data_7CDO
#
_model_server_result.job_id            3PLCp6hGjaVtlZsAkHyYBQ 
_model_server_result.datetime_utc      '2025-08-31 23:19:53' 
_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          7cdo 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
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_entry.id    7CDO 
#
_exptl.entry_id    7CDO 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              102.046 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'MALONATE ION' 
_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            7CDO 
_cell.length_a            78.377 
_cell.length_b            78.377 
_cell.length_c            38.785 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
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_symmetry.entry_id                 7CDO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    'P 4nw 2abw' 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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                      2 
_struct_asym.id                             B 
_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
disulf ? disulf1 A SG CYS 6 A CYS 6 1_555 A SG CYS 127 A CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf2 A SG CYS 30 A CYS 30 1_555 A SG CYS 115 A CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf3 A SG CYS 64 A CYS 64 1_555 A SG CYS 80 A CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf4 A SG CYS 76 A CYS 76 1_555 A SG CYS 94 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
metalc ? metalc1 A O SER 60 A SER 60 1_555 C NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? 
metalc ? metalc2 A O CYS 64 A CYS 64 1_555 C NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? 
metalc ? metalc3 A OG SER 72 A SER 72 1_555 C NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? 
metalc ? metalc4 A O ARG 73 A ARG 73 1_555 C NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? 
metalc ? metalc5 B O6 MLI . A MLI 201 1_555 C NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? 
metalc ? metalc6 B O7 MLI . A MLI 201 1_555 C NA NA . A NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? 
#
_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                     7CDO 
_atom_sites.fract_transf_matrix[1][1]    0.012759 
_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]    0.012759 
_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]    0.025783 
_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
B 2 MLI A 1 201 201 MLI MLI . 
C 3 NA A 1 202 1 NA NA . 
D 4 HOH A 1 301 25 HOH HOH . 
D 4 HOH A 2 302 7 HOH HOH . 
D 4 HOH A 3 303 35 HOH HOH . 
D 4 HOH A 4 304 21 HOH HOH . 
D 4 HOH A 5 305 32 HOH HOH . 
D 4 HOH A 6 306 16 HOH HOH . 
D 4 HOH A 7 307 11 HOH HOH . 
D 4 HOH A 8 308 3 HOH HOH . 
D 4 HOH A 9 309 4 HOH HOH . 
D 4 HOH A 10 310 17 HOH HOH . 
D 4 HOH A 11 311 1 HOH HOH . 
D 4 HOH A 12 312 38 HOH HOH . 
D 4 HOH A 13 313 41 HOH HOH . 
D 4 HOH A 14 314 10 HOH HOH . 
D 4 HOH A 15 315 13 HOH HOH . 
D 4 HOH A 16 316 29 HOH HOH . 
D 4 HOH A 17 317 28 HOH HOH . 
D 4 HOH A 18 318 14 HOH HOH . 
D 4 HOH A 19 319 19 HOH HOH . 
D 4 HOH A 20 320 6 HOH HOH . 
D 4 HOH A 21 321 18 HOH HOH . 
D 4 HOH A 22 322 45 HOH HOH . 
D 4 HOH A 23 323 23 HOH HOH . 
D 4 HOH A 24 324 2 HOH HOH . 
D 4 HOH A 25 325 12 HOH HOH . 
D 4 HOH A 26 326 15 HOH HOH . 
D 4 HOH A 27 327 47 HOH HOH . 
D 4 HOH A 28 328 5 HOH HOH . 
D 4 HOH A 29 329 30 HOH HOH . 
D 4 HOH A 30 330 9 HOH HOH . 
D 4 HOH A 31 331 37 HOH HOH . 
D 4 HOH A 32 332 36 HOH HOH . 
D 4 HOH A 33 333 31 HOH HOH . 
D 4 HOH A 34 334 20 HOH HOH . 
D 4 HOH A 35 335 33 HOH HOH . 
D 4 HOH A 36 336 22 HOH HOH . 
D 4 HOH A 37 337 43 HOH HOH . 
D 4 HOH A 38 338 49 HOH HOH . 
D 4 HOH A 39 339 42 HOH HOH . 
D 4 HOH A 40 340 8 HOH HOH . 
D 4 HOH A 41 341 26 HOH HOH . 
D 4 HOH A 42 342 48 HOH HOH . 
D 4 HOH A 43 343 27 HOH HOH . 
D 4 HOH A 44 344 34 HOH HOH . 
D 4 HOH A 45 345 39 HOH HOH . 
D 4 HOH A 46 346 44 HOH HOH . 
D 4 HOH A 47 347 46 HOH HOH . 
D 4 HOH A 48 348 24 HOH HOH . 
D 4 HOH A 49 349 40 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 . . . B 2 11.065 9.542 -14.963 1 18.17 ? C1 MLI 201 A 1 
HETATM 2 C C2 MLI . . . B 2 11.83 8.62 -14.012 1 22.77 ? C2 MLI 201 A 1 
HETATM 3 C C3 MLI . . . B 2 10.722 10.945 -14.449 1 22.78 ? C3 MLI 201 A 1 
HETATM 4 O O6 MLI . . . B 2 12.061 7.436 -14.391 1 17.47 ? O6 MLI 201 A 1 
HETATM 5 O O7 MLI . . . B 2 12.184 9.078 -12.896 1 18.25 ? O7 MLI 201 A 1 
HETATM 6 O O8 MLI . . . B 2 10.166 11.741 -15.237 1 25.61 ? O8 MLI 201 A 1 
HETATM 7 O O9 MLI . . . B 2 10.994 11.234 -13.266 1 19.21 ? O9 MLI 201 A 1 
#
_model_server_stats.io_time_ms              90 
_model_server_stats.parse_time_ms           194 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           615 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           7 
#