data_7EM3
#
_model_server_result.job_id            nD1tzOcAPzNfTLtOzAounA 
_model_server_result.datetime_utc      '2025-02-18 00:17:31' 
_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          7em3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":502}' 
#
_entry.id    7EM3 
#
_exptl.entry_id    7EM3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              522.196 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono 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 
_cell.angle_gamma         90 
_cell.entry_id            7EM3 
_cell.length_a            109.818 
_cell.length_b            185.947 
_cell.length_c            106.238 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7EM3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    'C 2c 2' 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C10 H17 N6 O13 P3' 
_chem_comp.formula_weight    522.196 
_chem_comp.id                CXC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(azanyl)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate' 
_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
O3G PG CXC doub 116 n n 
O1G PG CXC sing 117 n n 
PG O3B CXC sing 118 n n 
PG O2G CXC sing 119 n n 
O3B PB CXC sing 120 n n 
O2B PB CXC doub 121 n n 
PB O1B CXC sing 122 n n 
PB O3A CXC sing 123 n n 
O2A PA CXC doub 124 n n 
O3' C3' CXC sing 125 n n 
O3A PA CXC sing 126 n n 
PA O1A CXC sing 127 n n 
PA O5' CXC sing 128 n n 
O2' C2' CXC sing 129 n n 
C3' C2' CXC sing 130 n n 
C3' C4' CXC sing 131 n n 
C2' C1' CXC sing 132 n n 
O5' C5' CXC sing 133 n n 
C4' C5' CXC sing 134 n n 
C4' O4' CXC sing 135 n n 
C1' O4' CXC sing 136 n n 
C1' N9 CXC sing 137 n n 
N9 C8 CXC sing 138 n y 
N9 C4 CXC sing 139 n y 
C8 N7 CXC doub 140 n y 
C4 N3 CXC doub 141 n y 
C4 C5 CXC sing 142 n y 
N7 C5 CXC sing 143 n y 
N3 C2 CXC sing 144 n y 
C5 C6 CXC doub 145 n y 
C2 N2 CXC sing 146 n n 
C2 N1 CXC doub 147 n y 
C6 N1 CXC sing 148 n y 
C6 N6 CXC sing 149 n n 
C5' H1 CXC sing 150 n n 
C5' H2 CXC sing 151 n n 
C4' H3 CXC sing 152 n n 
C1' H4 CXC sing 153 n n 
C2' H5 CXC sing 154 n n 
O2' H6 CXC sing 155 n n 
C3' H7 CXC sing 156 n n 
O3' H8 CXC sing 157 n n 
C8 H9 CXC sing 158 n n 
N2 H10 CXC sing 159 n n 
N2 H11 CXC sing 160 n n 
N6 H12 CXC sing 161 n n 
N6 H13 CXC sing 162 n n 
O1A H14 CXC sing 163 n n 
O1B H15 CXC sing 164 n n 
O1G H16 CXC sing 165 n n 
O2G H17 CXC sing 166 n n 
#
_atom_sites.entry_id                     7EM3 
_atom_sites.fract_transf_matrix[1][1]    0.009106 
_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]    0.005378 
_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]    0.009413 
_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 CX0 A 1 501 501 CX0 CXC . 
D 3 CXC A 1 502 502 CXC CXC . 
