data_8GKS # _model_server_result.job_id c-ByvboLmADU97ktV9BTcw _model_server_result.datetime_utc '2024-11-27 17:07:57' _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 8gks # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":701}' # _entry.id 8GKS # _exptl.entry_id 8GKS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 441.437 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'N-{4-[3-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)propyl]benzoyl}-L-glutamic 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 8GKS _cell.length_a 157.927 _cell.length_b 157.927 _cell.length_c 206.67 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GKS _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,I 1 1 B,G,H,J 1 1,2 A,C,D,E,F,I 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' 12_564 x,x-y+1,-z-1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -78.9635 136.768794 -34.445 # 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 E 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 269 A LYS 280 1_555 F C4A PLP . A PLP 602 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.265 ? covale ? covale2 B NZ LYS 269 B LYS 280 1_555 H C4A PLP . B PLP 602 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.268 ? # _chem_comp.formula 'C21 H23 N5 O6' _chem_comp.formula_weight 441.437 _chem_comp.id Y6U _chem_comp.mon_nstd_flag . _chem_comp.name 'N-{4-[3-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)propyl]benzoyl}-L-glutamic 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 N11 C2 Y6U sing 402 n n N3 C2 Y6U sing 403 n n N3 C4 Y6U sing 404 n n C2 N1 Y6U doub 405 n n O10 C4 Y6U doub 406 n n C4 C8 Y6U sing 407 n n N1 C9 Y6U sing 408 n n C8 C9 Y6U doub 409 n y C8 N7 Y6U sing 410 n y C9 C5 Y6U sing 411 n y N7 C29 Y6U sing 412 n n N7 C6 Y6U sing 413 n y C5 C6 Y6U doub 414 n y C29 C30 Y6U sing 415 n n C30 C31 Y6U sing 416 n n C31 C32 Y6U sing 417 n n C15 C32 Y6U doub 418 n y C15 C13 Y6U sing 419 n y C32 C16 Y6U sing 420 n y C13 C12 Y6U doub 421 n y C16 C14 Y6U doub 422 n y O27 C26 Y6U doub 423 n n C12 C14 Y6U sing 424 n y C12 C17 Y6U sing 425 n n N19 C17 Y6U sing 426 n n N19 C20 Y6U sing 427 n n C26 O28 Y6U sing 428 n n C26 C20 Y6U sing 429 n n C17 O18 Y6U doub 430 n n C20 C21 Y6U sing 431 n n C21 C22 Y6U sing 432 n n C22 C23 Y6U sing 433 n n C23 O24 Y6U doub 434 n n C23 O25 Y6U sing 435 n n C5 H1 Y6U sing 436 n n C6 H2 Y6U sing 437 n n C14 H3 Y6U