data_2ZI6 # _model_server_result.job_id PhQYzKPDiybrhuCN9c1x6w _model_server_result.datetime_utc '2024-11-13 04:14:22' _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 2zi6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":3302}' # _entry.id 2ZI6 # _exptl.entry_id 2ZI6 _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 4 _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 2ZI6 _cell.length_a 138.25 _cell.length_b 138.51 _cell.length_c 118.67 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZI6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # 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 dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_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,E,F,G,H,I,J,M,N 1 1 C,K,O 2 1,2 D,L,P 3 1,3 # 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_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 138.25 0 59.335 3 'crystal symmetry operation' 3_654 -x+1,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 138.25 0 -59.335 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 I N N ? 3 J N N ? 3 K N N ? 3 L 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 2ZI6 _atom_sites.fract_transf_matrix[1][1] 0.007233 _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] 0.00722 _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] 0.008427 _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 E 2 UDP A 1 1301 1301 UDP UDP . F 2 UDP A 1 2301 2301 UDP UDP . G 2 UDP A 1 3301 3301 UDP UDP . H 2 UDP A 1 4301 4301 UDP UDP . I 3 3D1 A 1 1302 1302 3D1 DAD . J 3 3D1 B 1 2302 2302 3D1 DAD . K 3 3D1 C 1 3302 3302 3D1 DAD . L 3 3D1 D 1 4302 4302 3D1 DAD . M 4 HOH A 1 7002 7002 HOH HOH . M 4 HOH A 2 7009 7009 HOH HOH . M 4 HOH A 3 7015 7015 HOH HOH . M 4 HOH A 4 7017 7017 HOH HOH . M 4 HOH A 5 7030 7030 HOH HOH . M 4 HOH A 6 7034 7034 HOH HOH . M 4 HOH A 7 7042 7042 HOH HOH . M 4 HOH A 8 7043 7043 HOH HOH . M 4 HOH A 9 7045 7045 HOH HOH . M 4 HOH A 10 7046 7046 HOH HOH . M 4 HOH A 11 7049 7049 HOH HOH . M 4 HOH A 12 7051 7051 HOH HOH . M 4 HOH A 13 7052 7052 HOH HOH . M 4 HOH A 14 7055 7055 HOH HOH . M 4 HOH A 15 7056 7056 HOH HOH . M 4 HOH A 16 7063 7063 HOH HOH . M 4 HOH A 17 7070 7070 HOH HOH . M 4 HOH A 18 7072 7072 HOH HOH . M 4 HOH A 19 7074 7074 HOH HOH . M 4 HOH A 20 7076 7076 HOH HOH . M 4 HOH A 21 7081 7081 HOH HOH . M 4 HOH A 22 7085 7085 HOH HOH . M 4 HOH A 23 7092 7092 HOH HOH . M 4 HOH A 24 7098 7098 HOH HOH . M 4 HOH A 25 7099 7099 HOH HOH . M 4 HOH A 26 7100 7100 HOH HOH . M 4 HOH A 27 7101 7101 HOH HOH . M 4 HOH A 28 7104 7104 HOH HOH . M 4 HOH A 29 7105 7105 HOH HOH . M 4 HOH A 30 7106 7106 HOH HOH . M 4 HOH A 31 7112 7112 HOH HOH . M 4 HOH A 32 7113 7113 HOH HOH . M 4 HOH A 33 7114 7114 HOH HOH . M 4 HOH A 34 7115 7115 HOH HOH . M 4 HOH A 35 7117 7117 HOH HOH . M 4 HOH A 36 7129 7129 HOH HOH . M 4 HOH A 37 7130 7130 HOH HOH . M 4 HOH A 38 7131 7131 HOH HOH . M 4 HOH A 39 7132 7132 HOH HOH . M 4 HOH A 40 7133 7133 HOH HOH . M 4 HOH A 41 7136 7136 HOH HOH . M 4 HOH A 42 7141 7141 HOH HOH . M 4 HOH A 43 7148 7148 HOH HOH . M 4 HOH A 44 7149 7149 HOH HOH . M 4 HOH A 45 7151 7151 HOH HOH . M 4 HOH A 46 7155 7155 HOH HOH . M 4 HOH A 47 7156 7156 HOH HOH . M 4 HOH A 48 7158 7158 HOH HOH . M 4 HOH A 49 7160 7160 HOH HOH . M 4 HOH A 50 7164 7164 HOH HOH . N 4 HOH B 1 7003 7003 HOH HOH . N 4 HOH B 2 7006 7006 HOH HOH . N 4 HOH B 3 7007 7007 HOH HOH . N 4 HOH B 4 7012 7012 HOH HOH . N 4 HOH B 5 7013 7013 HOH HOH . N 4 HOH B 6 7019 7019 HOH HOH . N 4 HOH B 7 7020 7020 HOH HOH . N 4 HOH B 8 7022 7022 HOH HOH . N 4 HOH B 9 7023 7023 HOH HOH . N 4 HOH B 10 7028 7028 HOH HOH . N 4 HOH B 11 7029 7029 HOH HOH . N 4 HOH B 12 7031 7031 HOH HOH . N 4 HOH B 13 7033 7033 HOH HOH . N 4 HOH B 14 7038 7038 HOH HOH . N 4 HOH B 15 7041 7041 HOH HOH . N 4 HOH B 16 7047 7047 HOH HOH . N 4 HOH B 17 7050 7050 HOH HOH . N 4 HOH B 18 7057 7057 HOH HOH . N 4 HOH B 19 7060 7060 HOH HOH . N 4 HOH B 20 7061 7061 HOH HOH . N 4 HOH B 21 7062 7062 HOH HOH . N 4 HOH B 22 7068 7068 HOH HOH . N 4 HOH B 23 7069 7069 HOH HOH . N 4 HOH B 24 7071 7071 HOH HOH . N 4 HOH B 25 7078 7078 HOH HOH . N 4 HOH B 26 7080 7080 HOH HOH . N 4 HOH B 27 7083 7083 HOH HOH . N 4 HOH B 28 7087 7087 HOH HOH . N 4 HOH B 29 7088 7088 HOH HOH . N 4 HOH B 30 7089 7089 HOH HOH . N 4 HOH B 31 7093 7093 HOH HOH . N 4 HOH B 32 7094 7094 HOH HOH . N 4 HOH B 33 7096 7096 HOH HOH . N 4 HOH B 34 7102 7102 HOH HOH . N 4 HOH B 35 7103 7103 HOH HOH . N 4 HOH B 36 7107 7107 HOH HOH . N 4 HOH B 37 7108 7108 HOH HOH . N 4 HOH B 38 7137 7137 HOH HOH . N 4 HOH B 39 7143 7143 HOH HOH . N 4 HOH B 40 7150 7150 HOH HOH . N 4 HOH B 41 7152 7152 HOH HOH . N 4 HOH B 42 7162 7162 HOH HOH . O 4 HOH C 1 7004 7004 HOH HOH . O 4 HOH C 2 7005 7005 HOH HOH . O 4 HOH C 3 7010 7010 HOH HOH . O 4 HOH C 4 7016 7016 HOH HOH . O 4 HOH C 5 7021 7021 HOH HOH . O 4 HOH C 6 7032 7032 HOH HOH . O 4 HOH C 7 7035 7035 HOH HOH . O 4 HOH C 8 7037 7037 HOH HOH . O 4 HOH C 9 7039 7039 HOH HOH . O 4 HOH C 10 7040 7040 HOH HOH . O 4 HOH C 11 7044 7044 HOH HOH . O 4 HOH C 12 7053 7053 HOH HOH . O 4 HOH C 13 7054 7054 HOH HOH . O 4 HOH C 14 7059 7059 HOH HOH . O 4 HOH C 15 7064 7064 HOH HOH . O 4 HOH C 16 7067 7067 HOH HOH . O 4 HOH C 17 7075 7075 HOH HOH . O 4 HOH C 18 7079 7079 HOH HOH . O 4 HOH C 19 7084 7084 HOH HOH . O 4 HOH C 20 7090 7090 HOH HOH . O 4 HOH C 21 7097 7097 HOH HOH . O 4 HOH C 22 7109 7109 HOH HOH . O 4 HOH C 23 7110 7110 HOH HOH . O 4 HOH C 24 7120 7120 HOH HOH . O 4 HOH C 25 7121 7121 HOH HOH . O 4 HOH C 26 7123 7123 HOH HOH . O 4 HOH C 27 7124 7124 HOH HOH . O 4 HOH C 28 7125 7125 HOH HOH . O 4 HOH C 29 7126 7126 HOH HOH . O 4 HOH C 30 7127 7127 HOH HOH . O 4 HOH C 31 7139 7139 HOH HOH . O 4 HOH C 32 7142 7142 HOH HOH . O 4 HOH C 33 7144 7144 HOH HOH . O 4 HOH C 34 7154 7154 HOH HOH . O 4 HOH C 35 7157 7157 HOH HOH . O 4 HOH C 36 7159 7159 HOH HOH . O 4 HOH C 37 7161 7161 HOH HOH . O 4 HOH C 38 7165 7165 HOH HOH . P 4 HOH D 1 7001 7001 HOH HOH . P 4 HOH D 2 7008 7008 HOH HOH . P 4 HOH D 3 7011 7011 HOH HOH . P 4 HOH D 4 7014 7014 HOH HOH . P 4 HOH D 5 7018 7018 HOH HOH . P 4 HOH D 6 7024 7024 HOH HOH . P 4 HOH D 7 7025 7025 HOH HOH . P 4 HOH D 8 7026 7026 HOH HOH . P 4 HOH D 9 7027 7027 HOH HOH . P 4 HOH D 10 7036 7036 HOH HOH . P 4 HOH D 11 7048 7048 HOH HOH . P 4 HOH D 12 7058 7058 HOH HOH . P 4 HOH D 13 7065 7065 HOH HOH . P 4 HOH D 14 7066 7066 HOH HOH . P 4 HOH D 15 7073 7073 HOH HOH . P 4 HOH D 16 7077 7077 HOH HOH . P 4 HOH D 17 7082 7082 HOH HOH . P 4 HOH D 18 7086 7086 HOH HOH . P 4 HOH D 19 7091 7091 HOH HOH . P 4 HOH D 20 7095 7095 HOH HOH . P 4 HOH D 21 7111 7111 HOH HOH . P 4 HOH D 22 7116 7116 HOH HOH . P 4 HOH D 23 7118 7118 HOH HOH . P 4 HOH D 24 7119 7119 HOH HOH . P 4 HOH D 25 7122 7122 HOH HOH . P 4 HOH D 26 7128 7128 HOH HOH . P 4 HOH D 27 7134 7134 HOH HOH . P 4 HOH D 28 7135 7135 HOH HOH . P 4 HOH D 29 7138 7138 HOH HOH . P 4 HOH D 30 7140 7140 HOH HOH . P 4 HOH D 31 7145 7145 HOH HOH . P 4 HOH D 32 7146 7146 HOH HOH . P 4 HOH D 33 7147 7147 HOH HOH . P 4 HOH D 34 7153 7153 HOH HOH . P 4 HOH D 35 7163 7163 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 . . . K 3 85.385 8.609 20.842 1 33.78 ? O5' 3D1 3302 C 1 HETATM 2 C C5' 3D1 . . . K 3 85.724 7.532 21.738 1 33.33 ? C5' 3D1 3302 C 1 HETATM 3 C C4' 3D1 . . . K 3 84.825 6.317 21.555 1 33.84 ? C4' 3D1 3302 C 1 HETATM 4 O O4' 3D1 . . . K 3 83.474 6.687 21.944 1 33.8 ? O4' 3D1 3302 C 1 HETATM 5 C C1' 3D1 . . . K 3 82.613 6.42 20.808 1 32.28 ? C1' 3D1 3302 C 1 HETATM 6 N N9 3D1 . . . K 3 81.544 7.408 20.877 1 29.83 ? N9 3D1 3302 C 1 HETATM 7 C C4 3D1 . . . K 3 81.612 8.722 20.889 1 28.6 ? C4 3D1 3302 C 1 HETATM 8 N N3 3D1 . . . K 3 82.75 9.437 21.142 1 27.63 ? N3 3D1 3302 C 1 HETATM 9 C C2 3D1 . . . K 3 82.684 10.867 21.221 1 26.64 ? C2 3D1 3302 C 1 HETATM 10 N N1 3D1 . . . K 3 81.367 11.384 21.147 1 26.19 ? N1 3D1 3302 C 1 HETATM 11 C C6 3D1 . . . K 3 80.239 10.753 20.857 1 26.55 ? C6 3D1 3302 C 1 HETATM 12 N N6 3D1 . . . K 3 79.099 11.316 20.665 1 29.44 ? N6 3D1 3302 C 1 HETATM 13 C C5 3D1 . . . K 3 80.374 9.297 20.803 1 26.72 ? C5 3D1 3302 C 1 HETATM 14 N N7 3D1 . . . K 3 79.488 8.302 20.632 1 26.52 ? N7 3D1 3302 C 1 HETATM 15 C C8 3D1 . . . K 3 80.214 7.137 20.675 1 27.66 ? C8 3D1 3302 C 1 HETATM 16 C C2' 3D1 . . . K 3 83.443 6.332 19.552 1 30.82 ? C2' 3D1 3302 C 1 HETATM 17 C C3' 3D1 . . . K 3 84.754 5.796 20.107 1 32.3 ? C3' 3D1 3302 C 1 HETATM 18 O O3' 3D1 . . . K 3 84.845 4.374 20.108 1 34.11 ? O3' 3D1 3302 C 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 18 #