data_8GKU # _model_server_result.job_id domlPnz0Em1FA_IXEUCmtA _model_server_result.datetime_utc '2024-10-10 11:20:47' _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 8gku # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 8GKU # _exptl.entry_id 8GKU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 487.481 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'N-{4-[5-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)pentyl]-2-fluorobenzoyl}-D-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 8GKU _cell.length_a 158.324 _cell.length_b 158.324 _cell.length_c 207.65 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GKU _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 _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 -79.162 137.112606 -34.608333 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _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 E C4A PLP . A PLP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale2 B NZ LYS 269 B LYS 280 1_555 F C4A PLP . B PLP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? # _chem_comp.formula 'C23 H26 F N5 O6' _chem_comp.formula_weight 487.481 _chem_comp.id ZV1 _chem_comp.mon_nstd_flag . _chem_comp.name 'N-{4-[5-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)pentyl]-2-fluorobenzoyl}-D-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 ZV1 doub 402 n n C26 C25 ZV1 sing 403 n n C26 O28 ZV1 sing 404 n n C25 C24 ZV1 sing 405 n n C24 C20 ZV1 sing 406 n n F35 C13 ZV1 sing 407 n n C20 N19 ZV1 sing 408 n n C20 C21 ZV1 sing 409 n n N03 C04 ZV1 sing 410 n n N03 C02 ZV1 sing 411 n n N19 C17 ZV1 sing 412 n n N11 C02 ZV1 sing 413 n n O17 C04 ZV1 doub 414 n n C13 C15 ZV1 doub 415 n y C13 C12 ZV1 sing 416 n y C15 C34 ZV1 sing 417 n y C04 C08 ZV1 sing 418 n n C17 C12 ZV1 sing 419 n n C17 O18 ZV1 doub 420 n n C02 N01 ZV1 doub 421 n n C12 C14 ZV1 doub 422 n y C34 C33 ZV1 sing 423 n n C34 C16 ZV1 doub 424 n y C33 C32 ZV1 sing 425 n n C21 O22 ZV1 doub 426 n n C21 O23 ZV1 sing 427 n n C14 C16 ZV1 sing 428 n y N01 C09 ZV1 sing 429 n n C08 C09 ZV1 doub 430 n y C08 N07 ZV1 sing 431 n y C32 C31 ZV1 sing 432 n n C30 C29 ZV1 sing 433 n n C30 C31 ZV1 sing 434 n n C29 N07 ZV1 sing 435 n n C09 C05 ZV1 sing 436 n y N07 C06 ZV1 sing 437 n y C05 C06 ZV1 doub 438 n y C14 H1 ZV1 sing 439 n n C15 H2 ZV1 sing 440 n n C16 H3 ZV1 sing 441 n n C20 H4 ZV1 sing 442 n n C24 H5 ZV1 sing 443 n n C24 H6 ZV1 sing 444 n n C25 H7 ZV1 sing 445 n n C25 H8 ZV1 sing 446 n n C29 H9 ZV1 sing 447 n n C29 H10 ZV1 sing 448 n n C30 H11 ZV1 sing 449 n n C30 H12 ZV1 sing 450 n n C31 H13 ZV1 sing 451 n n C31 H14 ZV1 sing 452 n n C32 H15 ZV1 sing 453 n n C32 H16 ZV1 sing 454 n n C33 H17 ZV1 sing 455 n n C33 H18 ZV1 sing 456 n n C05 H19 ZV1 sing 457 