data_8AK5
#
_model_server_result.job_id            6R_oiIgjkdnmoofaXZMMgQ 
_model_server_result.datetime_utc      '2024-11-18 04:30:48' 
_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          8ak5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":402}' 
#
_entry.id    8AK5 
#
_exptl.entry_id    8AK5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              559.316 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' 
_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            8AK5 
_cell.length_a            90.986 
_cell.length_b            90.986 
_cell.length_c            144.318 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8AK5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,H,I,J,K,T 1 1 
B,L,M,N,O,P,Q,R,S,U 2 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 M N 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 SG CYS 135 A CYS 141 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? 
metalc ? metalc2 A SG CYS 138 A CYS 144 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? 
metalc ? metalc3 A SG CYS 160 A CYS 166 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc4 A SG CYS 171 A CYS 177 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc5 B SG CYS 135 B CYS 141 1_555 N ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc6 B SG CYS 138 B CYS 144 1_555 N ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc7 B SG CYS 160 B CYS 166 1_555 N ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc8 B SG CYS 171 B CYS 177 1_555 N ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? 
#
_chem_comp.formula           'C15 H23 N5 O14 P2' 
_chem_comp.formula_weight    559.316 
_chem_comp.id                AR6 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     Adenosine-5-Diphosphoribose 
#
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
N1 C2 AR6 doub 13 n y 
N1 C6 AR6 sing 14 n y 
C2 N3 AR6 sing 15 n y 
N3 C4 AR6 doub 16 n y 
C4 C5 AR6 sing 17 n y 
C4 N9 AR6 sing 18 n y 
C5 C6 AR6 doub 19 n y 
C5 N7 AR6 sing 20 n y 
C6 N6 AR6 sing 21 n n 
N7 C8 AR6 doub 22 n y 
C8 N9 AR6 sing 23 n y 
N9 C1' AR6 sing 24 n n 
PA O1A AR6 sing 25 n n 
PA O2A AR6 doub 26 n n 
PA O3A AR6 sing 27 n n 
PA O5' AR6 sing 28 n n 
PB O1B AR6 sing 29 n n 
PB O2B AR6 doub 30 n n 
PB O3A AR6 sing 31 n n 
PB O5D AR6 sing 32 n n 
C1' C2' AR6 sing 33 n n 
C1' O4' AR6 sing 34 n n 
C1D O1D AR6 sing 35 n n 
C1D C2D AR6 sing 36 n n 
C1D O4D AR6 sing 37 n n 
C2' O2' AR6 sing 38 n n 
C2' C3' AR6 sing 39 n n 
C2D O2D AR6 sing 40 n n 
C2D C3D AR6 sing 41 n n 
C3' O3' AR6 sing 42 n n 
C3' C4' AR6 sing 43 n n 
C3D O3D AR6 sing 44 n n 
C3D C4D AR6 sing 45 n n 
C4' O4' AR6 sing 46 n n 
C4' C5' AR6 sing 47 n n 
C4D O4D AR6 sing 48 n n 
C4D C5D AR6 sing 49 n n 
C5' O5' AR6 sing 50 n n 
C5D O5D AR6 sing 51 n n 
C2 H2 AR6 sing 52 n n 
N6 HN6 AR6 sing 53 n n 
N6 HN6A AR6 sing 54 n n 
C8 H8 AR6 sing 55 n n 
C1' H1' AR6 sing 56 n n 
C1D H1D AR6 sing 57 n n 
C2' H2' AR6 sing 58 n n 
O2' HO2' AR6 sing 59 n n 
C2D H2D AR6 sing 60 n n 
O2D HO2D AR6 sing 61 n n 
C3' H3' AR6 sing 62 n n 
O3' HO3' AR6 sing 63 n n 
C3D H3D AR6 sing 64 n n 
O3D HO3D AR6 sing 65 n n 
C4' H4' AR6 sing 66 n n 
C4D H4D AR6 sing 67 n n 
C5' H5' AR6 sing 68 n n 
C5' "H5'A" AR6 sing 69 n n 
C5D H5D AR6 sing 70 n n 
C5D H5DA AR6 sing 71 n n 
O1A H1A AR6 sing 72 n n 
O1B H1B AR6 sing 73 n n 
O1D HD1 AR6 sing 74 n n 
#
_atom_sites.entry_id                     8AK5 
_atom_sites.fract_transf_matrix[1][1]    0.010991 
_atom_sites.fract_transf_matrix[1][2]    0.006345 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012691 
_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]    0.006929 
_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 AR6 A 1 401 500 AR6 AR6 . 
