data_1FDZ # _model_server_result.job_id 27vrcAFDYfQM4UiYHB4G9A _model_server_result.datetime_utc '2024-11-29 01:38:09' _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 1fdz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":308}' # _entry.id 1FDZ # _exptl.entry_id 1FDZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 88.062 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PYRUVIC ACID' _entity.pdbx_number_of_molecules 4 _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 1FDZ _cell.length_a 121 _cell.length_b 121 _cell.length_c 196.12 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1FDZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H 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 165 A LYS 165 1_555 E CA PYR . A PYR 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.47 ? covale ? covale2 B NZ LYS 165 B LYS 165 1_555 F CA PYR . B PYR 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale3 C NZ LYS 165 C LYS 165 1_555 G CA PYR . C PYR 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale4 D NZ LYS 165 D LYS 165 1_555 H CA PYR . D PYR 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? # _chem_comp.formula 'C3 H4 O3' _chem_comp.formula_weight 88.062 _chem_comp.id PYR _chem_comp.mon_nstd_flag . _chem_comp.name 'PYRUVIC 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 C O PYR doub 277 n n C OXT PYR sing 278 n n C CA PYR sing 279 n n OXT HXT PYR sing 280 n n CA O3 PYR doub 281 n n CA CB PYR sing 282 n n CB HB1 PYR sing 283 n n CB HB2 PYR sing 284 n n CB HB3 PYR sing 285 n n # _atom_sites.entry_id 1FDZ _atom_sites.fract_transf_matrix[1][1] 0.008264 _atom_sites.fract_transf_matrix[1][2] 0.004771 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009543 _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] 0.005099 _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 E 2 PYR A 1 302 302 PYR PYR . F 2 PYR B 1 304 304 PYR PYR . G 2 PYR C 1 306 306 PYR PYR . H 2 PYR D 1 308 308 PYR PYR . I 3 HOH A 1 401 401 HOH HOH . I 3 HOH A 2 402 402 HOH HOH . I 3 HOH A 3 403 403 HOH HOH . I 3 HOH A 4 404 404 HOH HOH . I 3 HOH A 5 405 405 HOH HOH . I 3 HOH A 6 406 406 HOH HOH . I 3 HOH A 7 407 407 HOH HOH . I 3 HOH A 8 408 408 HOH HOH . I 3 HOH A 9 409 409 HOH HOH . I 3 HOH A 10 410 410 HOH HOH . I 3 HOH A 11 436 436 HOH HOH . I 3 HOH A 12 500 500 HOH HOH . I 3 HOH A 13 503 503 HOH HOH . I 3 HOH A 14 510 510 HOH HOH . I 3 