data_3E9Y # _model_server_result.job_id ZIJEgQsQ0YJWD4mvsRTsjw _model_server_result.datetime_utc '2024-11-06 01:30:32' _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 3e9y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":700}' # _entry.id 3E9Y # _exptl.entry_id 3E9Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 468.359 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-HYDROXYETHYLIDENE)-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE' _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 3E9Y _cell.length_a 178.866 _cell.length_b 178.866 _cell.length_c 186.078 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3E9Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 software_defined_assembly 1 ? tetrameric 4 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G 1 1,2 A,B,C,D,E,F,G 2 1,3,4,2 # 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' 10_665 -y+1,-x+1,-z+1/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 89.433 154.9025 62.026 3 'crystal symmetry operation' 4_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 89.433 154.9025 0 4 'crystal symmetry operation' 7_555 y,x,-z+1/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 62.026 # _struct_asym.details ? _struct_asym.entity_id 5 _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 C PRO 253 A PRO 339 1_555 A N CSD 254 A CSD 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C CSD 254 A CSD 340 1_555 A N ASP 255 A ASP 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? metalc ? metalc1 A OD1 ASP 452 A ASP 538 1_555 D MG MG . A MG 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc2 A OD1 ASN 479 A ASN 565 1_555 D MG MG . A MG 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc3 A O HIS 481 A HIS 567 1_555 D MG MG . A MG 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc4 D MG MG . A MG 699 1_555 E O1A TDM . A TDM 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc5 D MG MG . A MG 699 1_555 E O1B TDM . A TDM 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? # _chem_comp.formula 'C14 H22 N4 O8 P2 S' _chem_comp.formula_weight 468.359 _chem_comp.id TDM _chem_comp.mon_nstd_flag . _chem_comp.name '2-[(2E)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-(1-HYDROXYETHYLIDENE)-4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '2-HYDROXYETHYLTHIAMIN DIPHOSPHATE' # 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 O1A PA TDM doub 472 n n PA O2A TDM sing 473 n n PA O3A TDM sing 474 n n PA O7 TDM sing 475 n n O2A H2A TDM sing 476 n n O3A PB TDM sing 477 n n PB O2B TDM sing 478 n n PB O3B TDM sing 479 n n PB O1B TDM doub 480 n n O2B H2B TDM sing 481 n n O3B H3B TDM sing 482 n n O7 C7 TDM sing 483 n n C7 C6 TDM sing 484 n n C7 H71 TDM sing 485 n n C7 H72 TDM sing 486 n n C6 C5 TDM sing 487 n n C6 H61 TDM sing 488 n n C6 H62 TDM