data_5CJU # _model_server_result.job_id Ud0DZNVjKImNS9zJ0IBOxQ _model_server_result.datetime_utc '2024-11-15 05:01:22' _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 5cju # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1102}' # _entry.id 5CJU # _exptl.entry_id 5CJU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 251.242 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-DEOXYADENOSINE" _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 120 _cell.entry_id 5CJU _cell.length_a 316.76 _cell.length_b 316.76 _cell.length_c 342.67 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CJU _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _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,H,I,J,K,L,M _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 3 _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 metalc ? metalc1 A NE2 HIS 59 A HIS 39 1_555 C CO B12 . A B12 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc2 A OG SER 243 A SER 223 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc3 A OD1 ASP 269 A ASP 249 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.695 ? metalc ? metalc4 A OD1 ASP 282 A ASP 262 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc5 A OE2 GLU 330 A GLU 310 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? metalc ? metalc6 A OE2 GLU 330 A GLU 310 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? metalc ? metalc7 A O THR 331 A THR 311 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? metalc ? metalc8 C CO B12 . A B12 1101 1_555 D C5' 5AD . A 5AD 1102 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.257 ? metalc ? metalc9 F O2B GDP . A GDP 1104 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc10 F O3B GDP . A GDP 1104 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc11 B NE2 HIS 59 B HIS 39 1_555 I CO B12 . B B12 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc12 B OG SER 243 B SER 223 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc13 B O ILE 268 B ILE 248 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? metalc ? metalc14 B OD1 ASP 269 B ASP 249 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.581 ? metalc ? metalc15 B OD1 ASP 282 B ASP 262 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc16 B OD2 ASP 282 B ASP 262 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.723 ? metalc ? metalc17 B OE2 GLU 330 B GLU 310 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc18 B OE2 GLU 330 B GLU 310 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.769 ? metalc ? metalc19 B O THR 331 B THR 311 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? metalc ? metalc20 K O2B GDP . B GDP 1103 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? metalc ? metalc21 K O3B GDP . B GDP 1103 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? # _chem_comp.formula 'C10 H13 N5 O3' _chem_comp.formula_weight 251.242 _chem_comp.id 5AD _chem_comp.mon_nstd_flag . _chem_comp.name "5'-DEOXYADENOSINE" _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 N1 C2 5AD doub 1 n y N1 C6 5AD sing 2 n y C2 N3 5AD sing 3 n y C2 H2 5AD sing 4 n n N3 C4 5AD doub 5 n y C4 N9 5AD sing 6 n y C4 C5 5AD sing 7 n y N9 C8 5AD sing 8 n y N9 C1' 5AD sing 9 n n C8 N7 5AD doub 10 n y C8 H8 5AD sing 11 n n N7 C5 5AD sing 12 n y C5 C6 5AD doub 13 n y C6 N6 5AD sing 14 n n N6 HN61 5AD sing 15 n n N6 HN62 5AD sing 16 n n C1' C2' 5AD sing 17 n n C1' O4' 5AD sing 18 n n C1' H1' 5AD sing 19 n n C2' C3' 5AD sing 20 n n C2' O2' 5AD sing 21 n n C2' H2' 5AD sing 22 n n C3' C4' 5AD sing 23 n n C3' O3' 5AD sing 24 n n C3' H3' 5AD sing 25 n n C4' C5' 5AD sing 26 n n C4' O4' 5AD sing 27 n n C4' H4' 5AD sing 28 n n C5' "H5'1" 5AD sing 29 n n C5' "H5'2" 5AD sing 30 n n C5' "H5'3" 5AD sing 31 n n O2' HO2' 5AD sing 32 n n O3' HO3' 5AD sing 33 n n # _atom_sites.entry_id 5CJU _atom_sites.fract_transf_matrix[1][1] 0.003157 _atom_sites.fract_transf_matrix[1][2] 0.001823 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003645 _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] 0.002918 _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 B12 A 1 1101 1198 B12 B12 . D 3 5AD A 1 1102 1199 5AD 5AD . E 4 BCO A 1 1103 1211 BCO BCO . F 5 GDP A 1 1104 1200 GDP GDP . G 6 MG A 1 1105 1 MG MG . H 6 MG A 1 1106 3 MG MG . I 2 B12 B 1 1101 1198 B12 B12 . J 4 BCO B 1 1102 1211 BCO BCO . K 5 GDP B 1 1103 1201 GDP GDP . L 6 MG B 1 1104 2 MG MG . M 6 MG B 1 1105 4 MG MG . # 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 5AD . A . D 3 -216.9 -102.961 -9.907 0.5 112.21 ? N1 5AD 1102 A 1 HETATM 2 N N1 5AD . B . D 3 -217.38 -102.194 -10.398 0.5 111.91 ? N1 5AD 1102 A 1 HETATM 3 C C2 5AD . A . D 3 -217.412 -102.096 -10.788 0.5 113.11 ? C2 5AD 1102 A 1 HETATM 4 C C2 5AD . B . D 3 -217.755 -101.125 -11.107 0.5 113.34 ? C2 5AD 1102 A 1 HETATM 5 N N3 5AD . A . D 3 -217.152 -100.793 -10.931 0.5 112.61 ? N3 5AD 1102 A 1 HETATM 6 N N3 5AD . B . D 3 -217.287 -99.876 -11.052 0.5 112.16 ? N3 5AD 1102 A 1 HETATM 7 C C4 5AD . A . D 3 -216.249 -100.381 -10.032 0.5 113.53 ? C4 5AD 1102 A 1 HETATM 8 C C4 5AD . B . D 3 -216.316 -99.767 -10.137 0.5 115.99 ? C4 5AD 1102 A 1 HETATM 9 N N9 5AD . A . D 3 -215.735 -99.116 -9.885 0.5 113.94 ? N9 5AD 1102 A 1 HETATM 10 N N9 5AD . B . D 3 -215.601 -98.64 -9.806 0.5 112.24 ? N9 5AD 1102 A 1 HETATM 11 C C8 5AD . A . D 3 -214.855 -99.194 -8.836 0.5 116.12 ? C8 5AD 1102 A 1 HETATM 12 C C8 5AD . B . D 3 -214.731 -99.029 -8.822 0.5 116.06 ? C8 5AD 1102 A 1 HETATM 13 N N7 5AD . A . D 3 -214.758 -100.389 -8.308 0.5 115.49 ? N7 5AD 1102 A 1 HETATM 14 N N7 5AD . B . D 3 -214.821 -100.296 -8.498 0.5 115.43 ? N7 5AD 1102 A 1 HETATM 15 C C5 5AD . A . D 3 -215.638 -101.154 -9.06 0.5 113.19 ? C5 5AD 1102 A 1 HETATM 16 C C5 5AD . B . D 3 -215.823 -100.777 -9.327 0.5 111.41 ? C5 5AD 1102 A 1 HETATM 17 C C6 5AD . A . D 3 -215.991 -102.516 -9.01 0.5 110.48 ? C6 5AD 1102 A 1 HETATM 18 C C6 5AD . B . D 3 -216.396 -102.054 -9.48 0.5 114.31 ? C6 5AD 1102 A 1 HETATM 19 N N6 5AD . A . D 3 -215.475 -103.386 -8.139 0.5 110.09 ? N6 5AD 1102 A 1 HETATM 20 N N6 5AD . B . D 3 -216.018 -103.126 -8.78 0.5 110.73 ? N6 5AD 1102 A 1 HETATM 21 C C1' 5AD . A . D 3 -216.042 -97.94 -10.692 0.5 115.09 ? C1' 5AD 1102 A 1 HETATM 22 C C1' 5AD . B . D 3 -215.737 -97.305 -10.379 0.5 116.93 ? C1' 5AD 1102 A 1 HETATM 23 C C2' 5AD . A . D 3 -217.144 -97.046 -10.107 0.5 115.17 ? C2' 5AD 1102 A 1 HETATM 24 C C2' 5AD . B . D 3 -216.822 -96.459 -9.707 0.5 115.57 ? C2' 5AD 1102 A 1 HETATM 25 C C3' 5AD . A . D 3 -216.342 -95.895 -9.499 0.5 116.08 ? C3' 5AD 1102 A 1 HETATM 26 C C3' 5AD . B . D 3 -216.189 -95.066 -9.697 0.5 115.36 ? C3' 5AD 1102 A 1 HETATM 27 C C4' 5AD . A . D 3 -215.159 -95.793 -10.451 0.5 116.23 ? C4' 5AD 1102 A 1 HETATM 28 C C4' 5AD . B . D 3 -214.705 -95.376 -9.53 0.5 115.38 ? C4' 5AD 1102 A 1 HETATM 29 C C5' 5AD . A . D 3 -213.916 -95.151 -9.883 0.5 114.14 ? C5' 5AD 1102 A 1 HETATM 30 C C5' 5AD . B . D 3 -214.221 -95.511 -8.106 0.5 115.68 ? C5' 5AD 1102 A 1 HETATM 31 O O4' 5AD . A . D 3 -214.865 -97.157 -10.811 0.5 114.22 ? O4' 5AD 1102 A 1 HETATM 32 O O4' 5AD . B . D 3 -214.504 -96.626 -10.22 0.5 114.56 ? O4' 5AD 1102 A 1 HETATM 33 O O2' 5AD . A . D 3 -218.022 -96.597 -11.134 0.5 115.69 ? O2' 5AD 1102 A 1 HETATM 34 O O2' 5AD . B . D 3 -218.019 -96.496 -10.475 0.5 115.75 ? O2' 5AD 1102 A 1 HETATM 35 O O3' 5AD . A . D 3 -217.065 -94.67 -9.519 0.5 116.94 ? O3' 5AD 1102 A 1 HETATM 36 O O3' 5AD . B . D 3 -216.397 -94.37 -10.92 0.5 115.95 ? O3' 5AD 1102 A 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #