data_8AK6 # _model_server_result.job_id G1KsFFZZ5RspEX63H3NGnw _model_server_result.datetime_utc '2024-11-29 14:04:46' _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 8ak6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":401}' # _entry.id 8AK6 # _exptl.entry_id 8AK6 _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 8AK6 _cell.length_a 90.995 _cell.length_b 90.995 _cell.length_c 144.163 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8AK6 _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,M,S 1 1 B,N,O,P,Q,R,T 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 N 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc2 A SG CYS 138 A CYS 144 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc3 A SG CYS 160 A CYS 166 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc4 A SG CYS 171 A CYS 177 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc5 B SG CYS 135 B CYS 141 1_555 O ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc6 B SG CYS 138 B CYS 144 1_555 O ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc7 B SG CYS 160 B CYS 166 1_555 O ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc8 B SG CYS 171 B CYS 177 1_555 O ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? # _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 42 n y N1 C6 AR6 sing 43 n y C2 N3 AR6 sing 44 n y N3 C4 AR6 doub 45 n y C4 C5 AR6 sing 46 n y C4 N9 AR6 sing 47 n y C5 C6 AR6 doub 48 n y C5 N7 AR6 sing 49 n y C6 N6 AR6 sing 50 n n N7 C8 AR6 doub 51 n y C8 N9 AR6 sing 52 n y N9 C1' AR6 sing 53 n n PA O1A AR6 sing 54 n n PA O2A AR6 doub 55 n n PA O3A AR6 sing 56 n n PA O5' AR6 sing 57 n n PB O1B AR6 sing 58 n n PB O2B AR6 doub 59 n n PB O3A AR6 sing 60 n n PB O5D AR6 sing 61 n n C1' C2' AR6 sing 62 n n C1' O4' AR6 sing 63 n n C1D O1D AR6 sing 64 n n C1D C2D AR6 sing 65 n n C1D O4D AR6 sing 66 n n C2' O2' AR6 sing 67 n n C2' C3' AR6 sing 68 n n C2D O2D AR6 sing 69 n n C2D C3D AR6 sing 70 n n C3' O3' AR6 sing 71 n n C3' C4' AR6 sing 72 n n C3D O3D AR6 sing 73 n n C3D C4D AR6 sing 74 n n C4' O4' AR6 sing 75 n n C4' C5' AR6 sing 76 n n C4D O4D AR6 sing 77 n n C4D C5D AR6 sing 78 n n C5' O5' AR6 sing 79 n n C5D O5D AR6 sing 80 n n C2 H2 AR6 sing 81 n n N6 HN6 AR6 sing 82 n n N6 HN6A AR6 sing 83 n n C8 H8 AR6 sing 84 n n C1' H1' AR6 sing 85 n n C1D H1D AR6 sing 86 n n C2' H2' AR6 sing 87 n n O2' HO2' AR6 sing 88 n n C2D H2D AR6 sing 89 n n O2D HO2D AR6 sing 90 n n C3' H3' AR6 sing 91 n n O3' HO3' AR6 sing 92 n n C3D H3D AR6 sing 93 n n O3D HO3D AR6 sing 94 n n C4' H4' AR6 sing 95 n n C4D H4D AR6 sing 96 n n C5' H5' AR6 sing 97 n n C5' "H5'A" AR6 sing 98 n n C5D H5D AR6 sing 99 n n C5D H5DA AR6 sing 100 n n O1A H1A AR6 sing 101 n n O1B H1B AR6 sing 102 n n O1D HD1 AR6 sing 103 n n # _atom_sites.entry_id 8AK6 _atom_sites.fract_transf_matrix[1][1] 0.01099 _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] 0.01269 _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] 0.006937 _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 08D A 1 403 502 08D 08D . F 5 PEG A 1 404 503 PEG PEG . G 6 EDO A 1 405 505 EDO EDO . H 6 EDO A 1 406 506 EDO EDO . I 6 EDO A 1 407 503 EDO EDO . J 7 SO4 A 1 408 1 SO4 SO4 . K 7 SO4 A 1 409 3 SO4 SO4 . L 7 SO4 A 1 410 4 SO4 SO4 . M 7 SO4 A 1 411 5 SO4 SO4 . N 2 AR6 B 1 401 500 AR6 AR6 . O 3 ZN B 1 402 501 ZN ZN . P 4 08D B 1 403 502 08D 08D . Q 6 EDO B 1 404 504 EDO EDO . R 7 SO4 B 1 405 2 SO4 SO4 . S 8 HOH A 1 501 12 HOH HOH . S 8 HOH A 2 502 32 HOH HOH . S 8 HOH A 3 503 5 HOH HOH . S 8 HOH A 4 504 2 HOH HOH . S 8 HOH A 5 505 45 HOH HOH . S 8 HOH A 6 506 44 HOH HOH . S 8 HOH A 7 507 10 HOH HOH . S 8 HOH A 8 508 35 HOH HOH . S 8 HOH A 9 509 23 HOH HOH . S 8 HOH A 10 510 54 HOH HOH . S 8 HOH A 11 511 6 HOH HOH . S 8 HOH A 12 512 42 HOH HOH . S 8 HOH A 13 513 15 HOH HOH . S 8 HOH A 14 514 19 HOH HOH . S 8 HOH A 15 515 29 HOH HOH . S 8 HOH A 16 516 55 HOH HOH . S 8 HOH A 17 517 33 HOH HOH . S 8 HOH A 18 518 27 HOH HOH . S 8 HOH A 19 519 25 HOH HOH . S 8 HOH A 20 520 52 HOH HOH . S 8 HOH A 21 521 36 HOH HOH . S 8 HOH A 22 522 26 HOH HOH . S 8 HOH A 23 523 39 HOH HOH . S 8 HOH A 24 524 1 HOH HOH . S 8 HOH A 25 525 50 HOH HOH . S 8 HOH A 26 526 46 HOH HOH . S 8 HOH A 27 527 43 HOH HOH . S 8 HOH A 28 528 47 HOH HOH . S 8 HOH A 29 529 49 HOH HOH . S 8 HOH A 30 530 17 HOH HOH . S 8 HOH A 31 531 53 HOH HOH . S 8 HOH A 32 532 34 HOH HOH . S 8 HOH A 33 533 31 HOH HOH . T 8 HOH B 1 501 3 HOH HOH . T 8 HOH B 2 502 30 HOH HOH . T 8 HOH B 3 503 7 HOH HOH . T 8 HOH B 4 504 22 HOH HOH . T 8 HOH B 5 505 8 HOH HOH . T 8 HOH B 6 506 41 HOH HOH . T 8 HOH B 7 507 20 HOH HOH . T 8 HOH B 8 508 24 HOH HOH . T 8 HOH B 9 509 38 HOH HOH . T 8 HOH B 10 510 21 HOH HOH . T 8 HOH B 11 511 28 HOH HOH . T 8 HOH B 12 512 18 HOH HOH . T 8 HOH B 13 513 9 HOH HOH . T 8 HOH B 14 514 13 HOH HOH . T 8 HOH B 15 515 40 HOH HOH . T 8 HOH B 16 516 37 HOH HOH . T 8 HOH B 17 517 48 HOH HOH . T 8 HOH B 18 518 4 HOH HOH . T 8 HOH B 19 519 14 HOH HOH . T 8 HOH B 20 520 51 HOH HOH . T 8 HOH B 21 521 11 HOH HOH . T 8 HOH B 22 522 16 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 . . . N 2 -19.255 24.576 36.947 1 38.07 ? N1 AR6 401 B 1 HETATM 2 C C2 AR6 . . . N 2 -19.435 25.443 37.953 1 35.81 ? C2 AR6 401 B 1 HETATM 3 N N3 AR6 . . . N 2 -20.548 