data_9DF1
#
_model_server_result.job_id            QenpGXtghvyLWrv2QnWTyg 
_model_server_result.datetime_utc      '2025-02-23 05:40:41' 
_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          9df1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":203}' 
#
_entry.id    9DF1 
#
_exptl.entry_id    9DF1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              104.061 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'MALONIC ACID' 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         86.3 
_cell.angle_beta          86.32 
_cell.angle_gamma         65.23 
_cell.entry_id            9DF1 
_cell.length_a            31.077 
_cell.length_b            36.177 
_cell.length_c            64.022 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9DF1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    'P 1' 
_symmetry.space_group_name_H-M     'P 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_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,M 1 1 
B,G,H,I,J,K,L,N 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 E N N 
? 4 H N N 
? 4 I N N 
? 4 J 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 A NZ LYS 108 B LYS 108 1_555 C C23 ZFJ . B ZFJ 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 doub 
covale ? covale2 B NZ LYS 108 A LYS 108 1_555 G C23 ZFJ . A ZFJ 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.503 doub 
#
_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 257 n n 
C1 O1B MLA doub 258 n n 
C1 C2 MLA sing 259 n n 
O1A H1A MLA sing 260 n n 
C2 C3 MLA sing 261 n n 
C2 HC21 MLA sing 262 n n 
C2 HC22 MLA sing 263 n n 
C3 O3A MLA doub 264 n n 
C3 O3B MLA sing 265 n n 
O3B H3B MLA sing 266 n n 
#
_atom_sites.entry_id                     9DF1 
_atom_sites.fract_transf_matrix[1][1]    0.032178 
_atom_sites.fract_transf_matrix[1][2]    -0.014848 
_atom_sites.fract_transf_matrix[1][3]    -0.001454 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.030443 
_atom_sites.fract_transf_matrix[2][3]    -0.001266 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.015665 
_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 ZFJ B 1 201 202 ZFJ LIG . 
D 3 ACY B 1 202 302 ACY ACT . 
E 4 MLA B 1 203 1 MLA MAL . 
F 5 GOL B 1 204 2 GOL GOL . 
G 2 ZFJ A 1 201 201 ZFJ LIG . 
H 4 MLA A 1 202 401 MLA MAL . 
I 4 MLA A 1 203 501 MLA MAL . 
J 4 MLA A 1 204 3 MLA MAL . 
K 5 GOL A 1 205 1 GOL GOL . 
L 5 GOL A 1 206 3 GOL GOL . 
M 6 HOH B 1 301 90 HOH HOH . 
M 6 HOH B 2 302 97 HOH HOH . 
M 6 HOH B 3 303 36 HOH HOH . 
M 6 HOH B 4 304 67 HOH HOH . 
M 6 HOH B 5 305 31 HOH HOH . 
M 6 HOH B 6 306 32 HOH HOH . 
M 6 HOH B 7 307 50 HOH HOH . 
M 6 HOH B 8 308 83 HOH HOH . 
M 6 HOH B 9 309 51 HOH HOH . 
M 6 HOH B 10 310 105 HOH HOH . 
M 6 HOH B 11 311 46 HOH HOH . 
M 6 HOH B 12 312 87 HOH HOH . 
M 6 HOH B 13 313 41 HOH HOH . 
M 6 HOH B 14 314 95 HOH HOH . 
M 6 HOH B 15 315 34 HOH HOH . 
M 6 HOH B 16 316 21 HOH HOH . 
M 6 HOH B 17 317 9 HOH HOH . 
M 6 HOH B 18 318 33 HOH HOH . 
M 6 HOH B 19 319 5 HOH HOH . 
M 6 HOH B 20 320 137 HOH HOH . 
M 6 HOH B 21 321 7 HOH HOH . 
M 6 HOH B 22 322 43 HOH HOH . 
M 6 HOH B 23 323 8 HOH HOH . 
M 6 HOH B 24 324 24 HOH HOH . 
M 6 HOH B 25 325 120 HOH HOH . 
M 6 HOH B 26 326 88 HOH HOH . 
