data_6XB5
#
_model_server_result.job_id            TnbWNpt2kfJOsJ1JJhRq9g 
_model_server_result.datetime_utc      '2025-06-28 11:13:35' 
_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          6xb5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":301}' 
#
_entry.id    6XB5 
#
_exptl.entry_id    6XB5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              692.427 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "2',5'-GpAp" 
_entity.pdbx_number_of_molecules    2 
_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            6XB5 
_cell.length_a            124.422 
_cell.length_b            124.422 
_cell.length_c            132.178 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6XB5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        80 
_symmetry.space_group_name_Hall    'I 4bw' 
_symmetry.space_group_name_H-M     'I 41' 
#
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D N N 
#
_chem_comp.formula           'C20 H26 N10 O14 P2' 
_chem_comp.formula_weight    692.427 
_chem_comp.id                9BG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "2',5'-GpAp" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl [(2~{R},3~{R},4~{R},5~{R})-2-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate' 
#
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
O18 C17 9BG sing 1 n n 
C15 C14 9BG sing 2 n n 
C15 O16 9BG sing 3 n n 
C14 C17 9BG sing 4 n n 
C14 O13 9BG sing 5 n n 
C17 C19 9BG sing 6 n n 
O13 C12 9BG sing 7 n n 
C19 O20 9BG sing 8 n n 
C19 C12 9BG sing 9 n n 
O20 P21 9BG sing 10 n n 
C12 N11 9BG sing 11 n n 
O45 P21 9BG doub 12 n n 
P21 O46 9BG sing 13 n n 
P21 O22 9BG sing 14 n n 
N11 C10 9BG sing 15 n y 
N11 C07 9BG sing 16 n y 
C10 N09 9BG doub 17 n y 
O22 C23 9BG sing 18 n n 
N06 C07 9BG sing 19 n n 
N06 C04 9BG sing 20 n n 
C07 C08 9BG doub 21 n y 
C23 C24 9BG sing 22 n n 
N05 C04 9BG sing 23 n n 
N09 C08 9BG sing 24 n y 
C04 N03 9BG doub 25 n n 
C08 C02 9BG sing 26 n n 
O28 P27 9BG doub 27 n n 
C24 O44 9BG sing 28 n n 
C24 C25 9BG sing 29 n n 
O44 C33 9BG sing 30 n n 
C43 N42 9BG doub 31 n y 
C43 N34 9BG sing 32 n y 
N03 C02 9BG sing 33 n n 
N42 C41 9BG sing 34 n y 
O30 P27 9BG sing 35 n n 
C02 O01 9BG doub 36 n n 
P27 O29 9BG sing 37 n n 
P27 O26 9BG sing 38 n n 
C25 O26 9BG sing 39 n n 
C25 C31 9BG sing 40 n n 
N34 C33 9BG sing 41 n n 
N34 C35 9BG sing 42 n y 
C33 C31 9BG sing 43 n n 
C41 C35 9BG doub 44 n y 
C41 C39 9BG sing 45 n y 
N40 C39 9BG sing 46 n n 
C31 O32 9BG sing 47 n n 
C35 N36 9BG sing 48 n y 
C39 N38 9BG doub 49 n y 
N36 C37 9BG doub 50 n y 
N38 C37 9BG sing 51 n y 
C10 H1 9BG sing 52 n n 
C17 H2 9BG sing 53 n n 
C24 H3 9BG sing 54 n n 
C12 H4 9BG sing 55 n n 
C14 H5 9BG sing 56 n n 
C19 H6 9BG sing 57 n n 
C23 H7 9BG sing 58 n n 
C23 H8 9BG sing 59 n n 
C25 H9 9BG sing 60 n n 
N05 H10 9BG sing 61 n n 
N05 H11 9BG sing 62 n n 
N06 H12 9BG sing 63 n n 
C15 H13 9BG sing 64 n n 
C15 H14 9BG sing 65 n n 
O16 H15 9BG sing 66 n n 
O18 H16 9BG sing 67 n n 
O29 H17 9BG sing 68 n n 
O30 H18 9BG sing 69 n n 
C31 H19 9BG sing 70 n n 
O32 H20 9BG sing 71 n n 
C33 H21 9BG sing 72 n n 
C37 H22 9BG sing 73 n n 
N40 H23 9BG sing 74 n n 
N40 H24 9BG sing 75 n n 
C43 H25 9BG sing 76 n n 
O46 H26 9BG sing 77 n n 
#
_atom_sites.entry_id                     6XB5 
_atom_sites.fract_transf_matrix[1][1]    0.008037 
_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]    0.008037 
_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]    0.007566 
_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 9BG A 1 301 1 9BG 9BG . 
D 2 9BG B 1 301 2 9BG 9BG . 
#
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 C10 9BG . . . D 2 8.451 -32.884 -43.263 1 100.27 ? C10 9BG 301 B 1 
HETATM 2 C C17 9BG . . . D 2 10.353 -36.369 -45.772 1 106.12 ? C17 9BG 301 B 1 
HETATM 3 C C24 9BG . . . D 2 14.809 -37.744 -44.237 1 94.43 ? C24 9BG 301 B 1 
HETATM 4 C C02 9BG . . . D 2 9.4 -33.694 -39.809 1 81.15 ? C02 9BG 301 B 1 
HETATM 5 C C04 9BG . . . D 2 10.546 -35.856 -40.314 1 84.07 ? C04 9BG 301 B 1 
HETATM 6 C C07 9BG . . . D 2 9.491 -34.465 -42.19 1 93.04 ? C07 9BG 301 B 1 
HETATM 7 C C08 9BG . . . D 2 9.086 -33.515 -41.294 1 80.35 ? C08 9BG 301 B 1 
HETATM 8 C C12 9BG . . . D 2 9.295 -34.757 -44.66 1 91.66 ? C12 9BG 301 B 1 
HETATM 9 C C14 9BG . . . D 2 8.874 -36.873 -45.609 1 108.59 ? C14 9BG 301 B 1 
HETATM 10 C C19 9BG . . . D 2 10.482 -35.269 -44.725 1 90 ? C19 9BG 301 B 1 
HETATM 11 C C23 9BG . . . D 2 14.773 -36.216 -44.381 1 91.57 ? C23 9BG 301 B 1 
HETATM 12 C C25 9BG . . . D 2 13.889 -38.169 -43.037 1 85.6 ? C25 9BG 301 B 1 
HETATM 13 N N34 9BG . . . D 2 17.14 -39.041 -41.84 1 76.13 ? N34 9BG 301 B 1 
HETATM 14 O O01 9BG . . . D 2 9.041 -32.856 -39.049 1 86.23 ? O01 9BG 301 B 1 
HETATM 15 N N03 9BG . . . D 2 10.12 -34.852 -39.363 1 89.22 ? N03 9BG 301 B 1 
HETATM 16 N N05 9BG . . . D 2 11.273 -37.043 -39.894 1 73.5 ? N05 9BG 301 B 1 
HETATM 17 N N06 9BG . . . D 2 10.237 -35.679 -41.728 1 83.73 ? N06 9BG 301 B 1 
HETATM 18 N N09 9BG . . . D 2 8.454 -32.547 -41.954 1 69.92 ? N09 9BG 301 B 1 
HETATM 19 N N11 9BG . . . D 2 9.093 -34.069 -43.395 1 101.44 ? N11 9BG 301 B 1 
HETATM 20 O O13 9BG . . . D 2 8.286 -36.02 -44.846 1 93.4 ? O13 9BG 301 B 1 
HETATM 21 C C15 9BG . . . D 2 8.8 -38.31 -44.984 1 96.9 ? C15 9BG 301 B 1 
HETATM 22 O O16 9BG . . . D 2 10.065 -38.906 -44.866 1 100.98 ? O16 9BG 301 B 1 
HETATM 23 O O18 9BG . . . D 2 10.587 -35.908 -47.037 1 100.43 ? O18 9BG 301 B 1 
HETATM 24 O O20 9BG . . . D 2 11.454 -34.187 -45.132 1 88.95 ? O20 9BG 301 B 1 
HETATM 25 P P21 9BG . . . D 2 13.054 -34.341 -44.79 1 87.29 ? P21 9BG 301 B 1 
HETATM 26 O O22 9BG . . . D 2 13.547 -35.893 -44.962 1 91.57 ? O22 9BG 301 B 1 
HETATM 27 O O26 9BG . . . D 2 13.323 -39.337 -43.339 1 101.85 ? O26 9BG 301 B 1 
HETATM 28 P P27 9BG . . . D 2 12.226 -40.16 -42.402 1 94.77 ? P27 9BG 301 B 1 
HETATM 29 O O28 9BG . . . D 2 12.913 -40.846 -41.176 1 121.55 ? O28 9BG 301 B 1 
HETATM 30 O O29 9BG . . . D 2 11.118 -39.192 -42.046 1 95.1 -1 O29 9BG 301 B 1 
HETATM 31 O O30 9BG . . . D 2 11.554 -41.181 -43.299 1 101.14 -1 O30 9BG 301 B 1 
HETATM 32 C C31 9BG . . . D 2 14.992 -38.25 -41.915 1 84.22 ? C31 9BG 301 B 1 
HETATM 33 O O32 9BG . . . D 2 14.46 -38.844 -40.664 1 89.07 ? O32 9BG 301 B 1 
HETATM 34 C C33 9BG . . . D 2 15.889 -38.958 -42.519 1 81.96 ? C33 9BG 301 B 1 
HETATM 35 C C35 9BG . . . D 2 17.75 -40.231 -41.678 1 92.36 ? C35 9BG 301 B 1 
HETATM 36 N N36 9BG . . . D 2 17.407 -41.481 -42.058 1 93.11 ? N36 9BG 301 B 1 
HETATM 37 C C37 9BG . . . D 2 18.217 -42.525 -41.757 1 95.74 ? C37 9BG 301 B 1 
HETATM 38 N N38 9BG . . . D 2 19.373 -42.321 -41.075 1 87.78 ? N38 9BG 301 B 1 
HETATM 39 C C39 9BG . . . D 2 19.721 -41.098 -40.699 1 80.91 ? C39 9BG 301 B 1 
HETATM 40 N N40 9BG . . . D 2 20.995 -41.163 -39.993 1 67.41 ? N40 9BG 301 B 1 
HETATM 41 C C41 9BG . . . D 2 18.894 -40.027 -41.004 1 84.71 ? C41 9BG 301 B 1 
HETATM 42 N N42 9BG . . . D 2 18.984 -38.71 -40.752 1 86.12 ? N42 9BG 301 B 1 
HETATM 43 C C43 9BG . . . D 2 17.904 -38.108 -41.269 1 75.93 ? C43 9BG 301 B 1 
HETATM 44 O O44 9BG . . . D 2 16.026 -38.116 -43.951 1 89.85 ? O44 9BG 301 B 1 
HETATM 45 O O45 9BG . . . D 2 13.276 -33.952 -43.353 1 72.87 ? O45 9BG 301 B 1 
HETATM 46 O O46 9BG . . . D 2 13.859 -33.47 -45.729 1 98.8 -1 O46 9BG 301 B 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           330 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           46 
#