sing 438 n n C13 H4 Y6U sing 439 n n C15 H5 Y6U sing 440 n n C16 H6 Y6U sing 441 n n C20 H7 Y6U sing 442 n n C21 H8 Y6U sing 443 n n C21 H9 Y6U sing 444 n n C22 H10 Y6U sing 445 n n C22 H11 Y6U sing 446 n n C29 H12 Y6U sing 447 n n C29 H13 Y6U sing 448 n n C30 H14 Y6U sing 449 n n C30 H15 Y6U sing 450 n n C31 H16 Y6U sing 451 n n C31 H17 Y6U sing 452 n n N11 H18 Y6U sing 453 n n N11 H19 Y6U sing 454 n n N19 H20 Y6U sing 455 n n N3 H21 Y6U sing 456 n n O25 H22 Y6U sing 457 n n O28 H23 Y6U sing 458 n n # _atom_sites.entry_id 8GKS _atom_sites.fract_transf_matrix[1][1] 0.006332 _atom_sites.fract_transf_matrix[1][2] 0.003656 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007312 _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] 0.004839 _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 GLY A 1 601 601 GLY GLY . D 3 Y6U A 1 701 701 Y6U G29 . E 3 Y6U A 1 702 701 Y6U G29 . F 4 PLP A 1 602 280 PLP LLP . G 2 GLY B 1 601 601 GLY GLY . H 4 PLP B 1 602 280 PLP LLP . I 5 HOH A 1 801 75 HOH HOH . I 5 HOH A 2 802 72 HOH HOH . I 5 HOH A 3 803 81 HOH HOH . I 5 HOH A 4 804 93 HOH HOH . I 5 HOH A 5 805 82 HOH HOH . I 5 HOH A 6 806 65 HOH HOH . I 5 HOH A 7 807 94 HOH HOH . I 5 HOH A 8 808 7 HOH HOH . I 5 HOH A 9 809 77 HOH HOH . I 5 HOH A 10 810 103 HOH HOH . I 5 HOH A 11 811 33 HOH HOH . I 5 HOH A 12 812 62 HOH HOH . I 5 HOH A 13 813 58 HOH HOH . I 5 HOH A 14 814 27 HOH HOH . I 5 HOH A 15 815 112 HOH HOH . I 5 HOH A 16 816 110 HOH HOH . I 5 HOH A 17 817 64 HOH HOH . I 5 HOH A 18 818 11 HOH HOH . I 5 HOH A 19 819 80 HOH HOH . I 5 HOH A 20 820 16 HOH HOH . I 5 HOH A 21 821 63 HOH HOH . I 5 HOH A 22 822 8 HOH HOH . I 5 HOH A 23 823 66 HOH HOH . I 5 HOH A 24 824 26 HOH HOH . I 5 HOH A 25 825 76 HOH HOH . I 5 HOH A 26 826 105 HOH HOH . I 5 HOH A 27 827 85 HOH HOH . I 5 HOH A 28 828 120 HOH HOH . I 5 HOH A 29 829 97 HOH HOH . I 5 HOH A 30 830 56 HOH HOH . I 5 HOH A 31 831 24 HOH HOH . I 5 HOH A 32 832 59 HOH HOH . I 5 HOH A 33 833 89 HOH HOH . I 5 HOH A 34 834 52 HOH HOH . I 5 HOH A 35 835 23 HOH HOH . I 5 HOH A 36 836 19 HOH HOH . I 5 HOH A 37 837 74 HOH HOH . I 5 HOH A 38 838 67 HOH HOH . I 5 HOH A 39 839 12 HOH HOH . I 5 HOH A 40 840 69 HOH HOH . I 5 HOH A 41 841 109 HOH HOH . I 5 HOH A 42 842 99 HOH HOH . I 5 HOH A 43 843 100 HOH HOH . I 5 HOH A 44 844 20 HOH HOH . I 5 HOH A 45 845 29 HOH HOH . I 5 HOH A 46 846 60 HOH HOH . I 5 HOH A 47 847 44 HOH HOH . I 5 HOH A 48 848 84 HOH