data_5CJV # _model_server_result.job_id -gjJb_6ooVcj6278OmsplA _model_server_result.datetime_utc '2024-11-24 11:58:21' _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 5cjv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1102}' # _entry.id 5CJV # _exptl.entry_id 5CJV _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 5CJV _cell.length_a 317.56 _cell.length_b 317.56 _cell.length_c 343.52 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CJV _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc2 A OG SER 243 A SER 223 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc3 A OD1 ASP 269 A ASP 249 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc4 A OD1 ASP 282 A ASP 262 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc5 A OD1 ASP 282 A ASP 262 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? metalc ? metalc6 A OE2 GLU 330 A GLU 310 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? metalc ? metalc7 A OE2 GLU 330 A GLU 310 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.629 ? metalc ? metalc8 A O THR 331 A THR 311 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? metalc ? metalc9 C CO B12 . A B12 1101 1_555 D C5' 5AD . A 5AD 1102 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.181 ? metalc ? metalc10 F O2B GDP . A GDP 1104 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc11 F O3B GDP . A GDP 1104 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc12 B NE2 HIS 59 B HIS 39 1_555 I CO B12 . B B12 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc13 B OG SER 243 B SER 223 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc14 B O ILE 268 B ILE 248 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.95 ? metalc ? metalc15 B OD1 ASP 269 B ASP 249 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc16 B OD1 ASP 282 B ASP 262 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc17 B OD1 ASP 282 B ASP 262 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? metalc ? metalc18 B OD2 ASP 282 B ASP 262 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? metalc ? metalc19 B OE2 GLU 330 B GLU 310 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc20 B OE2 GLU 330 B GLU 310 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? metalc ? metalc21 B O THR 331 B THR 311 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? metalc ? metalc22 K O2B GDP . B GDP 1103 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc23 K O3B GDP . B GDP 1103 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? # _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 5CJV _atom_sites.fract_transf_matrix[1][1] 0.003149 _atom_sites.fract_transf_matrix[1][2] 0.001818 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003636 _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] 0.002911 _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 IVC A 1 1103 1211 IVC IVC . 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 IVC B 1 1102 1211 IVC IVC . 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 -217.642 -103.141 -10.352 0.5 110.24 ? N1 5AD 1102 A 1 HETATM 2 N N1 5AD . B . D 3 -217.843 -102.443 -10.559 0.5 110.57 ? N1 5AD 1102 A 1 HETATM 3 C C2 5AD . A . D 3 -218.057 -102.141 -11.135 0.5 111.04 ? C2 5AD 1102 A 1 HETATM 4 C C2 5AD . B . D 3 -218.204 -101.364 -11.26 0.5 110.95 ? C2 5AD 1102 A 1 HETATM 5 N N3 5AD . A . D 3 -217.704 -100.854 -11.109 0.5 111.21 ? N3 5AD 1102 A 1 HETATM 6 N N3 5AD . B . D 3 -217.754 -100.111 -11.161 0.5 111.29 ? N3 5AD 1102 A 1 HETATM 7 C C4 5AD . A . D 3 -216.811 -100.62 -10.138 0.5 112.15 ? C4 5AD 1102 A 1 HETATM 8 C C4 5AD . B . D 3 -216.821 -100.009 -10.206 0.5 112.57 ? C4 5AD 1102 A 1 HETATM 9 N N9 5AD . A . D 3 -216.221 -99.422 -9.817 0.5 112.96 ? N9 5AD 1102 A 1 HETATM 10 N N9 5AD . B . D 3 -216.138 -98.881 -9.821 0.5 114.34 ? N9 5AD 1102 A 1 HETATM 11 C C8 5AD . A . D 3 -215.391 -99.689 -8.76 0.5 112.87 ? C8 5AD 1102 A 1 HETATM 12 C C8 5AD . B . D 3 -215.302 -99.279 -8.811 0.5 113.26 ? C8 5AD 1102 A 1 HETATM 13 N N7 5AD . A . D 3 -215.394 -100.944 -8.381 0.5 112.95 ? N7 5AD 1102 A 1 HETATM 14 N N7 5AD . B . D 3 -215.387 -100.554 -8.519 0.5 113.34 ? N7 5AD 1102 A 1 HETATM 15 C C5 5AD . A . D 3 -216.292 -101.547 -9.25 0.5 110.6 ? C5 5AD 1102 A 1 HETATM 16 C C5 5AD . B . D 3 -216.347 -101.03 -9.399 0.5 111.4 ? C5 5AD 1102 A 1 HETATM 17 C C6 5AD . A . D 3 -216.74 -102.876 -9.38 0.5 109.56 ? C6 5AD 1102 A 1 HETATM 18 C C6 5AD . B . D 3 -216.898 -102.311 -9.602 0.5 110.85 ? C6 5AD 1102 A 1 HETATM 19 N N6 5AD . A . D 3 -216.321 -103.88 -8.606 0.5 107.8 ? N6 5AD 1102 A 1 HETATM 20 N N6 5AD . B . D 3 -216.535 -103.393 -8.908 0.5 108.19 ? N6 5AD 1102 A 1 HETATM 21 C C1' 5AD . A . D 3 -216.427 -98.133 -10.471 0.5 114.51 ? C1' 5AD 1102 A 1 HETATM 22 C C1' 5AD . B . D 3 -216.272 -97.534 -10.368 0.5 114 ? C1' 5AD 1102 A 1 HETATM 23 C C2' 5AD . A . D 3 -217.605 -97.326 -9.9 0.5 115.66 ? C2' 5AD 1102 A 1 HETATM 24 C C2' 5AD . B . D 3 -217.377 -96.711 -9.703 0.5 115.33 ? C2' 5AD 1102 A 1 HETATM 25 C C3' 5AD . A . D 3 -216.963 -95.988 -9.51 0.5 114.75 ? C3' 5AD 1102 A 1 HETATM 26 C C3' 5AD . B . D 3 -216.783 -95.302 -9.722 0.5 114.77 ? C3' 5AD 1102 A 1 HETATM 27 C C4' 5AD . A . D 3 -215.663 -95.981 -10.301 0.5 114.85 ? C4' 5AD 1102 A 1 HETATM 28 C C4' 5AD . B . D 3 -215.289 -95.562 -9.547 0.5 114.87 ? C4' 5AD 1102 A 1 HETATM 29 C C5' 5AD . A . D 3 -214.552 -95.135 -9.726 0.5 114.16 ? C5' 5AD 1102 A 1 HETATM 30 C C5' 5AD . B . D 3 -214.792 -95.594 -8.122 0.5 115.87 ? C5' 5AD 1102 A 1 HETATM 31 O O4' 5AD . A . D 3 -215.252 -97.357 -10.312 0.5 115.49 ? O4' 5AD 1102 A 1 HETATM 32 O O4' 5AD . B . D 3 -215.051 -96.846 -10.162 0.5 115.62 ? O4' 5AD 1102 A 1 HETATM 33 O O2' 5AD . A . D 3 -218.623 -97.162 -10.881 0.5 115.13 ? O2' 5AD 1102 A 1 HETATM 34 O O2' 5AD . B . D 3 -218.576 -96.797 -10.464 0.5 114.91 ? O2' 5AD 1102 A 1 HETATM 35 O O3' 5AD . A . D 3 -217.758 -94.876 -9.906 0.5 114.44 ? O3' 5AD 1102 A 1 HETATM 36 O O3' 5AD . B . D 3 -217.011 -94.634 -10.957 0.5 113.98 ? O3' 5AD 1102 A 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #