data_7EM2
#
_model_server_result.job_id            Ko9_p0xNhRqpNYUeR18Kjg 
_model_server_result.datetime_utc      '2024-11-13 09:45:33' 
_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          7em2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":502}' 
#
_entry.id    7EM2 
#
_exptl.entry_id    7EM2 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              524.165 
_entity.id                          3 
_entity.src_method                  nat 
_entity.type                        non-polymer 
_entity.pdbx_description            '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-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            7EM2 
_cell.length_a            109.848 
_cell.length_b            185.138 
_cell.length_c            105.81 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7EM2 
_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        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,E,F,G 
_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 H15 N4 O15 P3' 
_chem_comp.formula_weight    524.165 
_chem_comp.id                CZF 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-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     'xanthosine triphosphate' 
#
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
O15 P3 CZF doub 127 n n 
P3 O10 CZF sing 128 n n 
P3 O14 CZF sing 129 n n 
P3 O13 CZF sing 130 n n 
O10 P2 CZF sing 131 n n 
O12 P2 CZF doub 132 n n 
P2 O11 CZF sing 133 n n 
P2 O7 CZF sing 134 n n 
O8 P1 CZF doub 135 n n 
O7 P1 CZF sing 136 n n 
P1 O9 CZF sing 137 n n 
P1 O5 CZF sing 138 n n 
O5 C8 CZF sing 139 n n 
C8 C6 CZF sing 140 n n 
C4 C3 CZF sing 141 n n 
C4 C6 CZF sing 142 n n 
C4 O3 CZF sing 143 n n 
C3 O2 CZF sing 144 n n 
C3 C1 CZF sing 145 n n 
O4 C6 CZF sing 146 n n 
O4 C1 CZF sing 147 n n 
C1 N4 CZF sing 148 n n 
N4 C10 CZF sing 149 n y 
N4 C5 CZF sing 150 n y 
C10 N3 CZF doub 151 n y 
C5 N2 CZF sing 152 n n 
C5 C7 CZF doub 153 n y 
N3 C7 CZF sing 154 n y 
N2 C2 CZF sing 155 n n 
C7 C9 CZF sing 156 n n 
C2 O1 CZF doub 157 n n 
C2 N1 CZF sing 158 n n 
C9 N1 CZF sing 159 n n 
C9 O6 CZF doub 160 n n 
C1 H1 CZF sing 161 n n 
C3 H2 CZF sing 162 n n 
C4 H3 CZF sing 163 n n 
C6 H4 CZF sing 164 n n 
C8 H5 CZF sing 165 n n 
C8 H6 CZF sing 166 n n 
C10 H7 CZF sing 167 n n 
N1 H8 CZF sing 168 n n 
N2 H9 CZF sing 169 n n 
O2 H10 CZF sing 170 n n 
O3 H11 CZF sing 171 n n 
O9 H12 CZF sing 172 n n 
O11 H13 CZF sing 173 n n 
O13 H14 CZF sing 174 n n 
O14 H15 CZF sing 175 n n 
#
_atom_sites.entry_id                     7EM2 
_atom_sites.fract_transf_matrix[1][1]    0.009103 
_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]    0.005401 
_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]    0.009451 
_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 CZC A 1 501 501 CZC CZC . 
D 3 CZF A 1 502 502 CZF CZF . 
E 2 CZC B 1 501 501 CZC CZC . 
F 4 HOH A 1 601 601 HOH HOH . 
F 4 HOH A 2 602 602 HOH HOH . 
G 4 HOH B 1 601 601 HOH HOH . 
G 4 HOH B 2 602 602 HOH HOH . 
G 4 HOH B 3 603 603 HOH HOH . 
G 4 HOH B 4 604 604 HOH HOH . 
G 4 HOH B 5 605 605 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 C C1 CZF . . . D 3 52.768 48.462 -22.067 1 100.07 ? C1 CZF 502 A 1 
HETATM 2 C C2 CZF . . . D 3 57.338 47.954 -21.582 1 102.01 ? C2 CZF 502 A 1 
HETATM 3 C C3 CZF . . . D 3 53.244 49.38 -23.156 1 106.55 ? C3 CZF 502 A 1 
HETATM 4 C C4 CZF . . . D 3 51.976 49.596 -23.936 1 104.46 ? C4 CZF 502 A 1 
HETATM 5 C C5 CZF . . . D 3 55.002 47.304 -21.669 1 87.55 ? C5 CZF 502 A 1 
HETATM 6 C C6 CZF . . . D 3 50.928 49.413 -22.823 1 99.09 ? C6 CZF 502 A 1 
HETATM 7 C C7 CZF . . . D 3 55.347 46.042 -21.395 1 89.53 ? C7 CZF 502 A 1 
HETATM 8 C C8 CZF . . . D 3 49.517 49.346 -23.398 1 87.5 ? C8 CZF 502 A 1 
HETATM 9 C C9 CZF . . . D 3 56.617 45.682 -21.211 1 97.9 ? C9 CZF 502 A 1 
HETATM 10 C C10 CZF . . . D 3 53.202 46.101 -21.604 1 86.89 ? C10 CZF 502 A 1 
HETATM 11 N N1 CZF . . . D 3 57.659 46.621 -21.297 1 99.23 ? N1 CZF 502 A 1 
HETATM 12 N N2 CZF . . . D 3 55.987 48.299 -21.77 1 90.75 ? N2 CZF 502 A 1 
HETATM 13 N N3 CZF . . . D 3 54.234 45.307 -21.356 1 88.47 ? N3 CZF 502 A 1 
HETATM 14 N N4 CZF . . . D 3 53.676 47.328 -21.801 1 88.47 ? N4 CZF 502 A 1 
HETATM 15 O O1 CZF . . . D 3 58.222 48.811 -21.654 1 107.84 ? O1 CZF 502 A 1 
HETATM 16 O O2 CZF . . . D 3 53.522 50.545 -22.452 1 113.48 ? O2 CZF 502 A 1 
HETATM 17 O O3 CZF . . . D 3 51.991 50.911 -24.533 1 102.63 ? O3 CZF 502 A 1 
HETATM 18 O O4 CZF . . . D 3 51.38 48.137 -22.413 1 105.14 ? O4 CZF 502 A 1 
HETATM 19 O O5 CZF . . . D 3 48.808 48.146 -23.096 1 70.73 ? O5 CZF 502 A 1 
HETATM 20 O O6 CZF . . . D 3 56.875 44.507 -20.959 1 105.7 ? O6 CZF 502 A 1 
HETATM 21 O O7 CZF . . . D 3 47.871 46.092 -24.712 1 119.65 ? O7 CZF 502 A 1 
HETATM 22 O O8 CZF . . . D 3 50.255 46.842 -24.855 1 97.15 ? O8 CZF 502 A 1 
HETATM 23 O O9 CZF . . . D 3 49.343 45.917 -22.489 1 93.78 ? O9 CZF 502 A 1 
HETATM 24 O O10 CZF . . . D 3 46.771 44.634 -26.768 1 131.43 ? O10 CZF 502 A 1 
HETATM 25 O O11 CZF . . . D 3 48.195 43.368 -25.229 1 86.41 ? O11 CZF 502 A 1 
HETATM 26 O O12 CZF . . . D 3 49.453 45.074 -26.605 1 113.02 ? O12 CZF 502 A 1 
HETATM 27 O O13 CZF . . . D 3 44.37 45.187 -27.729 1 129.2 ? O13 CZF 502 A 1 
HETATM 28 O O14 CZF . . . D 3 46.027 47.137 -27.198 1 131.53 ? O14 CZF 502 A 1 
HETATM 29 O O15 CZF . . . D 3 46.442 45.56 -29.196 1 135.73 ? O15 CZF 502 A 1 
HETATM 30 P P1 CZF . . . D 3 49.074 46.741 -23.698 1 97.42 ? P1 CZF 502 A 1 
HETATM 31 P P2 CZF . . . D 3 48.172 44.856 -25.883 1 117.43 ? P2 CZF 502 A 1 
HETATM 32 P P3 CZF . . . D 3 45.952 45.638 -27.799 1 135.03 ? P3 CZF 502 A 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           32 
#