data_3EA4 # _model_server_result.job_id 9tIAOa78wv2qbZg9EfQe9w _model_server_result.datetime_utc '2025-02-17 05:54:56' _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 3ea4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":698}' # _entry.id 3EA4 # _exptl.entry_id 3EA4 _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 3EA4 _cell.length_a 178.468 _cell.length_b 178.468 _cell.length_c 184.948 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EA4 _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 89.234 154.557822 61.649333 3 'crystal symmetry operation' 4_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 89.234 154.557822 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 61.649333 # _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? metalc ? metalc1 A OD1 ASP 452 A ASP 538 1_555 F MG MG . A MG 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc2 A OD1 ASN 479 A ASN 565 1_555 F MG MG . A MG 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc3 A O HIS 481 A HIS 567 1_555 F MG MG . A MG 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc4 E O1A TDM . A TDM 698 1_555 F MG MG . A MG 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc5 E O1B TDM . A TDM 698 1_555 F MG MG . A MG 699 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? # _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 476 n n PA O2A TDM sing 477 n n PA O3A TDM sing 478 n n PA O7 TDM sing 479 n n O2A H2A TDM sing 480 n n O3A PB TDM sing 481 n n PB O2B TDM sing 482 n n PB O3B TDM sing 483 n n PB O1B TDM doub 484 n n O2B H2B TDM sing 485 n n O3B H3B TDM sing 486 n n O7 C7 TDM sing 487 n n C7 C6 TDM sing 488 n n C7 H71 TDM sing 489 n n C7 H72 TDM sing 490 n n C6 C5 TDM sing 491 n n C6 H61 TDM sing 492 n n C6 H62 TDM sing 493 n n C5 S1 TDM sing 494 n n C5 C4 TDM doub 495 n n S1 C2 TDM sing 496 n n C2 C27 TDM doub 497 e n C2 N3 TDM sing 498 n n C27 C29 TDM sing 499 n n C27 O28 TDM sing 500 n n C29 H291 TDM sing 501 n n C29 H292 TDM sing 502 n n C29 H293 TDM sing 503 n n O28 H28 TDM sing 504 n n N3 C4 TDM sing 505 n n N3 C7' TDM sing 506 n n C4 CM4 TDM sing 507 n n CM4 HM41 TDM sing 508 n n CM4 HM42 TDM sing 509 n n CM4 HM43 TDM sing 510 n n C7' C5' TDM sing 511 n n C7' "H7'1" TDM sing 512 n n C7' "H7'2" TDM sing 513 n n C5' C4' TDM doub 514 n y C5' C6' TDM sing 515 n y C4' N4' TDM sing 516 n n C4' N3' TDM sing 517 n y N4' "H4'1" TDM sing 518 n n N4' "H4'2" TDM sing 519 n n N3' C2' TDM doub 520 n y C2' CM2 TDM sing 521 n n C2' N1' TDM sing 522 n y CM2 HM21 TDM sing 523 n n CM2 HM22 TDM sing 524 n n CM2 HM23 TDM sing 525 n n N1' C6' TDM doub 526 n y C6' H6' TDM sing 527 n n # _atom_sites.entry_id 3EA4 _atom_sites.fract_transf_matrix[1][1] 0.005603 _atom_sites.fract_transf_matrix[1][2] 0.003235 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00647 _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] 0.005407 _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 2SM A 1 695 695 2SM MSM . C 3 FAB A 1 696 696 FAB FAB . D 4 NHE A 1 697 697 NHE NHE . E 5 TDM A 1 698 698 TDM TDM . F 6 MG A 1 699 699 MG MG . G 7 HOH A 1 700 1 HOH HOH . G 7 HOH A 2 701 2 HOH HOH . G 7 HOH A 3 702 3 HOH HOH . G 7 HOH A 4 703 4 HOH HOH . G 7 HOH A 5 704 5 HOH HOH . G 7 HOH A 6 705 6 HOH HOH . G 7 HOH A 7 706 7 HOH HOH . G 7 HOH A 8 707 8 HOH HOH . G 7 HOH A 9 708 9 HOH HOH . G 7 HOH A 10 709 10 HOH HOH . G 7 HOH A 11 710 11 HOH HOH . G 7 HOH A 12 711 12 HOH HOH . G 7 HOH A 13 712 13 HOH HOH . G 7 HOH A 14 713 14 HOH HOH . G 7 HOH A 15 714 15 HOH HOH . G 7 HOH A 16 715 16 HOH HOH . G 7 HOH A 17 716 17 HOH HOH . G 7 HOH A 18 717 18 HOH HOH . G 7 HOH A 19 718 19 HOH HOH . G 7 HOH A 20 719 20 HOH HOH . G 7 HOH A 21 720 21 HOH HOH . G 7 HOH A 22 721 22 HOH HOH . G 7 HOH A 23 722 23 HOH HOH . G 7 HOH A 24 723 24 HOH HOH . G 7 HOH A 25 724 25 HOH HOH . G 7 HOH A 26 725 26 HOH HOH . G 7 HOH A 27 726 27 HOH HOH . G 7 HOH A 28 727 28 HOH HOH . G 7 HOH A 29 728 29 HOH HOH . G 7 HOH A 30 729 30 HOH HOH . G 7 HOH A 31 730 31 HOH HOH . G 7 HOH A 32 731 32 HOH HOH . G 7 HOH A 33 732 33 HOH HOH . G 7 HOH A 34 733 34 HOH HOH . G 7 HOH A 35 734 35 HOH HOH . G 7 HOH A 36 735 36 HOH HOH . G 7 HOH A 37 736 37 HOH HOH . G 7 HOH A 38 737 38 HOH HOH . G 7 HOH A 39 738 39 HOH HOH . G 7 HOH A 40 739 40 HOH HOH . G 7 HOH A 41 740 41 HOH HOH . G 7 HOH A 42 741 42 HOH HOH . G 7 HOH A 43 742 43 HOH HOH . G 7 HOH A 44 743 44 HOH HOH . G 7 HOH A 45 744 45 HOH HOH . G 7 HOH A 46 745 46 HOH HOH . G 7 HOH A 47 746 47 HOH HOH . G 7 HOH A 48 747 48 HOH HOH . G 7 HOH A 49 748 49 HOH HOH . G 7 HOH A 50 749 50 HOH HOH . G 7 HOH A 51 750 51 HOH HOH . G 7 HOH A 52 751 52 HOH HOH . G 7 HOH A 53 752 53 HOH HOH . G 7 HOH A 54 753 54 HOH HOH . G 7 HOH A 55 754 55 HOH HOH . G 7 HOH A 56 755 56 HOH HOH . G 7 HOH A 57 756 57 HOH HOH . G 7 HOH A 58 757 58 HOH HOH . G 7 HOH A 59 758 59 HOH HOH . G 7 HOH A 60 759 60 HOH HOH . G 7 HOH A 61 760 61 HOH HOH . G 7 HOH A 62 761 62 HOH HOH . G 7 HOH A 63 762 63 HOH HOH . G 7 HOH A 64 763 64 HOH HOH . G 7 HOH A 65 764 65 HOH HOH . G 7 HOH A 66 765 66 HOH HOH . G 7 HOH A 67 766 67 HOH HOH . G 7 HOH A 68 767 68 HOH HOH . G 7 HOH A 69 768 69 HOH HOH . G 7 HOH A 70 769 70 HOH HOH . G 7 HOH A 71 770 71 HOH HOH . G 7 HOH A 72 771 72 HOH HOH . G 7 HOH A 73 772 73 HOH HOH . G 7 HOH A 74 773 74 HOH HOH . G 7 HOH A 75 774 75 HOH HOH . G 7 HOH A 76 775 76 HOH HOH . G 7 HOH A 77 776 77 HOH HOH . G 7 HOH A 78 777 78 HOH HOH . G 7 HOH A 79 778 79 HOH HOH . G 7 HOH A 80 779 80 HOH HOH . G 7 HOH A 81 780 81 HOH HOH . G 7 HOH A 82 781 82 HOH HOH . G 7 HOH A 83 782 83 HOH HOH . G 7 HOH A 84 783 84 HOH HOH . G 7 HOH A 85 784 85 HOH HOH . G 7 HOH A 86 785 86 HOH HOH . G 7 HOH A 87 786 87 HOH HOH . G 7 HOH A 88 787 88 HOH HOH . G 7 HOH A 89 788 89 HOH HOH . G 7 HOH A 90 789 90 HOH HOH . G 