data_8AKE
#
_model_server_result.job_id            Ac11QUSEe-yX4S-5ctx2RA 
_model_server_result.datetime_utc      '2024-11-18 04:41:13' 
_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          8ake 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    8AKE 
#
_exptl.entry_id    8AKE 
_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            8AKE 
_cell.length_a            91.106 
_cell.length_b            91.106 
_cell.length_c            143.428 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8AKE 
_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,P 1 1 
B,K,L,M,N,O,Q 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 L 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? 
metalc ? metalc2 A SG CYS 138 A CYS 144 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc3 A SG CYS 160 A CYS 166 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? 
metalc ? metalc4 A SG CYS 171 A CYS 177 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? 
metalc ? metalc5 B SG CYS 135 B CYS 141 1_555 M ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? 
metalc ? metalc6 B SG CYS 138 B CYS 144 1_555 M ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc7 B SG CYS 160 B CYS 166 1_555 M ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? 
metalc ? metalc8 B SG CYS 171 B CYS 177 1_555 M ZN ZN . B ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? 
#
_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                     8AKE 
_atom_sites.fract_transf_matrix[1][1]    0.010976 
_atom_sites.fract_transf_matrix[1][2]    0.006337 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012674 
_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]    0.006972 
_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 NCA A 1 403 502 NCA NCA . 
F 5 EDO A 1 404 504 EDO EDO . 
G 6 PEG A 1 405 503 PEG PEG . 
H 7 SO4 A 1 406 1 SO4 SO4 . 
I 7 SO4 A 1 407 3 SO4 SO4 . 
J 7 SO4 A 1 408 4 SO4 SO4 . 
K 6 PEG B 1 401 505 PEG PEG . 
L 2 AR6 B 1 402 500 AR6 AR6 . 
M 3 ZN B 1 403 501 ZN ZN . 
N 4 NCA B 1 404 502 NCA NCA . 
O 7 SO4 B 1 405 2 SO4 SO4 . 
P 8 HOH A 1 501 25 HOH HOH . 
P 8 HOH A 2 502 80 HOH HOH . 
P 8 HOH A 3 503 41 HOH HOH . 
P 8 HOH A 4 504 48 HOH HOH . 
P 8 HOH A 5 505 20 HOH HOH . 
P 8 HOH A 6 506 76 HOH HOH . 
P 8 HOH A 7 507 84 HOH HOH . 
P 8 HOH A 8 508 96 HOH HOH . 
P 8 HOH A 9 509 36 HOH HOH . 
P 8 HOH A 10 510 32 HOH HOH . 
P 8 HOH A 11 511 92 HOH HOH . 
P 8 HOH A 12 512 94 HOH HOH . 
P 8 HOH A 13 513 55 HOH HOH . 
P 8 HOH A 14 514 13 HOH HOH . 
P 8 HOH A 15 515 46 HOH HOH . 
P 8 HOH A 16 516 33 HOH HOH . 
P 8 HOH A 17 517 22 HOH HOH . 
P 8 HOH A 18 518 79 HOH HOH . 
P 8 HOH A 19 519 26 HOH HOH . 
P 8 HOH A 20 520 69 HOH HOH . 
P 8 HOH A 21 521 73 HOH HOH . 
P 8 HOH A 22 522 64 HOH HOH . 
P 8 HOH A 23 523 82 HOH HOH . 
P 8 HOH A 24 524 87 HOH HOH . 
P 8 HOH A 25 525 58 HOH HOH . 
P 8 HOH A 26 526 34 HOH HOH . 
P 8 HOH A 27 527 10 HOH HOH . 
P 8 HOH A 28 528 77 HOH HOH . 
P 8 HOH A 29 529 52 HOH HOH . 
P 8 HOH A 30 530 24 HOH HOH . 
P 8 HOH A 31 531 27 HOH HOH . 
P 8 HOH A 32 532 6 HOH HOH . 
P 8 HOH A 33 533 8 HOH HOH . 
P 8 HOH A 34 534 65 HOH HOH . 
P 8 HOH A 35 535 2 HOH HOH . 
P 8 HOH A 36 536 44 HOH HOH . 
P 8 HOH A 37 537 61 HOH HOH . 
P 8 HOH A 38 538 28 HOH HOH . 
P 8 HOH A 39 539 35 HOH HOH . 
