data_3TFD
#
_model_server_result.job_id            fAWeRQSyvDg1sS-jpgAM0w 
_model_server_result.datetime_utc      '2024-11-30 08:47:33' 
_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          3tfd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":190}' 
#
_entry.id    3TFD 
#
_exptl.entry_id    3TFD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              104.061 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'MALONIC ACID' 
_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         90 
_cell.entry_id            3TFD 
_cell.length_a            123.17 
_cell.length_b            123.17 
_cell.length_c            123.17 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3TFD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        198 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 3' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 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,F 1 1 
B,D,E,G 2 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                      3 
_struct_asym.id                             E 
_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 105 A HIS 105 1_555 C FE HEM . A HEM 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? 
metalc ? metalc2 B NE2 HIS 105 B HIS 105 1_555 D FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? 
#
_chem_comp.formula           'C3 H4 O4' 
_chem_comp.formula_weight    104.061 
_chem_comp.id                MLA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'MALONIC ACID' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'DICARBOXYLIC ACID C3;PROPANEDIOLIC ACID;METHANEDICARBOXYLIC ACID' 
#
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 O1A MLA sing 319 n n 
C1 O1B MLA doub 320 n n 
C1 C2 MLA sing 321 n n 
O1A H1A MLA sing 322 n n 
C2 C3 MLA sing 323 n n 
C2 HC21 MLA sing 324 n n 
C2 HC22 MLA sing 325 n n 
C3 O3A MLA doub 326 n n 
C3 O3B MLA sing 327 n n 
O3B H3B MLA sing 328 n n 
#
_atom_sites.entry_id                     3TFD 
_atom_sites.fract_transf_matrix[1][1]    0.008119 
_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]    0.008119 
_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]    0.008119 
_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 HEM A 1 500 500 HEM HEM . 
D 2 HEM B 1 501 501 HEM HEM . 
E 3 MLA B 1 190 184 MLA MLA . 
F 4 HOH A 1 190 190 HOH HOH . 
F 4 HOH A 2 191 191 HOH HOH . 
F 4 HOH A 3 192 192 HOH HOH . 
F 4 HOH A 4 193 193 HOH HOH . 
F 4 HOH A 5 194 194 HOH HOH . 
F 4 HOH A 6 195 195 HOH HOH . 
F 4 HOH A 7 196 196 HOH HOH . 
F 4 HOH A 8 197 197 HOH HOH . 
F 4 HOH A 9 198 198 HOH HOH . 
F 4 HOH A 10 199 199 HOH HOH . 
F 4 HOH A 11 200 200 HOH HOH . 
F 4 HOH A 12 201 201 HOH HOH . 
F 4 HOH A 13 202 202 HOH HOH . 
F 4 HOH A 14 203 203 HOH HOH . 
F 4 HOH A 15 204 204 HOH HOH . 
F 4 HOH A 16 205 205 HOH HOH . 
F 4 HOH A 17 206 206 HOH HOH . 
F 4 HOH A 18 207 207 HOH HOH . 
F 4 HOH A 19 208 208 HOH HOH . 
F 4 HOH A 20 209 209 HOH HOH . 
F 4 HOH A 21 210 210 HOH HOH . 
F 4 HOH A 22 211 211 HOH HOH . 
F 4 HOH A 23 212 212 HOH HOH . 
F 4 HOH A 24 213 213 HOH HOH . 
F 4 HOH A 25 214 214 HOH HOH . 
F 4 HOH A 26 215 215 HOH HOH . 
F 4 HOH A 27 216 216 HOH HOH . 
F 4 HOH A 28 217 217 HOH HOH . 
F 4 HOH A 29 218 218 HOH HOH . 
F 4 HOH A 30 219 219 HOH HOH . 
F 4 HOH A 31 220 220 HOH HOH . 
F 4 HOH A 32 221 221 HOH HOH . 
F 4 HOH A 33 222 222 HOH HOH . 
F 4 HOH A 34 223 223 HOH HOH . 
F 4 HOH A 35 224 224 HOH HOH . 
F 4 HOH A 36 225 225 HOH HOH . 
F 4 HOH A 37 226 226 HOH HOH . 
F 4 HOH A 38 227 227 HOH HOH . 
F 4 HOH A 39 228 228 HOH HOH . 
F 4 HOH A 40 229 229 HOH HOH . 
F 4 HOH A 41 230 230 HOH HOH . 
F 4 HOH A 42 231 231 HOH HOH . 
F 4 HOH A 43 232 232 HOH HOH . 
F 4 HOH A 44 233 233 HOH HOH . 
F 4 HOH A 45 234 234 HOH HOH . 
F 4 HOH A 46 235 235 HOH HOH . 
F 4 HOH A 47 236 236 HOH HOH . 
F 4 HOH A 48 237 237 HOH HOH . 
F 4 HOH A 49 238 238 HOH HOH . 
F 4 HOH A 50 239 239 HOH HOH . 
F 4 HOH A 51 240 240 HOH HOH . 
F 4 HOH A 52 241 241 HOH HOH . 
F 4 HOH A 53 242 242 HOH HOH . 
F 4 HOH A 54 243 243 HOH HOH . 
F 4 HOH A 55 244 244 HOH HOH . 
F 4 HOH A 56 245 245 HOH HOH . 
F 4 HOH A 57 246 246 HOH HOH . 
F 4 HOH A 58 247 247 HOH HOH . 
F 4 HOH A 59 248 248 HOH HOH . 
F 4 HOH A 60 249 249 HOH HOH . 
F 4 HOH A 61 250 250 HOH HOH . 
F 4 HOH A 62 251 251 HOH HOH . 
F 4 HOH A 63 252 252 HOH HOH . 
F 4 HOH A 64 253 253 HOH HOH . 
F 4 HOH A 65 254 254 HOH HOH . 
F 4 HOH A 66 255 255 HOH HOH . 
F 4 HOH A 67 256 256 HOH HOH . 
F 4 HOH A 68 257 257 HOH HOH . 
F 4 HOH A 69 258 258 HOH HOH . 
F 4 HOH A 70 259 259 HOH HOH . 
F 4 HOH A 71 260 260 HOH HOH . 
F 4 HOH A 72 261 261 HOH HOH . 
F 4 HOH A 73 262 262 HOH HOH . 
F 4 HOH A 74 263 263 HOH HOH . 
F 4 HOH A 75 264 264 HOH HOH . 
F 4 HOH A 76 265 265 HOH HOH . 
F 4 HOH A 77 266 266 HOH HOH . 
F 4 HOH A 78 267 267 HOH HOH . 
F 4 HOH A 79 268 268 HOH HOH . 
F 4 HOH A 80 269 184 HOH HOH . 
F 4 HOH A 81 270 185 HOH HOH . 
F 4 HOH A 82 271 186 HOH HOH . 
F 4 HOH A 83 272 187 HOH HOH . 
F 4 HOH A 84 273 188 HOH HOH . 
F 4 HOH A 85 274 189 HOH HOH . 
G 4 HOH B 1 191 191 HOH HOH . 
G 4 HOH B 2 192 192 HOH HOH . 
G 4 HOH B 3 193 193 HOH HOH . 
G 4 HOH B 4 194 194 HOH HOH . 
G 4 HOH B 5 195 195 HOH HOH . 
G 4 HOH B 6 196 196 HOH HOH . 
G 4 HOH B 7 197 197 HOH HOH . 
G 4 HOH B 8 198 198 HOH HOH . 
G 4 HOH B 9 199 199 HOH HOH . 
G 4 HOH B 10 200 200 HOH HOH . 
G 4 HOH B 11 201 201 HOH HOH . 
G 4 HOH B 12 202 202 HOH HOH . 
G 4 HOH B 13 203 203 HOH HOH . 
G 4 HOH B 14 204 204 HOH HOH . 
G 4 HOH B 15 205 205 HOH HOH . 
G 4 HOH B 16 206 206 HOH HOH . 
G 4 HOH B 17 207 207 HOH HOH . 
G 4 HOH B 18 208 208 HOH HOH . 
G 4 HOH B 19 209 209 HOH HOH . 
G 4 HOH B 20 210 210 HOH HOH . 
G 4 HOH B 21 211 211 HOH HOH . 
G 4 HOH B 22 212 212 HOH HOH . 
G 4 HOH B 23 213 213 HOH HOH . 
G 4 HOH B 24 214 214 HOH HOH . 
G 4 HOH B 25 215 215 HOH HOH . 
G 4 HOH B 26 216 216 HOH HOH . 
G 4 HOH B 27 217 217 HOH HOH . 
G 4 HOH B 28 218 218 HOH HOH . 
G 4 HOH B 29 219 219 HOH HOH . 
G 4 HOH B 30 220 220 HOH HOH . 
G 4 HOH B 31 221 221 HOH HOH . 
G 4 HOH B 32 222 222 HOH HOH . 
G 4 HOH B 33 223 223 HOH HOH . 
G 4 HOH B 34 224 224 HOH HOH . 
G 4 HOH B 35 225 225 HOH HOH . 
G 4 HOH B 36 226 226 HOH HOH . 
G 4 HOH B 37 227 227 HOH HOH . 
G 4 HOH B 38 228 228 HOH HOH . 
G 4 HOH B 39 229 229 HOH HOH . 
G 4 HOH B 40 230 230 HOH HOH . 
G 4 HOH B 41 231 231 HOH HOH . 
G 4 HOH B 42 232 232 HOH HOH . 
G 4 HOH B 43 233 233 HOH HOH . 
G 4 HOH B 44 234 234 HOH HOH . 
G 4 HOH B 45 235 235 HOH HOH . 
G 4 HOH B 46 236 236 HOH HOH . 
G 4 HOH B 47 237 237 HOH HOH . 
G 4 HOH B 48 238 238 HOH HOH . 
G 4 HOH B 49 239 239 HOH HOH . 
G 4 HOH B 50 240 240 HOH HOH . 
G 4 HOH B 51 241 241 HOH HOH . 
G 4 HOH B 52 242 242 HOH HOH . 
G 4 HOH B 53 243 243 HOH HOH . 
G 4 HOH B 54 244 244 HOH HOH . 
G 4 HOH B 55 245 245 HOH HOH . 
G 4 HOH B 56 246 246 HOH HOH . 
G 4 HOH B 57 247 247 HOH HOH . 
G 4 HOH B 58 248 248 HOH HOH . 
G 4 HOH B 59 249 249 HOH HOH . 
G 4 HOH B 60 250 250 HOH HOH . 
G 4 HOH B 61 251 251 HOH HOH . 
G 4 HOH B 62 252 252 HOH HOH . 
G 4 HOH B 63 253 253 HOH HOH . 
G 4 HOH B 64 254 254 HOH HOH . 
G 4 HOH B 65 255 255 HOH HOH . 
G 4 HOH B 66 256 256 HOH HOH . 
G 4 HOH B 67 257 257 HOH HOH . 
G 4 HOH B 68 258 258 HOH HOH . 
G 4 HOH B 69 259 259 HOH HOH . 
G 4 HOH B 70 260 260 HOH HOH . 
G 4 HOH B 71 261 261 HOH HOH . 
G 4 HOH B 72 262 262 HOH HOH . 
G 4 HOH B 73 263 263 HOH HOH . 
G 4 HOH B 74 264 264 HOH HOH . 
G 4 HOH B 75 265 265 HOH HOH . 
G 4 HOH B 76 266 266 HOH HOH . 
G 4 HOH B 77 267 267 HOH HOH . 
G 4 HOH B 78 268 268 HOH HOH . 
G 4 HOH B 79 269 269 HOH HOH . 
G 4 HOH B 80 270 270 HOH HOH . 
G 4 HOH B 81 271 271 HOH HOH . 
G 4 HOH B 82 272 272 HOH HOH . 
G 4 HOH B 83 273 273 HOH HOH . 
G 4 HOH B 84 274 274 HOH HOH . 
G 4 HOH B 85 275 275 HOH HOH . 
G 4 HOH B 86 276 276 HOH HOH . 
G 4 HOH B 87 277 277 HOH HOH . 
G 4 HOH B 88 278 278 HOH HOH . 
G 4 HOH B 89 279 279 HOH HOH . 
G 4 HOH B 90 280 280 HOH HOH . 
G 4 HOH B 91 281 281 HOH HOH . 
G 4 HOH B 92 282 282 HOH HOH . 
G 4 HOH B 93 283 283 HOH HOH . 
G 4 HOH B 94 284 284 HOH HOH . 
G 4 HOH B 95 285 285 HOH HOH . 
G 4 HOH B 96 286 286 HOH HOH . 
G 4 HOH B 97 287 287 HOH HOH . 
G 4 HOH B 98 288 288 HOH HOH . 
G 4 HOH B 99 289 289 HOH HOH . 
G 4 HOH B 100 290 185 HOH HOH . 
G 4 HOH B 101 291 186 HOH HOH . 
G 4 HOH B 102 292 187 HOH HOH . 
G 4 HOH B 103 293 188 HOH HOH . 
G 4 HOH B 104 294 189 HOH HOH . 
G 4 HOH B 105 295 190 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 MLA . . . E 3 24.524 77.423 70.854 1 50.56 ? C1 MLA 190 B 1 
HETATM 2 O O1A MLA . . . E 3 25.735 77.727 70.674 1 50.59 ? O1A MLA 190 B 1 
HETATM 3 O O1B MLA . . . E 3 23.668 78.307 71.128 1 50.63 ? O1B MLA 190 B 1 
HETATM 4 C C2 MLA . . . E 3 24.091 76.007 70.718 1 48.41 ? C2 MLA 190 B 1 
HETATM 5 C C3 MLA . . . E 3 23.765 75.613 69.322 1 61.22 ? C3 MLA 190 B 1 
HETATM 6 O O3A MLA . . . E 3 23.202 76.453 68.573 1 59.01 ? O3A MLA 190 B 1 
HETATM 7 O O3B MLA . . . E 3 24.052 74.464 68.895 1 67.62 ? O3B MLA 190 B 1 
#
_model_server_stats.io_time_ms              72 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           365 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           7 
#