#
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' CXC . . . D 3 48.828 47.831 -23.215 1 82.85 ? O5' CXC 502 A 1 
HETATM 2 C C5' CXC . . . D 3 49.957 48.533 -22.708 1 89.02 ? C5' CXC 502 A 1 
HETATM 3 C C4' CXC . . . D 3 50.379 49.903 -23.328 1 101.78 ? C4' CXC 502 A 1 
HETATM 4 O O4' CXC . . . D 3 51.165 50.573 -22.318 1 101.8 ? O4' CXC 502 A 1 
HETATM 5 C C1' CXC . . . D 3 52.63 50.386 -22.643 1 101.71 ? C1' CXC 502 A 1 
HETATM 6 N N1 CXC . . . D 3 57.164 48.106 -21.155 1 102.22 ? N1 CXC 502 A 1 
HETATM 7 C C6 CXC . . . D 3 56.178 47.216 -21.402 1 91.26 ? C6 CXC 502 A 1 
HETATM 8 C C2 CXC . . . D 3 56.903 49.429 -21.294 1 111.06 ? C2 CXC 502 A 1 
HETATM 9 N N3 CXC . . . D 3 55.661 49.826 -21.683 1 115 ? N3 CXC 502 A 1 
HETATM 10 C C4 CXC . . . D 3 54.67 48.932 -21.944 1 100.89 ? C4 CXC 502 A 1 
HETATM 11 C C5 CXC . . . D 3 54.958 47.622 -21.792 1 95.54 ? C5 CXC 502 A 1 
HETATM 12 C C2' CXC . . . D 3 52.597 50.738 -24.138 1 109.94 ? C2' CXC 502 A 1 
HETATM 13 O O2' CXC . . . D 3 52.224 52.151 -24.407 1 107.57 ? O2' CXC 502 A 1 
HETATM 14 C C3' CXC . . . D 3 51.461 49.815 -24.51 1 119.41 ? C3' CXC 502 A 1 
HETATM 15 O O3' CXC . . . D 3 50.97 50.243 -25.827 1 136.01 ? O3' CXC 502 A 1 
HETATM 16 C C8 CXC . . . D 3 52.928 47.819 -22.428 1 94.73 ? C8 CXC 502 A 1 
HETATM 17 N N2 CXC . . . D 3 57.859 50.34 -21.039 1 112.05 ? N2 CXC 502 A 1 
HETATM 18 N N6 CXC . . . D 3 56.354 45.896 -21.276 1 74.91 ? N6 CXC 502 A 1 
HETATM 19 N N7 CXC . . . D 3 53.864 46.941 -22.086 1 94.26 ? N7 CXC 502 A 1 
HETATM 20 N N9 CXC . . . D 3 53.382 49.066 -22.345 1 94.59 ? N9 CXC 502 A 1 
HETATM 21 O O1A CXC . . . D 3 50.388 46.724 -24.91 1 118.82 ? O1A CXC 502 A 1 
HETATM 22 O O1B CXC . . . D 3 48.153 43.601 -25.721 1 105.1 ? O1B CXC 502 A 1 
HETATM 23 O O1G CXC . . . D 3 44.451 45.953 -27.88 1 148.68 ? O1G CXC 502 A 1 
HETATM 24 O O2A CXC . . . D 3 48.364 48.16 -25.619 1 126.35 ? O2A CXC 502 A 1 
HETATM 25 O O2B CXC . . . D 3 49.099 45.667 -26.896 1 131.63 ? O2B CXC 502 A 1 
HETATM 26 O O2G CXC . . . D 3 45.901 47.721 -26.79 1 145.59 ? O2G CXC 502 A 1 
HETATM 27 O O3A CXC . . . D 3 48.115 45.879 -24.673 1 135.87 ? O3A CXC 502 A 1 
HETATM 28 O O3B CXC . . . D 3 46.434 45.372 -26.616 1 144.8 ? O3B CXC 502 A 1 
HETATM 29 O O3G CXC . . . D 3 46.747 46.4 -28.774 1 152.87 ? O3G CXC 502 A 1 
HETATM 30 P PA CXC . . . D 3 49.001 47.202 -24.679 1 120.84 ? PA CXC 502 A 1 
HETATM 31 P PB CXC . . . D 3 48.035 45.04 -26.066 1 130.65 ? PB CXC 502 A 1 
HETATM 32 P PG CXC . . . D 3 45.788 46.546 -27.675 1 147.54 ? PG CXC 502 A 1 
#
_model_server_stats.io_time_ms              57 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           32 
#