data_6ZU4 # _model_server_result.job_id VdrFgzti_fpK4xy8ANh1dg _model_server_result.datetime_utc '2025-01-10 10:25:56' _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 6zu4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 6ZU4 # _exptl.entry_id 6ZU4 _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 6ZU4 _cell.length_a 91.407 _cell.length_b 91.407 _cell.length_c 144.277 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6ZU4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 J 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc2 A SG CYS 138 A CYS 144 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc3 A SG CYS 160 A CYS 166 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc4 A SG CYS 171 A CYS 177 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc5 B SG CYS 135 B CYS 141 1_555 K ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc6 B SG CYS 138 B CYS 144 1_555 K ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc7 B SG CYS 160 B CYS 166 1_555 K ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc8 B SG CYS 171 B CYS 177 1_555 K ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? # _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 71 n y N1 C6 AR6 sing 72 n y C2 N3 AR6 sing 73 n y N3 C4 AR6 doub 74 n y C4 C5 AR6 sing 75 n y C4 N9 AR6 sing 76 n y C5 C6 AR6 doub 77 n y C5 N7 AR6 sing 78 n y C6 N6 AR6 sing 79 n n N7 C8 AR6 doub 80 n y C8 N9 AR6 sing 81 n y N9 C1' AR6 sing 82 n n PA O1A AR6 sing 83 n n PA O2A AR6 doub 84 n n PA O3A AR6 sing 85 n n PA O5' AR6 sing 86 n n PB O1B AR6 sing 87 n n PB O2B AR6 doub 88 n n PB O3A AR6 sing 89 n n PB O5D AR6 sing 90 n n C1' C2' AR6 sing 91 n n C1' O4' AR6 sing 92 n n C1D O1D AR6 sing 93 n n C1D C2D AR6 sing 94 n n C1D O4D AR6 sing 95 n n C2' O2' AR6 sing 96 n n C2' C3' AR6 sing 97 n n C2D O2D AR6 sing 98 n n C2D C3D AR6 sing 99 n n C3' O3' AR6 sing 100 n n C3' C4' AR6 sing 101 n n C3D O3D AR6 sing 102 n n C3D C4D AR6 sing 103 n n C4' O4' AR6 sing 104 n n C4' C5' AR6 sing 105 n n C4D O4D AR6 sing 106 n n C4D C5D AR6 sing 107 n n C5' O5' AR6 sing 108 n n C5D O5D AR6 sing 109 n n C2 H2 AR6 sing 110 n n N6 HN6 AR6 sing 111 n n N6 HN6A AR6 sing 112 n n C8 H8 AR6 sing 113 n n C1' H1' AR6 sing 114 n n C1D H1D AR6 sing 115 n n C2' H2' AR6 sing 116 n n O2' HO2' AR6 sing 117 n n C2D H2D AR6 sing 118 n n O2D HO2D AR6 sing 119 n n C3' H3' AR6 sing 120 n n O3' HO3' AR6 sing 121 n n C3D H3D AR6 sing 122 n n O3D HO3D AR6 sing 123 n n C4' H4' AR6 sing 124 n n C4D H4D AR6 sing 125 n n C5' H5' AR6 sing 126 n n C5' "H5'A" AR6 sing 127 n n C5D H5D AR6 sing 128 n n C5D H5DA AR6 sing 129 n n O1A H1A AR6 sing 130 n n O1B H1B AR6 sing 131 n n O1D HD1 AR6 sing 132 n n # _atom_sites.entry_id 6ZU4 _atom_sites.fract_transf_matrix[1][1] 0.01094 _atom_sites.fract_transf_matrix[1][2] 0.006316 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012633 _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] 0.006931 _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 GOL A 1 403 701 GOL GOL . F 5 SO4 A 1 404 3 SO4 SO4 . G 5 SO4 A 1 405 5 SO4 SO4 . H 5 SO4 A 1 406 7 SO4 SO4 . I 5 SO4 A 1 407 8 SO4 SO4 . J 2 AR6 B 1 401 500 AR6 AR6 . K 3 ZN B 1 402 501 ZN ZN . L 6 115 B 1 403 601 115 115 . M 4 GOL B 1 404 701 GOL GOL . N 5 SO4 B 1 405 1 SO4 SO4 . O 5 SO4 B 1 406 2 SO4 SO4 . P 5 SO4 B 1 407 4 SO4 SO4 . Q 5 SO4 B 1 408 6 SO4 SO4 . R 5 SO4 B 1 409 9 SO4 SO4 . S 7 HOH