sing 489 n n C5 S1 TDM sing 490 n n C5 C4 TDM doub 491 n n S1 C2 TDM sing 492 n n C2 C27 TDM doub 493 e n C2 N3 TDM sing 494 n n C27 C29 TDM sing 495 n n C27 O28 TDM sing 496 n n C29 H291 TDM sing 497 n n C29 H292 TDM sing 498 n n C29 H293 TDM sing 499 n n O28 H28 TDM sing 500 n n N3 C4 TDM sing 501 n n N3 C7' TDM sing 502 n n C4 CM4 TDM sing 503 n n CM4 HM41 TDM sing 504 n n CM4 HM42 TDM sing 505 n n CM4 HM43 TDM sing 506 n n C7' C5' TDM sing 507 n n C7' "H7'1" TDM sing 508 n n C7' "H7'2" TDM sing 509 n n C5' C4' TDM doub 510 n y C5' C6' TDM sing 511 n y C4' N4' TDM sing 512 n n C4' N3' TDM sing 513 n y N4' "H4'1" TDM sing 514 n n N4' "H4'2" TDM sing 515 n n N3' C2' TDM doub 516 n y C2' CM2 TDM sing 517 n n C2' N1' TDM sing 518 n y CM2 HM21 TDM sing 519 n n CM2 HM22 TDM sing 520 n n CM2 HM23 TDM sing 521 n n N1' C6' TDM doub 522 n y C6' H6' TDM sing 523 n n # _atom_sites.entry_id 3E9Y _atom_sites.fract_transf_matrix[1][1] 0.005591 _atom_sites.fract_transf_matrix[1][2] 0.003228 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006456 _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] 0.005374 _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 1MS A 1 695 695 1MS 1MS . C 3 NHE A 1 696 696 NHE NHE . D 4 MG A 1 699 699 MG MG . E 5 TDM A 1 700 700 TDM TDM . F 6 FAB A 1 701 701 FAB FAB . G 7 HOH A 1 702 2 HOH HOH . G 7 HOH A 2 703 3 HOH HOH . G 7 HOH A 3 704 4 HOH HOH . G 7 HOH A 4 705 5 HOH HOH . G 7 HOH A 5 706 6 HOH HOH . G 7 HOH A 6 707 8 HOH HOH . G 7 HOH A 7 708 10 HOH HOH . G 7 HOH A 8 709 12 HOH HOH . G 7 HOH A 9 710 16 HOH HOH . G 7 HOH A 10 711 18 HOH HOH . G 7 HOH A 11 712 19 HOH HOH . G 7 HOH A 12 713 20 HOH HOH . G 7 HOH A 13 714 21 HOH HOH . G 7 HOH A 14 715 23 HOH HOH . G 7 HOH A 15 716 25 HOH HOH . G 7 HOH A 16 717 32 HOH HOH . G 7 HOH A 17 718 34 HOH HOH . G 7 HOH A 18 719 35 HOH HOH . G 7 HOH A 19 720 37 HOH HOH . G 7 HOH A 20 721 38 HOH HOH . G 7 HOH A 21 722 40 HOH HOH . G 7 HOH A 22 723 43 HOH HOH . G 7 HOH A 23 724 44 HOH HOH . G 7 HOH A 24 725 45 HOH HOH . G 7 HOH A 25 726 46 HOH HOH . G 7 HOH A 26 727 47 HOH HOH . G 7 HOH A 27 728 50 HOH HOH . G 7 HOH A 28 729 51 HOH HOH . G 7 HOH A 29 730 53 HOH HOH . G 7 HOH A 30 731 54 HOH HOH . G 7 HOH A 31 732 57 HOH HOH . G 7 HOH A 32 733 60 HOH HOH . G 7 HOH A 33 734 62 HOH HOH . G 7 HOH A 34 735 63 HOH HOH . G 7 HOH A 35 736 67 HOH HOH . G 7 HOH A 36 737 68 HOH HOH . G 7 HOH A 37 738 78 HOH HOH . G 7 HOH A 38 739 82 HOH HOH . G 7 HOH A 39 740 83 HOH HOH . G 7 HOH A 40 741 85 HOH HOH . G 7 HOH A 41 742 90 HOH HOH . G 7 HOH A 42 743 93 HOH HOH . G 7 HOH A 43 744 95 HOH HOH . G 7 HOH A 44 745 96 HOH HOH . G 7 HOH A 45 746 97 HOH HOH . G 7 HOH A 46 747 98 HOH HOH . G 7 HOH A 47 748 102 HOH HOH . G 7 HOH A 48 749 103 HOH HOH . G 7 HOH A 49 750 104 HOH HOH . G 7 HOH A 50 751 107 HOH HOH . G 