P 8 HOH A 40 540 93 HOH HOH . 
P 8 HOH A 41 541 38 HOH HOH . 
P 8 HOH A 42 542 50 HOH HOH . 
P 8 HOH A 43 543 29 HOH HOH . 
P 8 HOH A 44 544 31 HOH HOH . 
P 8 HOH A 45 545 1 HOH HOH . 
P 8 HOH A 46 546 5 HOH HOH . 
P 8 HOH A 47 547 37 HOH HOH . 
P 8 HOH A 48 548 75 HOH HOH . 
P 8 HOH A 49 549 81 HOH HOH . 
P 8 HOH A 50 550 59 HOH HOH . 
P 8 HOH A 51 551 42 HOH HOH . 
P 8 HOH A 52 552 19 HOH HOH . 
P 8 HOH A 53 553 95 HOH HOH . 
Q 8 HOH B 1 501 49 HOH HOH . 
Q 8 HOH B 2 502 86 HOH HOH . 
Q 8 HOH B 3 503 85 HOH HOH . 
Q 8 HOH B 4 504 83 HOH HOH . 
Q 8 HOH B 5 505 60 HOH HOH . 
Q 8 HOH B 6 506 45 HOH HOH . 
Q 8 HOH B 7 507 53 HOH HOH . 
Q 8 HOH B 8 508 91 HOH HOH . 
Q 8 HOH B 9 509 90 HOH HOH . 
Q 8 HOH B 10 510 88 HOH HOH . 
Q 8 HOH B 11 511 74 HOH HOH . 
Q 8 HOH B 12 512 63 HOH HOH . 
Q 8 HOH B 13 513 66 HOH HOH . 
Q 8 HOH B 14 514 14 HOH HOH . 
Q 8 HOH B 15 515 18 HOH HOH . 
Q 8 HOH B 16 516 30 HOH HOH . 
Q 8 HOH B 17 517 21 HOH HOH . 
Q 8 HOH B 18 518 39 HOH HOH . 
Q 8 HOH B 19 519 15 HOH HOH . 
Q 8 HOH B 20 520 16 HOH HOH . 
Q 8 HOH B 21 521 56 HOH HOH . 
Q 8 HOH B 22 522 9 HOH HOH . 
Q 8 HOH B 23 523 70 HOH HOH . 
Q 8 HOH B 24 524 71 HOH HOH . 
Q 8 HOH B 25 525 47 HOH HOH . 
Q 8 HOH B 26 526 12 HOH HOH . 
Q 8 HOH B 27 527 57 HOH HOH . 
Q 8 HOH B 28 528 67 HOH HOH . 
Q 8 HOH B 29 529 3 HOH HOH . 
Q 8 HOH B 30 530 40 HOH HOH . 
Q 8 HOH B 31 531 17 HOH HOH . 
Q 8 HOH B 32 532 51 HOH HOH . 
Q 8 HOH B 33 533 62 HOH HOH . 
Q 8 HOH B 34 534 43 HOH HOH . 
Q 8 HOH B 35 535 68 HOH HOH . 
Q 8 HOH B 36 536 78 HOH HOH . 
Q 8 HOH B 37 537 4 HOH HOH . 
Q 8 HOH B 38 538 7 HOH HOH . 
Q 8 HOH B 39 539 72 HOH HOH . 
Q 8 HOH B 40 540 23 HOH HOH . 
Q 8 HOH B 41 541 54 HOH HOH . 
Q 8 HOH B 42 542 89 HOH HOH . 
