data_4WK1
#
_model_server_result.job_id            PPJC6g84cATreYxKciFJOg 
_model_server_result.datetime_utc      '2025-02-18 00:49:49' 
_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          4wk1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    4WK1 
#
_exptl.entry_id    4WK1 
_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         120 
_cell.entry_id            4WK1 
_cell.length_a            68.1 
_cell.length_b            68.1 
_cell.length_c            135.74 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4WK1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        155 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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    1,2,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_445 -y-1,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -34.05 -58.97633 0 
3 'crystal symmetry operation' 3_545 -x+y,-x-1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 34.05 -58.97633 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 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 A O GLN 31 A GLN 11 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? 
metalc ? metalc2 A O GLN 31 A GLN 11 1_555 C CA CA . A CA 202 11_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? 
metalc ? metalc3 A OE1 GLU 35 A GLU 15 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? 
metalc ? metalc4 A OE2 GLU 35 A GLU 15 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? 
metalc ? metalc5 A OE1 GLU 35 A GLU 15 1_555 C CA CA . A CA 202 11_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? 
metalc ? metalc6 A OE2 GLU 35 A GLU 15 1_555 C CA CA . A CA 202 11_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? 
metalc ? metalc7 C CA CA . A CA 202 1_555 D O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? 
metalc ? metalc8 C CA CA . A CA 202 1_555 D O HOH . A HOH 302 11_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? 
#
_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                     4WK1 
_atom_sites.fract_transf_matrix[1][1]    0.014684 
_atom_sites.fract_transf_matrix[1][2]    0.008478 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016956 
_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]    0.007367 
_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 1 201 1 2BA 2BA . 
C 3 CA A 1 202 4 CA CA . 
D 4 HOH A 1 301 11 HOH HOH . 
D 4 HOH A 2 302 43 HOH HOH . 
D 4 HOH A 3 303 51 HOH HOH . 
D 4 HOH A 4 304 55 HOH HOH . 
D 4 HOH A 5 305 72 HOH HOH . 
D 4 HOH A 6 306 5 HOH HOH . 
D 4 HOH A 7 307 73 HOH HOH . 
D 4 HOH A 8 308 12 HOH HOH . 
D 4 HOH A 9 309 9 HOH HOH . 
D 4 HOH A 10 310 13 HOH HOH . 
D 4 HOH A 11 311 4 HOH HOH . 
D 4 HOH A 12 312 66 HOH HOH . 
D 4 HOH A 13 313 61 HOH HOH . 
D 4 HOH A 14 314 24 HOH HOH . 
D 4 HOH A 15 315 8 HOH HOH . 
D 4 HOH A 16 316 69 HOH HOH . 
D 4 HOH A 17 317 64 HOH HOH . 
D 4 HOH A 18 318 14 HOH HOH . 
D 4 HOH A 19 319 6 HOH HOH . 
D 4 HOH A 20 320 29 HOH HOH . 
D 4 HOH A 21 321 67 HOH HOH . 
D 4 HOH A 22 322 65 HOH HOH . 
D 4 HOH A 23 323 59 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 14.238 -28.817 12.446 1 47 ? P 2BA 201 A 1 
HETATM 2 O O1P 2BA . . . B 2 14.848 -29.245 11.14 1 50.49 ? O1P 2BA 201 A 1 
HETATM 3 O O2P 2BA . . . B 2 13.595 -27.405 12.187 1 51.76 ? O2P 2BA 201 A 1 
HETATM 4 O O5' 2BA . . . B 2 13.168 -29.947 12.791 1 50.07 ? O5' 2BA 201 A 1 
