data_5CFN
#
_model_server_result.job_id            FrTyL0fAVYiFaOjB5MHUYA 
_model_server_result.datetime_utc      '2025-02-18 02:04:39' 
_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          5cfn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":402}' 
#
_entry.id    5CFN 
#
_exptl.entry_id    5CFN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              658.412 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide" 
_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         120 
_cell.entry_id            5CFN 
_cell.length_a            81.662 
_cell.length_b            81.662 
_cell.length_c            98.76 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5CFN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        144 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31' 
#
_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 H24 N10 O12 P2' 
_chem_comp.formula_weight    658.412 
_chem_comp.id                2BA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate" 
#
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
P O1P 2BA doub 1 n n 
P O2P 2BA sing 2 n n 
P O5' 2BA sing 3 n n 
P "O3'1" 2BA sing 4 n n 
O5' C5' 2BA sing 5 n n 
C5' C4' 2BA sing 6 n n 
C4' O4' 2BA sing 7 n n 
C4' C3' 2BA sing 8 n n 
O4' C1' 2BA sing 9 n n 
C3' O3' 2BA sing 10 n n 
C3' C2' 2BA sing 11 n n 
O3' P1 2BA sing 12 n n 
C2' O2' 2BA sing 13 n n 
C2' C1' 2BA sing 14 n n 
C1' N9 2BA sing 15 n n 
N9 C8 2BA sing 16 n y 
N9 C4 2BA sing 17 n y 
C8 N7 2BA doub 18 n y 
N7 C5 2BA sing 19 n y 
C5 C6 2BA doub 20 n y 
C5 C4 2BA sing 21 n y 
C6 N6 2BA sing 22 n n 
C6 N1 2BA sing 23 n y 
N1 C2 2BA doub 24 n y 
C2 N3 2BA sing 25 n y 
N3 C4 2BA doub 26 n y 
P1 O1P1 2BA doub 27 n n 
P1 O2P1 2BA sing 28 n n 
P1 "O5'1" 2BA sing 29 n n 
"O5'1" "C5'1" 2BA sing 30 n n 
"C5'1" "C4'1" 2BA sing 31 n n 
"C4'1" "O4'1" 2BA sing 32 n n 
"C4'1" "C3'1" 2BA sing 33 n n 
"O4'1" "C1'1" 2BA sing 34 n n 
"C3'1" "O3'1" 2BA sing 35 n n 
"C3'1" "C2'1" 2BA sing 36 n n 
"C2'1" "O2'1" 2BA sing 37 n n 
"C2'1" "C1'1" 2BA sing 38 n n 
"C1'1" N91 2BA sing 39 n n 
N91 C81 2BA sing 40 n y 
N91 C41 2BA sing 41 n y 
C81 N71 2BA doub 42 n y 
N71 C51 2BA sing 43 n y 
C51 C61 2BA doub 44 n y 
C51 C41 2BA sing 45 n y 
C61 N61 2BA sing 46 n n 
C61 N11 2BA sing 47 n y 
N11 C21 2BA doub 48 n y 
C21 N31 2BA sing 49 n y 
N31 C41 2BA doub 50 n y 
C5' H5' 2BA sing 51 n n 
C5' "H5'A" 2BA sing 52 n n 
C4' H4' 2BA sing 53 n n 
C3' H3' 2BA sing 54 n n 
C2' H2' 2BA sing 55 n n 
O2' HO2' 2BA sing 56 n n 
C1' H1' 2BA sing 57 n n 
C8 H8 2BA sing 58 n n 
N6 HN6 2BA sing 59 n n 
N6 HN6A 2BA sing 60 n n 
C2 H2 2BA sing 61 n n 
"C5'1" HC5' 2BA sing 62 n n 
"C5'1" HC5A 2BA sing 63 n n 
"C4'1" HC4' 2BA sing 64 n n 
"C3'1" HC3' 2BA sing 65 n n 
"C2'1" HC2' 2BA sing 66 n n 
"O2'1" HO2A 2BA sing 67 n n 
"C1'1" HC1' 2BA sing 68 n n 
C81 HC8 2BA sing 69 n n 
N61 H1N6 2BA sing 70 n n 
N61 H1NA 2BA sing 71 n n 
C21 HC2 2BA sing 72 n n 
O2P H2P 2BA sing 73 n n 
O2P1 H2OP 2BA sing 74 n n 
#
_atom_sites.entry_id                     5CFN 
_atom_sites.fract_transf_matrix[1][1]    0.012246 
_atom_sites.fract_transf_matrix[1][2]    0.00707 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01414 
_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]    0.010126 
_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 2BA A 1 401 1 2BA LIG . 
D 2 2BA A 1 402 2 2BA LIG . 
