data_4PNE
#
_model_server_result.job_id            -4xbeBL7yRLt89gsVZ7bCA 
_model_server_result.datetime_utc      '2025-07-30 15:52:13' 
_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          4pne 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":302}' 
#
_entry.id    4PNE 
#
_exptl.entry_id    4PNE 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              102.046 
_entity.id                          3 
_entity.src_method                  syn 
_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          97.49 
_cell.angle_gamma         90 
_cell.entry_id            4PNE 
_cell.length_a            41.74 
_cell.length_b            69.35 
_cell.length_c            83.63 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4PNE 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 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 
PISA dimeric 2 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,G 1 1 
B,E,F,H 2 1 
A,B,C,D,E,F,G,H 3 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 D N N 
? 3 F 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 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                     4PNE 
_atom_sites.fract_transf_matrix[1][1]    0.023958 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003148 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01442 
_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]    0.01206 
_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 SAH A 1 301 301 SAH SAH . 
D 3 MLI A 1 302 302 MLI MLI . 
E 2 SAH B 1 301 301 SAH SAH . 
F 3 MLI B 1 302 302 MLI MLI . 
G 4 HOH A 1 401 401 HOH HOH . 
G 4 HOH A 2 402 402 HOH HOH . 
G 4 HOH A 3 403 403 HOH HOH . 
G 4 HOH A 4 404 404 HOH HOH . 
G 4 HOH A 5 405 405 HOH HOH . 
G 4 HOH A 6 406 406 HOH HOH . 
G 4 HOH A 7 407 407 HOH HOH . 
G 4 HOH A 8 408 408 HOH HOH . 
G 4 HOH A 9 409 409 HOH HOH . 
G 4 HOH A 10 410 410 HOH HOH . 
G 4 HOH A 11 411 411 HOH HOH . 
G 4 HOH A 12 412 412 HOH HOH . 
G 4 HOH A 13 413 413 HOH HOH . 
G 4 HOH A 14 414 414 HOH HOH . 
G 4 HOH A 15 415 415 HOH HOH . 
G 4 HOH A 16 416 416 HOH HOH . 
G 4 HOH A 17 417 417 HOH HOH . 
G 4 HOH A 18 418 418 HOH HOH . 
G 4 HOH A 19 419 419 HOH HOH . 
G 4 HOH A 20 420 420 HOH HOH . 
G 4 HOH A 21 421 421 HOH HOH . 
G 4 HOH A 22 422 422 HOH HOH . 
G 4 HOH A 23 423 423 HOH HOH . 
G 4 HOH A 24 424 424 HOH HOH . 
G 4 HOH A 25 425 425 HOH HOH . 
G 4 HOH A 26 426 426 HOH HOH . 
G 4 HOH A 27 427 427 HOH HOH . 
G 4 HOH A 28 428 429 HOH HOH . 
G 4 HOH A 29 429 430 HOH HOH . 
G 4 HOH A 30 430 431 HOH HOH . 
G 4 HOH A 31 431 432 HOH HOH . 
G 4 HOH A 32 432 433 HOH HOH . 
G 4 HOH A 33 433 434 HOH HOH . 
G 4 HOH A 34 434 435 HOH HOH . 
G 4 HOH A 35 435 436 HOH HOH . 
G 4 HOH A 36 436 437 HOH HOH . 
G 4 HOH A 37 437 438 HOH HOH . 
G 4 HOH A 38 438 439 HOH HOH . 
G 4 HOH A 39 439 440 HOH HOH . 
G 4 HOH A 40 440 441 HOH HOH . 
G 4 HOH A 41 441 428 HOH HOH . 
G 4 HOH A 42 442 442 HOH HOH . 
G 4 HOH A 43 443 443 HOH HOH . 
G 4 HOH A 44 444 444 HOH HOH . 
G 4 HOH A 45 445 445 HOH HOH . 
G 4 HOH A 46 446 446 HOH HOH . 
G 4 HOH A 47 447 447 HOH HOH . 
G 4 HOH A 48 448 448 HOH HOH . 
G 4 HOH A 49 449 449 HOH HOH . 
G 4 HOH A 50 450 450 HOH HOH . 
G 4 HOH A 51 451 451 HOH HOH . 
G 4 HOH A 52 452 452 HOH HOH . 