n n C06 H20 ZV1 sing 458 n n N11 H22 ZV1 sing 459 n n N11 H23 ZV1 sing 460 n n N19 H24 ZV1 sing 461 n n O23 H25 ZV1 sing 462 n n O28 H26 ZV1 sing 463 n n N03 H21 ZV1 sing 464 n n # _atom_sites.entry_id 8GKU _atom_sites.fract_transf_matrix[1][1] 0.006316 _atom_sites.fract_transf_matrix[1][2] 0.003647 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007293 _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] 0.004816 _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 ZV1 A 1 601 601 ZV1 355 . D 3 GLY A 1 602 701 GLY GLY . E 4 PLP A 1 603 280 PLP LLP . F 4 PLP B 1 601 280 PLP LLP . G 5 HOH A 1 701 14 HOH HOH . G 5 HOH A 2 702 19 HOH HOH . G 5 HOH A 3 703 7 HOH HOH . G 5 HOH A 4 704 46 HOH HOH . G 5 HOH A 5 705 39 HOH HOH . G 5 HOH A 6 706 58 HOH HOH . G 5 HOH A 7 707 12 HOH HOH . G 5 HOH A 8 708 59 HOH HOH . G 5 HOH A 9 709 53 HOH HOH . G 5 HOH A 10 710 8 HOH HOH . G 5 HOH A 11 711 63 HOH HOH . G 5 HOH A 12 712 70 HOH HOH . G 5 HOH A 13 713 13 HOH HOH . G 5 HOH A 14 714 3 HOH HOH . G 5 HOH A 15 715 32 HOH HOH . G 5 HOH A 16 716 62 HOH HOH . G 5 HOH A 17 717 49 HOH HOH . G 5 HOH A 18 718 9 HOH HOH . G 5 HOH A 19 719 29 HOH HOH . G 5 HOH A 20 720 31 HOH HOH . G 5 HOH A 21 721 4 HOH HOH . G 5 HOH A 22 722 41 HOH HOH . G 5 HOH A 23 723 61 HOH HOH . G 5 HOH A 24 724 2 HOH HOH . G 5 HOH A 25 725 43 HOH HOH . G 5 HOH A 26 726 68 HOH HOH . G 5 HOH A 27 727 35 HOH HOH . G 5 HOH A 28 728 34 HOH HOH . G 5 HOH A 29 729 66 HOH HOH . G 5 HOH A 30 730 37 HOH HOH . G 5 HOH A 31 731 26 HOH HOH . G 5 HOH A 32 732 30 HOH HOH . G 5 HOH A 33 733 48 HOH HOH . G 5 HOH A 34 734 50 HOH HOH . G 5 HOH A 35 735 15 HOH HOH . G 5 HOH A 36 736 52 HOH HOH . G 5 HOH A 37 737 56 HOH HOH . G 5 HOH A 38 738 47 HOH HOH . G 5 HOH A 39 739 18 HOH HOH . G 5 HOH A 40 740 28 HOH HOH . G 5 HOH A 41 741 55 HOH HOH . G 5 HOH A 42 742 64 HOH HOH . G 5 HOH A 43 743 16 HOH HOH . H 5 HOH B 1 701 45 HOH HOH . H 5 HOH B 2 702 22 HOH HOH . H 5 HOH B 3 703 21 HOH HOH . H 5 HOH B 4 704 25 HOH HOH . H 5 HOH B 5 705 20 HOH HOH . H 5 HOH B 6 706 57 HOH HOH . H 5 HOH B 7 707 10 HOH HOH . H 5 HOH B 8 708 27 HOH HOH . H 5 HOH B 9 709 65 HOH HOH . H 5 HOH B 10 710 5 HOH HOH . H 5 HOH B 11 711 23 HOH HOH . H 5 HOH B 12 712 69 HOH HOH . H 5 HOH B 13 713 1 HOH HOH . H 5 HOH B 14 714 11 HOH HOH . H 5 HOH B 15 715 60 HOH HOH . H 5 HOH B 16 716 40 HOH HOH . H 5 HOH B 17 717 17 HOH HOH . H 5 HOH B 18 718 54 HOH HOH . H 5 HOH B 19 719 67 HOH HOH . H 5 HOH B 20 720 36 HOH HOH . H 5 HOH B 21 721 24 HOH HOH . H 5 HOH B 22 722 51 HOH HOH . H 5 HOH B 23 723 44 HOH HOH . H 5 HOH B 24 724 33 HOH HOH . H 5 HOH B 25 725 42 HOH HOH . H 5 HOH B 26 726 38 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 C12 ZV1 . . . C 2 -37.073 74.025 3.639 1 