data_8GKZ # _model_server_result.job_id BJV7QUULXwDwQ83pECUiEw _model_server_result.datetime_utc '2024-10-10 11:27:27' _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 8gkz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":601}' # _entry.id 8GKZ # _exptl.entry_id 8GKZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 479.482 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'N-{4-[4-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)butyl]-3-fluorothiophene-2-carbonyl}-L-glutamic acid' _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 120 _cell.entry_id 8GKZ _cell.length_a 158.25 _cell.length_b 158.25 _cell.length_c 207.99 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GKZ _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 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 _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' 12_564 x,x-y+1,-z-1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -79.125 137.04852 -34.665 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 D C4A PLP . A PLP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 B NZ LYS 269 B LYS 280 1_555 G C4A PLP . B PLP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? # _chem_comp.formula 'C20 H22 F N5 O6 S' _chem_comp.formula_weight 479.482 _chem_comp.id Y72 _chem_comp.mon_nstd_flag . _chem_comp.name 'N-{4-[4-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)butyl]-3-fluorothiophene-2-carbonyl}-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 O27 C26 Y72 doub 402 n n O18 C17 Y72 doub 403 n n S14 C13 Y72 sing 404 n y S14 C15 Y72 sing 405 n y O10 C04 Y72 doub 406 n n N03 C04 Y72 sing 407 n n N03 C02 Y72 sing 408 n n N11 C02 Y72 sing 409 n n C17 C13 Y72 sing 410 n n C17 N19 Y72 sing 411 n n C21 C20 Y72 sing 412 n n C21 C22 Y72 sing 413 n n C13 C12 Y72 doub 414 n y C15 C16 Y72 doub 415 n y C26 C20 Y72 sing 416 n n C26 O28 Y72 sing 417 n n C04 C08 Y72 sing 418 n n C02 N01 Y72 doub 419 n n C20 N19 Y72 sing 420 n n C22 C23 Y72 sing 421 n n C16 C12 Y72 sing 422 n y C16 C32 Y72 sing 423 n n C12 F33 Y72 sing 424 n n C08 C09 Y72 doub 425 n y C08 N05 Y72 sing 426 n y C31 C32 Y72 sing 427 n n C31 C30 Y72 sing 428 n n N01 C09 Y72 sing 429 n n C23 O25 Y72 doub 430 n n C23 O24 Y72 sing 431 n n C29 C30 Y72 sing 432 n n C29 N05 Y72 sing 433 n n C09 C07 Y72 sing 434 n y N05 C06 Y72 sing 435 n y C07 C06 Y72 doub 436 n y C15 H1 Y72 sing 437 n n C20 H2 Y72 sing 438 n n C06 H3 Y72 sing 439 n n C07 H4 Y72 sing 440 n n C21 H5 Y72 sing 441 n n C21 H6 Y72 sing 442 n n C22 H7 Y72 sing 443 n n C22 H8 Y72 sing 444 n n C29 H9 Y72 sing 445 n n C29 H10 Y72 sing 446 n n C30 H11 Y72 sing 447 n n C30 H12 Y72 sing 448 n n C31 H13 Y72 sing 449 n n C31 H14 Y72 sing 450 n n C32 H15 Y72 sing 451 n n C32 H16 Y72 sing 452 n n N03 H17 Y72 sing 453 n n N11 H18 Y72 sing 454 n n N11 H19 Y72 sing 455 n n N19 H20 Y72 sing 456 n n O24 H21 Y72 sing 457 n n O28 H22 Y72 sing 458 n n # _atom_sites.entry_id 8GKZ _atom_sites.fract_transf_matrix[1][1] 0.006319 _atom_sites.fract_transf_matrix[1][2] 0.003648 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007297 _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] 0.004808 _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 1 601 602 GLY GLY . D 3 PLP A 1 602 280 PLP LLP . E 4 Y72 B 1 601 601 Y72 G62 . F 2 GLY B 1 602 601 GLY GLY . G 3 PLP B 1 603 280 PLP LLP . H 5 HOH A 1 701 13 HOH HOH . H 5 HOH A 2 702 21 HOH HOH . H 5 HOH A 3 703 14 HOH HOH . H 5 HOH A 4 704 15 HOH HOH . H 5 HOH A 5 705 20 HOH HOH . H 5 HOH A 6 706 8 HOH HOH . H 5 HOH A 7 707 19 HOH HOH . H 5 HOH A 8 708 5 HOH HOH . H 5 HOH A 9 709 9 HOH HOH . H 5 HOH A 10 710 6 HOH HOH . H 5 HOH A 11 711 18 HOH HOH . H 5 HOH A 12 712 7 HOH HOH . H 5 HOH A 13 713 23 HOH HOH . H 5 HOH A 14 714 16 HOH HOH . H 5 HOH A 15 715 12 HOH HOH . I 5 HOH B 1 701 11 HOH HOH . I 5 HOH B 2 702 1 HOH HOH . I 5 HOH B 3 703 22 HOH HOH . I 5 HOH B 4 704 10 HOH HOH . I 5 HOH B 5 705 17 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 C15 Y72 . . . E 4 -38.583 70.778 3.21 0.91 72.75 ? C15 Y72 601 B 1 HETATM 2 C C17 Y72 . . . E 4 -37.134 74.552 3.72 0.91 83.19 ? C17 Y72 601 B 1 HETATM 3 C C20 Y72 . . . E 4 -36.519 76.362 5.51 0.91 94.12 ? C20 Y72 601 B 1 HETATM 4 C C16 Y72 . . . E 4 -37.311 70.694 3.801 0.91 82.38 ? C16 Y72 601 B 1 HETATM 5 C C09 Y72 . . . E 4 -38.428 64.686 5.878 0.91 94.41 ? C09 Y72 601 B 1 HETATM 6 C C06 Y72 . . . E 4 -37.282 65.938 7.373 0.91 98.47 ? C06 Y72 601 B 1 HETATM 7 O O18 Y72 . . . E 4 -37.079 75.266 2.773 0.91 70.62 ? O18 Y72 601 B 1 HETATM 8 C C12 Y72 . . . E 4 -36.71 71.986 4.014 0.91 85.54 ? C12 Y72 601 B 1 HETATM 9 C C04 Y72 . . . E 4 -37.196 65.094 3.859 0.91 96.92 ? C04 Y72 601 B 1 HETATM 10 C C02 Y72 . . . E 4 -39.041 63.704 3.862 0.91 86.56 ? C02 Y72 601 B 1 HETATM 11 C C07 Y72 . . . E 4 -38.372 65.082 7.248 0.91 98.11 ? C07 Y72 601 B 1 HETATM 12 C C08 Y72 . . . E 4 -37.377 65.316 5.255 0.91 96.66 ? C08 Y72 601 B 1 HETATM 13 C C13 Y72 . . . E 4 -37.498 73.071 3.59 0.91 83.59 ? C13 Y72 601 B 1 HETATM 14 C C21 Y72 . . . E 4 -35.296 76.904 4.771 0.91 96.36 ? C21 Y72 601 B 1 HETATM 15 C C22 Y72 . . . E 4 -34.293 77.558 5.726 0.91 95.9 ? C22 Y72 601 B 1 HETATM 16 C C23 Y72 . . . E 4 -34.591 79.038 5.972 0.91 92.84 ? C23 Y72 601 B 1 HETATM 17 C C26 Y72 . . . E 4 -37.725 77.29 5.347 0.91 88.93 ? C26 Y72 601 B 1 HETATM 18 C C29 Y72 . . . E 4 -35.55 66.872 5.907 0.91 91.5 ? C29 Y72 601 B 1 HETATM 19 C C30 Y72 . . . E 4 -35.838 68.292 6.39 0.91 84.55 ? C30 Y72 601 B 1 HETATM 20 C C31 Y72 . . . E 4 -35.666 69.365 5.312 0.91 83.61 ? C31 Y72 601 B 1 HETATM 21 C C32 Y72 . . . E 4 -36.677 69.336 4.159 0.91 86.85 ? C32 Y72 601 B 1 HETATM 22 F F33 Y72 . . . E 4 -35.483 72.189 4.576 0.91 87.39 ? F33 Y72 601 B 1 HETATM 23 N N01 Y72 . . . E 4 -39.25 63.88 5.159 0.91 89.6 ? N01 Y72 601 B 1 HETATM 24 N N03 Y72 . . . E 4 -38.039 64.293 3.22 0.91 97.9 ? N03 Y72 601 B 1 HETATM 25 N N05 Y72 . . . E 4 -36.716 66.054 6.183 0.91 97.57 ? N05 Y72 601 B 1 HETATM 26 N N11 Y72 . . . E 4 -39.933 62.839 3.11 0.91 68 ? N11 Y72 601 B 1 HETATM 27 N N19 Y72 . . . E 4 -36.872 75.014 5.08 0.91 93.33 ? N19 Y72 601 B 1 HETATM 28 O O10 Y72 . . . E 4 -36.147 65.701 3.154 0.91 89.51 ? O10 Y72 601 B 1 HETATM 29 O O24 Y72 . . . E 4 -34.393 79.585 7.244 0.91 97.57 ? O24 Y72 601 B 1 HETATM 30 O O25 Y72 . . . E 4 -35.278 79.779 5.003 0.91 82.45 ? O25 Y72 601 B 1 HETATM 31 O O27 Y72 . . . E 4 -38.638 77.405 6.403 0.91 78.23 ? O27 Y72 601 B 1 HETATM 32 O O28 Y72 . . . E 4 -38.065 77.783 4.077 0.91 86.37 ? O28 Y72 601 B 1 HETATM 33 S S14 Y72 . . . E 4 -38.925 72.417 2.974 0.91 80.69 ? S14 Y72 601 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 33 #