G 4 HOH A 53 453 453 HOH HOH . 
G 4 HOH A 54 454 454 HOH HOH . 
G 4 HOH A 55 455 455 HOH HOH . 
G 4 HOH A 56 456 456 HOH HOH . 
G 4 HOH A 57 457 457 HOH HOH . 
G 4 HOH A 58 458 458 HOH HOH . 
G 4 HOH A 59 459 459 HOH HOH . 
G 4 HOH A 60 460 460 HOH HOH . 
G 4 HOH A 61 461 461 HOH HOH . 
G 4 HOH A 62 462 462 HOH HOH . 
G 4 HOH A 63 463 463 HOH HOH . 
G 4 HOH A 64 464 464 HOH HOH . 
G 4 HOH A 65 465 465 HOH HOH . 
G 4 HOH A 66 466 466 HOH HOH . 
G 4 HOH A 67 467 467 HOH HOH . 
G 4 HOH A 68 468 468 HOH HOH . 
G 4 HOH A 69 469 469 HOH HOH . 
G 4 HOH A 70 470 470 HOH HOH . 
G 4 HOH A 71 471 471 HOH HOH . 
G 4 HOH A 72 472 472 HOH HOH . 
G 4 HOH A 73 473 473 HOH HOH . 
G 4 HOH A 74 474 474 HOH HOH . 
G 4 HOH A 75 475 475 HOH HOH . 
G 4 HOH A 76 476 476 HOH HOH . 
G 4 HOH A 77 477 477 HOH HOH . 
G 4 HOH A 78 478 478 HOH HOH . 
G 4 HOH A 79 479 479 HOH HOH . 
G 4 HOH A 80 480 480 HOH HOH . 
G 4 HOH A 81 481 481 HOH HOH . 
G 4 HOH A 82 482 482 HOH HOH . 
G 4 HOH A 83 483 483 HOH HOH . 
G 4 HOH A 84 484 484 HOH HOH . 
G 4 HOH A 85 485 485 HOH HOH . 
G 4 HOH A 86 486 486 HOH HOH . 
G 4 HOH A 87 487 487 HOH HOH . 
G 4 HOH A 88 488 488 HOH HOH . 
G 4 HOH A 89 489 489 HOH HOH . 
G 4 HOH A 90 490 490 HOH HOH . 
G 4 HOH A 91 491 491 HOH HOH . 
G 4 HOH A 92 492 492 HOH HOH . 
G 4 HOH A 93 493 493 HOH HOH . 
G 4 HOH A 94 494 494 HOH HOH . 
G 4 HOH A 95 495 495 HOH HOH . 
G 4 HOH A 96 496 496 HOH HOH . 
G 4 HOH A 97 497 497 HOH HOH . 
G 4 HOH A 98 498 498 HOH HOH . 
G 4 HOH A 99 499 499 HOH HOH . 
G 4 HOH A 100 500 500 HOH HOH . 
G 4 HOH A 101 501 501 HOH HOH . 
G 4 HOH A 102 502 502 HOH HOH . 
G 4 HOH A 103 503 503 HOH HOH . 
G 4 HOH A 104 504 504 HOH HOH . 
G 4 HOH A 105 505 505 HOH HOH . 
G 4 HOH A 106 506 506 HOH HOH . 
G 4 HOH A 107 507 507 HOH HOH . 
G 4 HOH A 108 508 508 HOH HOH . 
G 4 HOH A 109 509 509 HOH HOH . 
G 4 HOH A 110 510 510 HOH HOH . 
G 4 HOH A 111 511 511 HOH HOH . 
G 4 HOH A 112 512 512 HOH HOH . 
G 4 HOH A 113 513 513 HOH HOH . 
G 4 HOH A 114 514 514 HOH HOH . 
G 4 HOH A 115 515 515 HOH HOH . 
H 4 HOH B 1 401 401 HOH HOH . 
H 4 HOH B 2 402 403 HOH HOH . 
H 4 HOH B 3 403 404 HOH HOH . 
H 4 HOH B 4 404 405 HOH HOH . 
H 4 HOH B 5 405 406 HOH HOH . 
H 4 HOH B 6 406 407 HOH HOH . 
H 4 HOH B 7 407 408 HOH HOH . 
H 4 HOH B 8 408 409 HOH HOH . 
