data_5IDZ # _model_server_result.job_id Kh9ESbEaBRASOCaj0SJndQ _model_server_result.datetime_utc '2024-10-20 22:33:56' _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 5idz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 5IDZ # _exptl.entry_id 5IDZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 195.11 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(3S)-1-hydroxy-2-oxopiperidin-3-yl]phosphonic acid' _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 5IDZ _cell.length_a 68.1 _cell.length_b 108.74 _cell.length_c 116.46 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IDZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 D N N ? 3 G 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 metalc ? metalc1 A OD2 ASP 245 A ASP 245 1_555 C MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc2 A OE2 GLU 293 A GLU 293 1_555 C MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc3 A OD2 ASP 318 A ASP 318 1_555 C MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc4 C MG MG . A MG 500 1_555 D O08 6BM . A 6BM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc5 C MG MG . A MG 500 1_555 D O07 6BM . A 6BM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc6 C MG MG . A MG 500 1_555 I O HOH . A HOH 623 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc7 B OD2 ASP 245 B ASP 245 1_555 F MG MG . B MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc8 B OE2 GLU 293 B GLU 293 1_555 F MG MG . B MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc9 B OD1 ASP 318 B ASP 318 1_555 F MG MG . B MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc10 F MG MG . B MG 500 1_555 G O07 6BM . B 6BM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc11 F MG MG . B MG 500 1_555 G O08 6BM . B 6BM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc12 F MG MG . B MG 500 1_555 J O HOH . B HOH 633 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? # _chem_comp.formula 'C5 H10 N O5 P' _chem_comp.formula_weight 195.11 _chem_comp.id 6BM _chem_comp.mon_nstd_flag . _chem_comp.name '[(3S)-1-hydroxy-2-oxopiperidin-3-yl]phosphonic 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 O08 C06 6BM doub 1 n n C05 C06 6BM sing 2 n n C05 C04 6BM sing 3 n n C05 P09 6BM sing 4 n n O10 P09 6BM doub 5 n n C06 N01 6BM sing 6 n n C04 C03 6BM sing 7 n n O11 P09 6BM sing 8 n n P09 O12 6BM sing 9 n n N01 O07 6BM sing 10 n n N01 C02 6BM sing 11 n n C03 C02 6BM sing 12 n n C02 H1 6BM sing 13 n n C02 H2 6BM sing 14 n n C03 H3 6BM sing 15 n n C03 H4 6BM sing 16 n n C04 H5 6BM sing 17 n n C04 H6 6BM sing 18 n n C05 H7 6BM sing 19 n n O07 H8 6BM sing 20 n n O11 H9 6BM sing 21 n n O12 H10 6BM sing 22 n n # _atom_sites.entry_id 5IDZ _atom_sites.fract_transf_matrix[1][1] 0.014684 _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] 0.009196 _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] 0.008587 _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 MG A 1 500 500 MG MG . D 3 6BM A 1 501 501 6BM HEX . E 4 PGE A 1 502 502 PGE PGE . F 2 MG B 1 500 500 MG MG . G 3 6BM B 1 501 501 6BM HEX . H 4 PGE B 1 502 502 PGE PGE . I 5 HOH A 1 601 585 HOH HOH . I 5 HOH A 2 602 532 HOH HOH . I 5 HOH A 3 603 527 HOH HOH . I 5 HOH A 4 604 547 HOH HOH . I 5 HOH A 5 605 588 HOH HOH . I 5 HOH A 6 606 577 HOH HOH . I 5 HOH A 7 607 529 HOH HOH . I 5 HOH A 8 608 511 HOH HOH . I 5 HOH A 9 609 513 HOH HOH . I 5 HOH A 10 610 523 HOH HOH . I 5 HOH A 11 611 531 HOH HOH . I 5 HOH A 12 612 567 HOH HOH . I 5 HOH A 13 613 586 HOH HOH . I 5 HOH A 14 614 515 HOH HOH . I 5 HOH A 15 615 543 HOH HOH . I 5 HOH A 16 616 587 HOH HOH . I 5 HOH A 17 617 561 HOH HOH . I 5 HOH A 18 618 589 HOH HOH . I 5 HOH A 19 619 521 HOH HOH . I 5 HOH A 20 620 520 HOH HOH . I 5 HOH A 21 621 584 HOH HOH . I 5 HOH A 22 622 510 HOH HOH . I 5 HOH A 23 623 509 HOH HOH . I 5 HOH A 24 624 524 HOH HOH . I 5 HOH A 25 625 553 HOH HOH . I 5 HOH A 26 626 580 HOH HOH . I 5 HOH A 27 627 559 HOH HOH . I 5 HOH A 28 628 558 HOH HOH . I 5 HOH A 29 629 504 HOH HOH . I 5 HOH A 30 630 548 HOH HOH . I 5 HOH A 31 631 566 HOH HOH . I 5 HOH A 32 632 549 HOH HOH . I 5 HOH A 33 633 542 HOH HOH . I 5 HOH A 34 634 516 HOH HOH . I 5 HOH A 35 635 550 HOH HOH . I 5 HOH A 36 636 545 HOH HOH . I 5 HOH A 37 637 570 HOH HOH . I 5 HOH A 38 638 569 HOH HOH . I 5 HOH A 39 639 565 HOH HOH . I 5 HOH A 40 640 519 HOH HOH . I 5 HOH A 41 641 562 HOH HOH . I 5 HOH A 42 642 535 HOH HOH . I 5 HOH A 43 643 514 HOH HOH . I 5 HOH A 44 644 517 HOH HOH . I 5 HOH A 45 645 526 HOH HOH . I 5 HOH A 46 646 551 HOH HOH . I 5 HOH A 47 647 525 HOH HOH . I 5 HOH A 48 648 519 HOH HOH . I 5 HOH A 49 649 503 HOH HOH . I 5 HOH A 50 650 506 HOH HOH . I 5 HOH A 51 651 591 HOH HOH . I 5 HOH A 52 652 534 HOH HOH . I 5 HOH A 53 653 512 HOH HOH . I 5 HOH A 54 654 536 HOH HOH . I 5 HOH A 55 655 528 HOH HOH . I 5 HOH A 56 656 507 HOH HOH . I 5 HOH A 57 657 541 HOH HOH . I 5 HOH A 58 658 572 HOH HOH . I 5 HOH A 59 659 582 HOH HOH . I 5 HOH A 60 660 530 HOH HOH . I 5 HOH A 61 661 518 HOH HOH . I 5 HOH A 62 662 568 HOH HOH . I 5 HOH A 63 663 508 HOH HOH . I 5 HOH A 64 664 554 HOH HOH . I 5 HOH A 65 665 540 HOH HOH . I 5 HOH A 66 666 552 HOH HOH . I 5 HOH A 67 667 583 HOH HOH . I 5 HOH A 68 668 574 HOH HOH . I 5 HOH A 69 669 571 HOH HOH . I 5 HOH A 70 670 533 HOH HOH . I 5 HOH A 71 671 592 HOH HOH . I 5 HOH A 72 672 556 HOH HOH . I 5 HOH A 73 673 538 HOH HOH . I 5 HOH A 74 674 505 HOH HOH . I 5 HOH A 75 675 546 HOH HOH . I 5 HOH A 76 676 544 HOH HOH . I 5 HOH A 77 677 560 HOH HOH . I 5 HOH A 78 678 573 HOH HOH . I 5 HOH A 79 679 563 HOH HOH . I 5 HOH A 80 680 564 HOH HOH . I 5 HOH A 81 681 575 HOH HOH . I 5 HOH A 82 682 537 HOH HOH . I 5 HOH A 83 683 590 HOH HOH . I 5 HOH A 84 684 578 HOH HOH . I 5 HOH A 85 685 576 HOH HOH . I 5 HOH A 86 686 555 HOH HOH . I 5 HOH A 87 687 581 HOH HOH . I 5 HOH A 88 688 538 HOH HOH . I 5 HOH A 89 689 579 HOH HOH . I 5 HOH A 90 690 539 HOH HOH . J 5 HOH B 1 601 563 HOH HOH . J 5 HOH B 2 602 566 HOH HOH . J 5 HOH B 3 603 531 HOH HOH . J 5 HOH B 4 604 506 HOH HOH . J 5 HOH B 5 605 520 HOH HOH . J 5 HOH B 6 606 541 HOH HOH . J 5 HOH B 7 607 512 HOH HOH . J 5 HOH B 8 608 547 HOH HOH . J 5 HOH B 9 609 564 HOH HOH . J 5 HOH B 10 610 554 HOH HOH . J 5 HOH B 11 611 542 HOH HOH . J 5 HOH B 12 612 518 HOH HOH . J 5 HOH B 13 613 559 HOH HOH . J 5 HOH B 14 614 551 HOH HOH . J 5 HOH B 15 615 530 HOH HOH . J 5 HOH B 16 616 523 HOH HOH . J 5 HOH B 17 617 557 HOH HOH . J 5 HOH B 18 618 552 HOH HOH . J 5 HOH B 19 619 508 HOH HOH . J 5 HOH B 20 620 561 HOH HOH . J 5 HOH B 21 621 548 HOH HOH . J 5 HOH B 22 622 545 HOH HOH . J 5 HOH B 23 623 527 HOH HOH . J 5 HOH B 24 624 529 HOH HOH . J 5 HOH B 25 625 535 HOH HOH . J 5 HOH B 26 626 524 HOH HOH . J 5 HOH B 27 627 525 HOH HOH . J 5 HOH B 28 628 522 HOH HOH . J 5 HOH B 29 629 505 HOH HOH . J 5 HOH B 30 630 562 HOH HOH . J 5 HOH B 31 631 515 HOH HOH . J 5 HOH B 32 632 507 HOH HOH . J 5 HOH B 33 633 528 HOH HOH . J 5 HOH B 34 634 560 HOH HOH . J 5 HOH B 35 635 550 HOH HOH . J 5 HOH B 36 636 555 HOH HOH . J 5 HOH B 37 637 546 HOH HOH . J 5 HOH B 38 638 532 HOH HOH . J 5 HOH B 39 639 509 HOH HOH . J 5 HOH B 40 640 543 HOH HOH . J 5 HOH B 41 641 522 HOH HOH . J 5 HOH B 42 642 517 HOH HOH . J 5 HOH B 43 643 540 HOH HOH . J 5 HOH B 44 644 553 HOH HOH . J 5 HOH B 45 645 549 HOH HOH . J 5 HOH B 46 646 503 HOH HOH . J 5 HOH B 47 647 516 HOH HOH . J 5 HOH B 48 648 504 HOH HOH . J 5 HOH B 49 649 544 HOH HOH . J 5 HOH B 50 650 565 HOH HOH . J 5 HOH B 51 651 510 HOH HOH . J 5 HOH B 52 652 513 HOH HOH . J 5 HOH B 53 653 534 HOH HOH . J 5 HOH B 54 654 526 HOH HOH . J 5 HOH B 55 655 536 HOH HOH . J 5 HOH B 56 656 514 HOH HOH . J 5 HOH B 57 657 533 HOH HOH . J 5 HOH B 58 658 558 HOH HOH . J 5 HOH B 59 659 539 HOH HOH . J 5 HOH B 60 660 511 HOH HOH . J 5 HOH B 61 661 556 HOH HOH . J 5 HOH B 62 662 521 HOH HOH . J 5 HOH B 63 663 537 HOH HOH . J 5 HOH B 64 664 557 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 N N01 6BM . . . D 3 76.569 220.544 -92.262 1 29.54 ? N01 6BM 501 A 1 HETATM 2 C C02 6BM . . . D 3 75.793 221.357 -91.297 1 21.96 ? C02 6BM 501 A 1 HETATM 3 C C03 6BM . . . D 3 74.287 221.489 -91.578 1 27.63 ? C03 6BM 501 A 1 HETATM 4 C C04 6BM . . . D 3 73.906 221.15 -93.012 1 27.81 ? C04 6BM 501 A 1 HETATM 5 C C05 6BM . . . D 3 74.431 219.792 -93.424 1 29.4 ? C05 6BM 501 A 1 HETATM 6 C C06 6BM . . . D 3 75.88 219.804 -93.292 1 26.68 ? C06 6BM 501 A 1 HETATM 7 O O07 6BM . . . D 3 77.915 220.564 -92.12 1 30.4 ? O07 6BM 501 A 1 HETATM 8 O O08 6BM . . . D 3 76.667 219.162 -94.045 1 30.3 ? O08 6BM 501 A 1 HETATM 9 P P09 6BM . . . D 3 73.481 218.188 -92.526 1 28.29 ? P09 6BM 501 A 1 HETATM 10 O O10 6BM . . . D 3 72.28 217.914 -93.397 1 37.2 ? O10 6BM 501 A 1 HETATM 11 O O11 6BM . . . D 3 74.522 217.088 -92.527 1 27.99 ? O11 6BM 501 A 1 HETATM 12 O O12 6BM . . . D 3 73.157 218.74 -91.159 1 26.69 ? O12 6BM 501 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 12 #