HOH A 15 512 512 HOH HOH . I 3 HOH A 16 513 513 HOH HOH . I 3 HOH A 17 520 520 HOH HOH . I 3 HOH A 18 521 521 HOH HOH . I 3 HOH A 19 524 524 HOH HOH . I 3 HOH A 20 526 526 HOH HOH . I 3 HOH A 21 529 529 HOH HOH . I 3 HOH A 22 530 530 HOH HOH . I 3 HOH A 23 532 532 HOH HOH . I 3 HOH A 24 535 535 HOH HOH . I 3 HOH A 25 540 540 HOH HOH . I 3 HOH A 26 545 545 HOH HOH . I 3 HOH A 27 546 546 HOH HOH . I 3 HOH A 28 548 548 HOH HOH . I 3 HOH A 29 551 551 HOH HOH . I 3 HOH A 30 552 552 HOH HOH . I 3 HOH A 31 554 554 HOH HOH . I 3 HOH A 32 558 558 HOH HOH . I 3 HOH A 33 562 562 HOH HOH . I 3 HOH A 34 563 563 HOH HOH . I 3 HOH A 35 567 567 HOH HOH . I 3 HOH A 36 572 572 HOH HOH . I 3 HOH A 37 574 574 HOH HOH . I 3 HOH A 38 577 577 HOH HOH . I 3 HOH A 39 578 578 HOH HOH . I 3 HOH A 40 582 582 HOH HOH . I 3 HOH A 41 588 588 HOH HOH . I 3 HOH A 42 591 591 HOH HOH . I 3 HOH A 43 592 592 HOH HOH . I 3 HOH A 44 600 600 HOH HOH . I 3 HOH A 45 602 602 HOH HOH . I 3 HOH A 46 603 603 HOH HOH . I 3 HOH A 47 604 604 HOH HOH . I 3 HOH A 48 608 608 HOH HOH . I 3 HOH A 49 614 614 HOH HOH . I 3 HOH A 50 618 618 HOH HOH . I 3 HOH A 51 620 620 HOH HOH . I 3 HOH A 52 1000 1000 HOH HOH . I 3 HOH A 53 1012 1012 HOH HOH . I 3 HOH A 54 1013 1013 HOH HOH . I 3 HOH A 55 1019 1019 HOH HOH . I 3 HOH A 56 1025 1025 HOH HOH . I 3 HOH A 57 1026 1026 HOH HOH . I 3 HOH A 58 1033 1033 HOH HOH . I 3 HOH A 59 1034 1034 HOH HOH . I 3 HOH A 60 1041 1041 HOH HOH . I 3 HOH A 61 1043 1043 HOH HOH . I 3 HOH A 62 1048 1048 HOH HOH . I 3 HOH A 63 1049 1049 HOH HOH . I 3 HOH A 64 1065 1065 HOH HOH . J 3 HOH B 1 411 411 HOH HOH . J 3 HOH B 2 412 412 HOH HOH . J 3 HOH B 3 413 413 HOH HOH . J 3 HOH B 4 414 414 HOH HOH . J 3 HOH B 5 415 415 HOH HOH . J 3 HOH B 6 416 416 HOH HOH . J 3 HOH B 7 417 417 HOH HOH . J 3 HOH B 8 419 419 HOH HOH . J 3 HOH B 9 420 420 HOH HOH . J 3 HOH B 10 421 421 HOH HOH . J 3 HOH B 11 425 425 HOH HOH . J 3 HOH B 12 458 458 HOH HOH . J 3 HOH B 13 459 459 HOH HOH . J 3 HOH B 14 501 501 HOH HOH . J 3 HOH B 15 506 506 HOH HOH . J 3 HOH B 16 508 508 HOH HOH . J 3 HOH B 17 511 511 HOH HOH . J 3 HOH B 18 514 514 HOH HOH . J 3 HOH B 19 519 519 HOH HOH . J 3 HOH B 20 522 522 HOH HOH . J 3 HOH B 21 531 531 HOH HOH . J 3 HOH B 22 537 537 HOH HOH . J 3 HOH B 23 542 542 HOH HOH . J 3 HOH B 24 550 550 HOH HOH . J 3 HOH B 25 555 555 HOH HOH . J 3 HOH B 26 557 557 HOH HOH . J 3 HOH B 27 569 569 HOH HOH . J 3 HOH B 28 571 571 HOH HOH . J 3 HOH B 29 573 573 HOH HOH . J 3 HOH B 30 580 580 HOH HOH . J 3 HOH B 31 586 586 HOH HOH . J 3 HOH B 32 593 593 HOH HOH . J 3 HOH B 33 598 598 HOH HOH . J 3 HOH B 34 607 607 HOH HOH . J 3 HOH B 35 621 621 HOH HOH . J 3 HOH B 36 622 622 HOH HOH . J 3 HOH B 37 1002 1002 HOH HOH . J 3 HOH B 38 1003 1003 HOH HOH . J 3 HOH B 39 1016 1016 HOH HOH . J 3 HOH B 40 1020 1020 HOH HOH . J 3 HOH B 41 1022 1022 HOH HOH . J 3 HOH B 42 1023 1023 HOH HOH . J 3 HOH B 43 1030 1030 HOH HOH . J 3 HOH B 44 1045 1045 HOH HOH . J 3 HOH B 45 1047 1047 HOH HOH . J 3 HOH B 46 1053 1053 HOH HOH . J 3 HOH B 47 1055 1055 HOH HOH . J 3 HOH B 48 1056 1056 HOH HOH . J 3 HOH B 49 1058 1058 HOH HOH . J 3 HOH B 50 1060 1060 HOH HOH . J 3 HOH B 51 1061 1061 HOH HOH . K 3 HOH C 1 426 426 HOH HOH . K 3 HOH C 2 427 427 HOH HOH . K 3 HOH C 3 428 428 HOH HOH . K 3 HOH C 4 429 429 HOH HOH . K 3 HOH C 5 431 431 HOH HOH . K 3 HOH C 6 432 432 HOH HOH . K 3 HOH C 7 437 437 HOH HOH . K 3 HOH C 8 439 439 HOH HOH . K 3 HOH C 9 505 505 HOH HOH . K 3 HOH C 10 515 515 HOH HOH . K 3 HOH C 11 518 518 HOH HOH . K 3 HOH C 12 533 533 HOH HOH . K 3 HOH C 13 544 544 HOH HOH . K 3 HOH C 14 547 547 HOH HOH . K 3 HOH C 15 560 560 HOH HOH . K 3 HOH C 16 561 561 HOH HOH . K 3 HOH C 17 565 565 HOH HOH . K 3 HOH C 18 568 568 HOH HOH . K 3 HOH C 19 585 585 HOH HOH . K 3 HOH C 20 587 587 HOH HOH . K 3 HOH C 21 589 589 HOH HOH . K 3 HOH C 22 590 590 HOH HOH . K 3 HOH C 23 594 594 HOH HOH . K 3 HOH C 24 595 595 HOH HOH . K 3 HOH C 25 596 596 HOH HOH . K 3 HOH C 26 605 605 HOH HOH . K 3 HOH C 27 606 606 HOH HOH . K 3 HOH C 28 610 610 HOH HOH . K 3 HOH C 29 1001 1001 HOH HOH . K 3 HOH C 30 1004 1004 HOH HOH . K 3 HOH C 31 1008 1008 HOH HOH . K 3 HOH C 32 1009 1009 HOH HOH . K 3 HOH C 33 1010 1010 HOH HOH . K 3 HOH C 34 1011 1011 HOH HOH . K 3 HOH C 35 1014 1014 HOH HOH . K 3 HOH C 36 1021 1021 HOH HOH . K 3 HOH C 37 1028 1028 HOH HOH . K 3 HOH C 38 1031 1031 HOH HOH . K 3 HOH C 39 1035 1035 HOH HOH . K 3 HOH C 40 1038 1038 HOH HOH . K 3 HOH C 41 1039 1039 HOH HOH . K 3 HOH C 42 1040 1040 HOH HOH . K 3 HOH C 43 1042 1042 HOH HOH . K 3 HOH C 44 1050 1050 HOH HOH . K 3 HOH C 45 1057 1057 HOH HOH . K 3 HOH C 46 1062 1062 HOH HOH . K 3 HOH C 47 1063 1063 HOH HOH . K 3 HOH C 48 1064 1064 HOH HOH . L 3 HOH D 1 418 418 HOH HOH . L 3 HOH D 2 441 441 HOH HOH . L 3 HOH D 3 442 442 HOH HOH . L 3 HOH D 4 