data_8ZW9
#
_model_server_result.job_id            I9N8ADUdhulQBQax05BHhA 
_model_server_result.datetime_utc      '2024-11-07 04:45:56' 
_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          8zw9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":701}' 
#
_entry.id    8ZW9 
#
_exptl.entry_id    8ZW9 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              639.296 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[(2S,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl 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            8ZW9 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8ZW9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_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    ? 
_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                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C15 H24 N5 O17 P3' 
_chem_comp.formula_weight    639.296 
_chem_comp.id                A1D8A 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[(2S,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl 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
O34 P31 A1D8A doub 1 n n 
P31 O30 A1D8A sing 2 n n 
P31 O33 A1D8A sing 3 n n 
P31 O32 A1D8A sing 4 n n 
O30 C29 A1D8A sing 5 n n 
O36 C35 A1D8A sing 6 n n 
C29 C28 A1D8A sing 7 n n 
C28 C35 A1D8A sing 8 n n 
C28 O27 A1D8A sing 9 n n 
C35 C37 A1D8A sing 10 n n 
N1 C2 A1D8A doub 11 n y 
N1 C6 A1D8A sing 12 n y 
C2 N3 A1D8A sing 13 n y 
O27 C26 A1D8A sing 14 n n 
O38 C37 A1D8A sing 15 n n 
C37 C26 A1D8A sing 16 n n 
N6 C6 A1D8A sing 17 n n 
C6 C5 A1D8A doub 18 n y 
N3 C4 A1D8A doub 19 n y 
C26 O2' A1D8A sing 20 n n 
C5 C4 A1D8A sing 21 n y 
C5 N7 A1D8A sing 22 n y 
C4 N9 A1D8A sing 23 n y 
O2' C2' A1D8A sing 24 n n 
N7 C8 A1D8A doub 25 n y 
N9 C1' A1D8A sing 26 n n 
N9 C8 A1D8A sing 27 n y 
C1' C2' A1D8A sing 28 n n 
C1' O4' A1D8A sing 29 n n 
C2' C3' A1D8A sing 30 n n 
O3' C3' A1D8A sing 31 n n 
O4' C4' A1D8A sing 32 n n 
C3' C4' A1D8A sing 33 n n 
C4' C5' A1D8A sing 34 n n 
C5' O5' A1D8A sing 35 n n 
O5' PA A1D8A sing 36 n n 
O2A PA A1D8A doub 37 n n 
PA O3A A1D8A sing 38 n n 
PA O1A A1D8A sing 39 n n 
O3A PB A1D8A sing 40 n n 
PB O3B A1D8A doub 41 n n 
PB O1B A1D8A sing 42 n n 
PB O2B A1D8A sing 43 n n 
C1' H1 A1D8A sing 44 n n 
C2' H2 A1D8A sing 45 n n 
C3' H3 A1D8A sing 46 n n 
C4' H4 A1D8A sing 47 n n 
C5' H5 A1D8A sing 48 n n 
C5' H6 A1D8A sing 49 n n 
C2 H7 A1D8A sing 50 n n 
C26 H8 A1D8A sing 51 n n 
C28 H9 A1D8A sing 52 n n 
C29 H10 A1D8A sing 53 n n 
C29 H11 A1D8A sing 54 n n 
C35 H12 A1D8A sing 55 n n 
C37 H13 A1D8A sing 56 n n 
C8 H14 A1D8A sing 57 n n 
N6 H15 A1D8A sing 58 n n 
N6 H16 A1D8A sing 59 n n 
O1A H17 A1D8A sing 60 n n 
O1B H18 A1D8A sing 61 n n 
O2B H19 A1D8A sing 62 n n 
O3' H20 A1D8A sing 63 n n 
O32 H21 A1D8A sing 64 n n 
O33 H22 A1D8A sing 65 n n 
O36 H23 A1D8A sing 66 n n 
O38 H24 A1D8A sing 67 n n 
#
_atom_sites.entry_id                     8ZW9 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
_pdbx_nonpoly_scheme.asym_id          D 
_pdbx_nonpoly_scheme.entity_id        4 
_pdbx_nonpoly_scheme.mon_id           A1D8A 
_pdbx_nonpoly_scheme.pdb_strand_id    B 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      701 
_pdbx_nonpoly_scheme.auth_seq_num     701 
_pdbx_nonpoly_scheme.pdb_mon_id       A1D8A 
_pdbx_nonpoly_scheme.auth_mon_id      PRD 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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' A1D8A . . . D 4 101.831 105.041 114.851 1 94.46 ? C1' A1D8A 701 B 1 
HETATM 2 C C2' A1D8A . . . D 4 101.99 103.493 114.302 1 102.94 ? C2' A1D8A 701 B 1 
HETATM 3 C C3' A1D8A . . . D 4 103.087 103.632 113.293 1 103.03 ? C3' A1D8A 701 B 1 
HETATM 4 C C4' A1D8A . . . D 4 103.027 105.154 112.911 1 95.58 ? C4' A1D8A 701 B 1 
HETATM 5 C C5' A1D8A . . . D 4 102.601 105.279 111.565 1 100.4 ? C5' A1D8A 701 B 1 
HETATM 6 O O2' A1D8A . . . D 4 102.446 102.599 115.386 1 108.17 ? O2' A1D8A 701 B 1 
HETATM 7 O O5' A1D8A . . . D 4 103.723 105.134 110.778 1 107.12 ? O5' A1D8A 701 B 1 
HETATM 8 C C2 A1D8A . . . D 4 100.316 107.111 118.41 1 96.66 ? C2 A1D8A 701 B 1 
HETATM 9 C C26 A1D8A . . . D 4 101.301 102.021 116.066 1 97.89 ? C26 A1D8A 701 B 1 
HETATM 10 C C28 A1D8A . . . D 4 101.501 102.011 118.566 1 92.91 ? C28 A1D8A 701 B 1 
HETATM 11 C C29 A1D8A . . . D 4 102.276 102.939 119.535 1 104.18 ? C29 A1D8A 701 B 1 
HETATM 12 C C35 A1D8A . . . D 4 102.299 101.098 118.088 1 88.9 ? C35 A1D8A 701 B 1 
HETATM 13 C C37 A1D8A . . . D 4 101.663 100.697 116.62 1 94.77 ? C37 A1D8A 701 B 1 
HETATM 14 C C4 A1D8A . . . D 4 100.176 105.914 116.457 1 102.36 ? C4 A1D8A 701 B 1 
HETATM 15 C C5 A1D8A . . . D 4 98.816 105.894 116.56 1 98.61 ? C5 A1D8A 701 B 1 
HETATM 16 C C6 A1D8A . . . D 4 98.221 106.528 117.661 1 96.9 ? C6 A1D8A 701 B 1 
HETATM 17 C C8 A1D8A . . . D 4 99.395 104.847 114.781 1 98 ? C8 A1D8A 701 B 1 
HETATM 18 N N1 A1D8A . . . D 4 98.989 107.112 118.542 1 96.63 ? N1 A1D8A 701 B 1 
HETATM 19 N N3 A1D8A . . . D 4 100.908 106.525 117.392 1 98.82 ? N3 A1D8A 701 B 1 
HETATM 20 N N6 A1D8A . . . D 4 96.746 106.534 117.821 1 97.58 ? N6 A1D8A 701 B 1 
HETATM 21 N N7 A1D8A . . . D 4 98.362 105.227 115.509 1 95.45 ? N7 A1D8A 701 B 1 
HETATM 22 N N9 A1D8A . . . D 4 100.497 105.254 115.345 1 97.15 ? N9 A1D8A 701 B 1 
HETATM 23 O O1A A1D8A . . . D 4 102.191 104.197 108.968 1 108.29 ? O1A A1D8A 701 B 1 
HETATM 24 O O1B A1D8A . . . D 4 101.27 106.244 107.148 1 102.11 ? O1B A1D8A 701 B 1 
HETATM 25 O O27 A1D8A . . . D 4 100.99 102.86 117.352 1 99.45 ? O27 A1D8A 701 B 1 
HETATM 26 O O2A A1D8A . . . D 4 104.592 103.991 108.709 1 106.66 ? O2A A1D8A 701 B 1 
HETATM 27 O O2B A1D8A . . . D 4 102.886 107.92 106.513 1 107.93 ? O2B A1D8A 701 B 1 
HETATM 28 O O3' A1D8A . . . D 4 104.44 103.315 113.943 1 109.14 ? O3' A1D8A 701 B 1 
HETATM 29 O O30 A1D8A . . . D 4 103.504 103.315 118.925 1 109.49 ? O30 A1D8A 701 B 1 
HETATM 30 O O32 A1D8A . . . D 4 105.51 104.857 119.522 1 100.34 ? O32 A1D8A 701 B 1 
HETATM 31 O O33 A1D8A . . . D 4 104.393 103.659 121.371 1 111.14 ? O33 A1D8A 701 B 1 
HETATM 32 O O34 A1D8A . . . D 4 105.827 102.411 119.759 1 98.35 ? O34 A1D8A 701 B 1 
HETATM 33 O O36 A1D8A . . . D 4 102.285 99.945 118.938 1 101.91 ? O36 A1D8A 701 B 1 
HETATM 34 O O38 A1D8A . . . D 4 100.473 99.898 116.8 1 100.92 ? O38 A1D8A 701 B 1 
HETATM 35 O O3A A1D8A . . . D 4 103.555 106.258 108.374 1 110.72 ? O3A A1D8A 701 B 1 
HETATM 36 O O3B A1D8A . . . D 4 103.248 105.598 105.881 1 104.09 ? O3B A1D8A 701 B 1 
HETATM 37 O O4' A1D8A . . . D 4 102.003 105.8 113.838 1 90.54 ? O4' A1D8A 701 B 1 
HETATM 38 P P31 A1D8A . . . D 4 104.84 103.574 119.912 1 118.06 ? P31 A1D8A 701 B 1 
HETATM 39 P PA A1D8A . . . D 4 103.509 104.871 109.182 1 112.91 ? PA A1D8A 701 B 1 
HETATM 40 P PB A1D8A . . . D 4 102.713 106.529 106.946 1 117.61 ? PB A1D8A 701 B 1 
#
_model_server_stats.io_time_ms              21 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    43 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           40 
#