25.745 38.612 1 39.25 ? N3 AR6 401 B 1 HETATM 4 C C4 AR6 . . . N 2 -21.565 24.996 38.163 1 37.77 ? C4 AR6 401 B 1 HETATM 5 C C5 AR6 . . . N 2 -21.549 24.093 37.128 1 38.33 ? C5 AR6 401 B 1 HETATM 6 C C6 AR6 . . . N 2 -20.323 23.886 36.477 1 39.39 ? C6 AR6 401 B 1 HETATM 7 N N6 AR6 . . . N 2 -20.144 23.005 35.491 1 40.43 ? N6 AR6 401 B 1 HETATM 8 N N7 AR6 . . . N 2 -22.808 23.532 36.965 1 44.52 ? N7 AR6 401 B 1 HETATM 9 C C8 AR6 . . . N 2 -23.551 24.1 37.887 1 41.4 ? C8 AR6 401 B 1 HETATM 10 N N9 AR6 . . . N 2 -22.846 25.017 38.624 1 43.14 ? N9 AR6 401 B 1 HETATM 11 P PA AR6 . . . N 2 -27.048 23.974 43.987 1 49.96 ? PA AR6 401 B 1 HETATM 12 P PB AR6 . . . N 2 -26.076 22.191 46.01 1 43.92 ? PB AR6 401 B 1 HETATM 13 C C1' AR6 . . . N 2 -23.266 25.785 39.774 1 42.45 ? C1' AR6 401 B 1 HETATM 14 O O1A AR6 . . . N 2 -27.565 24.868 45.071 1 55.98 ? O1A AR6 401 B 1 HETATM 15 O O1B AR6 . . . N 2 -25.246 20.96 45.961 1 47.03 ? O1B AR6 401 B 1 HETATM 16 C C1D AR6 . . . N 2 -30.648 20.4 47.684 1 57.59 ? C1D AR6 401 B 1 HETATM 17 O O1D AR6 . . . N 2 -31.724 20.55 48.533 1 63.73 ? O1D AR6 401 B 1 HETATM 18 C C2' AR6 . . . N 2 -24.581 26.545 39.712 1 37.63 ? C2' AR6 401 B 1 HETATM 19 O O2' AR6 . . . N 2 -24.319 27.873 39.295 1 40.09 ? O2' AR6 401 B 1 HETATM 20 O O2A AR6 . . . N 2 -27.811 23.84 42.71 1 57.72 ? O2A AR6 401 B 1 HETATM 21 O O2B AR6 . . . N 2 -25.387 23.467 46.339 1 43.48 ? O2B AR6 401 B 1 HETATM 22 C C2D AR6 . . . N 2 -30.095 18.975 47.817 1 50.83 ? C2D AR6 401 B 1 HETATM 23 O O2D AR6 . . . N 2 -30.338 18.375 49.069 1 63.68 ? O2D AR6 401 B 1 HETATM 24 C C3' AR6 . . . N 2 -25.06 26.501 41.175 1 38.24 ? C3' AR6 401 B 1 HETATM 25 O O3' AR6 . . . N 2 -24.788 27.741 41.82 1 41.26 ? O3' AR6 401 B 1 HETATM 26 O O3A AR6 . . . N 2 -26.85 22.498 44.618 1 46.73 ? O3A AR6 401 B 1 HETATM 27 C C3D AR6 . . . N 2 -28.593 19.16 47.67 1 53.22 ? C3D AR6 401 B 1 HETATM 28 O O3D AR6 . . . N 2 -27.866 18.084 48.25 1 49.01 ? O3D AR6 401 B 1 HETATM 29 C C4' AR6 . . . N 2 -24.283 25.345 41.83 1 38.28 ? C4' AR6 401 B 1 HETATM 30 O O4' AR6 . . . N 2 -23.379 24.856 40.82 1 41.57 ? O4' AR6 401 B 1 HETATM 31 C C4D AR6 . . . N 2 -28.423 20.471 48.444 1 50.71 ? C4D AR6 401 B 1 HETATM 32 O O4D AR6 . . . N 2 -29.562 21.278 48.048 1 56.44 ? O4D AR6 401 B 1 HETATM 33 C C5' AR6 . . . N 2 -25.09 24.159 42.282 1 48.58 ? C5' AR6 401 B 1 HETATM 34 O O5' AR6 . . . N 2 -25.533 24.351 43.647 1 56.12 ? O5' AR6 401 B 1 HETATM 35 C C5D AR6 . . . N 2 -27.162 21.235 48.177 1 53.33 ? C5D AR6 401 B 1 HETATM 36 O O5D AR6 . . . N 2 -27.344 21.942 46.94 1 48.73 ? O5D AR6 401 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #