data_2A5C # _model_server_result.job_id UCA_lDR4tDm23q8u-5G3bA _model_server_result.datetime_utc '2024-12-21 17:16:14' _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 2a5c # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 2A5C # _exptl.entry_id 2A5C _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 269.257 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 8-OXODEOXYADENOSINE _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 90 _cell.angle_gamma 90 _cell.entry_id 2A5C _cell.length_a 70.584 _cell.length_b 79.052 _cell.length_c 42.997 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2A5C _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 2_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 ? 3 D N N ? 3 F N 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 disulf ? disulf1 A SG CYS 4 A CYS 4 1_555 A SG CYS 83 A CYS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? disulf ? disulf2 B SG CYS 4 B CYS 4 1_555 B SG CYS 83 B CYS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? covale ? covale1 A ND2 ASN 17 A ASN 17 1_555 C C1 NAG . A NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale2 B ND2 ASN 17 B ASN 17 1_555 E C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? # _chem_comp.formula 'C10 H15 N5 O4' _chem_comp.formula_weight 269.257 _chem_comp.id 8DA _chem_comp.mon_nstd_flag . _chem_comp.name 8-OXODEOXYADENOSINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O19 C5' 8DA sing 1 n n O19 H19 8DA sing 2 n n C5' C4' 8DA sing 3 n n C5' "H5'1" 8DA sing 4 n n C5' "H5'2" 8DA sing 5 n n C4' C3' 8DA sing 6 n n C4' O4' 8DA sing 7 n n C4' H4' 8DA sing 8 n n C3' O3' 8DA sing 9 n n C3' C2' 8DA sing 10 n n C3' H3' 8DA sing 11 n n O3' H1 8DA sing 12 n n O4' C1' 8DA sing 13 n n C1' C2' 8DA sing 14 n n C1' N9 8DA sing 15 n n C1' H1' 8DA sing 16 n n C2' "H2'1" 8DA sing 17 n n C2' "H2'2" 8DA sing 18 n n N9 C4 8DA sing 19 n n N9 C8 8DA sing 20 n n C4 N3 8DA doub 21 n n C4 C5 8DA sing 22 n n N3 C2 8DA sing 23 n n C5 N7 8DA sing 24 n n C5 C6 8DA doub 25 n n N7 C8 8DA sing 26 n n N7 HN7 8DA sing 27 n n C8 O18 8DA doub 28 n n C6 N6 8DA sing 29 n n C6 N1 8DA sing 30 n n N6 HN61 8DA sing 31 n n N6 HN62 8DA sing 32 n n N1 C2 8DA sing 33 n n N1 HN1 8DA sing 34 n n C2 H21 8DA sing 35 n n C2 H22 8DA sing 36 n n # _atom_sites.entry_id 2A5C _atom_sites.fract_transf_matrix[1][1] 0.014168 _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] 0.01265 _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] 0.023257 _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 NAG A 1 302 302 NAG NAG . D 3 8DA A 1 303 101 8DA 8DA . E 2 NAG B 1 301 301 NAG NAG . F 3 8DA B 1 201 201 8DA 8DA . G 4 HOH A 1 304 2 HOH HOH . G 4 HOH A 2 305 3 HOH HOH . G 4 HOH A 3 306 4 HOH HOH . G 4 HOH A 4 307 5 HOH HOH . G 4 HOH A 5 308 7 HOH HOH . G 4 HOH A 6 309 8 HOH HOH . G 4 HOH A 7 310 11 HOH HOH . G 4 HOH A 8 311 12 HOH HOH . G 4 HOH A 9 312 13 HOH HOH . G 4 HOH A 10 313 14 HOH HOH . G 4 HOH A 11 314 16 HOH HOH . G 4 HOH A 12 315 19 HOH HOH . G 4 HOH A 13 316 21 HOH HOH . G 4 HOH A 14 317 22 HOH HOH . G 4 HOH A 15 318 25 HOH HOH . G 4 HOH A 16 319 26 HOH HOH . H 4 HOH B 1 302 1 HOH HOH . H 4 HOH B 2 303 6 HOH HOH . H 4 HOH B 3 304 9 HOH HOH . H 4 HOH B 4 305 10 HOH HOH . H 4 HOH B 5 306 15 HOH HOH . H 4 HOH B 6 307 17 HOH HOH . H 4 HOH B 7 308 18 HOH HOH . H 4 HOH B 8 309 20 HOH HOH . H 4 HOH B 9 310 23 HOH HOH . H 4 HOH B 10 311 24 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 O19 8DA . . . D 3 2.879 9.862 22.351 1 44.84 ? O19 8DA 303 A 1 HETATM 2 C C5' 8DA . . . D 3 1.574 10.107 21.832 1 50.97 ? C5' 8DA 303 A 1 HETATM 3 C C4' 8DA . . . D 3 1.209 11.604 21.87 1 54.94 ? C4' 8DA 303 A 1 HETATM 4 C C3' 8DA . . . D 3 -0.265 11.67 21.941 1 56.96 ? C3' 8DA 303 A 1 HETATM 5 O O3' 8DA . . . D 3 -0.355 12.911 21.26 1 58.59 ? O3' 8DA 303 A 1 HETATM 6 O O4' 8DA . . . D 3 1.631 12.242 23.074 1 58.64 ? O4' 8DA 303 A 1 HETATM 7 C C1' 8DA . . . D 3 0.566 12.6 23.959 1 58.48 ? C1' 8DA 303 A 1 HETATM 8 C C2' 8DA . . . D 3 -0.706 12.165 23.285 1 58.37 ? C2' 8DA 303 A 1 HETATM 9 N N9 8DA . . . D 3 0.711 12.126 25.364 1 58.44 ? N9 8DA 303 A 1 HETATM 10 C C4 8DA . . . D 3 1.63 11.352 25.941 1 57.84 ? C4 8DA 303 A 1 HETATM 11 N N3 8DA . . . D 3 2.773 10.707 25.352 1 56.66 ? N3 8DA 303 A 1 HETATM 12 C C5 8DA . . . D 3 1.353 11.209 27.389 1 59.78 ? C5 8DA 303 A 1 HETATM 13 N N7 8DA . . . D 3 0.222 11.922 27.641 1 58.53 ? N7 8DA 303 A 1 HETATM 14 C C8 8DA . . . D 3 -0.083 12.437 26.411 1 59.03 ? C8 8DA 303 A 1 HETATM 15 O O18 8DA . . . D 3 -1.121 13.186 26.247 1 59.88 ? O18 8DA 303 A 1 HETATM 16 C C6 8DA . . . D 3 2.262 10.401 28.111 1 59.69 ? C6 8DA 303 A 1 HETATM 17 N N6 8DA . . . D 3 2.049 10.23 29.443 1 58.63 ? N6 8DA 303 A 1 HETATM 18 N N1 8DA . . . D 3 3.336 9.807 27.489 1 58.41 ? N1 8DA 303 A 1 HETATM 19 C C2 8DA . . . D 3 3.574 9.973 26.162 1 58.58 ? C2 8DA 303 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 19 #