7 HOH A 91 790 91 HOH HOH . G 7 HOH A 92 791 92 HOH HOH . G 7 HOH A 93 792 93 HOH HOH . G 7 HOH A 94 793 94 HOH HOH . G 7 HOH A 95 794 95 HOH HOH . G 7 HOH A 96 795 96 HOH HOH . G 7 HOH A 97 796 97 HOH HOH . G 7 HOH A 98 797 98 HOH HOH . G 7 HOH A 99 798 99 HOH HOH . G 7 HOH A 100 799 100 HOH HOH . G 7 HOH A 101 800 101 HOH HOH . G 7 HOH A 102 801 102 HOH HOH . G 7 HOH A 103 802 103 HOH HOH . G 7 HOH A 104 803 104 HOH HOH . G 7 HOH A 105 804 105 HOH HOH . G 7 HOH A 106 805 106 HOH HOH . G 7 HOH A 107 806 107 HOH HOH . G 7 HOH A 108 807 108 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 70.384 51.63 42.289 0.9 56.46 ? O1A TDM 698 A 1 HETATM 2 P PA TDM . . . E 5 69.518 52.793 42.622 0.9 56.3 ? PA TDM 698 A 1 HETATM 3 O O2A TDM . . . E 5 70.184 54.121 42.074 0.9 55.47 ? O2A TDM 698 A 1 HETATM 4 O O3A TDM . . . E 5 69.347 53.038 44.189 0.9 55.2 ? O3A TDM 698 A 1 HETATM 5 P PB TDM . . . E 5 69.037 51.889 45.25 0.9 52.75 ? PB TDM 698 A 1 HETATM 6 O O2B TDM . . . E 5 69.787 52.139 46.5 0.9 53.03 ? O2B TDM 698 A 1 HETATM 7 O O3B TDM . . . E 5 67.442 51.889 45.511 0.9 52.58 ? O3B TDM 698 A 1 HETATM 8 O O1B TDM . . . E 5 69.408 50.451 44.605 0.9 52.53 ? O1B TDM 698 A 1 HETATM 9 O O7 TDM . . . E 5 68.026 52.695 42.021 0.9 60.16 ? O7 TDM 698 A 1 HETATM 10 C C7 TDM . . . E 5 66.934 53.513 42.466 0.9 64.15 ? C7 TDM 698 A 1 HETATM 11 C C6 TDM . . . E 5 65.661 52.68 42.354 0.9 68.84 ? C6 TDM 698 A 1 HETATM 12 C C5 TDM . . . E 5 64.376 53.507 42.23 0.9 69.65 ? C5 TDM 698 A 1 HETATM 13 S S1 TDM . . . E 5 63.609 54.139 43.64 0.9 70.62 ? S1 TDM 698 A 1 HETATM 14 C C2 TDM . . . E 5 62.291 54.875 42.811 0.9 70.23 ? C2 TDM 698 A 1 HETATM 15 C C27 TDM . . . E 5 61.286 55.559 43.381 0.9 70.08 ? C27 TDM 698 A 1 HETATM 16 C C29 TDM . . . E 5 61.225 55.746 44.903 0.9 69.79 ? C29 TDM 698 A 1 HETATM 17 O O28 TDM . . . E 5 60.165 56.177 42.486 0.9 70.21 ? O28 TDM 698 A 1 HETATM 18 N N3 TDM . . . E 5 62.509 54.594 41.309 0.9 70.27 ? N3 TDM 698 A 1 HETATM 19 C C4 TDM . . . E 5 63.628 53.856 41.082 0.9 70.07 ? C4 TDM 698 A 1 HETATM 20 C CM4 TDM . . . E 5 64.068 53.431 39.674 0.9 70.07 ? CM4 TDM 698 A 1 HETATM 21 C C7' TDM . . . E 5 61.604 55.085 40.236 0.9 69.84 ? C7' TDM 698 A 1 HETATM 22 C C5' TDM . . . E 5 62.241 56.325 39.544 0.9 69.72 ? C5' TDM 698 A 1 HETATM 23 C C4' TDM . . . E 5 62.615 57.524 40.178 0.9 69.69 ? C4' TDM 698 A 1 HETATM 24 N N4' TDM . . . E 5 62.439 57.714 41.482 0.9 68.9 ? N4' TDM 698 A 1 HETATM 25 N N3' TDM . . . E 5 63.173 58.521 39.462 0.9 69.84 ? N3' TDM 698 A 1 HETATM 26 C C2' TDM . . . E 5 63.381 58.392 38.138 0.9 69.67 ? C2' TDM 698 A 1 HETATM 27 C CM2 TDM . . . E 5 64.015 59.553 37.37 0.9 69.34 ? CM2 TDM 698 A 1 HETATM 28 N N1' TDM . . . E 5 63.033 57.256 37.498 0.9 69.29 ? N1' TDM 698 A 1 HETATM 29 C C6' TDM . . . E 5 62.481 56.245 38.164 0.9 69.53 ? C6' TDM 698 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 29 #