data_3PHB # _model_server_result.job_id pg6NE2A8nPDcFCjj0Z6_Eg _model_server_result.datetime_utc '2024-11-07 16:34:16' _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 3phb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":292}' # _entry.id 3PHB # _exptl.entry_id 3PHB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 279.295 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.33 _cell.angle_gamma 90 _cell.entry_id 3PHB _cell.length_a 269.27 _cell.length_b 52.632 _cell.length_c 128.119 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PHB _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_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,B,F,G,H,I,J,K,L,U,V,W,X,Y,Z,DA 1 1 C,D,E,M,N,O,P,Q,R,S,T,AA,BA,CA 2 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 G N N ? 2 J N N ? 2 N N N ? 2 Q N N ? 2 S N N ? 2 W N N # _chem_comp.formula 'C12 H17 N5 O3' _chem_comp.formula_weight 279.295 _chem_comp.id IM5 _chem_comp.mon_nstd_flag . _chem_comp.name 2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DADMe-ImmG # 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 N1 IM5 sing 173 n n N1 C6 IM5 sing 174 n n N1 HN1 IM5 sing 175 n n N2 C2 IM5 sing 176 n n N3 C2 IM5 doub 177 n n N2 HN2 IM5 sing 178 n n N2 HN2A IM5 sing 179 n n N3 C4 IM5 sing 180 n n C9 C4 IM5 sing 181 n y C4 C5 IM5 doub 182 n y C5 N7 IM5 sing 183 n y C5 C6 IM5 sing 184 n n C6 O6 IM5 doub 185 n n C8 N7 IM5 sing 186 n y C9 C8 IM5 doub 187 n y C8 H8 IM5 sing 188 n n C10 C9 IM5 sing 189 n n C10 N1' IM5 sing 190 n n N1' C2' IM5 sing 191 n n N1' C6' IM5 sing 192 n n C10 H10 IM5 sing 193 n n C10 H10A IM5 sing 194 n n C2' C3' IM5 sing 195 n n C2' H2' IM5 sing 196 n n C2' "H2'A" IM5 sing 197 n n O3' C3' IM5 sing 198 n n C3' C4' IM5 sing 199 n n C3' H3' IM5 sing 200 n n O3' HO3' IM5 sing 201 n n C6' C4' IM5 sing 202 n n C4' C5' IM5 sing 203 n n C4' H4' IM5 sing 204 n n C5' O5' IM5 sing 205 n n C5' H5' IM5 sing 206 n n C5' "H5'A" IM5 sing 207 n n O5' HO5' IM5 sing 208 n n C6' H6' IM5 sing 209 n n C6' "H6'A" IM5 sing 210 n n N7 HN7 IM5 sing 211 n n # _atom_sites.entry_id 3PHB _atom_sites.fract_transf_matrix[1][1] 0.003714 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000021 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019 _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] 0.007805 _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 G 2 IM5 E 1 290 1 IM5 IM5 . H 