data_4U5N # _model_server_result.job_id rArjU4Aqax8TqpidJzC5tg _model_server_result.datetime_utc '2024-11-22 15:08:39' _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 4u5n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 4U5N # _exptl.entry_id 4U5N _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 619.754 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N~2~-[4-(pyridin-3-yl)benzyl]-L-lysyl-N-[(1R,2S,3R)-1-{[(2R)-1-amino-1-oxo-3-phenylpropan-2-yl]amino}-1,3-dihydroxybutan-2-yl]glycinamide _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 90 _cell.entry_id 4U5N _cell.length_a 78.501 _cell.length_b 91.08 _cell.length_c 98.965 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4U5N _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 MONOMERIC _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C33 H45 N7 O5' _chem_comp.formula_weight 619.754 _chem_comp.id 3D4 _chem_comp.mon_nstd_flag . _chem_comp.name N~2~-[4-(pyridin-3-yl)benzyl]-L-lysyl-N-[(1R,2S,3R)-1-{[(2R)-1-amino-1-oxo-3-phenylpropan-2-yl]amino}-1,3-dihydroxybutan-2-yl]glycinamide _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 NZ CE 3D4 sing 1 n n CE CD 3D4 sing 2 n n CD CG 3D4 sing 3 n n NAC CBH 3D4 sing 4 n n OAD CBH 3D4 doub 5 n n CBH CBR 3D4 sing 6 n n CG CB 3D4 sing 7 n n CAJ CAN 3D4 doub 8 n y CAJ CAI 3D4 sing 9 n y CAN CBM 3D4 sing 10 n y CB CA 3D4 sing 11 n n CBR NBG 3D4 sing 12 n n CBR CBB 3D4 sing 13 n n NBG CBK 3D4 sing 14 n n NBD CAZ 3D4 sing 15 n n NBD C 3D4 sing 16 n n CAI CAK 3D4 doub 17 n y OAE CBI 3D4 doub 18 n n CAZ CBI 3D4 sing 19 n n CBI NBF 3D4 sing 20 n n CBM CBB 3D4 sing 21 n n CBM CAO 3D4 doub 22 n y CA C 3D4 sing 23 n n CA N 3D4 sing 24 n n NBF CBS 3D4 sing 25 n n C O 3D4 doub 26 n n CBS CBK 3D4 sing 27 n n CBS CBP 3D4 sing 28 n n CBK OAG 3D4 sing 29 n n CAK CAO 3D4 sing 30 n y N CBA 3D4 sing 31 n n OAH CBP 3D4 sing 32 n n CBP CAA 3D4 sing 33 n n CAQ CAS 3D4 doub 34 n y CAQ CBL 3D4 sing 35 n y CBA CBL 3D4 sing 36 n n CAS CBN 3D4 sing 37 n y CBL CAR 3D4 doub 38 n y CAU NBC 3D4 doub 39 n y CAU CBO 3D4 sing 40 n y CBN CBO 3D4 sing 41 n n CBN CAT 3D4 doub 42 n y CAR CAT 3D4 sing 43 n y NBC CAM 3D4 sing 44 n y CBO CAP 3D4 doub 45 n y CAM CAL 3D4 doub 46 n y CAP CAL 3D4 sing 47 n y N H1 3D4 sing 48 n n CA H3 3D4 sing 49 n n CAA H4 3D4 sing 50 n n CAA H5 3D4 sing 51 n n CAA H6 3D4 sing 52 n n CAI H7 3D4 sing 53 n n CAJ H8 3D4 sing 54 n n CAK H9 3D4 sing 55 n n CAL H10 3D4 sing 56 n n CAM H11 3D4 sing 57 n n CAN H12 3D4 sing 58 n n CAO H13 3D4 sing 59 n n CAP H14 3D4 sing 60 n n CAQ H15 3D4 sing 61 n n CAR H16 3D4 sing 62 n n CAS H17 3D4 sing 63 n n CAT H18 3D4 sing 64 n n CAU H19 3D4 sing 65 n n CAZ H20 3D4 sing 66 n n CAZ H21 3D4 sing 67 n n NAC H22 3D4 sing 68 n n NAC H23 3D4 sing 69 n n OAG H24 3D4 sing 70 n n OAH H25 3D4 sing 71 n n CB H26 3D4 sing 72 n n CB H27 3D4 sing 73 n n CBA H28 3D4 sing 74 n n CBA H29 3D4 sing 75 n n CBB H30 3D4 sing 76 n n CBB H31 3D4 sing 77 n n CBK H32 3D4 sing 78 n n CBP H33 3D4 sing 79 n n CBR H34 3D4 sing 80 n n CBS H35 3D4 sing 81 n n NBD H36 3D4 sing 82 n n NBF H37 3D4 sing 83 n n NBG H38 3D4 sing 84 n n CG H40 3D4 sing 85 n n CG H41 3D4 sing 86 n n CD H42 3D4 sing 87 n n CD H43 3D4 sing 88 n n CE H44 3D4 sing 89 n n CE H45 3D4 sing 90 n n NZ H46 3D4 sing 91 n n NZ H47 3D4 sing 92 n n # _atom_sites.entry_id 4U5N _atom_sites.fract_transf_matrix[1][1] 0.012739 _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] 0.010979 _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] 0.010105 _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 B 2 3D4 A 1 501 1 3D4 DRG . C 3 HOH A 1 601 57 HOH HOH . C 3 HOH A 2 602 62 HOH HOH . C 3 HOH A 3 603 53 HOH HOH . C 3 HOH A 4 604 49 HOH HOH . C 3 HOH A 5 605 18 HOH HOH . C 3 HOH A 6 606 20 HOH HOH . C 3 HOH A 7 607 66 HOH HOH . C 3 HOH A 8 608 23 HOH HOH . C 3 HOH A 9 609 35 HOH HOH . C 3 HOH A 10 610 5 HOH HOH . C 3 HOH A 11 611 30 HOH HOH . C 3 HOH A 12 612 3 HOH HOH . C 3 HOH A 13 613 24 HOH HOH . C 3 HOH A 14 614 1 HOH HOH . C 3 HOH A 15 615 86 HOH HOH . C 3 HOH A 16 616 58 HOH HOH . C 3 HOH A 17 617 64 HOH HOH . C 3 HOH A 18 618 52 HOH HOH . C 3 HOH A 19 619 8 HOH HOH . C 3 HOH A 20 620 72 HOH HOH . C 3 HOH A 21 621 21 HOH HOH . C 3 HOH A 22 622 26 HOH HOH . C 3 HOH A 23 623 85 HOH HOH . C 3 HOH A 24 624 32 HOH HOH . C 3 HOH A 25 625 81 HOH HOH . C 3 HOH A 26 626 107 HOH HOH . C 3 HOH A 27 627 59 HOH HOH . C 3 HOH A 28 628 10 HOH HOH . C 3 HOH A 29 629 78 HOH HOH . C 3 HOH A 30 630 37 HOH HOH . C 3 HOH A 31 631 83 HOH HOH . C 3 HOH A 32 632 93 HOH HOH . C 3 HOH A 33 633 100 HOH HOH . C 3 HOH A 34 634 55 HOH HOH . C 3 HOH A 35 635 108 HOH HOH . C 3 HOH A 36 636 2 HOH HOH . C 3 HOH A 37 637 4 HOH HOH . C 3 HOH A 38 638 6 HOH HOH . C 3 HOH A 39 639 7 HOH HOH . C 3 HOH A 40 640 9 HOH HOH . C 3 HOH A 41 641 11 HOH HOH . C 3 HOH A 42 642 12 HOH HOH . C 3 HOH A 43 643 13 HOH HOH . C 3 HOH A 44 644 14 HOH HOH . C 3 HOH A 45 645 15 HOH HOH . C 3 HOH A 46 646 16 HOH HOH . C 3 HOH A 47 647 17 HOH HOH . C 3 HOH A 48 648 19 HOH HOH . C 3 HOH A 49 649 22 HOH HOH . C 3 HOH A 50 650 25 HOH HOH . C 3 HOH A 51 651 27 HOH HOH . C 3 HOH A 52 652 28 HOH HOH . C 3 HOH A 53 653 29 HOH HOH . C 3 HOH A 54 654 31 HOH HOH . C 3 HOH A 55 655 33 HOH HOH . C 3 HOH A 56 656 34 HOH HOH . C 3 HOH A 57 657 36 HOH HOH . C 3 HOH A 58 658 38 HOH HOH . C 3 HOH A 59 659 39 HOH HOH . C 3 HOH A 60 660 40 HOH HOH . C 3 HOH A 61 661 41 HOH HOH . C 3 HOH A 62 662 42 HOH HOH . C 3 HOH A 63 663 43 HOH HOH . C 3 HOH A 64 664 44 HOH HOH . C 3 HOH A 65 665 45 HOH HOH . C 3 HOH A 66 666 46 HOH HOH . C 3 HOH A 67 667 47 HOH HOH . C 3 HOH A 68 668 48 HOH HOH . C 3 HOH A 69 669 50 HOH HOH . C 3 HOH A 70 670 51 HOH HOH . C 3 HOH A 71 671 54 HOH HOH . C 3 HOH A 72 672 56 HOH HOH . C 3 HOH A 73 673 60 HOH HOH . C 3 HOH A 74 674 61 HOH HOH . C 3 HOH A 75 675 63 HOH HOH . C 3 HOH A 76 676 65 HOH HOH . C 3 HOH A 77 677 67 HOH HOH . C 3 HOH A 78 678 68 HOH HOH . C 3 HOH A 79 679 69 HOH HOH . C 3 HOH A 80 680 70 HOH HOH . C 3 HOH A 81 681 71 HOH HOH . C 3 HOH A 82 682 73 HOH HOH . C 3 HOH A 83 683 74 HOH HOH . C 3 HOH A 84 684 75 HOH HOH . C 3 HOH A 85 685 76 HOH HOH . C 3 HOH A 86 686 77 HOH HOH . C 3 HOH A 87 687 79 HOH HOH . C 3 HOH A 88 688 80 HOH HOH . C 3 HOH A 89 689 82 HOH HOH . C 3 HOH A 90 690 84 HOH HOH . C 3 HOH A 91 691 87 HOH HOH . C 3 HOH A 92 692 88 HOH HOH . C 3 HOH A 93 693 89 HOH HOH . C 3 HOH A 94 694 90 HOH HOH . C 3 HOH A 95 695 91 HOH HOH . C 3 HOH A 96 696 92 HOH HOH . C 3 HOH A 97 697 94 HOH HOH . C 3 HOH A 98 698 95 HOH HOH . C 3 HOH A 99 699 96 HOH HOH . C 3 HOH A 100 700 97 HOH HOH . C 3 HOH A 101 701 98 HOH HOH . C 3 HOH A 102 702 99 HOH HOH . C 3 HOH A 103 703 101 HOH HOH . C 3 HOH A 104 704 102 HOH HOH . C 3 HOH A 105 705 103 HOH HOH . C 3 HOH A 106 706 104 HOH HOH . C 3 HOH A 107 707 105 HOH HOH . C 3 HOH A 108 708 106 HOH HOH . C 3 HOH A 109 709 109 HOH HOH . C 3 HOH A 110 710 110 HOH HOH . C 3 HOH A 111 711 111 HOH HOH . C 3 HOH A 112 712 112 HOH HOH . C 3 HOH A 113 713 113 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 N 3D4 . . . B 2 2.745 37.356 9.104 1 63.34 ? N 3D4 501 A 1 HETATM 2 C CA 3D4 . . . B 2 2.416 36.502 7.95 1 60.88 ? CA 3D4 501 A 1 HETATM 3 C CAA 3D4 . . . B 2 3.25 28.756 10.544 1 81.13 ? CAA 3D4 501 A 1 HETATM 4 C CAI 3D4 . . . B 2 -4.302 24.858 7.559 1 80.76 ? CAI 3D4 501 A 1 HETATM 5 C CAJ 3D4 . . . B 2 -3.561 25.23 6.449 1 74.35 ? CAJ 3D4 501 A 1 HETATM 6 C CAK 3D4 . . . B 2 -3.718 24.812 8.813 1 86.07 ? CAK 3D4 501 A 1 HETATM 7 C CAL 3D4 . . . B 2 -0.089 30.244 12.903 1 64.17 ? CAL 3D4 501 A 1 HETATM 8 C CAM 3D4 . . . B 2 -1.317 29.846 12.405 1 61.55 ? CAM 3D4 501 A 1 HETATM 9 C CAN 3D4 . . . B 2 -2.229 25.558 6.605 1 83.93 ? CAN 3D4 501 A 1 HETATM 10 C CAO 3D4 . . . B 2 -2.378 25.14 8.965 1 97.84 ? CAO 3D4 501 A 1 HETATM 11 C CAP 3D4 . . . B 2 0.394 31.495 12.546 1 60.34 ? CAP 3D4 501 A 1 HETATM 12 C CAQ 3D4 . . . B 2 0.041 35.505 9.799 1 55.88 ? CAQ 3D4 501 A 1 HETATM 13 C CAR 3D4 . . . B 2 1.634 35.517 11.612 1 58.46 ? CAR 3D4 501 A 1 HETATM 14 C CAS 3D4 . . . B 2 -0.433 34.261 10.184 1 52.91 ? CAS 3D4 501 A 1 HETATM 15 C CAT 3D4 . . . B 2 1.158 34.273 12.011 1 58.64 ? CAT 3D4 501 A 1 HETATM 16 C CAU 3D4 . . . B 2 -1.597 31.819 11.256 1 60.31 ? CAU 3D4 501 A 1 HETATM 17 C CAZ 3D4 . . . B 2 2.472 32.581 7.678 1 67.28 ? CAZ 3D4 501 A 1 HETATM 18 C C 3D4 . . . B 2 2.892 35.061 8.183 1 63.14 ? C 3D4 501 A 1 HETATM 19 O O 3D4 . . . B 2 3.81 34.823 8.897 1 64.43 ? O 3D4 501 A 1 HETATM 20 N NAC 3D4 . . . B 2 2.181 25.912 5.083 1 83.13 ? NAC 3D4 501 A 1 HETATM 21 O OAD 3D4 . . . B 2 0.317 24.68 5.597 1 89.24 ? OAD 3D4 501 A 1 HETATM 22 O OAE 3D4 . . . B 2 0.17 32.117 7.562 1 69.94 ? OAE 3D4 501 A 1 HETATM 23 O OAG 3D4 . . . B 2 0.601 28.352 9.268 1 104.2 ? OAG 3D4 501 A 1 HETATM 24 O OAH 3D4 . . . B 2 4.598 30.387 9.55 1 92.22 ? OAH 3D4 501 A 1 HETATM 25 C CB 3D4 . . . B 2 2.908 37.03 6.605 1 58.43 ? CB 3D4 501 A 1 HETATM 26 C CBA 3D4 . . . B 2 1.615 37.498 10.049 1 57.76 ? CBA 3D4 501 A 1 HETATM 27 C CBB 3D4 . . . B 2 -0.137 25.863 8.03 1 101.49 ? CBB 3D4 501 A 1 HETATM 28 C CBH 3D4 . . . B 2 0.939 25.669 5.809 1 89.29 ? CBH 3D4 501 A 1 HETATM 29 C CBI 3D4 . . . B 2 1.244 31.662 7.774 1 72.54 ? CBI 3D4 501 A 1 HETATM 30 C CBK 3D4 . . . B 2 1.761 28.074 8.53 1 92.93 ? CBK 3D4 501 A 1 HETATM 31 C CBL 3D4 . . . B 2 1.075 36.133 10.5 1 56.88 ? CBL 3D4 501 A 1 HETATM 32 C CBM 3D4 . . . B 2 -1.624 25.51 7.86 1 95.03 ? CBM 3D4 501 A 1 HETATM 33 C CBN 3D4 . . . B 2 0.13 33.662 11.3 1 60.1 ? CBN 3D4 501 A 1 HETATM 34 C CBO 3D4 . . . B 2 -0.38 32.294 11.722 1 62.65 ? CBO 3D4 501 A 1 HETATM 35 C CBP 3D4 . . . B 2 3.177 29.853 9.731 1 91.67 ? CBP 3D4 501 A 1 HETATM 36 C CBR 3D4 . . . B 2 0.426 26.67 6.85 1 88.95 ? CBR 3D4 501 A 1 HETATM 37 C CBS 3D4 . . . B 2 2.452 29.432 8.433 1 89.51 ? CBS 3D4 501 A 1 HETATM 38 N NBC 3D4 . . . B 2 -2.032 30.628 11.616 1 60.88 ? NBC 3D4 501 A 1 HETATM 39 N NBD 3D4 . . . B 2 2.146 33.991 7.528 1 59.26 ? NBD 3D4 501 A 1 HETATM 40 N NBF 3D4 . . . B 2 1.292 30.252 8.133 1 77.34 ? NBF 3D4 501 A 1 HETATM 41 N NBG 3D4 . . . B 2 1.491 27.643 7.152 1 88.2 ? NBG 3D4 501 A 1 HETATM 42 C CG 3D4 . . . B 2 2.138 38.292 6.226 1 55.84 ? CG 3D4 501 A 1 HETATM 43 C CD 3D4 . . . B 2 1.283 38.095 4.986 1 49.99 ? CD 3D4 501 A 1 HETATM 44 C CE 3D4 . . . B 2 0.835 39.414 4.354 1 50.24 ? CE 3D4 501 A 1 HETATM 45 N NZ 3D4 . . . B 2 -0.379 39.203 3.58 1 46.06 ? NZ 3D4 501 A 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 45 #