data_8AKF
#
_model_server_result.job_id            YX_6j9MwJ4e_wkfgcx0_CA 
_model_server_result.datetime_utc      '2024-12-02 08:34:57' 
_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          8akf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    8AKF 
#
_exptl.entry_id    8AKF 
_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            8AKF 
_cell.length_a            91.033 
_cell.length_b            91.033 
_cell.length_c            143.095 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8AKF 
_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,L,U 1 1 
B,M,N,O,P,Q,R,S,T,V 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? 
metalc ? metalc2 A SG CYS 138 A CYS 144 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? 
metalc ? metalc3 A SG CYS 160 A CYS 166 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? 
metalc ? metalc4 A SG CYS 171 A CYS 177 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? 
metalc ? metalc5 B SG CYS 135 B CYS 141 1_555 N ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? 
metalc ? metalc6 B SG CYS 138 B CYS 144 1_555 N ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc7 B SG CYS 160 B CYS 166 1_555 N ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? 
metalc ? metalc8 B SG CYS 171 B CYS 177 1_555 N ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? 
#
_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 31 n y 
N1 C6 AR6 sing 32 n y 
C2 N3 AR6 sing 33 n y 
N3 C4 AR6 doub 34 n y 
C4 C5 AR6 sing 35 n y 
C4 N9 AR6 sing 36 n y 
C5 C6 AR6 doub 37 n y 
C5 N7 AR6 sing 38 n y 
C6 N6 AR6 sing 39 n n 
N7 C8 AR6 doub 40 n y 
C8 N9 AR6 sing 41 n y 
N9 C1' AR6 sing 42 n n 
PA O1A AR6 sing 43 n n 
PA O2A AR6 doub 44 n n 
PA O3A AR6 sing 45 n n 
PA O5' AR6 sing 46 n n 
PB O1B AR6 sing 47 n n 
PB O2B AR6 doub 48 n n 
PB O3A AR6 sing 49 n n 
PB O5D AR6 sing 50 n n 
C1' C2' AR6 sing 51 n n 
C1' O4' AR6 sing 52 n n 
C1D O1D AR6 sing 53 n n 
C1D C2D AR6 sing 54 n n 
C1D O4D AR6 sing 55 n n 
C2' O2' AR6 sing 56 n n 
C2' C3' AR6 sing 57 n n 
C2D O2D AR6 sing 58 n n 
C2D C3D AR6 sing 59 n n 
C3' O3' AR6 sing 60 n n 
C3' C4' AR6 sing 61 n n 
C3D O3D AR6 sing 62 n n 
C3D C4D AR6 sing 63 n n 
C4' O4' AR6 sing 64 n n 
C4' C5' AR6 sing 65 n n 
C4D O4D AR6 sing 66 n n 
C4D C5D AR6 sing 67 n n 
C5' O5' AR6 sing 68 n n 
C5D O5D AR6 sing 69 n n 
C2 H2 AR6 sing 70 n n 
N6 HN6 AR6 sing 71 n n 
N6 HN6A AR6 sing 72 n n 
C8 H8 AR6 sing 73 n n 
C1' H1' AR6 sing 74 n n 
C1D H1D AR6 sing 75 n n 
C2' H2' AR6 sing 76 n n 
O2' HO2' AR6 sing 77 n n 
C2D H2D AR6 sing 78 n n 
O2D HO2D AR6 sing 79 n n 
C3' H3' AR6 sing 80 n n 
O3' HO3' AR6 sing 81 n n 
C3D H3D AR6 sing 82 n n 
O3D HO3D AR6 sing 83 n n 
C4' H4' AR6 sing 84 n n 
C4D H4D AR6 sing 85 n n 
C5' H5' AR6 sing 86 n n 
C5' "H5'A" AR6 sing 87 n n 
C5D H5D AR6 sing 88 n n 
C5D H5DA AR6 sing 89 n n 
O1A H1A AR6 sing 90 n n 
O1B H1B AR6 sing 91 n n 
O1D HD1 AR6 sing 92 n n 
#
_atom_sites.entry_id                     8AKF 
_atom_sites.fract_transf_matrix[1][1]    0.010985 
_atom_sites.fract_transf_matrix[1][2]    0.006342 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012684 
_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]    0.006988 
_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 PEG A 1 403 502 PEG PEG . 
F 4 PEG A 1 404 502 PEG PEG . 
G 5 SO4 A 1 405 3 SO4 SO4 . 
H 5 SO4 A 1 406 4 SO4 SO4 . 