M 6 HOH B 27 327 77 HOH HOH . 
M 6 HOH B 28 328 58 HOH HOH . 
M 6 HOH B 29 329 129 HOH HOH . 
M 6 HOH B 30 330 26 HOH HOH . 
M 6 HOH B 31 331 13 HOH HOH . 
M 6 HOH B 32 332 1 HOH HOH . 
M 6 HOH B 33 333 133 HOH HOH . 
M 6 HOH B 34 334 61 HOH HOH . 
M 6 HOH B 35 335 101 HOH HOH . 
M 6 HOH B 36 336 2 HOH HOH . 
M 6 HOH B 37 337 40 HOH HOH . 
M 6 HOH B 38 338 91 HOH HOH . 
M 6 HOH B 39 339 47 HOH HOH . 
M 6 HOH B 40 340 93 HOH HOH . 
M 6 HOH B 41 341 14 HOH HOH . 
M 6 HOH B 42 342 18 HOH HOH . 
M 6 HOH B 43 343 60 HOH HOH . 
M 6 HOH B 44 344 44 HOH HOH . 
M 6 HOH B 45 345 16 HOH HOH . 
M 6 HOH B 46 346 56 HOH HOH . 
M 6 HOH B 47 347 162 HOH HOH . 
M 6 HOH B 48 348 25 HOH HOH . 
M 6 HOH B 49 349 55 HOH HOH . 
M 6 HOH B 50 350 92 HOH HOH . 
M 6 HOH B 51 351 72 HOH HOH . 
M 6 HOH B 52 352 114 HOH HOH . 
M 6 HOH B 53 353 30 HOH HOH . 
M 6 HOH B 54 354 94 HOH HOH . 
M 6 HOH B 55 355 75 HOH HOH . 
M 6 HOH B 56 356 159 HOH HOH . 
M 6 HOH B 57 357 122 HOH HOH . 
M 6 HOH B 58 358 124 HOH HOH . 
M 6 HOH B 59 359 52 HOH HOH . 
M 6 HOH B 60 360 65 HOH HOH . 
M 6 HOH B 61 361 53 HOH HOH . 
M 6 HOH B 62 362 78 HOH HOH . 
M 6 HOH B 63 363 153 HOH HOH . 
M 6 HOH B 64 364 111 HOH HOH . 
M 6 HOH B 65 365 140 HOH HOH . 
M 6 HOH B 66 366 145 HOH HOH . 
M 6 HOH B 67 367 146 HOH HOH . 
M 6 HOH B 68 368 135 HOH HOH . 
M 6 HOH B 69 369 147 HOH HOH . 
M 6 HOH B 70 370 154 HOH HOH . 
M 6 HOH B 71 371 128 HOH HOH . 
M 6 HOH B 72 372 148 HOH HOH . 
M 6 HOH B 73 373 109 HOH HOH . 
N 6 HOH A 1 301 71 HOH HOH . 
N 6 HOH A 2 302 152 HOH HOH . 
N 6 HOH A 3 303 64 HOH HOH . 
N 6 HOH A 4 304 70 HOH HOH . 
N 6 HOH A 5 305 59 HOH HOH . 
N 6 HOH A 6 306 79 HOH HOH . 
N 6 HOH A 7 307 73 HOH HOH . 
N 6 HOH A 8 308 119 HOH HOH . 
N 6 HOH A 9 309 121 HOH HOH . 
N 6 HOH A 10 310 35 HOH HOH . 
N 6 HOH A 11 311 48 HOH HOH . 
N 6 HOH A 12 312 17 HOH HOH . 
N 6 HOH A 13 313 84 HOH HOH . 
N 6 HOH A 14 314 28 HOH HOH . 
N 6 HOH A 15 315 110 HOH HOH . 
N 6 HOH A 16 316 80 HOH HOH . 
N 6 HOH A 17 317 89 HOH HOH . 
N 6 HOH A 18 318 4 HOH HOH . 
N 6 HOH A 19 319 69 HOH HOH . 
N 6 HOH A 20 320 10 HOH HOH . 