H 4 HOH B 9 409 410 HOH HOH . 
H 4 HOH B 10 410 411 HOH HOH . 
H 4 HOH B 11 411 412 HOH HOH . 
H 4 HOH B 12 412 413 HOH HOH . 
H 4 HOH B 13 413 414 HOH HOH . 
H 4 HOH B 14 414 415 HOH HOH . 
H 4 HOH B 15 415 416 HOH HOH . 
H 4 HOH B 16 416 417 HOH HOH . 
H 4 HOH B 17 417 418 HOH HOH . 
H 4 HOH B 18 418 419 HOH HOH . 
H 4 HOH B 19 419 420 HOH HOH . 
H 4 HOH B 20 420 421 HOH HOH . 
H 4 HOH B 21 421 422 HOH HOH . 
H 4 HOH B 22 422 423 HOH HOH . 
H 4 HOH B 23 423 424 HOH HOH . 
H 4 HOH B 24 424 425 HOH HOH . 
H 4 HOH B 25 425 426 HOH HOH . 
H 4 HOH B 26 426 427 HOH HOH . 
H 4 HOH B 27 427 428 HOH HOH . 
H 4 HOH B 28 428 429 HOH HOH . 
H 4 HOH B 29 429 430 HOH HOH . 
H 4 HOH B 30 430 402 HOH HOH . 
H 4 HOH B 31 431 431 HOH HOH . 
H 4 HOH B 32 432 432 HOH HOH . 
H 4 HOH B 33 433 433 HOH HOH . 
H 4 HOH B 34 434 434 HOH HOH . 
H 4 HOH B 35 435 435 HOH HOH . 
H 4 HOH B 36 436 436 HOH HOH . 
H 4 HOH B 37 437 437 HOH HOH . 
H 4 HOH B 38 438 438 HOH HOH . 
H 4 HOH B 39 439 439 HOH HOH . 
H 4 HOH B 40 440 440 HOH HOH . 
H 4 HOH B 41 441 441 HOH HOH . 
H 4 HOH B 42 442 442 HOH HOH . 
H 4 HOH B 43 443 443 HOH HOH . 
H 4 HOH B 44 444 444 HOH HOH . 
H 4 HOH B 45 445 445 HOH HOH . 
H 4 HOH B 46 446 446 HOH HOH . 
H 4 HOH B 47 447 447 HOH HOH . 
H 4 HOH B 48 448 448 HOH HOH . 
H 4 HOH B 49 449 449 HOH HOH . 
H 4 HOH B 50 450 450 HOH HOH . 
H 4 HOH B 51 451 451 HOH HOH . 
H 4 HOH B 52 452 452 HOH HOH . 
H 4 HOH B 53 453 453 HOH HOH . 
H 4 HOH B 54 454 454 HOH HOH . 
H 4 HOH B 55 455 455 HOH HOH . 
H 4 HOH B 56 456 456 HOH HOH . 
H 4 HOH B 57 457 457 HOH HOH . 
H 4 HOH B 58 458 458 HOH HOH . 
H 4 HOH B 59 459 459 HOH HOH . 
H 4 HOH B 60 460 460 HOH HOH . 
H 4 HOH B 61 461 461 HOH HOH . 
H 4 HOH B 62 462 462 HOH HOH . 
H 4 HOH B 63 463 463 HOH HOH . 
H 4 HOH B 64 464 464 HOH HOH . 
H 4 HOH B 65 465 465 HOH HOH . 
H 4 HOH B 66 466 466 HOH HOH . 
H 4 HOH B 67 467 467 HOH HOH . 
H 4 HOH B 68 468 468 HOH HOH . 
H 4 HOH B 69 469 469 HOH HOH . 
H 4 HOH B 70 470 470 HOH HOH . 
H 4 HOH B 71 471 471 HOH HOH . 
H 4 HOH B 72 472 472 HOH HOH . 
H 4 HOH B 73 473 473 HOH HOH . 
H 4 HOH B 74 474 474 HOH HOH . 
H 4 HOH B 75 475 475 HOH HOH . 
H 4 HOH B 76 476 476 HOH HOH . 
H 4 HOH B 77 477 477 HOH HOH . 
H 4 HOH B 78 478 478 HOH HOH . 
H 4 HOH B 79 479 479 HOH HOH . 
H 4 HOH B 80 480 480 HOH HOH . 
H 4 HOH B 81 481 481 HOH HOH . 
H 4 HOH B 82 482 482 HOH HOH . 
H 4 HOH B 83 483 483 HOH HOH . 
H 4 HOH B 84 484 484 HOH HOH . 
H 4 HOH B 85 485 485 HOH HOH . 
H 4 HOH B 86 486 486 HOH HOH . 
H 4 HOH B 87 487 487 HOH HOH . 
H 4 HOH B 88 488 488 HOH HOH . 
H 4 HOH B 89 489 489 HOH HOH . 
H 4 HOH B 90 490 490 HOH HOH . 
H 4 HOH B 91 491 491 HOH HOH . 
H 4 HOH B 92 492 492 HOH HOH . 
H 4 HOH B 93 493 493 HOH HOH . 
H 4 HOH B 94 494 494 HOH HOH . 
H 4 HOH B 95 495 495 HOH HOH . 
H 4 HOH B 96 496 496 HOH HOH . 
H 4 HOH B 97 497 497 HOH HOH . 
H 4 HOH B 98 498 498 HOH HOH . 
H 4 HOH B 99 499 499 HOH HOH . 
H 4 HOH B 100 500 500 HOH HOH . 
H 4 HOH B 101 501 501 HOH HOH . 
H 4 HOH B 102 502 502 HOH HOH . 
H 4 HOH B 103 503 503 HOH HOH . 
H 4 HOH B 104 504 504 HOH HOH . 
H 4 HOH B 105 505 505 HOH HOH . 
H 4 HOH B 106 506 506 HOH HOH . 
H 4 HOH B 107 507 507 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 . A . F 3 11.957 34.686 25.484 0.53 13.46 ? C1 MLI 302 B 1 
HETATM 2 C C1 MLI . B . F 3 11.34 35.017 24.977 0.46 14.06 ? C1 MLI 302 B 1 
HETATM 3 C C2 MLI . A . F 3 11.551 34.36 24.054 0.53 18.19 ? C2 MLI 302 B 1 
HETATM 4 C C2 MLI . B . F 3 12.689 34.406 25.321 0.46 11.35 ? C2 MLI 302 B 1 
HETATM 5 C C3 MLI . A . F 3 10.979 35.475 26.351 0.53 16.97 ? C3 MLI 302 B 1 
HETATM 6 C C3 MLI . B . F 3 10.804 36.021 25.987 0.46 15.37 ? C3 MLI 302 B 1 
HETATM 7 O O6 MLI . A . F 3 10.395 34.607 23.656 0.53 23.66 ? O6 MLI 302 B 1 
HETATM 8 O O6 MLI . B . F 3 13.109 34.438 26.489 0.46 19.58 ? O6 MLI 302 B 1 
HETATM 9 O O7 MLI . A . F 3 12.377 33.795 23.272 0.53 16 ? O7 MLI 302 B 1 
HETATM 10 O O7 MLI . B . F 3 13.388 33.841 24.452 0.46 15.43 ? O7 MLI 302 B 1 
HETATM 11 O O8 MLI . A . F 3 11.396 35.836 27.49 0.53 15.55 ? O8 MLI 302 B 1 
HETATM 12 O O8 MLI . B . F 3 11.103 35.983 27.217 0.46 17.17 ? O8 MLI 302 B 1 
HETATM 13 O O9 MLI . A . F 3 9.791 35.789 26.024 0.53 19.27 ? O9 MLI 302 B 1 
HETATM 14 O O9 MLI . B . F 3 9.988 36.89 25.582 0.46 16.45 ? O9 MLI 302 B 1 
HETATM 15 H H11 MLI . A . F 3 12.153 33.845 25.939 0.53 16.15 ? H11 MLI 302 B 1 
HETATM 16 H H11 MLI . B . F 3 10.699 34.283 24.935 0.46 16.87 ? H11 MLI 302 B 1 
HETATM 17 H H12 MLI . A . F 3 12.793 35.189 25.449 0.53 16.15 ? H12 MLI 302 B 1 
HETATM 18 H H12 MLI . B . F 3 11.385 35.435 24.096 0.46 16.87 ? H12 MLI 302 B 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           349 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           18 
#