I 5 SO4 A 1 407 6 SO4 SO4 . 
J 5 SO4 A 1 408 7 SO4 SO4 . 
K 6 3AB A 1 409 1 3AB 3AB . 
L 7 CL A 1 410 1 CL CL . 
M 2 AR6 B 1 401 500 AR6 AR6 . 
N 3 ZN B 1 402 501 ZN ZN . 
O 8 EDO B 1 403 503 EDO EDO . 
P 5 SO4 B 1 404 1 SO4 SO4 . 
Q 5 SO4 B 1 405 2 SO4 SO4 . 
R 5 SO4 B 1 406 5 SO4 SO4 . 
S 5 SO4 B 1 407 8 SO4 SO4 . 
T 6 3AB B 1 408 2 3AB 3AB . 
U 9 HOH A 1 501 32 HOH HOH . 
U 9 HOH A 2 502 23 HOH HOH . 
U 9 HOH A 3 503 11 HOH HOH . 
U 9 HOH A 4 504 7 HOH HOH . 
U 9 HOH A 5 505 48 HOH HOH . 
U 9 HOH A 6 506 39 HOH HOH . 
U 9 HOH A 7 507 27 HOH HOH . 
U 9 HOH A 8 508 14 HOH HOH . 
U 9 HOH A 9 509 5 HOH HOH . 
U 9 HOH A 10 510 30 HOH HOH . 
U 9 HOH A 11 511 36 HOH HOH . 
U 9 HOH A 12 512 45 HOH HOH . 
U 9 HOH A 13 513 19 HOH HOH . 
U 9 HOH A 14 514 25 HOH HOH . 
U 9 HOH A 15 515 15 HOH HOH . 
U 9 HOH A 16 516 42 HOH HOH . 
U 9 HOH A 17 517 50 HOH HOH . 
U 9 HOH A 18 518 49 HOH HOH . 
U 9 HOH A 19 519 46 HOH HOH . 
U 9 HOH A 20 520 44 HOH HOH . 
U 9 HOH A 21 521 31 HOH HOH . 
U 9 HOH A 22 522 16 HOH HOH . 
U 9 HOH A 23 523 20 HOH HOH . 
U 9 HOH A 24 524 38 HOH HOH . 
U 9 HOH A 25 525 1 HOH HOH . 
U 9 HOH A 26 526 4 HOH HOH . 
U 9 HOH A 27 527 43 HOH HOH . 
U 9 HOH A 28 528 21 HOH HOH . 
V 9 HOH B 1 501 33 HOH HOH . 
V 9 HOH B 2 502 47 HOH HOH . 
V 9 HOH B 3 503 12 HOH HOH . 
V 9 HOH B 4 504 10 HOH HOH . 
V 9 HOH B 5 505 17 HOH HOH . 
V 9 HOH B 6 506 22 HOH HOH . 
V 9 HOH B 7 507 37 HOH HOH . 
V 9 HOH B 8 508 8 HOH HOH . 
V 9 HOH B 9 509 24 HOH HOH . 
V 9 HOH B 10 510 9 HOH HOH . 
V 9 HOH B 11 511 18 HOH HOH . 
V 9 HOH B 12 512 13 HOH HOH . 
V 9 HOH B 13 513 28 HOH HOH . 
V 9 HOH B 14 514 29 HOH HOH . 
V 9 HOH B 15 515 41 HOH HOH . 
V 9 HOH B 16 516 2 HOH HOH . 
V 9 HOH B 17 517 26 HOH HOH . 
V 9 HOH B 18 518 34 HOH HOH . 
V 9 HOH B 19 519 3 HOH HOH . 
V 9 HOH B 20 520 35 HOH HOH . 
V 9 HOH B 21 521 40 HOH HOH . 
V 9 HOH B 22 522 51 HOH HOH . 
