data_3DP9 # _model_server_result.job_id 8vumNr4bqnhuFZ8TV9y2fg _model_server_result.datetime_utc '2024-11-25 11:25:56' _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 3dp9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 3DP9 # _exptl.entry_id 3DP9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 335.468 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(butylsulfanyl)methyl]pyrrolidin-3-ol _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 115.35 _cell.angle_gamma 90 _cell.entry_id 3DP9 _cell.length_a 67.738 _cell.length_b 54.332 _cell.length_c 69.786 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DP9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N N # _chem_comp.formula 'C16 H25 N5 O S' _chem_comp.formula_weight 335.468 _chem_comp.id BIG _chem_comp.mon_nstd_flag . _chem_comp.name (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(butylsulfanyl)methyl]pyrrolidin-3-ol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'butylthio-DADMe-Immucillin A' # 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 C2 N3 BIG doub 70 n y C2 N1 BIG sing 71 n y C5 C4 BIG doub 72 n y C5 N7 BIG sing 73 n y C5 C6 BIG sing 74 n y C4 N3 BIG sing 75 n y C4 C9 BIG sing 76 n y C8 N7 BIG sing 77 n y C8 C9 BIG doub 78 n y O3' C3' BIG sing 79 n n C3' C4' BIG sing 80 n n C3' C2' BIG sing 81 n n C4' C5' BIG sing 82 n n C4' C1' BIG sing 83 n n C5' S5' BIG sing 84 n n S5' C20 BIG sing 85 n n C20 C21 BIG sing 86 n n C21 C22 BIG sing 87 n n C22 C23 BIG sing 88 n n C1' N1' BIG sing 89 n n N1' C2' BIG sing 90 n n N1' C10 BIG sing 91 n n C10 C9 BIG sing 92 n n C6 N6 BIG sing 93 n n C6 N1 BIG doub 94 n y C2 H2 BIG sing 95 n n C8 H8 BIG sing 96 n n O3' HO3' BIG sing 97 n n C3' H3' BIG sing 98 n n C4' H4' BIG sing 99 n n C5' H5' BIG sing 100 n n C5' "H5'A" BIG sing 101 n n C20 H20 BIG sing 102 n n C20 H20A BIG sing 103 n n C21 H21 BIG sing 104 n n C21 H21A BIG sing 105 n n C22 H22 BIG sing 106 n n C22 H22A BIG sing 107 n n C23 H23 BIG sing 108 n n C23 H23A BIG sing 109 n n C23 H23B BIG sing 110 n n C1' H1' BIG sing 111 n n C1' "H1'A" BIG sing 112 n n C2' H2' BIG sing 113 n n C2' "H2'A" BIG sing 114 n n C10 H10 BIG sing 115 n n C10 H10A BIG sing 116 n n N7 HN7 BIG sing 117 n n N6 HN6 BIG sing 118 n n N6 HN6A BIG sing 119 n n # _atom_sites.entry_id 3DP9 _atom_sites.fract_transf_matrix[1][1] 0.014763 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006994 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018405 _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] 0.015856 _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 BIG A 1 301 301 BIG BIG . D 3 IOD C 1 300 300 IOD IOD . E 2 BIG C 1 301 301 BIG BIG . F 4 HOH A 1 302 2 HOH HOH . F 4 HOH A 2 303 4 HOH HOH . F 4 HOH A 3 304 5 HOH HOH . F 4 HOH A 4 305 6 HOH HOH . F 4 HOH A 5 306 8 HOH HOH . F 4 HOH A 6 307 9 HOH HOH . F 4 HOH A 7 308 10 HOH HOH . F 4 HOH A 8 309 11 HOH HOH . F 4 HOH A 9 310 13 HOH HOH . F 4 HOH A 10 311 14 HOH HOH . F 4 HOH A 11 312 15 HOH HOH . F 4 HOH A 12 313 16 HOH HOH . F 4 HOH A 13 314 17 HOH HOH . F 4 HOH A 14 315 18 HOH HOH . F 4 HOH A 15 316 22 HOH HOH . F 4 HOH A 16 317 27 HOH HOH . F 4 HOH A 17 318 28 HOH HOH . F 4 HOH A 18 319 29 HOH HOH . F 4 HOH A 19 320 30 HOH HOH . F 4 HOH A 20 321 32 HOH HOH . F 4 HOH A 21 322 33 HOH HOH . F 4 HOH A 22 323 35 HOH HOH . F 4 HOH A 23 324 38 HOH HOH . F 4 HOH A 24 325 39 HOH HOH . F 4 HOH A 25 326 40 HOH HOH . F 4 HOH A 26 327 41 HOH HOH . F 4 HOH A 27 328 44 HOH HOH . F 4 HOH A 28 329 45 HOH HOH . F 4 HOH A 29 330 46 HOH HOH . F 4 HOH A 30 331 47 HOH HOH . F 4 HOH A 31 332 49 HOH HOH . F 4 HOH A 32 333 50 HOH HOH . F 4 HOH A 33 334 51 HOH HOH . F 4 HOH A 34 335 59 HOH HOH . F 4 HOH A 35 336 60 HOH HOH . F 4 HOH A 36 337 61 HOH HOH . F 4 HOH A 37 338 63 HOH HOH . F 4 HOH A 38 339 65 HOH HOH . G 4 HOH C 1 302 1 HOH HOH . G 4 HOH C 2 303 3 HOH HOH . G 4 HOH C 3 304 7 HOH HOH . G 4 HOH C 4 305 12 HOH HOH . G 4 HOH C 5 306 19 HOH HOH . G 4 HOH C 6 307 20 HOH HOH . G 4 HOH C 7 308 21 HOH HOH . G 4 HOH C 8 309 23 HOH HOH . G 4 HOH C 9 310 24 HOH HOH . G 4 HOH C 10 311 25 HOH HOH . G 4 HOH C 11 312 26 HOH HOH . G 4 HOH C 12 313 31 HOH HOH . G 4 HOH C 13 314 34 HOH HOH . G 4 HOH C 14 315 36 HOH HOH . G 4 HOH C 15 316 37 HOH HOH . G 4 HOH C 16 317 42 HOH HOH . G 4 HOH C 17 318 43 HOH HOH . G 4 HOH C 18 319 48 HOH HOH . G 4 HOH C 19 320 52 HOH HOH . G 4 HOH C 20 321 53 HOH HOH . G 4 HOH C 21 322 54 HOH HOH . G 4 HOH C 22 323 55 HOH HOH . G 4 HOH C 23 324 56 HOH HOH . G 4 HOH C 24 325 57 HOH HOH . G 4 HOH C 25 326 58 HOH HOH . G 4 HOH C 26 327 62 HOH HOH . G 4 HOH C 27 328 64 HOH HOH . G 4 HOH C 28 329 66 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 C2 BIG . . . C 2 -1.321 -4.128 5.295 1 23.76 ? C2 BIG 301 A 1 HETATM 2 C C5 BIG . . . C 2 -3.934 -3.464 4.593 1 26.1 ? C5 BIG 301 A 1 HETATM 3 C C4 BIG . . . C 2 -3.235 -2.914 5.756 1 27.28 ? C4 BIG 301 A 1 HETATM 4 C C8 BIG . . . C 2 -5.326 -2.046 5.613 1 27.62 ? C8 BIG 301 A 1 HETATM 5 O O3' BIG . . . C 2 -1.263 2.082 8.214 1 28.08 ? O3' BIG 301 A 1 HETATM 6 C C3' BIG . . . C 2 -1.219 1.114 7.158 1 30.03 ? C3' BIG 301 A 1 HETATM 7 C C4' BIG . . . C 2 -2.117 1.51 5.992 1 30.33 ? C4' BIG 301 A 1 HETATM 8 C C5' BIG . . . C 2 -1.644 0.896 4.676 1 30.2 ? C5' BIG 301 A 1 HETATM 9 S S5' BIG . . . C 2 -0.393 1.862 3.883 1 31.5 ? S5' BIG 301 A 1 HETATM 10 C C20 BIG . . . C 2 -1.338 3.108 3.054 1 32.38 ? C20 BIG 301 A 1 HETATM 11 C C21 BIG . . . C 2 -0.402 4.151 2.453 1 36.02 ? C21 BIG 301 A 1 HETATM 12 C C22 BIG . . . C 2 -1.135 5.457 2.161 1 37.7 ? C22 BIG 301 A 1 HETATM 13 C C23 BIG . . . C 2 -0.977 5.826 0.704 1 38.46 ? C23 BIG 301 A 1 HETATM 14 C C1' BIG . . . C 2 -3.459 0.879 6.322 1 30.28 ? C1' BIG 301 A 1 HETATM 15 N N1' BIG . . . C 2 -3.255 0.114 7.571 1 29.54 ? N1' BIG 301 A 1 HETATM 16 C C2' BIG . . . C 2 -1.825 -0.155 7.709 1 28.55 ? C2' BIG 301 A 1 HETATM 17 C C10 BIG . . . C 2 -3.975 -1.176 7.647 1 28.74 ? C10 BIG 301 A 1 HETATM 18 N N7 BIG . . . C 2 -5.158 -2.903 4.555 1 27.13 ? N7 BIG 301 A 1 HETATM 19 C C6 BIG . . . C 2 -3.159 -4.431 3.79 1 25.68 ? C6 BIG 301 A 1 HETATM 20 N N6 BIG . . . C 2 -3.684 -5.023 2.689 1 25.34 ? N6 BIG 301 A 1 HETATM 21 N N3 BIG . . . C 2 -1.962 -3.258 6.082 1 25.46 ? N3 BIG 301 A 1 HETATM 22 C C9 BIG . . . C 2 -4.176 -1.981 6.396 1 27.6 ? C9 BIG 301 A 1 HETATM 23 N N1 BIG . . . C 2 -1.892 -4.695 4.204 1 25.33 ? N1 BIG 301 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 23 #