Q 8 HOH B 43 543 11 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 -29.768 9.638 24.307 1 28.65 ? N1 AR6 401 A 1 
HETATM 2 C C2 AR6 . . . C 2 -30.544 9.482 23.226 1 32.42 ? C2 AR6 401 A 1 
HETATM 3 N N3 AR6 . . . C 2 -31.108 10.405 22.448 1 32.13 ? N3 AR6 401 A 1 
HETATM 4 C C4 AR6 . . . C 2 -30.855 11.637 22.911 1 27.39 ? C4 AR6 401 A 1 
HETATM 5 C C5 AR6 . . . C 2 -30.113 11.952 24.028 1 23.88 ? C5 AR6 401 A 1 
HETATM 6 C C6 AR6 . . . C 2 -29.539 10.891 24.757 1 26.95 ? C6 AR6 401 A 1 
HETATM 7 N N6 AR6 . . . C 2 -28.771 11.066 25.827 1 30.02 ? N6 AR6 401 A 1 
HETATM 8 N N7 AR6 . . . C 2 -30.074 13.311 24.193 1 22.85 ? N7 AR6 401 A 1 
HETATM 9 C C8 AR6 . . . C 2 -30.801 13.804 23.213 1 28.25 ? C8 AR6 401 A 1 
HETATM 10 N N9 AR6 . . . C 2 -31.305 12.822 22.395 1 24.56 ? N9 AR6 401 A 1 
HETATM 11 P PA AR6 . . . C 2 -31.842 17.226 17.231 1 29.12 ? PA AR6 401 A 1 
HETATM 12 P PB AR6 . . . C 2 -29.762 16.773 15.15 1 28.16 ? PB AR6 401 A 1 
HETATM 13 C C1' AR6 . . . C 2 -32.125 12.939 21.191 1 22.18 ? C1' AR6 401 A 1 
HETATM 14 O O1A AR6 . . . C 2 -32.738 17.582 16.104 1 31.9 ? O1A AR6 401 A 1 
HETATM 15 O O1B AR6 . . . C 2 -28.277 16.566 15.26 1 29.74 ? O1B AR6 401 A 1 
HETATM 16 C C1D AR6 . . . C 2 -29.742 21.91 13.485 1 27.99 ? C1D AR6 401 A 1 
HETATM 17 O O1D AR6 . . . C 2 -30.237 22.963 12.693 1 28.56 ? O1D AR6 401 A 1 
HETATM 18 C C2' AR6 . . . C 2 -33.294 13.918 21.213 1 18.84 ? C2' AR6 401 A 1 
HETATM 19 O O2' AR6 . . . C 2 -34.495 13.335 21.599 1 21.3 ? O2' AR6 401 A 1 
HETATM 20 O O2A AR6 . . . C 2 -31.785 17.986 18.523 1 29.14 ? O2A AR6 401 A 1 
HETATM 21 O O2B AR6 . . . C 2 -30.597 15.724 14.509 1 23.47 ? O2B AR6 401 A 1 
HETATM 22 C C2D AR6 . . . C 2 -28.229 21.713 13.269 1 29.45 ? C2D AR6 401 A 1 
HETATM 23 O O2D AR6 . . . C 2 -27.819 22.132 11.981 1 30.72 ? O2D AR6 401 A 1 
HETATM 24 C C3' AR6 . . . C 2 -33.407 14.378 19.76 1 20.87 ? C3' AR6 401 A 1 
HETATM 25 O O3' AR6 . . . C 2 -34.512 13.804 19.089 1 16.6 ? O3' AR6 401 A 1 
HETATM 26 O O3A AR6 . . . C 2 -30.35 17.114 16.622 1 35.68 ? O3A AR6 401 A 1 
HETATM 27 C C3D AR6 . . . C 2 -28.055 20.213 13.52 1 30.92 ? C3D AR6 401 A 1 
HETATM 28 O O3D AR6 . . . C 2 -26.846 19.614 13.027 1 30.68 ? O3D AR6 401 A 1 
HETATM 29 C C4' AR6 . . . C 2 -32.061 14.005 19.148 1 23.81 ? C4' AR6 401 A 1 
HETATM 30 O O4' AR6 . . . C 2 -31.27 13.353 20.173 1 23.71 ? O4' AR6 401 A 1 
HETATM 31 C C4D AR6 . . . C 2 -29.293 19.72 12.769 1 28.14 ? C4D AR6 401 A 1 
HETATM 32 O O4D AR6 . . . C 2 -30.324 20.669 13.116 1 26.6 ? O4D AR6 401 A 1 
HETATM 33 C C5' AR6 . . . C 2 -31.292 15.164 18.618 1 27.38 ? C5' AR6 401 A 1 
HETATM 34 O O5' AR6 . . . C 2 -32.119 15.741 17.601 1 27.11 ? O5' AR6 401 A 1 
HETATM 35 C C5D AR6 . . . C 2 -29.776 18.322 13.063 1 33.58 ? C5D AR6 401 A 1 
HETATM 36 O O5D AR6 . . . C 2 -30.049 18.181 14.488 1 30.32 ? O5D AR6 401 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           328 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           36 
#