443 443 HOH HOH . L 3 HOH D 5 445 445 HOH HOH . L 3 HOH D 6 446 446 HOH HOH . L 3 HOH D 7 447 447 HOH HOH . L 3 HOH D 8 448 448 HOH HOH . L 3 HOH D 9 449 449 HOH HOH . L 3 HOH D 10 450 450 HOH HOH . L 3 HOH D 11 451 451 HOH HOH . L 3 HOH D 12 453 453 HOH HOH . L 3 HOH D 13 455 455 HOH HOH . L 3 HOH D 14 456 456 HOH HOH . L 3 HOH D 15 457 457 HOH HOH . L 3 HOH D 16 502 502 HOH HOH . L 3 HOH D 17 504 504 HOH HOH . L 3 HOH D 18 507 507 HOH HOH . L 3 HOH D 19 509 509 HOH HOH . L 3 HOH D 20 516 516 HOH HOH . L 3 HOH D 21 517 517 HOH HOH . L 3 HOH D 22 523 523 HOH HOH . L 3 HOH D 23 527 527 HOH HOH . L 3 HOH D 24 528 528 HOH HOH . L 3 HOH D 25 534 534 HOH HOH . L 3 HOH D 26 536 536 HOH HOH . L 3 HOH D 27 538 538 HOH HOH . L 3 HOH D 28 539 539 HOH HOH . L 3 HOH D 29 541 541 HOH HOH . L 3 HOH D 30 543 543 HOH HOH . L 3 HOH D 31 549 549 HOH HOH . L 3 HOH D 32 556 556 HOH HOH . L 3 HOH D 33 559 559 HOH HOH . L 3 HOH D 34 566 566 HOH HOH . L 3 HOH D 35 570 570 HOH HOH . L 3 HOH D 36 575 575 HOH HOH . L 3 HOH D 37 576 576 HOH HOH . L 3 HOH D 38 581 581 HOH HOH . L 3 HOH D 39 583 583 HOH HOH . L 3 HOH D 40 584 584 HOH HOH . L 3 HOH D 41 601 601 HOH HOH . L 3 HOH D 42 609 609 HOH HOH . L 3 HOH D 43 611 611 HOH HOH . L 3 HOH D 44 612 612 HOH HOH . L 3 HOH D 45 613 613 HOH HOH . L 3 HOH D 46 615 615 HOH HOH . L 3 HOH D 47 616 616 HOH HOH . L 3 HOH D 48 623 623 HOH HOH . L 3 HOH D 49 1005 1005 HOH HOH . L 3 HOH D 50 1006 1006 HOH HOH . L 3 HOH D 51 1007 1007 HOH HOH . L 3 HOH D 52 1015 1015 HOH HOH . L 3 HOH D 53 1017 1017 HOH HOH . L 3 HOH D 54 1018 1018 HOH HOH . L 3 HOH D 55 1024 1024 HOH HOH . L 3 HOH D 56 1027 1027 HOH HOH . L 3 HOH D 57 1032 1032 HOH HOH . L 3 HOH D 58 1036 1036 HOH HOH . L 3 HOH D 59 1037 1037 HOH HOH . L 3 HOH D 60 1044 1044 HOH HOH . L 3 HOH D 61 1046 1046 HOH HOH . L 3 HOH D 62 1051 1051 HOH HOH . L 3 HOH D 63 1052 1052 HOH HOH . L 3 HOH D 64 1054 1054 HOH HOH . L 3 HOH D 65 1059 1059 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 C PYR . . . H 2 -18.004 -88.767 -7.302 1 21.54 ? C PYR 308 D 1 HETATM 2 O O PYR . . . H 2 -17.983 -89.96 -7.701 1 30.89 ? O PYR 308 D 1 HETATM 3 O OXT PYR . . . H 2 -18.959 -88.006 -7.03 1 25.86 ? OXT PYR 308 D 1 HETATM 4 C CA PYR . . . H 2 -16.63 -88.213 -7.08 1 13.51 ? CA PYR 308 D 1 HETATM 5 C CB PYR . . . H 2 -15.41 -88.72 -7.797 1 13.13 ? CB PYR 308 D 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 5 #