#
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 P P 2BA . . . D 2 -23.509 -39.618 -0.074 1 116.78 ? P 2BA 402 A 1 
HETATM 2 O O1P 2BA . . . D 2 -24.485 -40.246 0.878 1 117.07 -1 O1P 2BA 402 A 1 
HETATM 3 O O2P 2BA . . . D 2 -22.781 -38.627 0.752 1 116.65 ? O2P 2BA 402 A 1 
HETATM 4 O O5' 2BA . . . D 2 -24.214 -38.729 -1.25 1 116.75 ? O5' 2BA 402 A 1 
HETATM 5 C C5' 2BA . . . D 2 -25.095 -39.397 -2.186 1 116.71 ? C5' 2BA 402 A 1 
HETATM 6 C C4' 2BA . . . D 2 -25.339 -38.501 -3.337 1 116.48 ? C4' 2BA 402 A 1 
HETATM 7 O O4' 2BA . . . D 2 -25.564 -36.933 -2.836 1 97.96 ? O4' 2BA 402 A 1 
HETATM 8 C C3' 2BA . . . D 2 -24.268 -38.443 -4.121 1 116.22 ? C3' 2BA 402 A 1 
HETATM 9 O O3' 2BA . . . D 2 -24.198 -39.589 -5.034 1 115.98 ? O3' 2BA 402 A 1 
HETATM 10 C C2' 2BA . . . D 2 -24.509 -37.14 -4.895 1 116.25 ? C2' 2BA 402 A 1 
HETATM 11 O O2' 2BA . . . D 2 -25.391 -37.331 -5.867 1 116.23 ? O2' 2BA 402 A 1 
HETATM 12 C C1' 2BA . . . D 2 -25.106 -36.165 -3.773 1 97.99 ? C1' 2BA 402 A 1 
HETATM 13 N N9 2BA . . . D 2 -24.061 -35.349 -3.285 1 98.21 ? N9 2BA 402 A 1 
HETATM 14 C C8 2BA . . . D 2 -23.065 -35.754 -2.504 1 98.24 ? C8 2BA 402 A 1 
HETATM 15 N N7 2BA . . . D 2 -22.249 -34.723 -2.238 1 98.44 ? N7 2BA 402 A 1 
HETATM 16 C C5 2BA . . . D 2 -22.732 -33.614 -2.87 1 98.95 ? C5 2BA 402 A 1 
HETATM 17 C C6 2BA . . . D 2 -22.31 -32.253 -2.96 1 99.47 ? C6 2BA 402 A 1 
HETATM 18 N N6 2BA . . . D 2 -21.161 -31.806 -2.308 1 99.49 ? N6 2BA 402 A 1 
HETATM 19 N N1 2BA . . . D 2 -23.071 -31.409 -3.707 1 99.74 ? N1 2BA 402 A 1 
HETATM 20 C C2 2BA . . . D 2 -24.163 -31.807 -4.333 1 99.54 ? C2 2BA 402 A 1 
HETATM 21 N N3 2BA . . . D 2 -24.583 -33.073 -4.27 1 99.08 ? N3 2BA 402 A 1 
HETATM 22 C C4 2BA . . . D 2 -23.894 -34.013 -3.545 1 98.75 ? C4 2BA 402 A 1 
HETATM 23 P P1 2BA . . . D 2 -22.736 -39.975 -5.652 1 124.52 ? P1 2BA 402 A 1 
HETATM 24 O O1P1 2BA . . . D 2 -22.775 -41.032 -6.673 1 124.87 -1 O1P1 2BA 402 A 1 
HETATM 25 O O2P1 2BA . . . D 2 -22.275 -38.698 -6.417 1 87.11 ? O2P1 2BA 402 A 1 
HETATM 26 O "O5'1" 2BA . . . D 2 -21.642 -40.196 -4.575 1 123.72 ? "O5'1" 2BA 402 A 1 
HETATM 27 C "C5'1" 2BA . . . D 2 -21.729 -41.383 -3.736 1 124.16 ? "C5'1" 2BA 402 A 1 
HETATM 28 C "C4'1" 2BA . . . D 2 -20.753 -41.22 -2.591 1 124.1 ? "C4'1" 2BA 402 A 1 
HETATM 29 O "O4'1" 2BA . . . D 2 -19.634 -40.764 -3.031 1 123.7 ? "O4'1" 2BA 402 A 1 
HETATM 30 C "C3'1" 2BA . . . D 2 -21.289 -40.088 -1.533 1 115.37 ? "C3'1" 2BA 402 A 1 
HETATM 31 O "O3'1" 2BA . . . D 2 -22.368 -40.633 -0.611 1 115.13 ? "O3'1" 2BA 402 A 1 
HETATM 32 C "C2'1" 2BA . . . D 2 -20.274 -39.775 -0.889 1 115.95 ? "C2'1" 2BA 402 A 1 
HETATM 33 O "O2'1" 2BA . . . D 2 -20.058 -40.761 0.246 1 116.37 ? "O2'1" 2BA 402 A 1 
HETATM 34 C "C1'1" 2BA . . . D 2 -19.101 -39.877 -1.93 1 122.87 ? "C1'1" 2BA 402 A 1 
HETATM 35 N N91 2BA . . . D 2 -18.784 -38.684 -2.38 1 122.18 ? N91 2BA 402 A 1 
HETATM 36 C C81 2BA . . . D 2 -19.473 -37.92 -3.26 1 122.22 ? C81 2BA 402 A 1 
HETATM 37 N N71 2BA . . . D 2 -18.868 -36.733 -3.503 1 122.07 ? N71 2BA 402 A 1 
HETATM 38 C C51 2BA . . . D 2 -17.738 -36.763 -2.728 1 121.8 ? C51 2BA 402 A 1 
HETATM 39 C C61 2BA . . . D 2 -16.733 -35.803 -2.579 1 121.36 ? C61 2BA 402 A 1 
HETATM 40 N N61 2BA . . . D 2 -16.751 -34.578 -3.265 1 121.03 ? N61 2BA 402 A 1 
HETATM 41 N N11 2BA . . . D 2 -15.742 -36.146 -1.729 1 121.39 ? N11 2BA 402 A 1 
HETATM 42 C C21 2BA . . . D 2 -15.735 -37.32 -1.083 1 121.42 ? C21 2BA 402 A 1 
HETATM 43 N N31 2BA . . . D 2 -16.674 -38.243 -1.203 1 121.59 ? N31 2BA 402 A 1 
HETATM 44 C C41 2BA . . . D 2 -17.68 -37.938 -2.045 1 121.83 ? C41 2BA 402 A 1 
#
_model_server_stats.io_time_ms              61 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           263 
_model_server_stats.encode_time_ms          15 
_model_server_stats.element_count           44 
#