data_9QYD
#
_model_server_result.job_id            uxi34nysNB0AFoIJvn2idA 
_model_server_result.datetime_utc      '2025-08-31 08:47:35' 
_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          9qyd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":402}' 
#
_entry.id    9QYD 
#
_exptl.entry_id    9QYD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              102.046 
_entity.id                          3 
_entity.src_method                  nat 
_entity.type                        non-polymer 
_entity.pdbx_description            'MALONATE ION' 
_entity.pdbx_number_of_molecules    2 
_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            9QYD 
_cell.length_a            39.701 
_cell.length_b            63.847 
_cell.length_c            69.53 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9QYD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        17 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 C N N 
? 3 D N N 
#
_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 250 n n 
C1 C3 MLI sing 251 n n 
C1 H11 MLI sing 252 n n 
C1 H12 MLI sing 253 n n 
C2 O6 MLI doub 254 n n 
C2 O7 MLI sing 255 n n 
C3 O8 MLI doub 256 n n 
C3 O9 MLI sing 257 n n 
#
_atom_sites.entry_id                     9QYD 
_atom_sites.fract_transf_matrix[1][1]    0.025188 
_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]    0.015662 
_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]    0.014382 
_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 GOL A 1 401 1 GOL GOL . 
C 3 MLI A 1 402 2 MLI MLI . 
D 3 MLI A 1 403 3 MLI MLI . 
E 2 GOL A 1 404 4 GOL GOL . 
F 4 HOH A 1 501 23 HOH HOH . 
F 4 HOH A 2 502 86 HOH HOH . 
F 4 HOH A 3 503 16 HOH HOH . 
F 4 HOH A 4 504 10 HOH HOH . 
F 4 HOH A 5 505 82 HOH HOH . 
F 4 HOH A 6 506 79 HOH HOH . 
F 4 HOH A 7 507 44 HOH HOH . 
F 4 HOH A 8 508 90 HOH HOH . 
F 4 HOH A 9 509 61 HOH HOH . 
F 4 HOH A 10 510 40 HOH HOH . 
F 4 HOH A 11 511 95 HOH HOH . 
F 4 HOH A 12 512 34 HOH HOH . 
F 4 HOH A 13 513 76 HOH HOH . 
F 4 HOH A 14 514 51 HOH HOH . 
F 4 HOH A 15 515 18 HOH HOH . 
F 4 HOH A 16 516 13 HOH HOH . 
F 4 HOH A 17 517 28 HOH HOH . 
F 4 HOH A 18 518 30 HOH HOH . 
F 4 HOH A 19 519 42 HOH HOH . 
F 4 HOH A 20 520 81 HOH HOH . 
F 4 HOH A 21 521 4 HOH HOH . 
F 4 HOH A 22 522 36 HOH HOH . 
F 4 HOH A 23 523 48 HOH HOH . 
F 4 HOH A 24 524 24 HOH HOH . 
F 4 HOH A 25 525 68 HOH HOH . 
F 4 HOH A 26 526 43 HOH HOH . 
F 4 HOH A 27 527 62 HOH HOH . 
F 4 HOH A 28 528 38 HOH HOH . 
F 4 HOH A 29 529 15 HOH HOH . 
F 4 HOH A 30 530 25 HOH HOH . 
F 4 HOH A 31 531 17 HOH HOH . 
F 4 HOH A 32 532 92 HOH HOH . 
F 4 HOH A 33 533 91 HOH HOH . 
F 4 HOH A 34 534 84 HOH HOH . 
F 4 HOH A 35 535 6 HOH HOH . 
F 4 HOH A 36 536 67 HOH HOH . 
F 4 HOH A 37 537 37 HOH HOH . 
F 4 HOH A 38 538 74 HOH HOH . 
F 4 HOH A 39 539 33 HOH HOH . 
F 4 HOH A 40 540 70 HOH HOH . 
F 4 HOH A 41 541 75 HOH HOH . 
F 4 HOH A 42 542 3 HOH HOH . 
F 4 HOH A 43 543 66 HOH HOH . 
F 4 HOH A 44 544 41 HOH HOH . 
F 4 HOH A 45 545 29 HOH HOH . 
F 4 HOH A 46 546 11 HOH HOH . 
F 4 HOH A 47 547 57 HOH HOH . 
F 4 HOH A 48 548 31 HOH HOH . 
F 4 HOH A 49 549 19 HOH HOH . 
F 4 HOH A 50 550 65 HOH HOH . 
F 4 HOH A 51 551 27 HOH HOH . 
F 4 HOH A 52 552 39 HOH HOH . 
F 4 HOH A 53 553 35 HOH HOH . 
F 4 HOH A 54 554 46 HOH HOH . 
F 4 HOH A 55 555 83 HOH HOH . 
F 4 HOH A 56 556 87 HOH HOH . 
F 4 HOH A 57 557 72 HOH HOH . 
F 4 HOH A 58 558 85 HOH HOH . 
F 4 HOH A 59 559 7 HOH HOH . 
F 4 HOH A 60 560 5 HOH HOH . 
F 4 HOH A 61 561 1 HOH HOH . 
F 4 HOH A 62 562 93 HOH HOH . 
F 4 HOH A 63 563 89 HOH HOH . 
F 4 HOH A 64 564 94 HOH HOH . 
F 4 HOH A 65 565 64 HOH HOH . 
F 4 HOH A 66 566 32 HOH HOH . 
F 4 HOH A 67 567 71 HOH HOH . 
F 4 HOH A 68 568 96 HOH HOH . 
F 4 HOH A 69 569 49 HOH HOH . 
F 4 HOH A 70 570 88 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 . . . C 3 13.292 -16.419 -16.658 1 63.35 ? C1 MLI 402 A 1 
HETATM 2 C C2 MLI . . . C 3 14.16 -15.159 -16.717 1 68.84 ? C2 MLI 402 A 1 
HETATM 3 C C3 MLI . . . C 3 13.257 -17.194 -15.344 1 62.35 ? C3 MLI 402 A 1 
HETATM 4 O O6 MLI . . . C 3 14.994 -15.058 -17.642 1 76.8 ? O6 MLI 402 A 1 
HETATM 5 O O7 MLI . . . C 3 13.977 -14.27 -15.868 1 76.54 ? O7 MLI 402 A 1 
HETATM 6 O O8 MLI . . . C 3 13.585 -18.393 -15.356 1 61.53 ? O8 MLI 402 A 1 
HETATM 7 O O9 MLI . . . C 3 12.871 -16.603 -14.331 1 56.23 ? O9 MLI 402 A 1 
#
_model_server_stats.io_time_ms              5 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           299 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           7 
#