HOH . I 5 HOH A 49 849 5 HOH HOH . I 5 HOH A 50 850 78 HOH HOH . I 5 HOH A 51 851 107 HOH HOH . I 5 HOH A 52 852 43 HOH HOH . I 5 HOH A 53 853 83 HOH HOH . I 5 HOH A 54 854 28 HOH HOH . I 5 HOH A 55 855 102 HOH HOH . I 5 HOH A 56 856 92 HOH HOH . I 5 HOH A 57 857 50 HOH HOH . I 5 HOH A 58 858 111 HOH HOH . I 5 HOH A 59 859 96 HOH HOH . I 5 HOH A 60 860 45 HOH HOH . I 5 HOH A 61 861 35 HOH HOH . I 5 HOH A 62 862 9 HOH HOH . I 5 HOH A 63 863 117 HOH HOH . I 5 HOH A 64 864 98 HOH HOH . I 5 HOH A 65 865 39 HOH HOH . I 5 HOH A 66 866 51 HOH HOH . I 5 HOH A 67 867 41 HOH HOH . I 5 HOH A 68 868 2 HOH HOH . I 5 HOH A 69 869 121 HOH HOH . I 5 HOH A 70 870 48 HOH HOH . I 5 HOH A 71 871 4 HOH HOH . I 5 HOH A 72 872 101 HOH HOH . I 5 HOH A 73 873 18 HOH HOH . I 5 HOH A 74 874 13 HOH HOH . I 5 HOH A 75 875 54 HOH HOH . I 5 HOH A 76 876 115 HOH HOH . I 5 HOH A 77 877 1 HOH HOH . I 5 HOH A 78 878 55 HOH HOH . I 5 HOH A 79 879 42 HOH HOH . I 5 HOH A 80 880 53 HOH HOH . I 5 HOH A 81 881 36 HOH HOH . I 5 HOH A 82 882 79 HOH HOH . I 5 HOH A 83 883 14 HOH HOH . I 5 HOH A 84 884 46 HOH HOH . J 5 HOH B 1 801 3 HOH HOH . J 5 HOH B 2 802 108 HOH HOH . J 5 HOH B 3 803 95 HOH HOH . J 5 HOH B 4 804 68 HOH HOH . J 5 HOH B 5 805 87 HOH HOH . J 5 HOH B 6 806 86 HOH HOH . J 5 HOH B 7 807 61 HOH HOH . J 5 HOH B 8 808 122 HOH HOH . J 5 HOH B 9 809 71 HOH HOH . J 5 HOH B 10 810 73 HOH HOH . J 5 HOH B 11 811 17 HOH HOH . J 5 HOH B 12 812 32 HOH HOH . J 5 HOH B 13 813 57 HOH HOH . J 5 HOH B 14 814 90 HOH HOH . J 5 HOH B 15 815 113 HOH HOH . J 5 HOH B 16 816 30 HOH HOH . J 5 HOH B 17 817 21 HOH HOH . J 5 HOH B 18 818 114 HOH HOH . J 5 HOH B 19 819 106 HOH HOH . J 5 HOH B 20 820 31 HOH HOH . J 5 HOH B 21 821 70 HOH HOH . J 5 HOH B 22 822 6 HOH HOH . J 5 HOH B 23 823 104 HOH HOH . J 5 HOH B 24 824 22 HOH HOH . J 5 HOH B 25 825 88 HOH HOH . J 5 HOH B 26 826 34 HOH HOH . J 5 HOH B 27 827 10 HOH HOH . J 5 HOH B 28 828 91 HOH HOH . J 5 HOH B 29 829 116 HOH HOH . J 5 HOH B 30 830 119 HOH HOH . J 5 HOH B 31 831 40 HOH HOH . J 5 HOH B 32 832 38 HOH HOH . J 5 HOH B 33 833 123 HOH HOH . J 5 HOH B 34 834 25 HOH HOH . J 5 HOH B 35 835 47 HOH HOH . J 5 HOH B 36 836 37 HOH HOH . J 5 HOH B 37 837 49 HOH HOH . J 5 HOH B 38 838 15 HOH HOH . J 5 HOH B 39 839 118 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 C2 Y6U . . . D 3 -39.066 63.427 3.534 1 58.33 ? C2 Y6U 701 A 1 HETATM 2 C C9 Y6U . . . D 3 -38.099 64.227 5.465 