3 PO4 E 1 291 2 PO4 PO4 . I 3 PO4 E 1 292 8 PO4 PO4 . J 2 IM5 Q 1 290 1 IM5 IM5 . K 3 PO4 Q 1 291 2 PO4 PO4 . L 3 PO4 Q 1 292 11 PO4 PO4 . M 3 PO4 S 1 290 9 PO4 PO4 . N 2 IM5 S 1 291 1 IM5 IM5 . O 3 PO4 S 1 292 2 PO4 PO4 . P 3 PO4 T 1 290 10 PO4 PO4 . Q 2 IM5 T 1 291 1 IM5 IM5 . R 3 PO4 T 1 292 2 PO4 PO4 . S 2 IM5 U 1 290 1 IM5 IM5 . T 3 PO4 U 1 291 2 PO4 PO4 . U 3 PO4 Y 1 290 7 PO4 PO4 . V 3 PO4 Y 1 291 12 PO4 PO4 . W 2 IM5 Y 1 292 1 IM5 IM5 . X 3 PO4 Y 1 293 2 PO4 PO4 . Y 4 HOH E 1 293 6 HOH HOH . Y 4 HOH E 2 294 8 HOH HOH . Y 4 HOH E 3 295 15 HOH HOH . Y 4 HOH E 4 296 16 HOH HOH . Y 4 HOH E 5 297 38 HOH HOH . Y 4 HOH E 6 298 50 HOH HOH . Y 4 HOH E 7 299 58 HOH HOH . Y 4 HOH E 8 300 63 HOH HOH . Y 4 HOH E 9 301 64 HOH HOH . Y 4 HOH E 10 302 65 HOH HOH . Y 4 HOH E 11 303 66 HOH HOH . Y 4 HOH E 12 304 67 HOH HOH . Y 4 HOH E 13 305 69 HOH HOH . Y 4 HOH E 14 306 70 HOH HOH . Y 4 HOH E 15 307 71 HOH HOH . Y 4 HOH E 16 308 79 HOH HOH . Z 4 HOH Q 1 293 7 HOH HOH . Z 4 HOH Q 2 294 12 HOH HOH . Z 4 HOH Q 3 295 18 HOH HOH . Z 4 HOH Q 4 296 20 HOH HOH . Z 4 HOH Q 5 297 22 HOH HOH . Z 4 HOH Q 6 298 26 HOH HOH . Z 4 HOH Q 7 299 28 HOH HOH . Z 4 HOH Q 8 300 32 HOH HOH . Z 4 HOH Q 9 301 44 HOH HOH . Z 4 HOH Q 10 302 48 HOH HOH . Z 4 HOH Q 11 303 52 HOH HOH . Z 4 HOH Q 12 304 53 HOH HOH . Z 4 HOH Q 13 305 72 HOH HOH . Z 4 HOH Q 14 306 73 HOH HOH . Z 4 HOH Q 15 307 75 HOH HOH . Z 4 HOH Q 16 308 76 HOH HOH . Z 4 HOH Q 17 309 77 HOH HOH . Z 4 HOH Q 18 310 78 HOH HOH . AA 4 HOH S 1 293 1 HOH HOH . AA 4 HOH S 2 294 23 HOH HOH . AA 4 HOH S 3 295 27 HOH HOH . AA 4 HOH S 4 296 30 HOH HOH . AA 4 HOH S 5 297 34 HOH HOH . AA 4 HOH S 6 298 35 HOH HOH . AA 4 HOH S 7 299 43 HOH HOH . AA 4 HOH S 8 300 45 HOH HOH . AA 4 HOH S 9 301 54 HOH HOH . AA 4 HOH S 10 302 60 HOH HOH . AA 4 HOH S 11 303 61 HOH HOH . AA 4 HOH S 12 304 80 HOH HOH . AA 4 HOH S 13 305 81 HOH HOH . AA 4 HOH S 14 306 82 HOH HOH . AA 4 HOH S 15 307 92 HOH HOH . BA 4 HOH T 1 293 5 HOH HOH . BA 4 HOH T 2 294 17 HOH HOH . BA 4 HOH T 3 295 21 HOH HOH . BA 4 HOH T 4 296 24 HOH HOH . BA 4 HOH T 5 297 33 HOH HOH . BA 4 HOH T 6 298 36 HOH HOH . BA 4 HOH T 7 299 51 HOH HOH . BA 4 HOH T 8 300 55 HOH HOH . BA 4 HOH T 9 301 83 HOH HOH . BA 4 HOH T 10 302 93 HOH HOH . CA 4 HOH U 1 292 3 HOH HOH . CA 4 HOH U 2 293 9 HOH HOH . CA 4 HOH U 3 294 10 HOH HOH . CA 4 HOH U 4 295 11 HOH HOH . CA 4 HOH U 5 296 31 HOH HOH . CA 4 HOH U 6 297 37 HOH HOH . CA 4 HOH U 7 298 40 HOH HOH . CA 4 HOH U 8 299 41 HOH HOH . CA 4 HOH U 9 300 42 HOH HOH . CA 4 HOH U 10 301 47 HOH HOH . CA 4 HOH U 11 302 56 HOH HOH . CA 4 HOH U 12 303 84 HOH HOH . CA 4 HOH U 13 304 85 HOH HOH . DA 4 HOH Y 1 294 2 HOH HOH . DA 4 HOH Y 2 295 4 HOH HOH . DA 4 HOH Y 3 296 13 HOH HOH . DA 4 HOH Y 4 297 19 HOH HOH . DA 4 HOH Y 5 298 25 HOH HOH . DA 4 HOH Y 6 299 29 HOH HOH . DA 4 HOH Y 7 300 49 HOH HOH . DA 4 HOH Y 8 301 57 HOH HOH . DA 4 HOH Y 9 302 59 HOH HOH . DA 4 HOH Y 10 303 68 HOH HOH . DA 4 HOH Y 11 304 74 HOH HOH . DA 4 HOH Y 12 305 87 HOH HOH . DA 4 HOH Y 13 306 88 HOH HOH . DA 4 HOH Y 14 307 89 HOH HOH . DA 4 HOH Y 15 308 90 HOH HOH . DA 4 HOH Y 16 309 91 HOH HOH . DA 4 HOH Y 17 310 94 HOH HOH . DA 4 HOH Y 18 311 95 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 IM5 . . . W 2 -14.26 8.908 -5.387 1 39.48 ? N1 IM5 292 Y 1 HETATM 2 C C2 IM5 . . . W 2 -14.803 7.783 -4.869 1 35.44 ? C2 IM5 292 Y 1 HETATM 3 N N2 IM5 . . . W 2 -15.762 7.142 -5.544 1 35.31 ? N2 IM5 292 Y 1 HETATM 4 N N3 IM5 . . . W 2 -14.418 7.258 -3.703 1 35.11 ? N3 IM5 292 Y 1 HETATM 5 C C4 IM5 . . . W 2 -13.457 7.875 -3.014 1 35.99 ? C4 IM5 292 Y 1 HETATM 6 C C5 IM5 . . . W 2 -12.801 9.104 -3.467 1 36.38 ? C5 IM5 292 Y 1 HETATM 7 C C6 IM5 . . . W 2 -13.284 9.611 -4.776 1 37.61 ? C6 IM5 292 Y 1 HETATM 8 O O6 IM5 . . . W 2 -12.831 10.642 -5.312 1 37.36 ? O6 IM5 292 Y 1 HETATM 9 N N7 IM5 . . . W 2 -11.907 9.431 -2.52 1 34.52 ? N7 IM5 292 Y 1 HETATM 10 C C8 IM5 . . . W 2 -11.93 8.524 -1.496 1 35.41 ? C8 IM5 292 Y 1 HETATM 11 C C9 IM5 . . . W 2 -12.867 7.507 -1.729 1 36.18 ? C9 IM5 292 Y 1 HETATM 12 N N1' IM5 . . . W 2 -12.581 5.08 -1.1 1 36.56 ? N1' IM5 292 Y 1 HETATM 13 C C10 IM5 . . . W 2 -13.27 6.339 -0.857 1 36.06 ? C10 IM5 292 Y 1 HETATM 14 C C2' IM5 . . . W 2 -13.252 4.358 -2.183 1 34.33 ? C2' IM5 292 Y 1 HETATM 15 C C3' IM5 . . . W 2 -12.186 3.367 -2.616 1 37.53 ? C3' IM5 292 Y 1 HETATM 16 O O3' IM5 . . . W 2 -12.337 2.114 -1.961 1 35.15 ? O3' IM5 292 Y 1 HETATM 17 C C4' IM5 . . . W 2 -10.856 3.98 -2.225 1 37.34 ? C4' IM5 292 Y 1 HETATM 18 C C5' IM5 . . . W 2 -10.058 4.247 -3.474 1 38.94 ? C5' IM5 292 Y 1 HETATM 19 O O5' IM5 . . . W 2 -8.947 5.045 -3.108 1 41.73 ? O5' IM5 292 Y 1 HETATM 20 C C6' IM5 . . . W 2 -11.18 5.274 -1.497 1 35.87 ? C6' IM5 292 Y 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 24 _model_server_stats.element_count 20 #