V 9 HOH B 23 523 6 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 . . . C 2 -29.788 9.522 24.224 1 30.94 ? N1 AR6 401 A 1 
HETATM 2 C C2 AR6 . . . C 2 -30.613 9.325 23.183 1 34.33 ? C2 AR6 401 A 1 
HETATM 3 N N3 AR6 . . . C 2 -31.256 10.217 22.435 1 30.37 ? N3 AR6 401 A 1 
HETATM 4 C C4 AR6 . . . C 2 -30.936 11.459 22.818 1 30.33 ? C4 AR6 401 A 1 
HETATM 5 C C5 AR6 . . . C 2 -30.11 11.825 23.865 1 30.33 ? C5 AR6 401 A 1 
HETATM 6 C C6 AR6 . . . C 2 -29.499 10.786 24.599 1 32.16 ? C6 AR6 401 A 1 
HETATM 7 N N6 AR6 . . . C 2 -28.663 10.957 25.624 1 30.85 ? N6 AR6 401 A 1 
HETATM 8 N N7 AR6 . . . C 2 -30.054 13.203 23.947 1 32.1 ? N7 AR6 401 A 1 
HETATM 9 C C8 AR6 . . . C 2 -30.778 13.632 22.946 1 28.67 ? C8 AR6 401 A 1 
HETATM 10 N N9 AR6 . . . C 2 -31.384 12.617 22.27 1 27.81 ? N9 AR6 401 A 1 
HETATM 11 P PA AR6 . . . C 2 -31.93 17.145 17.055 1 42.08 ? PA AR6 401 A 1 
HETATM 12 P PB AR6 . . . C 2 -29.852 16.737 15.044 1 31.28 ? PB AR6 401 A 1 
HETATM 13 C C1' AR6 . . . C 2 -32.279 12.738 21.115 1 29.04 ? C1' AR6 401 A 1 
HETATM 14 O O1A AR6 . . . C 2 -32.917 17.43 15.969 1 37.28 ? O1A AR6 401 A 1 
HETATM 15 O O1B AR6 . . . C 2 -28.412 16.403 15.129 1 31.9 ? O1B AR6 401 A 1 
HETATM 16 C C1D AR6 . . . C 2 -29.737 21.735 13.454 1 34.28 ? C1D AR6 401 A 1 
HETATM 17 O O1D AR6 . . . C 2 -30.298 22.89 12.92 1 38.66 ? O1D AR6 401 A 1 
HETATM 18 C C2' AR6 . . . C 2 -33.42 13.757 21.216 1 24.09 ? C2' AR6 401 A 1 
HETATM 19 O O2' AR6 . . . C 2 -34.598 13.078 21.589 1 28.55 ? O2' AR6 401 A 1 
HETATM 20 O O2A AR6 . . . C 2 -32.043 17.983 18.291 1 38.49 ? O2A AR6 401 A 1 
HETATM 21 O O2B AR6 . . . C 2 -30.794 15.681 14.622 1 28.27 ? O2B AR6 401 A 1 
HETATM 22 C C2D AR6 . . . C 2 -28.24 21.536 13.158 1 37.81 ? C2D AR6 401 A 1 
HETATM 23 O O2D AR6 . . . C 2 -27.814 21.955 11.873 1 39.31 ? O2D AR6 401 A 1 
HETATM 24 C C3' AR6 . . . C 2 -33.528 14.302 19.777 1 24.44 ? C3' AR6 401 A 1 
HETATM 25 O O3' AR6 . . . C 2 -34.582 13.635 19.128 1 23.38 ? O3' AR6 401 A 1 
HETATM 26 O O3A AR6 . . . C 2 -30.412 17.229 16.478 1 41.48 ? O3A AR6 401 A 1 
HETATM 27 C C3D AR6 . . . C 2 -28.098 20.021 13.307 1 36.37 ? C3D AR6 401 A 1 
HETATM 28 O O3D AR6 . . . C 2 -26.886 19.515 12.737 1 31.51 ? O3D AR6 401 A 1 
HETATM 29 C C4' AR6 . . . C 2 -32.196 13.946 19.113 1 27.26 ? C4' AR6 401 A 1 
HETATM 30 O O4' AR6 . . . C 2 -31.436 13.187 20.091 1 24.5 ? O4' AR6 401 A 1 
HETATM 31 C C4D AR6 . . . C 2 -29.367 19.596 12.57 1 33.52 ? C4D AR6 401 A 1 
HETATM 32 O O4D AR6 . . . C 2 -30.363 20.595 12.904 1 35.15 ? O4D AR6 401 A 1 
HETATM 33 C C5' AR6 . . . C 2 -31.359 15.091 18.631 1 30.24 ? C5' AR6 401 A 1 
HETATM 34 O O5' AR6 . . . C 2 -31.943 15.599 17.403 1 35.31 ? O5' AR6 401 A 1 
HETATM 35 C C5D AR6 . . . C 2 -29.923 18.229 12.868 1 35.68 ? C5D AR6 401 A 1 
HETATM 36 O O5D AR6 . . . C 2 -30.127 18.115 14.292 1 33.81 ? O5D AR6 401 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           28 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           36 
#