95.97 ? C12 ZV1 601 A 1 HETATM 2 C C13 ZV1 . . . C 2 -37.955 73.209 2.951 1 88.48 ? C13 ZV1 601 A 1 HETATM 3 C C14 ZV1 . . . C 2 -36.069 73.464 4.408 1 86.98 ? C14 ZV1 601 A 1 HETATM 4 C C15 ZV1 . . . C 2 -37.826 71.831 3.025 1 76.77 ? C15 ZV1 601 A 1 HETATM 5 C C16 ZV1 . . . C 2 -35.937 72.087 4.483 1 76.95 ? C16 ZV1 601 A 1 HETATM 6 C C17 ZV1 . . . C 2 -37.226 75.542 3.558 1 101.66 ? C17 ZV1 601 A 1 HETATM 7 C C20 ZV1 . . . C 2 -38.663 77.516 2.782 1 122.81 ? C20 ZV1 601 A 1 HETATM 8 C C21 ZV1 . . . C 2 -38.644 78.177 4.161 1 130.87 ? C21 ZV1 601 A 1 HETATM 9 C C24 ZV1 . . . C 2 -37.647 78.194 1.863 1 117.8 ? C24 ZV1 601 A 1 HETATM 10 C C25 ZV1 . . . C 2 -38.328 78.751 0.613 1 116.07 ? C25 ZV1 601 A 1 HETATM 11 C C26 ZV1 . . . C 2 -38.385 80.277 0.605 1 114.38 ? C26 ZV1 601 A 1 HETATM 12 C C29 ZV1 . . . C 2 -35.126 66.166 5.626 1 83.76 ? C29 ZV1 601 A 1 HETATM 13 C C30 ZV1 . . . C 2 -35.421 67.588 5.142 1 90.01 ? C30 ZV1 601 A 1 HETATM 14 C C31 ZV1 . . . C 2 -36.511 68.288 5.954 1 89.84 ? C31 ZV1 601 A 1 HETATM 15 C C32 ZV1 . . . C 2 -37.397 69.198 5.104 1 87.49 ? C32 ZV1 601 A 1 HETATM 16 C C33 ZV1 . . . C 2 -36.675 69.756 3.878 1 81.09 ? C33 ZV1 601 A 1 HETATM 17 C C02 ZV1 . . . C 2 -39.323 63.538 3.604 1 85.68 ? C02 ZV1 601 A 1 HETATM 18 C C04 ZV1 . . . C 2 -37.19 64.831 3.546 1 90.98 ? C04 ZV1 601 A 1 HETATM 19 C C05 ZV1 . . . C 2 -37.952 64.508 7.143 1 93.45 ? C05 ZV1 601 A 1 HETATM 20 C C06 ZV1 . . . C 2 -36.766 65.227 7.193 1 91.25 ? C06 ZV1 601 A 1 HETATM 21 C C08 ZV1 . . . C 2 -37.191 64.89 5.078 1 89.32 ? C08 ZV1 601 A 1 HETATM 22 C C09 ZV1 . . . C 2 -38.221 64.291 5.784 1 85.86 ? C09 ZV1 601 A 1 HETATM 23 C C34 ZV1 . . . C 2 -36.817 71.272 3.791 1 76.3 ? C34 ZV1 601 A 1 HETATM 24 F F35 ZV1 . . . C 2 -38.947 73.766 2.197 1 91.31 ? F35 ZV1 601 A 1 HETATM 25 N N01 ZV1 . . . C 2 -39.32 63.596 5.069 1 74.8 ? N01 ZV1 601 A 1 HETATM 26 N N03 ZV1 . . . C 2 -38.251 64.16 2.853 1 94.66 ? N03 ZV1 601 A 1 HETATM 27 N N07 ZV1 . . . C 2 -36.344 65.443 5.957 1 85.03 ? N07 ZV1 601 A 1 HETATM 28 N N11 ZV1 . . . C 2 -40.398 62.857 2.91 1 94.16 ? N11 ZV1 601 A 1 HETATM 29 N N19 ZV1 . . . C 2 -38.408 76.088 2.907 1 113.61 ? N19 ZV1 601 A 1 HETATM 30 O O17 ZV1 . . . C 2 -36.321 65.335 2.918 1 77.27 ? O17 ZV1 601 A 1 HETATM 31 O O18 ZV1 . . . C 2 -36.394 76.245 4.028 1 96.75 ? O18 ZV1 601 A 1 HETATM 32 O O22 ZV1 . . . C 2 -38.324 79.389 4.273 1 135.17 ? O22 ZV1 601 A 1 HETATM 33 O O23 ZV1 . . . C 2 -38.951 77.509 5.184 1 129.39 ? O23 ZV1 601 A 1 HETATM 34 O O27 ZV1 . . . C 2 -39.237 80.867 -0.11 1 108.97 ? O27 ZV1 601 A 1 HETATM 35 O O28 ZV1 . . . C 2 -37.585 80.943 1.313 1 110.7 ? O28 ZV1 601 A 1 # _model_server_stats.io_time_ms 121 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 35 #