data_5Y8N # _model_server_result.job_id gEsDP_lepIO92_otafePgg _model_server_result.datetime_utc '2024-11-15 03:13:20' _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 5y8n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":307}' # _entry.id 5Y8N # _exptl.entry_id 5Y8N _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 146.141 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2~{S})-2-methylpentanedioic 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 120 _cell.entry_id 5Y8N _cell.length_a 129.16 _cell.length_b 129.16 _cell.length_c 70.43 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Y8N _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,E,F,G,H,I,J,K,L,M,N _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 6 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C6 H10 O4' _chem_comp.formula_weight 146.141 _chem_comp.id 9ON _chem_comp.mon_nstd_flag . _chem_comp.name '(2~{S})-2-methylpentanedioic acid' _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 O12 C7 9ON doub 1 n n C4 C7 9ON sing 2 n n C4 C5 9ON sing 3 n n C4 C3 9ON sing 4 n n C7 O10 9ON sing 5 n n C2 C3 9ON sing 6 n n C2 C1 9ON sing 7 n n O9 C1 9ON doub 8 n n C1 O8 9ON sing 9 n n O10 H1 9ON sing 10 n n C4 H2 9ON sing 11 n n C5 H3 9ON sing 12 n n C5 H4 9ON sing 13 n n C5 H5 9ON sing 14 n n C3 H6 9ON sing 15 n n C3 H7 9ON sing 16 n n C2 H8 9ON sing 17 n n C2 H9 9ON sing 18 n n O8 H10 9ON sing 19 n n # _atom_sites.entry_id 5Y8N _atom_sites.fract_transf_matrix[1][1] 0.007742 _atom_sites.fract_transf_matrix[1][2] 0.00447 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00894 _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] 0.014198 _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 NAD A 1 301 301 NAD NAD . D 3 SER A 1 302 302 SER SER . E 3 SER A 1 303 303 SER SER . F 4 GOL A 1 304 304 GOL GOL . G 4 GOL A 1 305 305 GOL GOL . H 5 AKR A 1 306 306 AKR AKR . I 6 9ON A 1 307 307 9ON 9ON . J 2 NAD B 1 301 301 NAD NAD . K 3 SER B 1 302 302 SER SER . L 5 AKR B 1 303 303 AKR AKR . M 7 HOH A 1 401 401 HOH HOH . M 7 HOH A 2 402 402 HOH HOH . M 7 HOH A 3 403 403 HOH HOH . M 7 HOH A 4 404 404 HOH HOH . M 7 HOH A 5 405 408 HOH HOH . M 7 HOH A 6 406 407 HOH HOH . M 7 HOH A 7 407 406 HOH HOH . M 7 HOH A 8 408 410 HOH HOH . M 7 HOH A 9 409 408 HOH HOH . M 7 HOH A 10 410 409 HOH HOH . M 7 HOH A 11 411 412 HOH HOH . M 7 HOH A 12 412 411 HOH HOH . M 7 HOH A 13 413 413 HOH HOH . M 7 HOH A 14 414 415 HOH HOH . M 7 HOH A 15 415 414 HOH HOH . M 7 HOH A 16 416 416 HOH HOH . M 7 HOH A 17 417 419 HOH HOH . M 7 HOH A 18 418 417 HOH HOH . M 7 HOH A 19 419 418 HOH HOH . M 7 HOH A 20 420 420 HOH HOH . M 7 HOH A 21 421 421 HOH HOH . M 7 HOH A 22 422 422 HOH HOH . M 7 HOH A 23 423 425 HOH HOH . M 7 HOH A 24 424 423 HOH HOH . M 7 HOH A 25 425 424 HOH HOH . M 7 HOH A 26 426 426 HOH HOH . M 7 HOH A 27 427 430 HOH HOH . M 7 HOH A 28 428 429 HOH HOH . M 7 HOH A 29 429 431 HOH HOH . M 7 HOH A 30 430 428 HOH HOH . M 7 HOH A 31 431 435 HOH HOH . M 7 HOH A 32 432 427 HOH HOH . M 7 HOH A 33 433 432 HOH HOH . M 7 HOH A 34 434 433 HOH HOH . M 7 HOH A 35 435 436 HOH HOH . M 7 HOH A 36 436 434 HOH HOH . M 7 HOH A 37 437 439 HOH HOH . M 7 HOH A 38 438 437 HOH HOH . M 7 HOH A 39 439 438 HOH HOH . M 7 HOH A 40 440 440 HOH HOH . M 7 HOH A 41 441 441 HOH HOH . M 7 HOH A 42 442 443 HOH HOH . M 7 HOH A 43 443 442 HOH HOH . M 7 HOH A 44 444 447 HOH HOH . M 7 HOH A 45 445 444 HOH HOH . M 7 HOH A 46 446 445 HOH HOH . M 7 HOH A 47 447 448 HOH HOH . M 7 HOH A 48 448 446 HOH HOH . M 7 HOH A 49 449 449 HOH HOH . M 7 HOH A 50 450 453 HOH HOH . M 7 HOH A 51 451 456 HOH HOH . M 7 HOH A 52 452 455 HOH HOH . M 7 HOH A 53 453 452 HOH HOH . M 7 HOH A 54 454 454 HOH HOH . M 7 HOH A 55 455 450 HOH HOH . M 7 HOH A 56 456 451 HOH HOH . M 7 HOH A 57 457 457 HOH HOH . M 7 HOH A 58 458 459 HOH HOH . M 7 HOH A 59 459 460 HOH HOH . M 7 HOH A 60 460 458 HOH HOH . M 7 HOH A 61 461 462 HOH HOH . M 7 HOH A 62 462 461 HOH HOH . M 7 HOH A 63 463 465 HOH HOH . M 7 HOH A 64 464 464 HOH HOH . M 7 HOH A 65 465 463 HOH HOH . M 7 HOH A 66 466 466 HOH HOH . M 7 HOH A 67 467 468 HOH HOH . M 7 HOH A 68 468 469 HOH HOH . M 7 HOH A 69 469 467 HOH HOH . M 7 HOH A 70 470 470 HOH HOH . M 7 HOH A 71 471 473 HOH HOH . M 7 HOH A 72 472 471 HOH HOH . M 7 HOH A 73 473 475 HOH HOH . M 7 HOH A 74 474 472 HOH HOH . M 7 HOH A 75 475 474 HOH HOH . M 7 HOH A 76 476 476 HOH HOH . M 7 HOH A 77 477 478 HOH HOH . M 7 HOH A 78 478 477 HOH HOH . M 7 HOH A 79 479 479 HOH HOH . M 7 HOH A 80 480 480 HOH HOH . M 7 HOH A 81 481 481 HOH HOH . M 7 HOH A 82 482 482 HOH HOH . M 7 HOH A 83 483 483 HOH HOH . M 7 HOH A 84 484 484 HOH HOH . M 7 HOH A 85 485 485 HOH HOH . M 7 HOH A 86 486 486 HOH HOH . M 7 HOH A 87 487 487 HOH HOH . M 7 HOH A 88 488 488 HOH HOH . M 7 HOH A 89 489 489 HOH HOH . M 7 HOH A 90 490 490 HOH HOH . M 7 HOH A 91 491 491 HOH HOH . M 7 HOH A 92 492 492 HOH HOH . M 7 HOH A 93 493 493 HOH HOH . M 7 HOH A 94 494 495 HOH HOH . M 7 HOH A 95 495 494 HOH HOH . M 7 HOH A 96 496 496 HOH HOH . M 7 HOH A 97 497 497 HOH HOH . M 7 HOH A 98 498 498 HOH HOH . M 7 HOH A 99 499 499 HOH HOH . M 7 HOH A 100 500 500 HOH HOH . M 7 HOH A 101 501 501 HOH HOH . M 7 HOH A 102 502 502 HOH HOH . M 7 HOH A 103 503 503 HOH HOH . M 7 HOH A 104 504 504 HOH HOH . M 7 HOH A 105 505 505 HOH HOH . M 7 HOH A 106 506 506 HOH HOH . M 7 HOH A 107 507 507 HOH HOH . M 7 HOH A 108 508 508 HOH HOH . M 7 HOH A 109 509 509 HOH HOH . M 7 HOH A 110 510 510 HOH HOH . M 7 HOH A 111 511 511 HOH HOH . M 7 HOH A 112 512 512 HOH HOH . M 7 HOH A 113 513 513 HOH HOH . M 7 HOH A 114 514 514 HOH HOH . M 7 HOH A 115 515 515 HOH HOH . M 7 HOH A 116 516 517 HOH HOH . M 7 HOH A 117 517 516 HOH HOH . M 7 HOH A 118 518 518 HOH HOH . M 7 HOH A 119 519 519 HOH HOH . M 7 HOH A 120 520 520 HOH HOH . M 7 HOH A 121 521 521 HOH HOH . M 7 HOH A 122 522 522 HOH HOH . M 7 HOH A 123 523 523 HOH HOH . M 7 HOH A 124 524 524 HOH HOH . M 7 HOH A 125 525 525 HOH HOH . M 7 HOH A 126 526 526 HOH HOH . M 7 HOH A 127 527 527 HOH HOH . M 7 HOH A 128 528 528 HOH HOH . M 7 HOH A 129 529 529 HOH HOH . M 7 HOH A 130 530 530 HOH HOH . M 7 HOH A 131 531 531 HOH HOH . M 7 HOH A 132 532 532 HOH HOH . M 7 HOH A 133 533 533 HOH HOH . M 7 HOH A 134 534 536 HOH HOH . M 7 HOH A 135 535 534 HOH HOH . M 7 HOH A 136 536 537 HOH HOH . M 7 HOH A 137 537 535 HOH HOH . M 7 HOH A 138 538 538 HOH HOH . N 7 HOH B 1 401 403 HOH HOH . N 7 HOH B 2 402 402 HOH HOH . N 7 HOH B 3 403 401 HOH HOH . N 7 HOH B 4 404 405 HOH HOH . N 7 HOH B 5 405 404 HOH HOH . N 7 HOH B 6 406 406 HOH HOH . N 7 HOH B 7 407 405 HOH HOH . N 7 HOH B 8 408 407 HOH HOH . N 7 HOH B 9 409 409 HOH HOH . N 7 HOH B 10 410 413 HOH HOH . N 7 HOH B 11 411 410 HOH HOH . N 7 HOH B 12 412 416 HOH HOH . N 7 HOH B 13 413 411 HOH HOH . N 7 HOH B 14 414 412 HOH HOH . N 7 HOH B 15 415 415 HOH HOH . N 7 HOH B 16 416 414 HOH HOH . N 7 HOH B 17 417 421 HOH HOH . N 7 HOH B 18 418 417 HOH HOH . N 7 HOH B 19 419 419 HOH HOH . N 7 HOH B 20 420 418 HOH HOH . N 7 HOH B 21 421 420 HOH HOH . N 7 HOH B 22 422 422 HOH HOH . N 7 HOH B 23 423 427 HOH HOH . N 7 HOH B 24 424 426 HOH HOH . N 7 HOH B 25 425 425 HOH HOH . N 7 HOH B 26 426 424 HOH HOH . N 7 HOH B 27 427 423 HOH HOH . N 7 HOH B 28 428 431 HOH HOH . N 7 HOH B 29 429 428 HOH HOH . N 7 HOH B 30 430 433 HOH HOH . N 7 HOH B 31 431 435 HOH HOH . N 7 HOH B 32 432 430 HOH HOH . N 7 HOH B 33 433 432 HOH HOH . N 7 HOH B 34 434 429 HOH HOH . N 7 HOH B 35 435 434 HOH HOH . N 7 HOH B 36 436 438 HOH HOH . N 7 HOH B 37 437 436 HOH HOH . N 7 HOH B 38 438 441 HOH HOH . N 7 HOH B 39 439 437 HOH HOH . N 7 HOH B 40 440 439 HOH HOH . N 7 HOH B 41 441 440 HOH HOH . N 7 HOH B 42 442 442 HOH HOH . N 7 HOH B 43 443 445 HOH HOH . N 7 HOH B 44 444 443 HOH HOH . N 7 HOH B 45 445 444 HOH HOH . N 7 HOH B 46 446 448 HOH HOH . N 7 HOH B 47 447 447 HOH HOH . N 7 HOH B 48 448 449 HOH HOH . N 7 HOH B 49 449 446 HOH HOH . N 7 HOH B 50 450 450 HOH HOH . N 7 HOH B 51 451 451 HOH HOH . N 7 HOH B 52 452 452 HOH HOH . N 7 HOH B 53 453 453 HOH HOH . N 7 HOH B 54 454 455 HOH HOH . N 7 HOH B 55 455 457 HOH HOH . N 7 HOH B 56 456 456 HOH HOH . N 7 HOH B 57 457 460 HOH HOH . N 7 HOH B 58 458 458 HOH HOH . N 7 HOH B 59 459 454 HOH HOH . N 7 HOH B 60 460 459 HOH HOH . N 7 HOH B 61 461 461 HOH HOH . N 7 HOH B 62 462 462 HOH HOH . N 7 HOH B 63 463 465 HOH HOH . N 7 HOH B 64 464 463 HOH HOH . N 7 HOH B 65 465 466 HOH HOH . N 7 HOH B 66 466 464 HOH HOH . N 7 HOH B 67 467 467 HOH HOH . N 7 HOH B 68 468 468 HOH HOH . N 7 HOH B 69 469 471 HOH HOH . N 7 HOH B 70 470 470 HOH HOH . N 7 HOH B 71 471 469 HOH HOH . N 7 HOH B 72 472 474 HOH HOH . N 7 HOH B 73 473 472 HOH HOH . N 7 HOH B 74 474 473 HOH HOH . N 7 HOH B 75 475 478 HOH HOH . N 7 HOH B 76 476 475 HOH HOH . N 7 HOH B 77 477 477 HOH HOH . N 7 HOH B 78 478 476 HOH HOH . N 7 HOH B 79 479 480 HOH HOH . N 7 HOH B 80 480 479 HOH HOH . N 7 HOH B 81 481 483 HOH HOH . N 7 HOH B 82 482 482 HOH HOH . N 7 HOH B 83 483 481 HOH HOH . N 7 HOH B 84 484 484 HOH HOH . N 7 HOH B 85 485 485 HOH HOH . N 7 HOH B 86 486 486 HOH HOH . N 7 HOH B 87 487 489 HOH HOH . N 7 HOH B 88 488 487 HOH HOH . N 7 HOH B 89 489 488 HOH HOH . N 7 HOH B 90 490 490 HOH HOH . N 7 HOH B 91 491 491 HOH HOH . N 7 HOH B 92 492 492 HOH HOH . N 7 HOH B 93 493 493 HOH HOH . N 7 HOH B 94 494 494 HOH HOH . N 7 HOH B 95 495 495 HOH HOH . N 7 HOH B 96 496 496 HOH HOH . N 7 HOH B 97 497 497 HOH HOH . N 7 HOH B 98 498 499 HOH HOH . N 7 HOH B 99 499 498 HOH HOH . N 7 HOH B 100 500 502 HOH HOH . N 7 HOH B 101 501 500 HOH HOH . N 7 HOH B 102 502 501 HOH HOH . N 7 HOH B 103 503 503 HOH HOH . N 7 HOH B 104 504 504 HOH HOH . N 7 HOH B 105 505 505 HOH HOH . N 7 HOH B 106 506 507 HOH HOH . N 7 HOH B 107 507 506 HOH HOH . N 7 HOH B 108 508 508 HOH HOH . N 7 HOH B 109 509 509 HOH HOH . N 7 HOH B 110 510 510 HOH HOH . N 7 HOH B 111 511 511 HOH HOH . N 7 HOH B 112 512 512 HOH HOH . N 7 HOH B 113 513 513 HOH HOH . N 7 HOH B 114 514 514 HOH HOH . N 7 HOH B 115 515 515 HOH HOH . N 7 HOH B 116 516 516 HOH HOH . N 7 HOH B 117 517 518 HOH HOH . N 7 HOH B 118 518 517 HOH HOH . N 7 HOH B 119 519 519 HOH HOH . N 7 HOH B 120 520 520 HOH HOH . N 7 HOH B 121 521 521 HOH HOH . N 7 HOH B 122 522 522 HOH HOH . N 7 HOH B 123 523 523 HOH HOH . N 7 HOH B 124 524 525 HOH HOH . N 7 HOH B 125 525 524 HOH HOH . N 7 HOH B 126 526 526 HOH HOH . N 7 HOH B 127 527 527 HOH HOH . N 7 HOH B 128 528 528 HOH HOH . N 7 HOH B 129 529 529 HOH HOH . N 7 HOH B 130 530 530 HOH HOH . N 7 HOH B 131 531 531 HOH HOH . N 7 HOH B 132 532 532 HOH HOH . N 7 HOH B 133 533 533 HOH HOH . N 7 HOH B 134 534 534 HOH HOH . N 7 HOH B 135 535 535 HOH HOH . N 7 HOH B 136 536 536 HOH HOH . N 7 HOH B 137 537 537 HOH HOH . N 7 HOH B 138 538 538 HOH HOH . N 7 HOH B 139 539 539 HOH HOH . N 7 HOH B 140 540 540 HOH HOH . N 7 HOH B 141 541 541 HOH HOH . N 7 HOH B 142 542 542 HOH HOH . N 7 HOH B 143 543 543 HOH HOH . N 7 HOH B 144 544 544 HOH HOH . N 7 HOH B 145 545 545 HOH HOH . N 7 HOH B 146 546 546 HOH HOH . N 7 HOH B 147 547 547 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 O O12 9ON . . . I 6 44.979 71.971 12.464 1 59.19 ? O12 9ON 307 A 1 HETATM 2 C C7 9ON . . . I 6 45.484 71.493 13.493 1 55.43 ? C7 9ON 307 A 1 HETATM 3 O O10 9ON . . . I 6 45.457 70.291 13.809 1 54.36 ? O10 9ON 307 A 1 HETATM 4 C C4 9ON . . . I 6 46.146 72.481 14.46 1 55.1 ? C4 9ON 307 A 1 HETATM 5 C C5 9ON . . . I 6 45.564 72.289 15.857 1 54.55 ? C5 9ON 307 A 1 HETATM 6 C C3 9ON . . . I 6 47.683 72.371 14.456 1 54.63 ? C3 9ON 307 A 1 HETATM 7 C C2 9ON . . . I 6 48.222 71.021 14.949 1 58.07 ? C2 9ON 307 A 1 HETATM 8 C C1 9ON . . . I 6 49.739 71.035 15.148 1 59.13 ? C1 9ON 307 A 1 HETATM 9 O O8 9ON . . . I 6 50.278 69.918 15.364 1 53.42 ? O8 9ON 307 A 1 HETATM 10 O O9 9ON . . . I 6 50.339 72.135 15.102 1 51.03 ? O9 9ON 307 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 10 #