C3 MLI . . . I 4 2.961 136.654 33.432 1 94.41 ? C3 MLI 202 B 1 HETATM 4 O O6 MLI . . . I 4 2.073 136.24 30.659 1 88.6 ? O6 MLI 202 B 1 HETATM 5 O O7 MLI . . . I 4 0.278 137.301 31.279 1 96.99 ? O7 MLI 202 B 1 HETATM 6 O O8 MLI . . . I 4 3.923 136.233 32.744 1 89.51 ? O8 MLI 202 B 1 HETATM 7 O O9 MLI . . . I 4 3.124 137.355 34.461 1 89.19 ? O9 MLI 202 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 7 #