data_9J1O # _model_server_result.job_id u2SnHLtxjQ-TNUisPXX1Pg _model_server_result.datetime_utc '2025-06-20 13:48:55' _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 9j1o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":101}' # _entry.id 9J1O # _exptl.entry_id 9J1O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 251.242 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol _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 90 _cell.entry_id 9J1O _cell.length_a 33.2 _cell.length_b 54.87 _cell.length_c 100.79 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9J1O _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,H,I _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 P DT 1 A DT 2 1_555 D O3' 3D1 . A 3D1 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.605 ? covale ? covale2 B P DC 1 B DC 2 1_555 E O3' THM . B THM 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.605 ? hydrog WATSON-CRICK hydrog1 A N3 DT 1 A DT 2 1_555 B N1 DA 15 B DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A O4 DT 1 A DT 2 1_555 B N6 DA 15 B DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A N1 DG 2 A DG 3 1_555 B N3 DC 14 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N2 DG 2 A DG 3 1_555 B O2 DC 14 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A O6 DG 2 A DG 3 1_555 B N4 DC 14 B DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N1 DA 3 A DA 4 1_555 B N3 DT 13 B DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N6 DA 3 A DA 4 1_555 B O4 DT 13 B DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N1 DA 4 A DA 5 1_555 B N3 DT 12 B DT 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N6 DA 4 A DA 5 1_555 B O4 DT 12 B DT 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DA 5 A DA 6 1_555 B N3 DT 11 B DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N6 DA 5 A DA 6 1_555 B O4 DT 11 B DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N1 DA 6 A DA 7 1_555 B N3 DT 10 B DT 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N6 DA 6 A DA 7 1_555 B O4 DT 10 B DT 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N1 DG 7 A DG 8 1_555 B N3 DC 9 B DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N2 DG 7 A DG 8 1_555 B O2 DC 9 B DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A O6 DG 7 A DG 8 1_555 B N4 DC 9 B DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N1 DG 8 A DG 9 1_555 B N3 DC 8 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N2 DG 8 A DG 9 1_555 B O2 DC 8 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O6 DG 8 A DG 9 1_555 B N4 DC 8 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N1 DG 9 A DG 10 1_555 B N3 DC 7 B DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N2 DG 9 A DG 10 1_555 B O2 DC 7 B DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A O6 DG 9 A DG 10 1_555 B N4 DC 7 B DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N1 DA 10 A DA 11 1_555 B N3 DT 6 B DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N6 DA 10 A DA 11 1_555 B O4 DT 6 B DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N1 DA 11 A DA 12 1_555 B N3 DT 5 B DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N6 DA 11 A DA 12 1_555 B O4 DT 5 B DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N3 DT 12 A DT 13 1_555 B N1 DA 4 B DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A O4 DT 12 A DT 13 1_555 B N6 DA 4 B DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A N3 DT 13 A DT 14 1_555 B N1 DA 3 B DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A O4 DT 13 A DT 14 1_555 B N6 DA 3 B DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A N1 DG 14 A DG 15 1_555 B N3 DC 2 B DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A N2 DG 14 A DG 15 1_555 B O2 DC 2 B DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 A O6 DG 14 A DG 15 1_555 B N4 DC 2 B DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 A N1 DG 15 A DG 16 1_555 B N3 DC 1 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 A N2 DG 15 A DG 16 1_555 B O2 DC 1 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 A O6 DG 15 A DG 16 1_555 B N4 DC 1 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H13 N5 O3' _chem_comp.formula_weight 251.242 _chem_comp.id 3D1 _chem_comp.mon_nstd_flag . _chem_comp.name (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2'-DEOXYADENOSINE" # 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 O5' C5' 3D1 sing 1 n n O5' H5' 3D1 sing 2 n n C5' C4' 3D1 sing 3 n n C5' "H5'1" 3D1 sing 4 n n C5' "H5'2" 3D1 sing 5 n n C4' O4' 3D1 sing 6 n n C4' C3' 3D1 sing 7 n n C4' H4' 3D1 sing 8 n n O4' C1' 3D1 sing 9 n n C1' N9 3D1 sing 10 n n C1' C2' 3D1 sing 11 n n C1' H1' 3D1 sing 12 n n N9 C4 3D1 sing 13 n y N9 C8 3D1 sing 14 n y C4 N3 3D1 doub 15 n y C4 C5 3D1 sing 16 n y N3 C2 3D1 sing 17 n y C2 N1 3D1 doub 18 n y C2 H2 3D1 sing 19 n n N1 C6 3D1 sing 20 n y C6 N6 3D1 sing 21 n n C6 C5 3D1 doub 22 n y N6 HN61 3D1 sing 23 n n N6 HN62 3D1 sing 24 n n C5 N7 3D1 sing 25 n y N7 C8 3D1 doub 26 n y C8 H8 3D1 sing 27 n n C2' C3' 3D1 sing 28 n n C2' "H2'1" 3D1 sing 29 n n C2' "H2'2" 3D1 sing 30 n n C3' O3' 3D1 sing 31 n n C3' H3' 3D1 sing 32 n n O3' H1 3D1 sing 33 n n # _atom_sites.entry_id 9J1O _atom_sites.fract_transf_matrix[1][1] 0.03012 _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] 0.018225 _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] 0.009922 _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 4 3D1 A 1 101 1 3D1 3D1 . E 5 THM B 1 101 1 THM THM . F 6 PG4 B 1 102 1 PG4 PG4 . G 7 HOH A 1 201 28 HOH HOH . G 7 HOH A 2 202 10 HOH HOH . G 7 HOH A 3 203 43 HOH HOH . G 7 HOH A 4 204 39 HOH HOH . G 7 HOH A 5 205 29 HOH HOH . G 7 HOH A 6 206 21 HOH HOH . G 7 HOH A 7 207 33 HOH HOH . G 7 HOH A 8 208 34 HOH HOH . H 7 HOH B 1 201 12 HOH HOH . H 7 HOH B 2 202 25 HOH HOH . H 7 HOH B 3 203 22 HOH HOH . H 7 HOH B 4 204 9 HOH HOH . H 7 HOH B 5 205 17 HOH HOH . H 7 HOH B 6 206 35 HOH HOH . H 7 HOH B 7 207 15 HOH HOH . H 7 HOH B 8 208 40 HOH HOH . H 7 HOH B 9 209 14 HOH HOH . H 7 HOH B 10 210 4 HOH HOH . H 7 HOH B 11 211 18 HOH HOH . H 7 HOH B 12 212 13 HOH HOH . H 7 HOH B 13 213 27 HOH HOH . H 7 HOH B 14 214 44 HOH HOH . I 7 HOH C 1 301 19 HOH HOH . I 7 HOH C 2 302 1 HOH HOH . I 7 HOH C 3 303 7 HOH HOH . I 7 HOH C 4 304 8 HOH HOH . I 7 HOH C 5 305 3 HOH HOH . I 7 HOH C 6 306 5 HOH HOH . I 7 HOH C 7 307 31 HOH HOH . I 7 HOH C 8 308 6 HOH HOH . I 7 HOH C 9 309 30 HOH HOH . I 7 HOH C 10 310 23 HOH HOH . I 7 HOH C 11 311 2 HOH HOH . I 7 HOH C 12 312 16 HOH HOH . I 7 HOH C 13 313 20 HOH HOH . I 7 HOH C 14 314 24 HOH HOH . I 7 HOH C 15 315 37 HOH HOH . I 7 HOH C 16 316 41 HOH HOH . I 7 HOH C 17 317 36 HOH HOH . I 7 HOH C 18 318 26 HOH HOH . I 7 HOH C 19 319 11 HOH HOH . I 7 HOH C 20 320 45 HOH HOH . I 7 HOH C 21 321 46 HOH HOH . I 7 HOH C 22 322 38 HOH HOH . I 7 HOH C 23 323 47 HOH HOH . I 7 HOH C 24 324 42 HOH HOH . I 7 HOH C 25 325 32 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 O5' 3D1 . . . D 4 -16.095 -0.03 42.979 1 65.26 ? O5' 3D1 101 A 1 HETATM 2 C C5' 3D1 . . . D 4 -16.755 0.655 41.922 1 57.7 ? C5' 3D1 101 A 1 HETATM 3 C C4' 3D1 . . . D 4 -15.872 1.729 41.332 1 55.7 ? C4' 3D1 101 A 1 HETATM 4 O O4' 3D1 . . . D 4 -14.674 1.136 40.793 1 63.41 ? O4' 3D1 101 A 1 HETATM 5 C C1' 3D1 . . . D 4 -14.832 0.949 39.382 1 54.6 ? C1' 3D1 101 A 1 HETATM 6 N N9 3D1 . . . D 4 -14.703 -0.48 39.082 1 53.86 ? N9 3D1 101 A 1 HETATM 7 C C4 3D1 . . . D 4 -15.654 -1.482 39.107 1 52.42 ? C4 3D1 101 A 1 HETATM 8 N N3 3D1 . . . D 4 -16.963 -1.374 39.384 1 51.79 ? N3 3D1 101 A 1 HETATM 9 C C2 3D1 . . . D 4 -17.571 -2.554 39.295 1 52.61 ? C2 3D1 101 A 1 HETATM 10 N N1 3D1 . . . D 4 -17.061 -3.752 38.985 1 50.56 ? N1 3D1 101 A 1 HETATM 11 C C6 3D1 . . . D 4 -15.738 -3.835 38.711 1 55.09 ? C6 3D1 101 A 1 HETATM 12 N N6 3D1 . . . D 4 -15.224 -5.02 38.397 1 54.82 ? N6 3D1 101 A 1 HETATM 13 C C5 3D1 . . . D 4 -14.986 -2.645 38.774 1 52.19 ? C5 3D1 101 A 1 HETATM 14 N N7 3D1 . . . D 4 -13.642 -2.385 38.554 1 53.19 ? N7 3D1 101 A 1 HETATM 15 C C8 3D1 . . . D 4 -13.521 -1.097 38.751 1 53.99 ? C8 3D1 101 A 1 HETATM 16 C C2' 3D1 . . . D 4 -16.17 1.565 38.992 1 53.88 ? C2' 3D1 101 A 1 HETATM 17 C C3' 3D1 . . . D 4 -16.485 2.49 40.166 1 56.94 ? C3' 3D1 101 A 1 HETATM 18 O O3' 3D1 . . . D 4 -15.838 3.75 40.028 1 56.58 ? O3' 3D1 101 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 34 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 432 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 18 #