N 6 HOH A 21 321 161 HOH HOH . 
N 6 HOH A 22 322 38 HOH HOH . 
N 6 HOH A 23 323 113 HOH HOH . 
N 6 HOH A 24 324 11 HOH HOH . 
N 6 HOH A 25 325 20 HOH HOH . 
N 6 HOH A 26 326 156 HOH HOH . 
N 6 HOH A 27 327 100 HOH HOH . 
N 6 HOH A 28 328 6 HOH HOH . 
N 6 HOH A 29 329 116 HOH HOH . 
N 6 HOH A 30 330 62 HOH HOH . 
N 6 HOH A 31 331 42 HOH HOH . 
N 6 HOH A 32 332 12 HOH HOH . 
N 6 HOH A 33 333 157 HOH HOH . 
N 6 HOH A 34 334 141 HOH HOH . 
N 6 HOH A 35 335 63 HOH HOH . 
N 6 HOH A 36 336 29 HOH HOH . 
N 6 HOH A 37 337 45 HOH HOH . 
N 6 HOH A 38 338 3 HOH HOH . 
N 6 HOH A 39 339 85 HOH HOH . 
N 6 HOH A 40 340 19 HOH HOH . 
N 6 HOH A 41 341 37 HOH HOH . 
N 6 HOH A 42 342 27 HOH HOH . 
N 6 HOH A 43 343 23 HOH HOH . 
N 6 HOH A 44 344 102 HOH HOH . 
N 6 HOH A 45 345 98 HOH HOH . 
N 6 HOH A 46 346 49 HOH HOH . 
N 6 HOH A 47 347 68 HOH HOH . 
N 6 HOH A 48 348 103 HOH HOH . 
N 6 HOH A 49 349 15 HOH HOH . 
N 6 HOH A 50 350 39 HOH HOH . 
N 6 HOH A 51 351 82 HOH HOH . 
N 6 HOH A 52 352 107 HOH HOH . 
N 6 HOH A 53 353 104 HOH HOH . 
N 6 HOH A 54 354 22 HOH HOH . 
N 6 HOH A 55 355 123 HOH HOH . 
N 6 HOH A 56 356 118 HOH HOH . 
N 6 HOH A 57 357 130 HOH HOH . 
N 6 HOH A 58 358 106 HOH HOH . 
N 6 HOH A 59 359 66 HOH HOH . 
N 6 HOH A 60 360 76 HOH HOH . 
N 6 HOH A 61 361 108 HOH HOH . 
N 6 HOH A 62 362 117 HOH HOH . 
N 6 HOH A 63 363 144 HOH HOH . 
N 6 HOH A 64 364 96 HOH HOH . 
N 6 HOH A 65 365 74 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 . . . I 4 -17.4 -0.204 -17.339 1 45.88 ? C1 MLA 203 A 1 
HETATM 2 O O1A MLA . . . I 4 -16.265 0.206 -16.972 1 48.89 ? O1A MLA 203 A 1 
HETATM 3 O O1B MLA . . . I 4 -18.45 0.367 -16.937 1 43.81 -1 O1B MLA 203 A 1 
HETATM 4 C C2 MLA . . . I 4 -17.506 -1.392 -18.285 1 41.5 ? C2 MLA 203 A 1 
HETATM 5 C C3 MLA . . . I 4 -16.939 -2.632 -17.604 1 48.27 ? C3 MLA 203 A 1 
HETATM 6 O O3A MLA . . . I 4 -17.462 -3.06 -16.539 1 60.65 -1 O3A MLA 203 A 1 
HETATM 7 O O3B MLA . . . I 4 -15.947 -3.222 -18.103 1 54.49 ? O3B MLA 203 A 1 
HETATM 8 H HC21 MLA . . . I 4 -17.003 -1.209 -19.094 1 49.83 ? HC21 MLA 203 A 1 
HETATM 9 H HC22 MLA . . . I 4 -18.437 -1.544 -18.51 1 49.83 ? HC22 MLA 203 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           293 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           9 
#