D 3 ZN A 1 402 501 ZN ZN . 
E 4 PCA A 1 403 502 PCA PCA . 
F 5 EDO A 1 404 507 EDO EDO . 
G 6 PGE A 1 405 508 PGE PGE . 
H 7 SO4 A 1 406 2 SO4 SO4 . 
I 7 SO4 A 1 407 4 SO4 SO4 . 
J 7 SO4 A 1 408 6 SO4 SO4 . 
K 7 SO4 A 1 409 7 SO4 SO4 . 
L 8 PEG B 1 401 505 PEG PEG . 
M 2 AR6 B 1 402 500 AR6 AR6 . 
N 3 ZN B 1 403 501 ZN ZN . 
O 4 PCA B 1 404 502 PCA PCA . 
P 8 PEG B 1 405 503 PEG PEG . 
Q 7 SO4 B 1 406 1 SO4 SO4 . 
R 7 SO4 B 1 407 3 SO4 SO4 . 
S 7 SO4 B 1 408 5 SO4 SO4 . 
T 9 HOH A 1 501 21 HOH HOH . 
T 9 HOH A 2 502 19 HOH HOH . 
T 9 HOH A 3 503 39 HOH HOH . 
T 9 HOH A 4 504 10 HOH HOH . 
T 9 HOH A 5 505 6 HOH HOH . 
T 9 HOH A 6 506 30 HOH HOH . 
T 9 HOH A 7 507 18 HOH HOH . 
T 9 HOH A 8 508 17 HOH HOH . 
T 9 HOH A 9 509 23 HOH HOH . 
T 9 HOH A 10 510 4 HOH HOH . 
T 9 HOH A 11 511 24 HOH HOH . 
T 9 HOH A 12 512 34 HOH HOH . 
T 9 HOH A 13 513 14 HOH HOH . 
T 9 HOH A 14 514 27 HOH HOH . 
T 9 HOH A 15 515 22 HOH HOH . 
T 9 HOH A 16 516 40 HOH HOH . 
T 9 HOH A 17 517 25 HOH HOH . 
T 9 HOH A 18 518 13 HOH HOH . 
T 9 HOH A 19 519 9 HOH HOH . 
T 9 HOH A 20 520 32 HOH HOH . 
T 9 HOH A 21 521 26 HOH HOH . 
T 9 HOH A 22 522 11 HOH HOH . 
T 9 HOH A 23 523 15 HOH HOH . 
T 9 HOH A 24 524 12 HOH HOH . 
T 9 HOH A 25 525 3 HOH HOH . 
U 9 HOH B 1 501 28 HOH HOH . 
U 9 HOH B 2 502 41 HOH HOH . 
U 9 HOH B 3 503 1 HOH HOH . 
U 9 HOH B 4 504 2 HOH HOH . 
U 9 HOH B 5 505 36 HOH HOH . 
U 9 HOH B 6 506 33 HOH HOH . 
U 9 HOH B 7 507 16 HOH HOH . 
U 9 HOH B 8 508 20 HOH HOH . 
U 9 HOH B 9 509 29 HOH HOH . 
U 9 HOH B 10 510 38 HOH HOH . 
U 9 HOH B 11 511 37 HOH HOH . 
U 9 HOH B 12 512 35 HOH HOH . 
U 9 HOH B 13 513 8 HOH HOH . 
U 9 HOH B 14 514 5 HOH HOH . 
U 9 HOH B 15 515 7 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 N N1 AR6 . . . M 2 -19.221 24.616 37.017 1 55.13 ? N1 AR6 402 B 1 
HETATM 2 C C2 AR6 . . . M 2 -19.342 25.466 38.053 1 46.97 ? C2 AR6 402 B 1 
HETATM 3 N N3 AR6 . . . M 2 -20.414 25.736 38.798 1 43.53 ? N3 AR6 402 B 1 
HETATM 4 C C4 AR6 . . . M 2 -21.472 25.021 38.367 1 46.08 ? C4 AR6 402 B 1 
HETATM 5 C C5 AR6 . . . M 2 -21.506 24.134 37.314 1 43.59 ? C5 AR6 402 B 1 
HETATM 6 C C6 AR6 . . . M 2 -20.314 23.923 36.604 1 43.38 ? C6 AR6 402 B 1 
HETATM 7 N N6 AR6 . . . M 2 -20.206 23.084 35.574 1 48.71 ? N6 AR6 402 B 1 
HETATM 8 N N7 AR6 . . . M 2 -22.789 23.621 37.17 1 52.33 ? N7 AR6 402 B 1 
HETATM 9 C C8 AR6 . . . M 2 -23.481 24.192 38.124 1 45.26 ? C8 AR6 402 B 1 
HETATM 10 N N9 AR6 . . . M 2 -22.743 25.044 38.87 1 44.21 ? N9 AR6 402 B 1 
HETATM 11 P PA AR6 . . . M 2 -27.12 23.812 43.979 1 53.28 ? PA AR6 402 B 1 
HETATM 12 P PB AR6 . . . M 2 -25.982 22.066 45.92 1 46.88 ? PB AR6 402 B 1 
HETATM 13 C C1' AR6 . . . M 2 -23.179 25.821 40.038 1 48.37 ? C1' AR6 402 B 1 
HETATM 14 O O1A AR6 . . . M 2 -27.741 24.502 45.151 1 56.64 ? O1A AR6 402 B 1 
HETATM 15 O O1B AR6 . . . M 2 -25.165 20.818 45.882 1 46.7 ? O1B AR6 402 B 1 
HETATM 16 C C1D AR6 . . . M 2 -30.556 20.337 47.651 1 56.88 ? C1D AR6 402 B 1 
HETATM 17 O O1D AR6 . . . M 2 -31.716 20.475 48.363 1 74.14 ? O1D AR6 402 B 1 
HETATM 18 C C2' AR6 . . . M 2 -24.53 26.513 39.943 1 43.13 ? C2' AR6 402 B 1 
HETATM 19 O O2' AR6 . . . M 2 -24.323 27.806 39.428 1 42.9 ? O2' AR6 402 B 1 
HETATM 20 O O2A AR6 . . . M 2 -27.849 23.702 42.673 1 49.98 ? O2A AR6 402 B 1 
HETATM 21 O O2B AR6 . . . M 2 -25.311 23.342 46.323 1 43.65 ? O2B AR6 402 B 1 
HETATM 22 C C2D AR6 . . . M 2 -29.985 18.926 47.809 1 54.64 ? C2D AR6 402 B 1 
HETATM 23 O O2D AR6 . . . M 2 -30.135 18.388 49.103 1 58.9 ? O2D AR6 402 B 1 
HETATM 24 C C3' AR6 . . . M 2 -24.986 26.563 41.409 1 48.9 ? C3' AR6 402 B 1 
HETATM 25 O O3' AR6 . . . M 2 -24.61 27.777 42.053 1 48.05 ? O3' AR6 402 B 1 
HETATM 26 O O3A AR6 . . . M 2 -26.679 22.355 44.497 1 51.68 ? O3A AR6 402 B 1 
HETATM 27 C C3D AR6 . . . M 2 -28.51 19.19 47.547 1 59.09 ? C3D AR6 402 B 1 
HETATM 28 O O3D AR6 . . . M 2 -27.629 18.151 47.947 1 54.42 ? O3D AR6 402 B 1 
HETATM 29 C C4' AR6 . . . M 2 -24.264 25.376 42.064 1 43.33 ? C4' AR6 402 B 1 
HETATM 30 O O4' AR6 . . . M 2 -23.279 24.92 41.115 1 50.48 ? O4' AR6 402 B 1 
HETATM 31 C C4D AR6 . . . M 2 -28.342 20.441 48.415 1 56.64 ? C4D AR6 402 B 1 
HETATM 32 O O4D AR6 . . . M 2 -29.542 21.215 48.169 1 61.38 ? O4D AR6 402 B 1 
HETATM 33 C C5' AR6 . . . M 2 -25.128 24.197 42.413 1 51.55 ? C5' AR6 402 B 1 
HETATM 34 O O5' AR6 . . . M 2 -25.692 24.427 43.716 1 51.4 ? O5' AR6 402 B 1 
HETATM 35 C C5D AR6 . . . M 2 -27.14 21.282 48.105 1 56.42 ? C5D AR6 402 B 1 
HETATM 36 O O5D AR6 . . . M 2 -27.3 21.793 46.773 1 49.06 ? O5D AR6 402 B 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           325 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           36 
#