data_6XB5 # _model_server_result.job_id Yz2u2glS8t4H9FogQigFhg _model_server_result.datetime_utc '2025-02-18 19:55:11' _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 6xb5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 6XB5 # _exptl.entry_id 6XB5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 692.427 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2',5'-GpAp" _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 6XB5 _cell.length_a 124.422 _cell.length_b 124.422 _cell.length_c 132.178 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XB5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 80 _symmetry.space_group_name_Hall 'I 4bw' _symmetry.space_group_name_H-M 'I 41' # _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N # _chem_comp.formula 'C20 H26 N10 O14 P2' _chem_comp.formula_weight 692.427 _chem_comp.id 9BG _chem_comp.mon_nstd_flag . _chem_comp.name "2',5'-GpAp" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl [(2~{R},3~{R},4~{R},5~{R})-2-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate' # 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 O18 C17 9BG sing 1 n n C15 C14 9BG sing 2 n n C15 O16 9BG sing 3 n n C14 C17 9BG sing 4 n n C14 O13 9BG sing 5 n n C17 C19 9BG sing 6 n n O13 C12 9BG sing 7 n n C19 O20 9BG sing 8 n n C19 C12 9BG sing 9 n n O20 P21 9BG sing 10 n n C12 N11 9BG sing 11 n n O45 P21 9BG doub 12 n n P21 O46 9BG sing 13 n n P21 O22 9BG sing 14 n n N11 C10 9BG sing 15 n y N11 C07 9BG sing 16 n y C10 N09 9BG doub 17 n y O22 C23 9BG sing 18 n n N06 C07 9BG sing 19 n n N06 C04 9BG sing 20 n n C07 C08 9BG doub 21 n y C23 C24 9BG sing 22 n n N05 C04 9BG sing 23 n n N09 C08 9BG sing 24 n y C04 N03 9BG doub 25 n n C08 C02 9BG sing 26 n n O28 P27 9BG doub 27 n n C24 O44 9BG sing 28 n n C24 C25 9BG sing 29 n n O44 C33 9BG sing 30 n n C43 N42 9BG doub 31 n y C43 N34 9BG sing 32 n y N03 C02 9BG sing 33 n n N42 C41 9BG sing 34 n y O30 P27 9BG sing 35 n n C02 O01 9BG doub 36 n n P27 O29 9BG sing 37 n n P27 O26 9BG sing 38 n n C25 O26 9BG sing 39 n n C25 C31 9BG sing 40 n n N34 C33 9BG sing 41 n n N34 C35 9BG sing 42 n y C33 C31 9BG sing 43 n n C41 C35 9BG doub 44 n y C41 C39 9BG sing 45 n y N40 C39 9BG sing 46 n n C31 O32 9BG sing 47 n n C35 N36 9BG sing 48 n y C39 N38 9BG doub 49 n y N36 C37 9BG doub 50 n y N38 C37 9BG sing 51 n y C10 H1 9BG sing 52 n n C17 H2 9BG sing 53 n n C24 H3 9BG sing 54 n n C12 H4 9BG sing 55 n n C14 H5 9BG sing 56 n n C19 H6 9BG sing 57 n n C23 H7 9BG sing 58 n n C23 H8 9BG sing 59 n n C25 H9 9BG sing 60 n n N05 H10 9BG sing 61 n n N05 H11 9BG sing 62 n n N06 H12 9BG sing 63 n n C15 H13 9BG sing 64 n n C15 H14 9BG sing 65 n n O16 H15 9BG sing 66 n n O18 H16 9BG sing 67 n n O29 H17 9BG sing 68 n n O30 H18 9BG sing 69 n n C31 H19 9BG sing 70 n n O32 H20 9BG sing 71 n n C33 H21 9BG sing 72 n n C37 H22 9BG sing 73 n n N40 H23 9BG sing 74 n n N40 H24 9BG sing 75 n n C43 H25 9BG sing 76 n n O46 H26 9BG sing 77 n n # _atom_sites.entry_id 6XB5 _atom_sites.fract_transf_matrix[1][1] 0.008037 _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] 0.008037 _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] 0.007566 _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 9BG A 1 301 1 9BG 9BG . D 2 9BG B 1 301 2 9BG 9BG . # 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 C C10 9BG . . . C 2 17.741 -17.38 -19.439 1 73.23 ? C10 9BG 301 A 1 HETATM 2 C C17 9BG . . . C 2 21.908 -16.502 -17.519 1 86.04 ? C17 9BG 301 A 1 HETATM 3 C C24 9BG . . . C 2 25.189 -19.074 -19.812 1 63.22 ? C24 9BG 301 A 1 HETATM 4 C C02 9BG . . . C 2 18.357 -17.246 -23.052 1 67.3 ? C02 9BG 301 A 1 HETATM 5 C C04 9BG . . . C 2 20.775 -16.647 -22.937 1 80.75 ? C04 9BG 301 A 1 HETATM 6 C C07 9BG . . . C 2 19.404 -16.976 -20.789 1 72.8 ? C07 9BG 301 A 1 HETATM 7 C C08 9BG . . . C 2 18.289 -17.255 -21.529 1 67.33 ? C08 9BG 301 A 1 HETATM 8 C C12 9BG . . . C 2 19.859 -16.84 -18.322 1 71.69 ? C12 9BG 301 A 1 HETATM 9 C C14 9BG . . . C 2 21.264 -15.081 -17.625 1 86.7 ? C14 9BG 301 A 1 HETATM 10 C C19 9BG . . . C 2 21.044 -17.353 -18.426 1 71.99 ? C19 9BG 301 A 1 HETATM 11 C C23 9BG . . . C 2 24.05 -20.099 -19.836 1 60.27 ? C23 9BG 301 A 1 HETATM 12 C C25 9BG . . . C 2 24.901 -17.927 -20.831 1 66.51 ? C25 9BG 301 A 1 HETATM 13 N N34 9BG . . . C 2 27.435 -19.805 -22.518 1 58.79 ? N34 9BG 301 A 1 HETATM 14 O O01 9BG . . . C 2 17.368 -17.499 -23.661 1 74.51 ? O01 9BG 301 A 1 HETATM 15 N N03 9BG . . . C 2 19.593 -16.945 -23.714 1 77.45 ? N03 9BG 301 A 1 HETATM 16 N N05 9BG . . . C 2 22.041 -16.333 -23.585 1 77.16 ? N05 9BG 301 A 1 HETATM 17 N N06 9BG . . . C 2 20.695 -16.658 -21.477 1 73.3 ? N06 9BG 301 A 1 HETATM 18 N N09 9BG . . . C 2 17.278 -17.505 -20.7 1 69.69 ? N09 9BG 301 A 1 HETATM 19 N N11 9BG . . . C 2 19.051 -17.056 -19.503 1 71.24 ? N11 9BG 301 A 1 HETATM 20 O O13 9BG . . . C 2 20.077 -15.249 -18.079 1 80.66 ? O13 9BG 301 A 1 HETATM 21 C C15 9BG . . . C 2 22.096 -14.217 -18.617 1 69.32 ? C15 9BG 301 A 1 HETATM 22 O O16 9BG . . . C 2 23.446 -14.566 -18.511 1 78.79 ? O16 9BG 301 A 1 HETATM 23 O O18 9BG . . . C 2 21.87 -16.958 -16.233 1 88.87 ? O18 9BG 301 A 1 HETATM 24 O O20 9BG . . . C 2 21.029 -18.756 -17.885 1 66.89 ? O20 9BG 301 A 1 HETATM 25 P P21 9BG . . . C 2 21.701 -19.904 -18.832 1 57.47 ? P21 9BG 301 A 1 HETATM 26 O O22 9BG . . . C 2 23.322 -19.848 -18.681 1 67.3 ? O22 9BG 301 A 1 HETATM 27 O O26 9BG . . . C 2 25.602 -16.871 -20.445 1 77.77 ? O26 9BG 301 A 1 HETATM 28 P P27 9BG . . . C 2 25.319 -15.349 -21.012 1 60.52 ? P27 9BG 301 A 1 HETATM 29 O O28 9BG . . . C 2 24.219 -15.408 -22.047 1 64.44 ? O28 9BG 301 A 1 HETATM 30 O O29 9BG . . . C 2 26.577 -14.807 -21.637 1 80.81 -1 O29 9BG 301 A 1 HETATM 31 O O30 9BG . . . C 2 24.966 -14.446 -19.858 1 76.59 -1 O30 9BG 301 A 1 HETATM 32 C C31 9BG . . . C 2 25.519 -18.572 -22.123 1 59.99 ? C31 9BG 301 A 1 HETATM 33 O O32 9BG . . . C 2 25.595 -17.539 -23.183 1 72.28 ? O32 9BG 301 A 1 HETATM 34 C C33 9BG . . . C 2 26.675 -18.931 -21.669 1 56.39 ? C33 9BG 301 A 1 HETATM 35 C C35 9BG . . . C 2 28.729 -19.539 -22.787 1 69.89 ? C35 9BG 301 A 1 HETATM 36 N N36 9BG . . . C 2 29.541 -18.528 -22.393 1 67.15 ? N36 9BG 301 A 1 HETATM 37 C C37 9BG . . . C 2 30.826 -18.492 -22.822 1 70.76 ? C37 9BG 301 A 1 HETATM 38 N N38 9BG . . . C 2 31.304 -19.463 -23.643 1 65.45 ? N38 9BG 301 A 1 HETATM 39 C C39 9BG . . . C 2 30.517 -20.45 -24.032 1 54.88 ? C39 9BG 301 A 1 HETATM 40 N N40 9BG . . . C 2 31.273 -21.33 -24.899 1 61.58 ? N40 9BG 301 A 1 HETATM 41 C C41 9BG . . . C 2 29.204 -20.499 -23.601 1 63.94 ? C41 9BG 301 A 1 HETATM 42 N N42 9BG . . . C 2 28.206 -21.361 -23.842 1 62.46 ? N42 9BG 301 A 1 HETATM 43 C C43 9BG . . . C 2 27.123 -20.933 -23.171 1 66.88 ? C43 9BG 301 A 1 HETATM 44 O O44 9BG . . . C 2 26.278 -19.653 -20.213 1 57.04 ? O44 9BG 301 A 1 HETATM 45 O O45 9BG . . . C 2 21.346 -19.663 -20.27 1 60.26 ? O45 9BG 301 A 1 HETATM 46 O O46 9BG . . . C 2 21.228 -21.261 -18.403 1 76.99 -1 O46 9BG 301 A 1 # _model_server_stats.io_time_ms 48 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 792 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 46 #