1 54.05 ? C9 Y6U 701 A 1 HETATM 3 C C12 Y6U . . . D 3 -36.821 72.286 3.87 1 53.35 ? C12 Y6U 701 A 1 HETATM 4 C C4 Y6U . . . D 3 -37.099 64.596 3.336 1 48.82 ? C4 Y6U 701 A 1 HETATM 5 C C5 Y6U . . . D 3 -37.844 64.532 6.811 1 51.04 ? C5 Y6U 701 A 1 HETATM 6 C C6 Y6U . . . D 3 -36.66 65.252 6.814 1 47.62 ? C6 Y6U 701 A 1 HETATM 7 C C23 Y6U . . . D 3 -39.4 77.339 0.924 1 81.56 ? C23 Y6U 701 A 1 HETATM 8 C C26 Y6U . . . D 3 -37.11 77.054 5.107 1 112.79 ? C26 Y6U 701 A 1 HETATM 9 C C8 Y6U . . . D 3 -37.063 64.774 4.734 1 53.68 ? C8 Y6U 701 A 1 HETATM 10 C C14 Y6U . . . D 3 -35.938 72.157 4.928 1 52.43 ? C14 Y6U 701 A 1 HETATM 11 C C13 Y6U . . . D 3 -37.452 71.162 3.35 1 51.19 ? C13 Y6U 701 A 1 HETATM 12 C C15 Y6U . . . D 3 -37.191 69.911 3.893 1 57.55 ? C15 Y6U 701 A 1 HETATM 13 C C16 Y6U . . . D 3 -35.677 70.907 5.469 1 59.26 ? C16 Y6U 701 A 1 HETATM 14 C C17 Y6U . . . D 3 -37.091 73.688 3.294 1 62.04 ? C17 Y6U 701 A 1 HETATM 15 C C20 Y6U . . . D 3 -37.179 76.225 3.829 1 93.69 ? C20 Y6U 701 A 1 HETATM 16 C C21 Y6U . . . D 3 -38.537 76.45 3.162 1 82.52 ? C21 Y6U 701 A 1 HETATM 17 C C22 Y6U . . . D 3 -38.473 77.581 2.121 1 80.05 ? C22 Y6U 701 A 1 HETATM 18 C C29 Y6U . . . D 3 -34.99 66.087 5.227 1 49.38 ? C29 Y6U 701 A 1 HETATM 19 C C30 Y6U . . . D 3 -35.334 67.434 4.58 1 56.62 ? C30 Y6U 701 A 1 HETATM 20 C C31 Y6U . . . D 3 -36.008 68.405 5.561 1 59.3 ? C31 Y6U 701 A 1 HETATM 21 C C32 Y6U . . . D 3 -36.3 69.783 4.949 1 60.69 ? C32 Y6U 701 A 1 HETATM 22 N N1 Y6U . . . D 3 -39.083 63.562 4.847 1 57.25 ? N1 Y6U 701 A 1 HETATM 23 N N11 Y6U . . . D 3 -40.136 62.707 2.893 1 64.51 ? N11 Y6U 701 A 1 HETATM 24 N N19 Y6U . . . D 3 -36.968 74.829 4.202 1 80.8 ? N19 Y6U 701 A 1 HETATM 25 N N3 Y6U . . . D 3 -38.099 63.929 2.786 1 53.65 ? N3 Y6U 701 A 1 HETATM 26 N N7 Y6U . . . D 3 -36.215 65.379 5.581 1 53.67 ? N7 Y6U 701 A 1 HETATM 27 O O10 Y6U . . . D 3 -36.096 65.114 2.519 1 42.18 ? O10 Y6U 701 A 1 HETATM 28 O O18 Y6U . . . D 3 -37.378 73.819 2.157 1 57.54 ? O18 Y6U 701 A 1 HETATM 29 O O24 Y6U . . . D 3 -39.776 76.171 0.646 1 79.44 ? O24 Y6U 701 A 1 HETATM 30 O O25 Y6U . . . D 3 -39.785 78.311 0.219 1 76.05 ? O25 Y6U 701 A 1 HETATM 31 O O27 Y6U . . . D 3 -37.499 78.249 5.11 1 117.25 ? O27 Y6U 701 A 1 HETATM 32 O O28 Y6U . . . D 3 -36.661 76.538 6.162 1 116.33 ? O28 Y6U 701 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 233 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #