data_3E6E # _model_server_result.job_id H1-U9GY-ObjAl48CYQ2fwA _model_server_result.datetime_utc '2024-12-04 20:03:36' _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 3e6e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":372}' # _entry.id 3E6E # _exptl.entry_id 3E6E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 333.234 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE _entity.pdbx_number_of_molecules 3 _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 90 _cell.entry_id 3E6E _cell.length_a 94.597 _cell.length_b 156.186 _cell.length_c 146.93 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3E6E _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # 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 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,F,G,I 1 1 B,E,H 2 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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N ? 2 F N N # _chem_comp.formula 'C11 H16 N3 O7 P' _chem_comp.formula_weight 333.234 _chem_comp.id DCS _chem_comp.mon_nstd_flag . _chem_comp.name D-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-N,O-CYCLOSERYLAMIDE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms D-PYRIDOXYL-N,O-CYCLOSERYLAMIDE-5-MONOPHOSPHATE # 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 N1 C2 DCS doub 83 n y N1 C6 DCS sing 84 n y C2 C2A DCS sing 85 n n C2 C3 DCS sing 86 n y C2A H2A1 DCS sing 87 n n C2A H2A2 DCS sing 88 n n C2A H2A3 DCS sing 89 n n C3 O3 DCS sing 90 n n C3 C4 DCS doub 91 n y O3 HO3 DCS sing 92 n n C4 C4A DCS sing 93 n n C4 C5 DCS sing 94 n y C4A N DCS sing 95 n n C4A H4A1 DCS sing 96 n n C4A H4A2 DCS sing 97 n n C5 C6 DCS doub 98 n y C5 C5A DCS sing 99 n n C6 H6 DCS sing 100 n n C5A O4P DCS sing 101 n n C5A H5A1 DCS sing 102 n n C5A H5A2 DCS sing 103 n n O4P P DCS sing 104 n n P O1P DCS doub 105 n n P O2P DCS sing 106 n n P O3P DCS sing 107 n n O2P HOP2 DCS sing 108 n n O3P HOP3 DCS sing 109 n n N CA DCS sing 110 n n N HN DCS sing 111 n n CA C DCS sing 112 n n CA CB DCS sing 113 n n CA HA DCS sing 114 n n C O DCS doub 115 n n C ND DCS sing 116 n n ND OG DCS sing 117 n n ND HND DCS sing 118 n n OG CB DCS sing 119 n n CB HB1 DCS sing 120 n n CB HB2 DCS sing 121 n n # _atom_sites.entry_id 3E6E _atom_sites.fract_transf_matrix[1][1] 0.010571 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006403 _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] 0.006806 _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 D 2 DCS A 1 372 372 DCS DCS . E 2 DCS B 1 372 372 DCS DCS . F 2 DCS C 1 372 372 DCS DCS . G 3 HOH A 1 373 373 HOH HOH . G 3 HOH A 2 374 374 HOH HOH . G 3 HOH A 3 375 375 HOH HOH . G 3 HOH A 4 376 376 HOH HOH . G 3 HOH A 5 377 377 HOH HOH . G 3 HOH A 6 378 378 HOH HOH . G 3 HOH A 7 379 379 HOH HOH . G 3 HOH A 8 380 380 HOH HOH . G 3 HOH A 9 381 381 HOH HOH . G 3 HOH A 10 382 382 HOH HOH . G 3 HOH A 11 383 383 HOH HOH . G 3 HOH A 12 384 384 HOH HOH . G 3 HOH A 13 385 385 HOH HOH . G 3 HOH A 14 386 386 HOH HOH . G 3 HOH A 15 387 387 HOH HOH . G 3 HOH A 16 388 388 HOH HOH . G 3 HOH A 17 389 389 HOH HOH . G 3 HOH A 18 390 390 HOH HOH . G 3 HOH A 19 391 391 HOH HOH . G 3 HOH A 20 392 392 HOH HOH . G 3 HOH A 21 393 393 HOH HOH . G 3 HOH A 22 394 394 HOH HOH . G 3 HOH A 23 395 395 HOH HOH . G 3 HOH A 24 396 396 HOH HOH . G 3 HOH A 25 397 397 HOH HOH . G 3 HOH A 26 398 398 HOH HOH . G 3 HOH A 27 399 399 HOH HOH . G 3 HOH A 28 400 400 HOH HOH . G 3 HOH A 29 401 401 HOH HOH . G 3 HOH A 30 402 402 HOH HOH . G 3 HOH A 31 403 403 HOH HOH . G 3 HOH A 32 404 404 HOH HOH . G 3 HOH A 33 405 405 HOH HOH . G 3 HOH A 34 406 406 HOH HOH . G 3 HOH A 35 407 407 HOH HOH . G 3 HOH A 36 408 408 HOH HOH . G 3 HOH A 37 409 409 HOH HOH . G 3 HOH A 38 410 410 HOH HOH . G 3 HOH A 39 411 411 HOH HOH . G 3 HOH A 40 412 412 HOH HOH . G 3 HOH A 41 413 413 HOH HOH . G 3 HOH A 42 414 414 HOH HOH . G 3 HOH A 43 415 415 HOH HOH . G 3 HOH A 44 416 416 HOH HOH . G 3 HOH A 45 417 417 HOH HOH . G 3 HOH A 46 418 418 HOH HOH . G 3 HOH A 47 419 419 HOH HOH . G 3 HOH A 48 420 420 HOH HOH . G 3 HOH A 49 421 421 HOH HOH . G 3 HOH A 50 422 422 HOH HOH . G 3 HOH A 51 423 423 HOH HOH . H 3 HOH B 1 373 373 HOH HOH . H 3 HOH B 2 374 374 HOH HOH . H 3 HOH B 3 375 375 HOH HOH . H 3 HOH B 4 376 376 HOH HOH . H 3 HOH B 5 377 377 HOH HOH . H 3 HOH B 6 378 378 HOH HOH . H 3 HOH B 7 379 379 HOH HOH . H 3 HOH B 8 380 380 HOH HOH . H 3 HOH B 9 381 381 HOH HOH . H 3 HOH B 10 382 382 HOH HOH . H 3 HOH B 11 383 383 HOH HOH . H 3 HOH B 12 384 384 HOH HOH . H 3 HOH B 13 385 385 HOH HOH . H 3 HOH B 14 386 386 HOH HOH . H 3 HOH B 15 387 387 HOH HOH . H 3 HOH B 16 388 388 HOH HOH . H 3 HOH B 17 389 389 HOH HOH . H 3 HOH B 18 390 390 HOH HOH . H 3 HOH B 19 391 391 HOH HOH . H 3 HOH B 20 392 392 HOH HOH . H 3 HOH B 21 393 393 HOH HOH . H 3 HOH B 22 394 394 HOH HOH . H 3 HOH B 23 395 395 HOH HOH . H 3 HOH B 24 396 396 HOH HOH . H 3 HOH B 25 397 397 HOH HOH . H 3 HOH B 26 398 398 HOH HOH . H 3 HOH B 27 399 399 HOH HOH . H 3 HOH B 28 400 400 HOH HOH . H 3 HOH B 29 401 401 HOH HOH . H 3 HOH B 30 402 402 HOH HOH . H 3 HOH B 31 403 403 HOH HOH . H 3 HOH B 32 404 404 HOH HOH . H 3 HOH B 33 405 405 HOH HOH . H 3 HOH B 34 406 406 HOH HOH . H 3 HOH B 35 407 407 HOH HOH . H 3 HOH B 36 408 408 HOH HOH . H 3 HOH B 37 409 409 HOH HOH . H 3 HOH B 38 410 410 HOH HOH . H 3 HOH B 39 411 411 HOH HOH . H 3 HOH B 40 412 412 HOH HOH . I 3 HOH C 1 373 373 HOH HOH . I 3 HOH C 2 374 374 HOH HOH . I 3 HOH C 3 375 375 HOH HOH . I 3 HOH C 4 376 376 HOH HOH . I 3 HOH C 5 377 377 HOH HOH . I 3 HOH C 6 378 378 HOH HOH . I 3 HOH C 7 379 379 HOH HOH . I 3 HOH C 8 380 380 HOH HOH . I 3 HOH C 9 381 381 HOH HOH . I 3 HOH C 10 382 382 HOH HOH . I 3 HOH C 11 383 383 HOH HOH . I 3 HOH C 12 384 384 HOH HOH . I 3 HOH C 13 385 385 HOH HOH . I 3 HOH C 14 386 386 HOH HOH . I 3 HOH C 15 387 387 HOH HOH . I 3 HOH C 16 388 388 HOH HOH . I 3 HOH C 17 389 389 HOH HOH . I 3 HOH C 18 390 390 HOH HOH . I 3 HOH C 19 391 391 HOH HOH . I 3 HOH C 20 392 392 HOH HOH . I 3 HOH C 21 393 393 HOH HOH . I 3 HOH C 22 394 394 HOH HOH . I 3 HOH C 23 395 395 HOH HOH . I 3 HOH C 24 396 396 HOH HOH . I 3 HOH C 25 397 397 HOH HOH . I 3 HOH C 26 398 398 HOH HOH . I 3 HOH C 27 399 399 HOH HOH . I 3 HOH C 28 400 400 HOH HOH . I 3 HOH C 29 401 401 HOH HOH . I 3 HOH C 30 402 402 HOH HOH . I 3 HOH C 31 403 403 HOH HOH . I 3 HOH C 32 404 404 HOH HOH . I 3 HOH C 33 405 405 HOH HOH . I 3 HOH C 34 406 406 HOH HOH . I 3 HOH C 35 407 407 HOH HOH . I 3 HOH C 36 408 408 HOH HOH . I 3 HOH C 37 409 409 HOH HOH . I 3 HOH C 38 410 410 HOH HOH . I 3 HOH C 39 411 411 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 N N1 DCS . . . D 2 21.181 -22.601 -26.952 1 29.63 ? N1 DCS 372 A 1 HETATM 2 C C2 DCS . . . D 2 22.292 -21.758 -26.62 1 29.64 ? C2 DCS 372 A 1 HETATM 3 C C2A DCS . . . D 2 23.146 -21.125 -27.702 1 31.69 ? C2A DCS 372 A 1 HETATM 4 C C3 DCS . . . D 2 22.552 -21.538 -25.263 1 29.97 ? C3 DCS 372 A 1 HETATM 5 O O3 DCS . . . D 2 23.582 -20.759 -24.864 1 30.58 ? O3 DCS 372 A 1 HETATM 6 C C4 DCS . . . D 2 21.695 -22.171 -24.273 1 30.89 ? C4 DCS 372 A 1 HETATM 7 C C4A DCS . . . D 2 21.961 -21.935 -22.799 1 34.27 ? C4A DCS 372 A 1 HETATM 8 C C5 DCS . . . D 2 20.584 -23.013 -24.722 1 28.15 ? C5 DCS 372 A 1 HETATM 9 C C6 DCS . . . D 2 20.362 -23.205 -26.04 1 28.49 ? C6 DCS 372 A 1 HETATM 10 C C5A DCS . . . D 2 19.637 -23.705 -23.773 1 26.89 ? C5A DCS 372 A 1 HETATM 11 O O4P DCS . . . D 2 18.867 -22.711 -23.092 1 27.14 ? O4P DCS 372 A 1 HETATM 12 P P DCS . . . D 2 17.745 -23.002 -22 1 25.04 ? P DCS 372 A 1 HETATM 13 O O1P DCS . . . D 2 16.715 -23.779 -22.662 1 26.02 ? O1P DCS 372 A 1 HETATM 14 O O2P DCS . . . D 2 18.349 -23.723 -20.884 1 24.66 ? O2P DCS 372 A 1 HETATM 15 O O3P DCS . . . D 2 17.213 -21.715 -21.565 1 25.99 ? O3P DCS 372 A 1 HETATM 16 N N DCS . . . D 2 21.906 -20.451 -22.485 1 37.03 ? N DCS 372 A 1 HETATM 17 C CA DCS . . . D 2 22.121 -19.982 -21.181 1 37.37 ? CA DCS 372 A 1 HETATM 18 C C DCS . . . D 2 23.311 -19.349 -20.714 1 38.21 ? C DCS 372 A 1 HETATM 19 O O DCS . . . D 2 24.441 -19.13 -21.447 1 39.09 ? O DCS 372 A 1 HETATM 20 N ND DCS . . . D 2 23.138 -19.009 -19.46 1 37.84 ? ND DCS 372 A 1 HETATM 21 O OG DCS . . . D 2 21.873 -19.398 -19.07 1 37.75 ? OG DCS 372 A 1 HETATM 22 C CB DCS . . . D 2 21.262 -19.99 -20.118 1 38.26 ? CB DCS 372 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 22 #