A 1 501 6 HOH HOH . S 7 HOH A 2 502 3 HOH HOH . S 7 HOH A 3 503 12 HOH HOH . S 7 HOH A 4 504 5 HOH HOH . S 7 HOH A 5 505 13 HOH HOH . S 7 HOH A 6 506 2 HOH HOH . S 7 HOH A 7 507 1 HOH HOH . S 7 HOH A 8 508 7 HOH HOH . S 7 HOH A 9 509 16 HOH HOH . S 7 HOH A 10 510 10 HOH HOH . S 7 HOH A 11 511 18 HOH HOH . T 7 HOH B 1 501 11 HOH HOH . T 7 HOH B 2 502 15 HOH HOH . T 7 HOH B 3 503 8 HOH HOH . T 7 HOH B 4 504 14 HOH HOH . T 7 HOH B 5 505 9 HOH HOH . T 7 HOH B 6 506 4 HOH HOH . T 7 HOH B 7 507 17 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 -29.823 9.599 24.476 1 34.01 ? N1 AR6 401 A 1 HETATM 2 C C2 AR6 . . . C 2 -30.561 9.384 23.378 1 39.16 ? C2 AR6 401 A 1 HETATM 3 N N3 AR6 . . . C 2 -31.184 10.256 22.589 1 37.17 ? N3 AR6 401 A 1 HETATM 4 C C4 AR6 . . . C 2 -30.983 11.512 23.03 1 34.91 ? C4 AR6 401 A 1 HETATM 5 C C5 AR6 . . . C 2 -30.264 11.89 24.132 1 34.94 ? C5 AR6 401 A 1 HETATM 6 C C6 AR6 . . . C 2 -29.641 10.876 24.88 1 33.77 ? C6 AR6 401 A 1 HETATM 7 N N6 AR6 . . . C 2 -28.866 11.132 25.933 1 30.4 ? N6 AR6 401 A 1 HETATM 8 N N7 AR6 . . . C 2 -30.306 13.271 24.271 1 35.42 ? N7 AR6 401 A 1 HETATM 9 C C8 AR6 . . . C 2 -31.047 13.678 23.273 1 31.63 ? C8 AR6 401 A 1 HETATM 10 N N9 AR6 . . . C 2 -31.472 12.678 22.502 1 29.49 ? N9 AR6 401 A 1 HETATM 11 P PA AR6 . . . C 2 -31.974 17.123 17.224 1 36.14 ? PA AR6 401 A 1 HETATM 12 P PB AR6 . . . C 2 -29.97 16.803 15.132 1 34.97 ? PB AR6 401 A 1 HETATM 13 C C1' AR6 . . . C 2 -32.286 12.806 21.311 1 32.13 ? C1' AR6 401 A 1 HETATM 14 O O1A AR6 . . . C 2 -32.975 17.484 16.195 1 34.17 ? O1A AR6 401 A 1 HETATM 15 O O1B AR6 . . . C 2 -28.536 16.46 15.381 1 35.66 ? O1B AR6 401 A 1 HETATM 16 C C1D AR6 . . . C 2 -29.757 21.739 13.438 1 40.28 ? C1D AR6 401 A 1 HETATM 17 O O1D AR6 . . . C 2 -30.253 22.75 12.685 1 33.66 ? O1D AR6 401 A 1 HETATM 18 C C2' AR6 . . . C 2 -33.427 13.812 21.393 1 28.58 ? C2' AR6 401 A 1 HETATM 19 O O2' AR6 . . . C 2 -34.561 13.205 21.983 1 26.76 ? O2' AR6 401 A 1 HETATM 20 O O2A AR6 . . . C 2 -31.906 17.916 18.483 1 38.87 ? O2A AR6 401 A 1 HETATM 21 O O2B AR6 . . . C 2 -30.905 15.784 14.562 1 32.01 ? O2B AR6 401 A 1 HETATM 22 C C2D AR6 . . . C 2 -28.24 21.679 13.244 1 38.83 ? C2D AR6 401 A 1 HETATM 23 O O2D AR6 . . . C 2 -27.828 22.197 11.989 1 43.67 ? O2D AR6 401 A 1 HETATM 24 C C3' AR6 . . . C 2 -33.57 14.274 19.921 1 30.57 ? C3' AR6 401 A 1 HETATM 25 O O3' AR6 . . . C 2 -34.662 13.711 19.18 1 28.64 ? O3' AR6 401 A 1 HETATM 26 O O3A AR6 . . . C 2 -30.53 17.202 16.563 1 33.39 ? O3A AR6 401 A 1 HETATM 27 C C3D AR6 . . . C 2 -28.002 20.184 13.4 1 36.9 ? C3D AR6 401 A 1 HETATM 28 O O3D AR6 . . . C 2 -26.829 19.726 12.733 1 39.82 ? O3D AR6 401 A 1 HETATM 29 C C4' AR6 . . . C 2 -32.242 13.883 19.255 1 29.09 ? C4' AR6 401 A 1 HETATM 30 O O4' AR6 . . . C 2 -31.443 13.296 20.304 1 35.02 ? O4' AR6 401 A 1 HETATM 31 C C4D AR6 . . . C 2 -29.209 19.608 12.652 1 38.97 ? C4D AR6 401 A 1 HETATM 32 O O4D AR6 . . . C 2 -30.294 20.489 12.951 1 37.59 ? O4D AR6 401 A 1 HETATM 33 C C5' AR6 . . . C 2 -31.417 15 18.668 1 35.36 ? C5' AR6 401 A 1 HETATM 34 O O5' AR6 . . . C 2 -32.103 15.565 17.538 1 33.33 ? O5' AR6 401 A 1 HETATM 35 C C5D AR6 . . . C 2 -29.623 18.191 12.987 1 35.69 ? C5D AR6 401 A 1 HETATM 36 O O5D AR6 . . . C 2 -30.084 18.176 14.336 1 37.17 ? 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 7 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 36 #