data_2C5H # _model_server_result.job_id Pccco-xGsmRbmqaruEut-g _model_server_result.datetime_utc '2025-03-06 09:52:31' _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 2c5h # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":500}' # _entry.id 2C5H # _exptl.entry_id 2C5H _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 (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol _entity.pdbx_number_of_molecules 3 _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 2C5H _cell.length_a 74.543 _cell.length_b 126.697 _cell.length_c 181.333 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2C5H _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -90.6665 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 H N N ? 3 I N N # _chem_comp.formula 'C10 H13 N5 O3' _chem_comp.formula_weight 251.242 _chem_comp.id 3D1 _chem_comp.mon_nstd_flag . _chem_comp.name (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2'-DEOXYADENOSINE" # 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 O5' C5' 3D1 sing 1 n n O5' H5' 3D1 sing 2 n n C5' C4' 3D1 sing 3 n n C5' "H5'1" 3D1 sing 4 n n C5' "H5'2" 3D1 sing 5 n n C4' O4' 3D1 sing 6 n n C4' C3' 3D1 sing 7 n n C4' H4' 3D1 sing 8 n n O4' C1' 3D1 sing 9 n n C1' N9 3D1 sing 10 n n C1' C2' 3D1 sing 11 n n C1' H1' 3D1 sing 12 n n N9 C4 3D1 sing 13 n y N9 C8 3D1 sing 14 n y C4 N3 3D1 doub 15 n y C4 C5 3D1 sing 16 n y N3 C2 3D1 sing 17 n y C2 N1 3D1 doub 18 n y C2 H2 3D1 sing 19 n n N1 C6 3D1 sing 20 n y C6 N6 3D1 sing 21 n n C6 C5 3D1 doub 22 n y N6 HN61 3D1 sing 23 n n N6 HN62 3D1 sing 24 n n C5 N7 3D1 sing 25 n y N7 C8 3D1 doub 26 n y C8 H8 3D1 sing 27 n n C2' C3' 3D1 sing 28 n n C2' "H2'1" 3D1 sing 29 n n C2' "H2'2" 3D1 sing 30 n n C3' O3' 3D1 sing 31 n n C3' H3' 3D1 sing 32 n n O3' H1 3D1 sing 33 n n # _atom_sites.entry_id 2C5H _atom_sites.fract_transf_matrix[1][1] 0.013415 _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] 0.007893 _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] 0.005515 _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 D 2 MET A 1 1301 1301 MET MET . E 3 3D1 A 1 500 500 3D1 3D1 . F 4 CL A 1 1302 1302 CL CL . G 2 MET B 1 1299 1299 MET MET . H 3 3D1 B 1 500 500 3D1 3D1 . I 3 3D1 C 1 500 500 3D1 3D1 . J 5 HOH A 1 2001 2001 HOH HOH . J 5 HOH A 2 2002 2002 HOH HOH . J 5 HOH A 3 2003 2003 HOH HOH . J 5 HOH A 4 2004 2004 HOH HOH . J 5 HOH A 5 2005 2005 HOH HOH . J 5 HOH A 6 2006 2006 HOH HOH . J 5 HOH A 7 2007 2007 HOH HOH . J 5 HOH A 8 2008 2008 HOH HOH . J 5 HOH A 9 2009 2009 HOH HOH . J 5 HOH A 10 2010 2010 HOH HOH . J 5 HOH A 11 2011 2011 HOH HOH . J 5 HOH A 12 2012 2012 HOH HOH . J 5 HOH A 13 2013 2013 HOH HOH . J 5 HOH A 14 2014 2014 HOH HOH . J 5 HOH A 15 2015 2015 HOH HOH . J 5 HOH A 16 2016 2016 HOH HOH . J 5 HOH A 17 2017 2017 HOH HOH . J 5 HOH A 18 2018 2018 HOH HOH . J 5 HOH A 19 2019 2019 HOH HOH . J 5 HOH A 20 2020 2020 HOH HOH . J 5 HOH A 21 2021 2021 HOH HOH . J 5 HOH A 22 2022 2022 HOH HOH . J 5 HOH A 23 2023 2023 HOH HOH . J 5 HOH A 24 2024 2024 HOH HOH . J 5 HOH A 25 2025 2025 HOH HOH . J 5 HOH A 26 2026 2026 HOH HOH . J 5 HOH A 27 2027 2027 HOH HOH . J 5 HOH A 28 2028 2028 HOH HOH . J 5 HOH A 29 2029 2029 HOH HOH . J 5 HOH A 30 2030 2030 HOH HOH . J 5 HOH A 31 2031 2031 HOH HOH . J 5 HOH A 32 2032 2032 HOH HOH . J 5 HOH A 33 2033 2033 HOH HOH . K 5 HOH B 1 2001 2001 HOH HOH . K 5 HOH B 2 2002 2002 HOH HOH . K 5 HOH B 3 2003 2003 HOH HOH . K 5 HOH B 4 2004 2004 HOH HOH . K 5 HOH B 5 2005 2005 HOH HOH . K 5 HOH B 6 2006 2006 HOH HOH . K 5 HOH B 7 2007 2007 HOH HOH . K 5 HOH B 8 2008 2008 HOH HOH . K 5 HOH B 9 2009 2009 HOH HOH . K 5 HOH B 10 2010 2010 HOH HOH . K 5 HOH B 11 2011 2011 HOH HOH . K 5 HOH B 12 2012 2012 HOH HOH . K 5 HOH B 13 2013 2013 HOH HOH . K 5 HOH B 14 2014 2014 HOH HOH . K 5 HOH B 15 2015 2015 HOH HOH . K 5 HOH B 16 2016 2016 HOH HOH . K 5 HOH B 17 2017 2017 HOH HOH . K 5 HOH B 18 2018 2018 HOH HOH . K 5 HOH B 19 2019 2019 HOH HOH . K 5 HOH B 20 2020 2020 HOH HOH . K 5 HOH B 21 2021 2021 HOH HOH . K 5 HOH B 22 2022 2022 HOH HOH . K 5 HOH B 23 2023 2023 HOH HOH . K 5 HOH B 24 2024 2024 HOH HOH . K 5 HOH B 25 2025 2025 HOH HOH . K 5 HOH B 26 2026 2026 HOH HOH . K 5 HOH B 27 2027 2027 HOH HOH . K 5 HOH B 28 2028 2028 HOH HOH . K 5 HOH B 29 2029 2029 HOH HOH . K 5 HOH B 30 2030 2030 HOH HOH . K 5 HOH B 31 2031 2031 HOH HOH . K 5 HOH B 32 2032 2032 HOH HOH . K 5 HOH B 33 2033 2033 HOH HOH . K 5 HOH B 34 2034 2034 HOH HOH . K 5 HOH B 35 2035 2035 HOH HOH . K 5 HOH B 36 2036 2036 HOH HOH . L 5 HOH C 1 2001 2001 HOH HOH . L 5 HOH C 2 2002 2002 HOH HOH . L 5 HOH C 3 2003 2003 HOH HOH . L 5 HOH C 4 2004 2004 HOH HOH . L 5 HOH C 5 2005 2005 HOH HOH . L 5 HOH C 6 2006 2006 HOH HOH . L 5 HOH C 7 2007 2007 HOH HOH . L 5 HOH C 8 2008 2008 HOH HOH . L 5 HOH C 9 2009 2009 HOH HOH . L 5 HOH C 10 2010 2010 HOH HOH . L 5 HOH C 11 2011 2011 HOH HOH . L 5 HOH C 12 2012 2012 HOH HOH . L 5 HOH C 13 2013 2013 HOH HOH . L 5 HOH C 14 2014 2014 HOH HOH . L 5 HOH C 15 2015 2015 HOH HOH . L 5 HOH C 16 2016 2016 HOH HOH . L 5 HOH C 17 2017 2017 HOH HOH . L 5 HOH C 18 2018 2018 HOH HOH . L 5 HOH C 19 2019 2019 HOH HOH . L 5 HOH C 20 2020 2020 HOH HOH . L 5 HOH C 21 2021 2021 HOH HOH . L 5 HOH C 22 2022 2022 HOH HOH . L 5 HOH C 23 2023 2023 HOH HOH . L 5 HOH C 24 2024 2024 HOH HOH . L 5 HOH C 25 2025 2025 HOH HOH . L 5 HOH C 26 2026 2026 HOH HOH . L 5 HOH C 27 2027 2027 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 O O5' 3D1 . . . I 3 -7.969 21.135 -19.643 1 6.46 ? O5' 3D1 500 C 1 HETATM 2 C C5' 3D1 . . . I 3 -7.218 21.948 -20.536 1 3.82 ? C5' 3D1 500 C 1 HETATM 3 C C4' 3D1 . . . I 3 -7.061 21.083 -21.768 1 4.32 ? C4' 3D1 500 C 1 HETATM 4 O O4' 3D1 . . . I 3 -8.201 21.167 -22.621 1 3.62 ? O4' 3D1 500 C 1 HETATM 5 C C1' 3D1 . . . I 3 -7.837 20.322 -23.682 1 2.92 ? C1' 3D1 500 C 1 HETATM 6 N N9 3D1 . . . I 3 -8.542 20.808 -24.929 1 2.51 ? N9 3D1 500 C 1 HETATM 7 C C4 3D1 . . . I 3 -9.09 20.022 -25.841 1 2.23 ? C4 3D1 500 C 1 HETATM 8 N N3 3D1 . . . I 3 -9.192 18.688 -25.962 1 2.88 ? N3 3D1 500 C 1 HETATM 9 C C2 3D1 . . . I 3 -9.786 18.123 -27.01 1 2.88 ? C2 3D1 500 C 1 HETATM 10 N N1 3D1 . . . I 3 -10.334 18.863 -27.978 1 2.64 ? N1 3D1 500 C 1 HETATM 11 C C6 3D1 . . . I 3 -10.284 20.208 -27.892 1 2.65 ? C6 3D1 500 C 1 HETATM 12 N N6 3D1 . . . I 3 -10.827 20.924 -28.859 1 2.89 ? N6 3D1 500 C 1 HETATM 13 C C5 3D1 . . . I 3 -9.649 20.831 -26.8 1 2.55 ? C5 3D1 500 C 1 HETATM 14 N N7 3D1 . . . I 3 -9.42 22.094 -26.436 1 2.42 ? N7 3D1 500 C 1 HETATM 15 C C8 3D1 . . . I 3 -8.747 22.07 -25.294 1 2.29 ? C8 3D1 500 C 1 HETATM 16 C C2' 3D1 . . . I 3 -6.278 20.372 -23.749 1 4.27 ? C2' 3D1 500 C 1 HETATM 17 C C3' 3D1 . . . I 3 -5.961 21.45 -22.73 1 4.06 ? C3' 3D1 500 C 1 HETATM 18 O O3' 3D1 . . . I 3 -4.691 21.217 -22.12 1 4.09 ? O3' 3D1 500 C 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 18 #