data_8SWR # _model_server_result.job_id ylnD93JhZ5-lKzKXnEbdSA _model_server_result.datetime_utc '2024-11-05 19:47:01' _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 8swr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":400}' # _entry.id 8SWR # _exptl.entry_id 8SWR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 279.295 _entity.id 2 _entity.src_method nat _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 108.3 _cell.angle_gamma 90 _cell.entry_id 8SWR _cell.length_a 89.43 _cell.length_b 111.005 _cell.length_c 97.87 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8SWR _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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,C,G,H,I,M,N,O 1 1 D,E,F,J,K,L,P,Q,R 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 I N N ? 2 J 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 190 n n N1 C6 IM5 sing 191 n n N1 HN1 IM5 sing 192 n n N2 C2 IM5 sing 193 n n N3 C2 IM5 doub 194 n n N2 HN2 IM5 sing 195 n n N2 HN2A IM5 sing 196 n n N3 C4 IM5 sing 197 n n C9 C4 IM5 sing 198 n y C4 C5 IM5 doub 199 n y C5 N7 IM5 sing 200 n y C5 C6 IM5 sing 201 n n C6 O6 IM5 doub 202 n n C8 N7 IM5 sing 203 n y C9 C8 IM5 doub 204 n y C8 H8 IM5 sing 205 n n C10 C9 IM5 sing 206 n n C10 N1' IM5 sing 207 n n N1' C2' IM5 sing 208 n n N1' C6' IM5 sing 209 n n C10 H10 IM5 sing 210 n n C10 H10A IM5 sing 211 n n C2' C3' IM5 sing 212 n n C2' H2' IM5 sing 213 n n C2' "H2'A" IM5 sing 214 n n O3' C3' IM5 sing 215 n n C3' C4' IM5 sing 216 n n C3' H3' IM5 sing 217 n n O3' HO3' IM5 sing 218 n n C6' C4' IM5 sing 219 n n C4' C5' IM5 sing 220 n n C4' H4' IM5 sing 221 n n C5' O5' IM5 sing 222 n n C5' H5' IM5 sing 223 n n C5' "H5'A" IM5 sing 224 n n O5' HO5' IM5 sing 225 n n C6' H6' IM5 sing 226 n n C6' "H6'A" IM5 sing 227 n n N7 HN7 IM5 sing 228 n n # _atom_sites.entry_id 8SWR _atom_sites.fract_transf_matrix[1][1] 0.011182 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003698 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009009 _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] 0.010762 _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 A 1 400 400 IM5 IM5 . H 3 SO4 A 1 401 401 SO4 SO4 . I 2 IM5 B 1 400 400 IM5 IM5 . J 2 IM5 D 1 400 400 IM5 IM5 . K 3 SO4 D 1 401 401 SO4 SO4 . L 4 GUN E 1 400 400 GUN GUN . M 5 HOH A 1 501 12 HOH HOH . M 5 HOH A 2 502 40 HOH HOH . M 5 HOH A 3 503 45 HOH HOH . M 5 HOH A 4 504 11 HOH HOH . M 5 HOH A 5 505 97 HOH HOH . M 5 HOH A 6 506 3 HOH HOH . M 5 HOH A 7 507 15 HOH HOH . M 5 HOH A 8 508 23 HOH HOH . M 5 HOH A 9 509 96 HOH HOH . M 5 HOH A 10 510 10 HOH HOH . M 5 HOH A 11 511 99 HOH HOH . M 5 HOH A 12 512 54 HOH HOH . M 5 HOH A 13 513 25 HOH HOH . M 5 HOH A 14 514 29 HOH HOH . M 5 HOH A 15 515 95 HOH HOH . M 5 HOH A 16 516 34 HOH HOH . M 5 HOH A 17 517 39 HOH HOH . M 5 HOH A 18 518 87 HOH HOH . M 5 HOH A 19 519 75 HOH HOH . M 5 HOH A 20 520 35 HOH HOH . M 5 HOH A 21 521 60 HOH HOH . M 5 HOH A 22 522 80 HOH HOH . M 5 HOH A 23 523 98 HOH HOH . N 5 HOH B 1 501 66 HOH HOH . N 5 HOH B 2 502 38 HOH HOH . N 5 HOH B 3 503 79 HOH HOH . N 5 HOH B 4 504 14 HOH HOH . N 5 HOH B 5 505 42 HOH HOH . N 5 HOH B 6 506 69 HOH HOH . N 5 HOH B 7 507 86 HOH HOH . N 5 HOH B 8 508 85 HOH HOH . N 5 HOH B 9 509 61 HOH HOH . N 5 HOH B 10 510 63 HOH HOH . N 5 HOH B 11 511 9 HOH HOH . N 5 HOH B 12 512 76 HOH HOH . N 5 HOH B 13 513 74 HOH HOH . N 5 HOH B 14 514 50 HOH HOH . N 5 HOH B 15 515 88 HOH HOH . O 5 HOH C 1 401 81 HOH HOH . O 5 HOH C 2 402 46 HOH HOH . O 5 HOH C 3 403 78 HOH HOH . O 5 HOH C 4 404 82 HOH HOH . O 5 HOH C 5 405 53 HOH HOH . O 5 HOH C 6 406 28 HOH HOH . O 5 HOH C 7 407 36 HOH HOH . P 5 HOH D 1 501 51 HOH HOH . P 5 HOH D 2 502 33 HOH HOH . P 5 HOH D 3 503 65 HOH HOH . P 5 HOH D 4 504 2 HOH HOH . P 5 HOH D 5 505 91 HOH HOH . P 5 HOH D 6 506 19 HOH HOH . P 5 HOH D 7 507 32 HOH HOH . P 5 HOH D 8 508 13 HOH HOH . P 5 HOH D 9 509 30 HOH HOH . P 5 HOH D 10 510 83 HOH HOH . P 5 HOH D 11 511 20 HOH HOH . P 5 HOH D 12 512 21 HOH HOH . P 5 HOH D 13 513 64 HOH HOH . P 5 HOH D 14 514 100 HOH HOH . P 5 HOH D 15 515 59 HOH HOH . P 5 HOH D 16 516 26 HOH HOH . P 5 HOH D 17 517 101 HOH HOH . P 5 HOH D 18 518 90 HOH HOH . P 5 HOH D 19 519 93 HOH HOH . P 5 HOH D 20 520 92 HOH HOH . P 5 HOH D 21 521 77 HOH HOH . Q 5 HOH E 1 501 24 HOH HOH . Q 5 HOH E 2 502 47 HOH HOH . Q 5 HOH E 3 503 72 HOH HOH . Q 5 HOH E 4 504 67 HOH HOH . Q 5 HOH E 5 505 89 HOH HOH . Q 5 HOH E 6 506 73 HOH HOH . Q 5 HOH E 7 507 68 HOH HOH . Q 5 HOH E 8 508 31 HOH HOH . Q 5 HOH E 9 509 27 HOH HOH . R 5 HOH F 1 401 84 HOH HOH . R 5 HOH F 2 402 17 HOH HOH . R 5 HOH F 3 403 1 HOH HOH . R 5 HOH F 4 404 22 HOH HOH . R 5 HOH F 5 405 70 HOH HOH . R 5 HOH F 6 406 71 HOH HOH . R 5 HOH F 7 407 52 HOH HOH . R 5 HOH F 8 408 37 HOH HOH . R 5 HOH F 9 409 18 HOH HOH . R 5 HOH F 10 410 7 HOH HOH . R 5 HOH F 11 411 6 HOH HOH . R 5 HOH F 12 412 44 HOH HOH . R 5 HOH F 13 413 62 HOH HOH . R 5 HOH F 14 414 16 HOH HOH . R 5 HOH F 15 415 41 HOH HOH . R 5 HOH F 16 416 43 HOH HOH . R 5 HOH F 17 417 4 HOH HOH . R 5 HOH F 18 418 57 HOH HOH . R 5 HOH F 19 419 5 HOH HOH . R 5 HOH F 20 420 8 HOH HOH . R 5 HOH F 21 421 49 HOH HOH . R 5 HOH F 22 422 56 HOH HOH . R 5 HOH F 23 423 48 HOH HOH . R 5 HOH F 24 424 55 HOH HOH . R 5 HOH F 25 425 94 HOH HOH . R 5 HOH F 26 426 58 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 . . . G 2 73.534 19.826 196.211 1 45.72 ? N1 IM5 400 A 1 HETATM 2 C C2 IM5 . . . G 2 74.183 18.623 196.307 1 46.31 ? C2 IM5 400 A 1 HETATM 3 N N2 IM5 . . . G 2 75.509 18.627 196.133 1 50.11 ? N2 IM5 400 A 1 HETATM 4 N N3 IM5 . . . G 2 73.55 17.5 196.563 1 47.52 ? N3 IM5 400 A 1 HETATM 5 C C4 IM5 . . . G 2 72.202 17.567 196.726 1 44.91 ? C4 IM5 400 A 1 HETATM 6 C C5 IM5 . . . G 2 71.491 18.768 196.639 1 43.33 ? C5 IM5 400 A 1 HETATM 7 C C6 IM5 . . . G 2 72.164 19.991 196.364 1 44.7 ? C6 IM5 400 A 1 HETATM 8 O O6 IM5 . . . G 2 71.659 21.112 196.259 1 49.46 ? O6 IM5 400 A 1 HETATM 9 N N7 IM5 . . . G 2 70.172 18.464 196.857 1 45.69 ? N7 IM5 400 A 1 HETATM 10 C C8 IM5 . . . G 2 70.066 17.12 197.074 1 48.68 ? C8 IM5 400 A 1 HETATM 11 C C9 IM5 . . . G 2 71.306 16.559 197.006 1 48.48 ? C9 IM5 400 A 1 HETATM 12 N N1' IM5 . . . G 2 71.992 14.71 198.527 1 60.79 ? N1' IM5 400 A 1 HETATM 13 C C10 IM5 . . . G 2 71.67 15.115 197.158 1 53.16 ? C10 IM5 400 A 1 HETATM 14 C C2' IM5 . . . G 2 72.739 15.715 199.292 0.52 56.6 ? C2' IM5 400 A 1 HETATM 15 C C3' IM5 . . . G 2 72.687 15.137 200.675 0.33 59.18 ? C3' IM5 400 A 1 HETATM 16 O O3' IM5 . . . G 2 73.563 14.026 200.794 0.69 61.9 ? O3' IM5 400 A 1 HETATM 17 C C4' IM5 . . . G 2 71.21 14.74 200.795 1 64.9 ? C4' IM5 400 A 1 HETATM 18 C C5' IM5 . . . G 2 70.346 15.816 201.423 1 58.6 ? C5' IM5 400 A 1 HETATM 19 O O5' IM5 . . . G 2 71.117 16.756 202.153 1 73.87 ? O5' IM5 400 A 1 HETATM 20 C C6' IM5 . . . G 2 70.802 14.429 199.353 0.63 61.77 ? C6' IM5 400 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #