data_4ND1 # _model_server_result.job_id -unfJeKwU12OVxlpMqbrVw _model_server_result.datetime_utc '2024-11-24 03:53:14' _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 4nd1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":402}' # _entry.id 4ND1 # _exptl.entry_id 4ND1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 89.05 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'OXAMIC 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 120 _cell.entry_id 4ND1 _cell.length_a 94.816 _cell.length_b 94.816 _cell.length_c 185.072 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ND1 _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 185.072 # 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 I 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 C ARG 4 A ARG 20 1_555 A N ARG 5 A ARG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C ALA 29 A ALA 46 1_555 A N ASP 30 A ASP 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale3 A C PHE 55 A PHE 73 1_555 A N GLY 56 A GLY 73 1_555 A ? ? B ? ? ? ? ? ? ? ? 1.332 ? covale ? covale4 A C THR 64 A THR 81 1_555 A N ASN 65 A ASN 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale5 A C ARG 85 A ARG 103 1_555 A N PRO 86 A PRO 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale6 A C PRO 113 A PRO 132 1_555 A N ASN 114 A ASN 132 1_555 A ? ? B ? ? ? ? ? ? ? ? 1.333 ? covale ? covale7 A C GLY 191 A GLY 209 1_555 A N GLY 192 A GLY 209 1_555 A ? ? B ? ? ? ? ? ? ? ? 1.333 ? covale ? covale8 A C VAL 193 A VAL 210 1_555 A N PRO 194 A PRO 210 1_555 A ? ? B ? ? ? ? ? ? ? ? 1.336 ? covale ? covale9 A C PRO 194 A PRO 210 1_555 A N LEU 195 A LEU 212 1_555 B ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale10 A C GLN 201 A GLN 218 1_555 A N GLY 202 A GLY 218 1_555 A ? ? B ? ? ? ? ? ? ? ? 1.33 ? covale ? covale11 A C LYS 228 A LYS 244 1_555 A N THR 229 A THR 244 1_555 A ? ? B ? ? ? ? ? ? ? ? 1.335 ? covale ? covale12 A C THR 229 A THR 244 1_555 A N GLY 230 A GLY 244 1_555 B ? ? C ? ? ? ? ? ? ? ? 1.331 ? covale ? covale13 A C GLY 269 A GLY 283 1_555 A N ILE 270 A ILE 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale14 A C GLU 284 A GLU 299 1_555 A N ASP 285 A ASP 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale15 B C ARG 4 B ARG 20 1_555 B N ARG 5 B ARG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale16 B C ALA 29 B ALA 46 1_555 B N ASP 30 B ASP 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale17 B C PHE 55 B PHE 73 1_555 B N GLY 56 B GLY 73 1_555 A ? ? B ? ? ? ? ? ? ? ? 1.332 ? covale ? covale18 B C THR 64 B THR 81 1_555 B N ASN 65 B ASN 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale19 B C ARG 85 B ARG 103 1_555 B N PRO 86 B PRO 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale20 B C PRO 113 B PRO 132 1_555 B N ASN 114 B ASN 132 1_555 A ? ? B ? ? ? ? ? ? ? ? 1.334 ? covale ? covale21 B C GLY 191 B GLY 209 1_555 B N GLY 192 B GLY 209 1_555 A ? ? B ? ? ? ? ? ? ? ? 1.332 ? covale ? covale22 B C VAL 193 B VAL 210 1_555 B N PRO 194 B PRO 210 1_555 A ? ? B ? ? ? ? ? ? ? ? 1.334 ? covale ? covale23 B C PRO 194 B PRO 210 1_555 B N LEU 195 B LEU 212 1_555 B ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale24 B C GLN 201 B GLN 218 1_555 B N GLY 202 B GLY 218 1_555 A ? ? B ? ? ? ? ? ? ? ? 1.33 ? covale ? covale25 B C LYS 228 B LYS 244 1_555 B N THR 229 B THR 244 1_555 A ? ? B ? ? ? ? ? ? ? ? 1.333 ? covale ? covale26 B C THR 229 B THR 244 1_555 B N GLY 230 B GLY 244 1_555 B ? ? C ? ? ? ? ? ? ? ? 1.328 ? covale ? covale27 B C GLY 269 B GLY 283 1_555 B N ILE 270 B ILE 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale28 B C GLU 284 B GLU 299 1_555 B N ASP 285 B ASP 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? # _chem_comp.formula 'C2 H3 N O3' _chem_comp.formula_weight 89.05 _chem_comp.id OXM _chem_comp.mon_nstd_flag . _chem_comp.name 'OXAMIC 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 C1 N1 OXM sing 325 n n C1 O1 OXM doub 326 n n C1 C2 OXM sing 327 n n N1 HN1 OXM sing 328 n n N1 HN2 OXM sing 329 n n C2 O2 OXM doub 330 n n C2 O3 OXM sing 331 n n O3 HO3 OXM sing 332 n n # _atom_sites.entry_id 4ND1 _atom_sites.fract_transf_matrix[1][1] 0.010547 _atom_sites.fract_transf_matrix[1][2] 0.006089 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012178 _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] 0.005403 _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 1 401 401 NAD NAD . D 3 OXM A 1 402 402 OXM OXM . E 4 GOL A 1 403 403 GOL GOL . F 4 GOL A 1 404 404 GOL GOL . G 4 GOL A 1 405 405 GOL GOL . H 2 NAD B 1 401 401 NAD NAD . I 3 OXM B 1 402 402 OXM OXM . J 4 GOL B 1 403 403 GOL GOL . K 5 HOH A 1 601 601 HOH HOH . K 5 HOH A 2 602 602 HOH HOH . K 5 HOH A 3 603 603 HOH HOH . K 5 HOH A 4 604 604 HOH HOH . K 5 HOH A 5 605 605 HOH HOH . K 5 HOH A 6 606 606 HOH HOH . K 5 HOH A 7 607 607 HOH HOH . K 5 HOH A 8 608 608 HOH HOH . K 5 HOH A 9 609 609 HOH HOH . K 5 HOH A 10 610 610 HOH HOH . K 5 HOH A 11 611 611 HOH HOH . K 5 HOH A 12 612 612 HOH HOH . K 5 HOH A 13 613 613 HOH HOH . K 5 HOH A 14 614 614 HOH HOH . K 5 HOH A 15 615 615 HOH HOH . K 5 HOH A 16 616 616 HOH HOH . K 5 HOH A 17 617 617 HOH HOH . K 5 HOH A 18 618 618 HOH HOH . K 5 HOH A 19 619 619 HOH HOH . K 5 HOH A 20 620 620 HOH HOH . K 5 HOH A 21 621 621 HOH HOH . K 5 HOH A 22 622 622 HOH HOH . K 5 HOH A 23 623 623 HOH HOH . K 5 HOH A 24 624 624 HOH HOH . K 5 HOH A 25 625 625 HOH HOH . K 5 HOH A 26 626 627 HOH HOH . K 5 HOH A 27 627 628 HOH HOH . K 5 HOH A 28 628 629 HOH HOH . K 5 HOH A 29 629 631 HOH HOH . K 5 HOH A 30 630 633 HOH HOH . K 5 HOH A 31 631 634 HOH HOH . K 5 HOH A 32 632 635 HOH HOH . K 5 HOH A 33 633 636 HOH HOH . K 5 HOH A 34 634 637 HOH HOH . K 5 HOH A 35 635 640 HOH HOH . K 5 HOH A 36 636 641 HOH HOH . K 5 HOH A 37 637 642 HOH HOH . K 5 HOH A 38 638 643 HOH HOH . K 5 HOH A 39 639 644 HOH HOH . K 5 HOH A 40 640 645 HOH HOH . K 5 HOH A 41 641 646 HOH HOH . K 5 HOH A 42 642 647 HOH HOH . K 5 HOH A 43 643 648 HOH HOH . K 5 HOH A 44 644 649 HOH HOH . K 5 HOH A 45 645 650 HOH HOH . K 5 HOH A 46 646 651 HOH HOH . K 5 HOH A 47 647 652 HOH HOH . K 5 HOH A 48 648 653 HOH HOH . K 5 HOH A 49 649 654 HOH HOH . K 5 HOH A 50 650 655 HOH HOH . K 5 HOH A 51 651 656 HOH HOH . K 5 HOH A 52 652 657 HOH HOH . K 5 HOH A 53 653 658 HOH HOH . K 5 HOH A 54 654 659 HOH HOH . K 5 HOH A 55 655 661 HOH HOH . K 5 HOH A 56 656 662 HOH HOH . K 5 HOH A 57 657 664 HOH HOH . K 5 HOH A 58 658 665 HOH HOH . K 5 HOH A 59 659 666 HOH HOH . K 5 HOH A 60 660 667 HOH HOH . K 5 HOH A 61 661 669 HOH HOH . K 5 HOH A 62 662 677 HOH HOH . K 5 HOH A 63 663 679 HOH HOH . K 5 HOH A 64 664 681 HOH HOH . K 5 HOH A 65 665 694 HOH HOH . K 5 HOH A 66 666 696 HOH HOH . K 5 HOH A 67 667 699 HOH HOH . K 5 HOH A 68 668 700 HOH HOH . K 5 HOH A 69 669 701 HOH HOH . K 5 HOH A 70 670 704 HOH HOH . K 5 HOH A 71 671 705 HOH HOH . K 5 HOH A 72 672 706 HOH HOH . K 5 HOH A 73 673 707 HOH HOH . K 5 HOH A 74 674 708 HOH HOH . K 5 HOH A 75 675 709 HOH HOH . K 5 HOH A 76 676 711 HOH HOH . K 5 HOH A 77 677 712 HOH HOH . K 5 HOH A 78 678 713 HOH HOH . K 5 HOH A 79 679 715 HOH HOH . K 5 HOH A 80 680 716 HOH HOH . K 5 HOH A 81 681 721 HOH HOH . K 5 HOH A 82 682 722 HOH HOH . K 5 HOH A 83 683 723 HOH HOH . K 5 HOH A 84 684 724 HOH HOH . K 5 HOH A 85 685 728 HOH HOH . K 5 HOH A 86 686 729 HOH HOH . K 5 HOH A 87 687 730 HOH HOH . K 5 HOH A 88 688 733 HOH HOH . K 5 HOH A 89 689 738 HOH HOH . K 5 HOH A 90 690 739 HOH HOH . K 5 HOH A 91 691 740 HOH HOH . K 5 HOH A 92 692 742 HOH HOH . K 5 HOH A 93 693 743 HOH HOH . K 5 HOH A 94 694 744 HOH HOH . K 5 HOH A 95 695 745 HOH HOH . K 5 HOH A 96 696 747 HOH HOH . K 5 HOH A 97 697 748 HOH HOH . K 5 HOH A 98 698 749 HOH HOH . K 5 HOH A 99 699 750 HOH HOH . L 5 HOH B 1 501 626 HOH HOH . L 5 HOH B 2 502 630 HOH HOH . L 5 HOH B 3 503 632 HOH HOH . L 5 HOH B 4 504 638 HOH HOH . L 5 HOH B 5 505 639 HOH HOH . L 5 HOH B 6 506 660 HOH HOH . L 5 HOH B 7 507 663 HOH HOH . L 5 HOH B 8 508 668 HOH HOH . L 5 HOH B 9 509 670 HOH HOH . L 5 HOH B 10 510 671 HOH HOH . L 5 HOH B 11 511 672 HOH HOH . L 5 HOH B 12 512 673 HOH HOH . L 5 HOH B 13 513 674 HOH HOH . L 5 HOH B 14 514 675 HOH HOH . L 5 HOH B 15 515 676 HOH HOH . L 5 HOH B 16 516 678 HOH HOH . L 5 HOH B 17 517 680 HOH HOH . L 5 HOH B 18 518 682 HOH HOH . L 5 HOH B 19 519 683 HOH HOH . L 5 HOH B 20 520 684 HOH HOH . L 5 HOH B 21 521 685 HOH HOH . L 5 HOH B 22 522 686 HOH HOH . L 5 HOH B 23 523 687 HOH HOH . L 5 HOH B 24 524 688 HOH HOH . L 5 HOH B 25 525 689 HOH HOH . L 5 HOH B 26 526 690 HOH HOH . L 5 HOH B 27 527 691 HOH HOH . L 5 HOH B 28 528 692 HOH HOH . L 5 HOH B 29 529 693 HOH HOH . L 5 HOH B 30 530 695 HOH HOH . L 5 HOH B 31 531 697 HOH HOH . L 5 HOH B 32 532 698 HOH HOH . L 5 HOH B 33 533 702 HOH HOH . L 5 HOH B 34 534 703 HOH HOH . L 5 HOH B 35 535 710 HOH HOH . L 5 HOH B 36 536 714 HOH HOH . L 5 HOH B 37 537 717 HOH HOH . L 5 HOH B 38 538 718 HOH HOH . L 5 HOH B 39 539 719 HOH HOH . L 5 HOH B 40 540 720 HOH HOH . L 5 HOH B 41 541 725 HOH HOH . L 5 HOH B 42 542 726 HOH HOH . L 5 HOH B 43 543 727 HOH HOH . L 5 HOH B 44 544 731 HOH HOH . L 5 HOH B 45 545 732 HOH HOH . L 5 HOH B 46 546 734 HOH HOH . L 5 HOH B 47 547 735 HOH HOH . L 5 HOH B 48 548 736 HOH HOH . L 5 HOH B 49 549 737 HOH HOH . L 5 HOH B 50 550 741 HOH HOH . L 5 HOH B 51 551 746 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 OXM . . . I 3 -3.202 45.233 80.552 1 43.69 ? C1 OXM 402 B 1 HETATM 2 N N1 OXM . . . I 3 -3.081 45.54 79.267 1 44.44 ? N1 OXM 402 B 1 HETATM 3 O O1 OXM . . . I 3 -4.01 44.401 80.929 1 44.38 ? O1 OXM 402 B 1 HETATM 4 C C2 OXM . . . I 3 -2.34 45.905 81.526 1 44.39 ? C2 OXM 402 B 1 HETATM 5 O O2 OXM . . . I 3 -1.327 46.517 81.117 1 44.07 ? O2 OXM 402 B 1 HETATM 6 O O3 OXM . . . I 3 -2.636 45.86 82.743 1 44.18 ? O3 OXM 402 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 6 #