data_8JBS # _model_server_result.job_id EUXYPYFQuH612N2DoygJJw _model_server_result.datetime_utc '2025-08-20 05:58:47' _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 8jbs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":302}' # _entry.id 8JBS # _exptl.entry_id 8JBS _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 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 120 _cell.entry_id 8JBS _cell.length_a 125.218 _cell.length_b 125.218 _cell.length_c 73.088 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8JBS _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 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 dimeric 2 author_and_software_defined_assembly 1 PISA monomeric 1 software_defined_assembly 2 PISA monomeric 1 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H 1 1 A,C,D,G 2 1 B,E,F,H 3 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 ? 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 metalc ? metalc1 A NE2 HIS 204 A HIS 122 1_555 C CO B12 . A B12 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc2 B NE2 HIS 204 B HIS 122 1_555 E CO B12 . B B12 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? # _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 8JBS _atom_sites.fract_transf_matrix[1][1] 0.007986 _atom_sites.fract_transf_matrix[1][2] 0.004611 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009222 _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] 0.013682 _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 1 301 301 B12 B12 . D 3 5AD A 1 302 302 5AD 5AD . E 2 B12 B 1 301 301 B12 B12 . F 3 5AD B 1 302 302 5AD 5AD . G 4 HOH A 1 401 35 HOH HOH . G 4 HOH A 2 402 14 HOH HOH . G 4 HOH A 3 403 49 HOH HOH . G 4 HOH A 4 404 11 HOH HOH . G 4 HOH A 5 405 2 HOH HOH . G 4 HOH A 6 406 10 HOH HOH . G 4 HOH A 7 407 50 HOH HOH . G 4 HOH A 8 408 3 HOH HOH . G 4 HOH A 9 409 34 HOH HOH . G 4 HOH A 10 410 6 HOH HOH . G 4 HOH A 11 411 9 HOH HOH . G 4 HOH A 12 412 48 HOH HOH . G 4 HOH A 13 413 4 HOH HOH . G 4 HOH A 14 414 22 HOH HOH . G 4 HOH A 15 415 26 HOH HOH . G 4 HOH A 16 416 18 HOH HOH . G 4 HOH A 17 417 27 HOH HOH . G 4 HOH A 18 418 25 HOH HOH . G 4 HOH A 19 419 16 HOH HOH . G 4 HOH A 20 420 28 HOH HOH . G 4 HOH A 21 421 24 HOH HOH . H 4 HOH B 1 401 12 HOH HOH . H 4 HOH B 2 402 51 HOH HOH . H 4 HOH B 3 403 43 HOH HOH . H 4 HOH B 4 404 15 HOH HOH . H 4 HOH B 5 405 52 HOH HOH . H 4 HOH B 6 406 20 HOH HOH . H 4 HOH B 7 407 33 HOH HOH . H 4 HOH B 8 408 53 HOH HOH . H 4 HOH B 9 409 37 HOH HOH . H 4 HOH B 10 410 17 HOH HOH . H 4 HOH B 11 411 31 HOH HOH . H 4 HOH B 12 412 38 HOH HOH . H 4 HOH B 13 413 23 HOH HOH . H 4 HOH B 14 414 5 HOH HOH . H 4 HOH B 15 415 13 HOH HOH . H 4 HOH B 16 416 42 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 5AD . . . F 3 56.319 -4.548 -6.737 1 42.02 ? N1 5AD 302 B 1 HETATM 2 C C2 5AD . . . F 3 55.946 -5.471 -5.836 1 40.62 ? C2 5AD 302 B 1 HETATM 3 N N3 5AD . . . F 3 55.788 -5.351 -4.519 1 37.78 ? N3 5AD 302 B 1 HETATM 4 C C4 5AD . . . F 3 56.04 -4.098 -4.124 1 41.12 ? C4 5AD 302 B 1 HETATM 5 N N9 5AD . . . F 3 55.974 -3.603 -2.854 1 46.49 ? N9 5AD 302 B 1 HETATM 6 C C8 5AD . . . F 3 56.345 -2.279 -2.929 1 46.48 ? C8 5AD 302 B 1 HETATM 7 N N7 5AD . . . F 3 56.621 -1.906 -4.161 1 44.08 ? N7 5AD 302 B 1 HETATM 8 C C5 5AD . . . F 3 56.433 -3.046 -4.924 1 42.83 ? C5 5AD 302 B 1 HETATM 9 C C6 5AD . . . F 3 56.577 -3.299 -6.296 1 40.49 ? C6 5AD 302 B 1 HETATM 10 N N6 5AD . . . F 3 56.912 -2.367 -7.182 1 45.24 ? N6 5AD 302 B 1 HETATM 11 C C1' 5AD . . . F 3 55.664 -4.349 -1.655 1 46.69 ? C1' 5AD 302 B 1 HETATM 12 C C2' 5AD . . . F 3 56.735 -4.212 -0.564 1 46.57 ? C2' 5AD 302 B 1 HETATM 13 C C3' 5AD . . . F 3 55.962 -3.669 0.644 1 50.18 ? C3' 5AD 302 B 1 HETATM 14 C C4' 5AD . . . F 3 54.52 -3.994 0.288 1 47.8 ? C4' 5AD 302 B 1 HETATM 15 C C5' 5AD . . . F 3 53.529 -3.06 0.908 1 53.13 ? C5' 5AD 302 B 1 HETATM 16 O O4' 5AD . . . F 3 54.452 -3.854 -1.143 1 42.2 ? O4' 5AD 302 B 1 HETATM 17 O O2' 5AD . . . F 3 57.336 -5.436 -0.22 1 42.26 ? O2' 5AD 302 B 1 HETATM 18 O O3' 5AD . . . F 3 56.325 -4.264 1.887 1 45.55 ? O3' 5AD 302 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 18 #