7 HOH A 51 752 109 HOH HOH . G 7 HOH A 52 753 115 HOH HOH . G 7 HOH A 53 754 120 HOH HOH . G 7 HOH A 54 755 127 HOH HOH . G 7 HOH A 55 756 129 HOH HOH . G 7 HOH A 56 757 131 HOH HOH . G 7 HOH A 57 758 132 HOH HOH . G 7 HOH A 58 759 134 HOH HOH . G 7 HOH A 59 760 141 HOH HOH . G 7 HOH A 60 761 142 HOH HOH . G 7 HOH A 61 762 144 HOH HOH . G 7 HOH A 62 763 146 HOH HOH . G 7 HOH A 63 764 148 HOH HOH . G 7 HOH A 64 765 151 HOH HOH . G 7 HOH A 65 766 154 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 O O1A TDM . . . E 5 70.671 51.833 42.524 0.9 56.83 ? O1A TDM 700 A 1 HETATM 2 P PA TDM . . . E 5 69.741 52.94 42.862 0.9 56.72 ? PA TDM 700 A 1 HETATM 3 O O2A TDM . . . E 5 70.316 54.324 42.339 0.9 56.56 ? O2A TDM 700 A 1 HETATM 4 O O3A TDM . . . E 5 69.554 53.151 44.456 0.9 55.57 ? O3A TDM 700 A 1 HETATM 5 P PB TDM . . . E 5 69.308 51.955 45.505 0.9 54.03 ? PB TDM 700 A 1 HETATM 6 O O2B TDM . . . E 5 70.128 52.113 46.731 0.9 54.17 ? O2B TDM 700 A 1 HETATM 7 O O3B TDM . . . E 5 67.731 51.933 45.845 0.9 53.74 ? O3B TDM 700 A 1 HETATM 8 O O1B TDM . . . E 5 69.592 50.549 44.766 0.9 54.1 ? O1B TDM 700 A 1 HETATM 9 O O7 TDM . . . E 5 68.284 52.808 42.195 0.9 59.12 ? O7 TDM 700 A 1 HETATM 10 C C7 TDM . . . E 5 67.185 53.64 42.594 0.9 61.84 ? C7 TDM 700 A 1 HETATM 11 C C6 TDM . . . E 5 65.914 52.8 42.545 0.9 65.31 ? C6 TDM 700 A 1 HETATM 12 C C5 TDM . . . E 5 64.63 53.632 42.48 0.9 66.08 ? C5 TDM 700 A 1 HETATM 13 S S1 TDM . . . E 5 63.937 54.276 43.918 0.9 66.93 ? S1 TDM 700 A 1 HETATM 14 C C2 TDM . . . E 5 62.591 55.018 43.16 0.9 66.37 ? C2 TDM 700 A 1 HETATM 15 C C27 TDM . . . E 5 61.627 55.714 43.788 0.9 66.32 ? C27 TDM 700 A 1 HETATM 16 C C29 TDM . . . E 5 61.66 55.893 45.31 0.9 66.14 ? C29 TDM 700 A 1 HETATM 17 O O28 TDM . . . E 5 60.478 56.343 42.998 0.9 66.35 ? O28 TDM 700 A 1 HETATM 18 N N3 TDM . . . E 5 62.737 54.724 41.654 0.9 66.39 ? N3 TDM 700 A 1 HETATM 19 C C4 TDM . . . E 5 63.836 53.984 41.372 0.9 66.28 ? C4 TDM 700 A 1 HETATM 20 C CM4 TDM . . . E 5 64.206 53.549 39.947 0.9 66.33 ? CM4 TDM 700 A 1 HETATM 21 C C7' TDM . . . E 5 61.792 55.22 40.626 0.9 66.06 ? C7' TDM 700 A 1 HETATM 22 C C5' TDM . . . E 5 62.451 56.423 39.907 0.9 65.67 ? C5' TDM 700 A 1 HETATM 23 C C4' TDM . . . E 5 62.914 57.596 40.521 0.9 65.54 ? C4' TDM 700 A 1 HETATM 24 N N4' TDM . . . E 5 62.802 57.789 41.831 0.9 65.15 ? N4' TDM 700 A 1 HETATM 25 N N3' TDM . . . E 5 63.483 58.567 39.782 0.9 65.65 ? N3' TDM 700 A 1 HETATM 26 C C2' TDM . . . E 5 63.622 58.429 38.453 0.9 65.62 ? C2' TDM 700 A 1 HETATM 27 C CM2 TDM . . . E 5 64.273 59.552 37.638 0.9 65.39 ? CM2 TDM 700 A 1 HETATM 28 N N1' TDM . . . E 5 63.188 57.309 37.843 0.9 65.27 ? N1' TDM 700 A 1 HETATM 29 C C6' TDM . . . E 5 62.619 56.327 38.524 0.9 65.43 ? C6' TDM 700 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 29 #