data_8K6F # _model_server_result.job_id kE5eH9SMe1YWB2-ogLUUAg _model_server_result.datetime_utc '2025-02-24 03:32:45' _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 8k6f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 8K6F # _exptl.entry_id 8K6F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.316 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' _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 90.3 _cell.angle_gamma 90 _cell.entry_id 8K6F _cell.length_a 54.69 _cell.length_b 214.227 _cell.length_c 79.563 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8K6F _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 5 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C15 H23 N5 O14 P2' _chem_comp.formula_weight 559.316 _chem_comp.id AR6 _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Adenosine-5-Diphosphoribose # 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 AR6 doub 13 n y N1 C6 AR6 sing 14 n y C2 N3 AR6 sing 15 n y N3 C4 AR6 doub 16 n y C4 C5 AR6 sing 17 n y C4 N9 AR6 sing 18 n y C5 C6 AR6 doub 19 n y C5 N7 AR6 sing 20 n y C6 N6 AR6 sing 21 n n N7 C8 AR6 doub 22 n y C8 N9 AR6 sing 23 n y N9 C1' AR6 sing 24 n n PA O1A AR6 sing 25 n n PA O2A AR6 doub 26 n n PA O3A AR6 sing 27 n n PA O5' AR6 sing 28 n n PB O1B AR6 sing 29 n n PB O2B AR6 doub 30 n n PB O3A AR6 sing 31 n n PB O5D AR6 sing 32 n n C1' C2' AR6 sing 33 n n C1' O4' AR6 sing 34 n n C1D O1D AR6 sing 35 n n C1D C2D AR6 sing 36 n n C1D O4D AR6 sing 37 n n C2' O2' AR6 sing 38 n n C2' C3' AR6 sing 39 n n C2D O2D AR6 sing 40 n n C2D C3D AR6 sing 41 n n C3' O3' AR6 sing 42 n n C3' C4' AR6 sing 43 n n C3D O3D AR6 sing 44 n n C3D C4D AR6 sing 45 n n C4' O4' AR6 sing 46 n n C4' C5' AR6 sing 47 n n C4D O4D AR6 sing 48 n n C4D C5D AR6 sing 49 n n C5' O5' AR6 sing 50 n n C5D O5D AR6 sing 51 n n C2 H2 AR6 sing 52 n n N6 HN6 AR6 sing 53 n n N6 HN6A AR6 sing 54 n n C8 H8 AR6 sing 55 n n C1' H1' AR6 sing 56 n n C1D H1D AR6 sing 57 n n C2' H2' AR6 sing 58 n n O2' HO2' AR6 sing 59 n n C2D H2D AR6 sing 60 n n O2D HO2D AR6 sing 61 n n C3' H3' AR6 sing 62 n n O3' HO3' AR6 sing 63 n n C3D H3D AR6 sing 64 n n O3D HO3D AR6 sing 65 n n C4' H4' AR6 sing 66 n n C4D H4D AR6 sing 67 n n C5' H5' AR6 sing 68 n n C5' "H5'A" AR6 sing 69 n n C5D H5D AR6 sing 70 n n C5D H5DA AR6 sing 71 n n O1A H1A AR6 sing 72 n n O1B H1B AR6 sing 73 n n O1D HD1 AR6 sing 74 n n # _atom_sites.entry_id 8K6F _atom_sites.fract_transf_matrix[1][1] 0.018285 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000096 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004668 _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] 0.012569 _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 G 4 ATP A 1 401 402 ATP ATP . H 4 ATP B 1 401 402 ATP ATP . I 5 AR6 D 1 401 401 AR6 AR6 . # 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 P PB AR6 . . . I 5 35.421 65.283 61.065 1 63.27 ? PB AR6 401 D 1 HETATM 2 O O1B AR6 . . . I 5 36.469 65.542 62.097 1 49.03 ? O1B AR6 401 D 1 HETATM 3 C C1D AR6 . . . I 5 31.902 68.748 62.383 1 64.46 ? C1D AR6 401 D 1 HETATM 4 O O1D AR6 . . . I 5 30.827 69.258 63.165 1 57.19 ? O1D AR6 401 D 1 HETATM 5 O O2B AR6 . . . I 5 35.685 65.599 59.627 1 62.99 ? O2B AR6 401 D 1 HETATM 6 C C2D AR6 . . . I 5 31.735 69.136 60.93 1 64.84 ? C2D AR6 401 D 1 HETATM 7 O O2D AR6 . . . I 5 30.374 69.437 60.641 1 71.84 ? O2D AR6 401 D 1 HETATM 8 O O3A AR6 . . . I 5 34.965 63.761 61.197 1 61.8 ? O3A AR6 401 D 1 HETATM 9 C C3D AR6 . . . I 5 32.109 67.914 60.144 1 66.27 ? C3D AR6 401 D 1 HETATM 10 O O3D AR6 . . . I 5 31.302 67.807 58.975 1 61.92 ? O3D AR6 401 D 1 HETATM 11 C C4D AR6 . . . I 5 31.841 66.778 61.108 1 68.12 ? C4D AR6 401 D 1 HETATM 12 O O4D AR6 . . . I 5 31.919 67.323 62.425 1 72.4 ? O4D AR6 401 D 1 HETATM 13 C C5D AR6 . . . I 5 32.834 65.642 60.95 1 64.98 ? C5D AR6 401 D 1 HETATM 14 O O5D AR6 . . . I 5 34.086 66.043 61.491 1 71.87 ? O5D AR6 401 D 1 HETATM 15 H H1D AR6 . . . I 5 32.857 69.147 62.75 1 77.12 ? H1D AR6 401 D 1 HETATM 16 H H2D AR6 . . . I 5 32.402 69.972 60.683 1 77.58 ? H2D AR6 401 D 1 HETATM 17 H HO2D AR6 . . . I 5 29.97 69.885 61.393 1 85.97 ? HO2D AR6 401 D 1 HETATM 18 H H3D AR6 . . . I 5 33.176 67.96 59.885 1 79.29 ? H3D AR6 401 D 1 HETATM 19 H HO3D AR6 . . . I 5 31.418 68.601 58.435 1 74.07 ? HO3D AR6 401 D 1 HETATM 20 H H4D AR6 . . . I 5 30.829 66.392 60.925 1 81.51 ? H4D AR6 401 D 1 HETATM 21 H H5D AR6 . . . I 5 32.939 65.388 59.893 1 77.74 ? H5D AR6 401 D 1 HETATM 22 H H5DA AR6 . . . I 5 32.462 64.763 61.48 1 77.74 ? H5DA AR6 401 D 1 HETATM 23 H HD1 AR6 . . . I 5 31.099 69.308 64.091 1 68.39 ? HD1 AR6 401 D 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 23 #