data_7JI4
#
_model_server_result.job_id            e_JB8AYMqrspWxudYVP9lA 
_model_server_result.datetime_utc      '2024-10-19 21:21:36' 
_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          7ji4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":401}' 
#
_entry.id    7JI4 
#
_exptl.entry_id    7JI4 
_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    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            7JI4 
_cell.length_a            54.411 
_cell.length_b            54.411 
_cell.length_c            96.526 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7JI4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C 
_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                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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                     7JI4 
_atom_sites.fract_transf_matrix[1][1]    0.018379 
_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]    0.018379 
_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]    0.01036 
_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
B 2 2BA A 1 401 1 2BA 2BA . 
C 3 HOH A 1 501 22 HOH HOH . 
C 3 HOH A 2 502 2 HOH HOH . 
C 3 HOH A 3 503 18 HOH HOH . 
C 3 HOH A 4 504 1 HOH HOH . 
C 3 HOH A 5 505 8 HOH HOH . 
C 3 HOH A 6 506 21 HOH HOH . 
C 3 HOH A 7 507 4 HOH HOH . 
C 3 HOH A 8 508 23 HOH HOH . 
C 3 HOH A 9 509 17 HOH HOH . 
C 3 HOH A 10 510 3 HOH HOH . 
C 3 HOH A 11 511 6 HOH HOH . 
C 3 HOH A 12 512 28 HOH HOH . 
C 3 HOH A 13 513 20 HOH HOH . 
C 3 HOH A 14 514 16 HOH HOH . 
C 3 HOH A 15 515 9 HOH HOH . 
C 3 HOH A 16 516 11 HOH HOH . 
C 3 HOH A 17 517 14 HOH HOH . 
C 3 HOH A 18 518 10 HOH HOH . 
C 3 HOH A 19 519 7 HOH HOH . 
C 3 HOH A 20 520 24 HOH HOH . 
C 3 HOH A 21 521 25 HOH HOH . 
C 3 HOH A 22 522 15 HOH HOH . 
C 3 HOH A 23 523 26 HOH HOH . 
C 3 HOH A 24 524 29 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 P P 2BA . . . B 2 15.092 29.316 45.83 1 53.82 ? P 2BA 401 A 1 
HETATM 2 O O1P 2BA . . . B 2 13.982 29.194 44.805 1 52.08 ? O1P 2BA 401 A 1 
HETATM 3 O O2P 2BA . . . B 2 15.653 28.002 45.965 1 59.16 -1 O2P 2BA 401 A 1 
HETATM 4 O O5' 2BA . . . B 2 16.254 30.295 45.179 1 55.08 ? O5' 2BA 401 A 1 
HETATM 5 C C5' 2BA . . . B 2 17.453 30.376 45.928 1 51.09 ? C5' 2BA 401 A 1 
HETATM 6 C C4' 2BA . . . B 2 18.237 31.517 45.124 1 57.42 ? C4' 2BA 401 A 1 
HETATM 7 O O4' 2BA . . . B 2 18.081 31.192 43.907 1 52.35 ? O4' 2BA 401 A 1 
HETATM 8 C C3' 2BA . . . B 2 17.52 32.91 45.216 1 49.08 ? C3' 2BA 401 A 1 
HETATM 9 O O3' 2BA . . . B 2 17.956 33.63 46.286 1 55.48 ? O3' 2BA 401 A 1 
HETATM 10 C C2' 2BA . . . B 2 18.077 33.525 43.948 1 50.65 ? C2' 2BA 401 A 1 
HETATM 11 O O2' 2BA . . . B 2 19.45 34.037 44.306 1 44.09 ? O2' 2BA 401 A 1 
HETATM 12 C C1' 2BA . . . B 2 18.187 32.561 43.061 1 42.99 ? C1' 2BA 401 A 1 
HETATM 13 N N9 2BA . . . B 2 17.156 32.681 42.13 1 51.16 ? N9 2BA 401 A 1 
HETATM 14 C C8 2BA . . . B 2 15.931 32.299 42.517 1 52.33 ? C8 2BA 401 A 1 
HETATM 15 N N7 2BA . . . B 2 15.081 32.505 41.506 1 50.9 ? N7 2BA 401 A 1 
HETATM 16 C C5 2BA . . . B 2 15.798 33.038 40.481 1 53.02 ? C5 2BA 401 A 1 
HETATM 17 C C6 2BA . . . B 2 15.442 33.444 39.223 1 48.47 ? C6 2BA 401 A 1 
HETATM 18 N N6 2BA . . . B 2 14.157 33.455 38.53 1 49.03 ? N6 2BA 401 A 1 
HETATM 19 N N1 2BA . . . B 2 16.371 33.921 38.396 1 53.14 ? N1 2BA 401 A 1 
HETATM 20 C C2 2BA . . . B 2 17.669 34.024 38.783 1 49.22 ? C2 2BA 401 A 1 
HETATM 21 N N3 2BA . . . B 2 18.012 33.647 40.008 1 47.94 ? N3 2BA 401 A 1 
HETATM 22 C C4 2BA . . . B 2 17.058 33.144 40.859 1 49.19 ? C4 2BA 401 A 1 
HETATM 23 P P1 2BA . . . B 2 16.681 34.474 47.069 1 52.35 ? P1 2BA 401 A 1 
HETATM 24 O O1P1 2BA . . . B 2 16.01 35.205 45.984 1 56.68 ? O1P1 2BA 401 A 1 
HETATM 25 O O2P1 2BA . . . B 2 17.001 35.402 48.219 1 54.35 -1 O2P1 2BA 401 A 1 
HETATM 26 O "O5'1" 2BA . . . B 2 15.779 33.092 47.475 1 63.64 ? "O5'1" 2BA 401 A 1 
HETATM 27 C "C5'1" 2BA . . . B 2 14.585 33.464 48.144 1 60.68 ? "C5'1" 2BA 401 A 1 
HETATM 28 C "C4'1" 2BA . . . B 2 13.858 32.094 48.387 1 59.03 ? "C4'1" 2BA 401 A 1 
HETATM 29 O "O4'1" 2BA . . . B 2 12.601 32.467 48.625 1 61.7 ? "O4'1" 2BA 401 A 1 
HETATM 30 C "C3'1" 2BA . . . B 2 13.888 31.235 47.127 1 57.06 ? "C3'1" 2BA 401 A 1 
HETATM 31 O "O3'1" 2BA . . . B 2 14.511 30.042 47.3 1 59.43 ? "O3'1" 2BA 401 A 1 
HETATM 32 C "C2'1" 2BA . . . B 2 12.374 30.897 46.92 1 60.27 ? "C2'1" 2BA 401 A 1 
HETATM 33 O "O2'1" 2BA . . . B 2 12.07 29.693 47.812 1 59.19 ? "O2'1" 2BA 401 A 1 
HETATM 34 C "C1'1" 2BA . . . B 2 11.738 31.912 47.385 1 63.68 ? "C1'1" 2BA 401 A 1 
HETATM 35 N N91 2BA . . . B 2 11.431 32.929 46.376 1 62.2 ? N91 2BA 401 A 1 
HETATM 36 C C81 2BA . . . B 2 12.006 32.912 45.111 1 60.02 ? C81 2BA 401 A 1 
HETATM 37 N N71 2BA . . . B 2 11.516 33.909 44.405 1 60.29 ? N71 2BA 401 A 1 
HETATM 38 C C51 2BA . . . B 2 10.619 34.55 45.21 1 59.82 ? C51 2BA 401 A 1 
HETATM 39 C C61 2BA . . . B 2 9.829 35.641 44.993 1 70 ? C61 2BA 401 A 1 
HETATM 40 N N61 2BA . . . B 2 9.875 36.314 43.712 1 75.95 ? N61 2BA 401 A 1 
HETATM 41 N N11 2BA . . . B 2 9.021 36.08 45.969 1 75.08 ? N11 2BA 401 A 1 
HETATM 42 C C21 2BA . . . B 2 8.979 35.447 47.179 1 70.48 ? C21 2BA 401 A 1 
HETATM 43 N N31 2BA . . . B 2 9.769 34.363 47.398 1 64.17 ? N31 2BA 401 A 1 
HETATM 44 C C41 2BA . . . B 2 10.583 33.932 46.406 1 62.03 ? C41 2BA 401 A 1 
#
_model_server_stats.io_time_ms              62 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           280 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           44 
#