HETATM 5 C C5' 2BA . . . B 2 12.366 -29.782 13.938 1 37.7 ? C5' 2BA 201 A 1 
HETATM 6 C C4' 2BA . . . B 2 11.518 -31.056 14.076 1 48.9 ? C4' 2BA 201 A 1 
HETATM 7 O O4' 2BA . . . B 2 10.844 -31.171 12.927 1 49.82 ? O4' 2BA 201 A 1 
HETATM 8 C C3' 2BA . . . B 2 12.417 -32.264 14.197 1 45.9 ? C3' 2BA 201 A 1 
HETATM 9 O O3' 2BA . . . B 2 12.681 -32.541 15.523 1 43.01 ? O3' 2BA 201 A 1 
HETATM 10 C C2' 2BA . . . B 2 11.472 -33.347 13.546 1 41.24 ? C2' 2BA 201 A 1 
HETATM 11 O O2' 2BA . . . B 2 10.586 -33.869 14.575 1 39.69 ? O2' 2BA 201 A 1 
HETATM 12 C C1' 2BA . . . B 2 10.763 -32.743 12.627 1 40.53 ? C1' 2BA 201 A 1 
HETATM 13 N N9 2BA . . . B 2 11.229 -33.064 11.319 1 45.05 ? N9 2BA 201 A 1 
HETATM 14 C C8 2BA . . . B 2 12.116 -32.174 10.813 1 41.22 ? C8 2BA 201 A 1 
HETATM 15 N N7 2BA . . . B 2 12.49 -32.603 9.56 1 42.71 ? N7 2BA 201 A 1 
HETATM 16 C C5 2BA . . . B 2 11.816 -33.774 9.318 1 39.07 ? C5 2BA 201 A 1 
HETATM 17 C C6 2BA . . . B 2 11.787 -34.68 8.225 1 43.74 ? C6 2BA 201 A 1 
HETATM 18 N N6 2BA . . . B 2 12.452 -34.703 6.969 1 37.72 ? N6 2BA 201 A 1 
HETATM 19 N N1 2BA . . . B 2 11.016 -35.764 8.272 1 40.25 ? N1 2BA 201 A 1 
HETATM 20 C C2 2BA . . . B 2 10.244 -36.022 9.363 1 40.89 ? C2 2BA 201 A 1 
HETATM 21 N N3 2BA . . . B 2 10.262 -35.15 10.444 1 36.69 ? N3 2BA 201 A 1 
HETATM 22 C C4 2BA . . . B 2 11.045 -34.037 10.383 1 37.28 ? C4 2BA 201 A 1 
HETATM 23 P P1 2BA . . . B 2 14.174 -33.066 15.858 1 44.15 ? P1 2BA 201 A 1 
HETATM 24 O O1P1 2BA . . . B 2 14.371 -34.384 15.123 1 45.23 ? O1P1 2BA 201 A 1 
HETATM 25 O O2P1 2BA . . . B 2 14.456 -33.346 17.328 1 51.01 ? O2P1 2BA 201 A 1 
HETATM 26 O "O5'1" 2BA . . . B 2 15.215 -31.977 15.105 1 44.4 ? "O5'1" 2BA 201 A 1 
HETATM 27 C "C5'1" 2BA . . . B 2 15.624 -30.945 15.965 1 46.08 ? "C5'1" 2BA 201 A 1 
HETATM 28 C "C4'1" 2BA . . . B 2 16.673 -30.12 15.273 1 53.1 ? "C4'1" 2BA 201 A 1 
HETATM 29 O "O4'1" 2BA . . . B 2 17.819 -30.713 15.335 1 51.97 ? "O4'1" 2BA 201 A 1 
HETATM 30 C "C3'1" 2BA . . . B 2 16.345 -29.888 13.654 1 53.84 ? "C3'1" 2BA 201 A 1 
HETATM 31 O "O3'1" 2BA . . . B 2 15.538 -28.667 13.488 1 44.91 ? "O3'1" 2BA 201 A 1 
HETATM 32 C "C2'1" 2BA . . . B 2 17.484 -29.741 13.115 1 62.94 ? "C2'1" 2BA 201 A 1 
HETATM 33 O "O2'1" 2BA . . . B 2 17.948 -28.309 13.266 1 55.69 ? "O2'1" 2BA 201 A 1 
HETATM 34 C "C1'1" 2BA . . . B 2 18.49 -30.621 13.957 1 52.89 ? "C1'1" 2BA 201 A 1 
HETATM 35 N N91 2BA . . . B 2 18.692 -31.83 13.458 1 52.78 ? N91 2BA 201 A 1 
HETATM 36 C C81 2BA . . . B 2 17.839 -32.873 13.293 1 51.1 ? C81 2BA 201 A 1 
HETATM 37 N N71 2BA . . . B 2 18.547 -33.907 12.755 1 53.28 ? N71 2BA 201 A 1 
HETATM 38 C C51 2BA . . . B 2 19.842 -33.496 12.598 1 51.02 ? C51 2BA 201 A 1 
HETATM 39 C C61 2BA . . . B 2 20.978 -34.152 12.098 1 65.75 ? C61 2BA 201 A 1 
HETATM 40 N N61 2BA . . . B 2 20.975 -35.515 11.613 1 66.86 ? N61 2BA 201 A 1 
HETATM 41 N N11 2BA . . . B 2 22.175 -33.498 12.053 1 73.05 ? N11 2BA 201 A 1 
HETATM 42 C C21 2BA . . . B 2 22.264 -32.207 12.497 1 72.38 ? C21 2BA 201 A 1 
HETATM 43 N N31 2BA . . . B 2 21.146 -31.564 12.985 1 61.88 ? N31 2BA 201 A 1 
HETATM 44 C C41 2BA . . . B 2 19.935 -32.221 13.037 1 53.76 ? C41 2BA 201 A 1 
#
_model_server_stats.io_time_ms              66 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           234 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           44 
#