data_8SUB # _model_server_result.job_id JVlIaDfOawV3lC-L56BUCQ _model_server_result.datetime_utc '2024-10-19 06:39:08' _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 8sub # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":501}' # _entry.id 8SUB # _exptl.entry_id 8SUB _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 559.316 _entity.id 3 _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 12 _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 90 _cell.entry_id 8SUB _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8SUB _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details heptadecameric _pdbx_struct_assembly.oligomeric_count 17 _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,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA _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 ? _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 ? 3 R N N ? 3 S N N ? 3 T N N ? 3 U N N ? 3 V N N ? 3 W N N ? 3 X N N ? 3 Y N N ? 3 Z N N ? 3 AA N N ? 3 BA N N ? 3 CA 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 M OG SER 184 M SER 184 1_555 EA MG MG . M MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? metalc ? metalc2 DA O3B ADP . M ADP 701 1_555 EA MG MG . M MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc3 N OG SER 184 N SER 184 1_555 GA MG MG . N MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? metalc ? metalc4 FA O3B ADP . N ADP 701 1_555 GA MG MG . N MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc5 HA O3B ADP . O ADP 701 1_555 IA MG MG . O MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc6 P OG SER 184 P SER 184 1_555 KA MG MG . P MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc7 JA O2B ADP . P ADP 701 1_555 KA MG MG . P MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc8 LA O1B ADP . Q ADP 701 1_555 MA MG MG . Q MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc9 LA O1A ADP . Q ADP 701 1_555 MA MG MG . Q MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.877 ? # _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 57 n y N1 C6 AR6 sing 58 n y C2 N3 AR6 sing 59 n y N3 C4 AR6 doub 60 n y C4 C5 AR6 sing 61 n y C4 N9 AR6 sing 62 n y C5 C6 AR6 doub 63 n y C5 N7 AR6 sing 64 n y C6 N6 AR6 sing 65 n n N7 C8 AR6 doub 66 n y C8 N9 AR6 sing 67 n y N9 C1' AR6 sing 68 n n PA O1A AR6 sing 69 n n PA O2A AR6 doub 70 n n PA O3A AR6 sing 71 n n PA O5' AR6 sing 72 n n PB O1B AR6 sing 73 n n PB O2B AR6 doub 74 n n PB O3A AR6 sing 75 n n PB O5D AR6 sing 76 n n C1' C2' AR6 sing 77 n n C1' O4' AR6 sing 78 n n C1D O1D AR6 sing 79 n n C1D C2D AR6 sing 80 n n C1D O4D AR6 sing 81 n n C2' O2' AR6 sing 82 n n C2' C3' AR6 sing 83 n n C2D O2D AR6 sing 84 n n C2D C3D AR6 sing 85 n n C3' O3' AR6 sing 86 n n C3' C4' AR6 sing 87 n n C3D O3D AR6 sing 88 n n C3D C4D AR6 sing 89 n n C4' O4' AR6 sing 90 n n C4' C5' AR6 sing 91 n n C4D O4D AR6 sing 92 n n C4D C5D AR6 sing 93 n n C5' O5' AR6 sing 94 n n C5D O5D AR6 sing 95 n n C2 H2 AR6 sing 96 n n N6 HN6 AR6 sing 97 n n N6 HN6A AR6 sing 98 n n C8 H8 AR6 sing 99 n n C1' H1' AR6 sing 100 n n C1D H1D AR6 sing 101 n n C2' H2' AR6 sing 102 n n O2' HO2' AR6 sing 103 n n C2D H2D AR6 sing 104 n n O2D HO2D AR6 sing 105 n n C3' H3' AR6 sing 106 n n O3' HO3' AR6 sing 107 n n C3D H3D AR6 sing 108 n n O3D HO3D AR6 sing 109 n n C4' H4' AR6 sing 110 n n C4D H4D AR6 sing 111 n n C5' H5' AR6 sing 112 n n C5' "H5'A" AR6 sing 113 n n C5D H5D AR6 sing 114 n n C5D H5DA AR6 sing 115 n n O1A H1A AR6 sing 116 n n O1B H1B AR6 sing 117 n n O1D HD1 AR6 sing 118 n n # _atom_sites.entry_id 8SUB _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _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] 1 _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 R 3 AR6 A 1 501 501 AR6 AR6 . S 3 AR6 B 1 501 501 AR6 AR6 . T 3 AR6 C 1 501 501 AR6 AR6 . U 3 AR6 D 1 501 501 AR6 AR6 . V 3 AR6 E 1 501 501 AR6 AR6 . W 3 AR6 F 1 501 501 AR6 AR6 . X 3 AR6 G 1 501 501 AR6 AR6 . Y 3 AR6 H 1 501 501 AR6 AR6 . Z 3 AR6 I 1 501 501 AR6 AR6 . AA 3 AR6 J 1 501 501 AR6 AR6 . BA 3 AR6 K 1 501 501 AR6 AR6 . CA 3 AR6 L 1 501 501 AR6 AR6 . DA 4 ADP M 1 701 701 ADP ADP . EA 5 MG M 1 702 703 MG MG . FA 4 ADP N 1 701 701 ADP ADP . GA 5 MG N 1 702 704 MG MG . HA 4 ADP O 1 701 701 ADP ADP . IA 5 MG O 1 702 705 MG MG . JA 4 ADP P 1 701 701 ADP ADP . KA 5 MG P 1 702 702 MG MG . LA 4 ADP Q 1 701 701 ADP ADP . MA 5 MG Q 1 702 706 MG MG . # 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 . . . Y 3 168.183 234.916 140.992 1 61.85 ? N1 AR6 501 H 1 HETATM 2 C C2 AR6 . . . Y 3 169.387 234.363 140.967 1 61.01 ? C2 AR6 501 H 1 HETATM 3 N N3 AR6 . . . Y 3 170.535 234.927 140.662 1 59.92 ? N3 AR6 501 H 1 HETATM 4 C C4 AR6 . . . Y 3 170.382 236.206 140.342 1 64.09 ? C4 AR6 501 H 1 HETATM 5 C C5 AR6 . . . Y 3 169.2 236.92 140.317 1 63.04 ? C5 AR6 501 H 1 HETATM 6 C C6 AR6 . . . Y 3 168.046 236.203 140.675 1 62.8 ? C6 AR6 501 H 1 HETATM 7 N N6 AR6 . . . Y 3 166.826 236.744 140.706 1 62.05 ? N6 AR6 501 H 1 HETATM 8 N N7 AR6 . . . Y 3 169.428 238.217 139.941 1 58.58 ? N7 AR6 501 H 1 HETATM 9 C C8 AR6 . . . Y 3 170.712 238.284 139.749 1 62.75 ? C8 AR6 501 H 1 HETATM 10 N N9 AR6 . . . Y 3 171.344 237.091 139.97 1 65.13 ? N9 AR6 501 H 1 HETATM 11 P PA AR6 . . . Y 3 176.248 239.769 142.854 1 85.77 ? PA AR6 501 H 1 HETATM 12 P PB AR6 . . . Y 3 178.253 238.803 144.609 1 82.8 ? PB AR6 501 H 1 HETATM 13 C C1' AR6 . . . Y 3 172.745 236.775 139.862 1 63 ? C1' AR6 501 H 1 HETATM 14 O O1A AR6 . . . Y 3 177.136 240.252 141.76 1 73.01 ? O1A AR6 501 H 1 HETATM 15 O O1B AR6 . . . Y 3 178.098 240.182 145.153 1 69.5 ? O1B AR6 501 H 1 HETATM 16 C C1D AR6 . . . Y 3 180.589 239.085 147.919 1 65.37 ? C1D AR6 501 H 1 HETATM 17 O O1D AR6 . . . Y 3 181.464 238.413 148.746 1 66.54 ? O1D AR6 501 H 1 HETATM 18 C C2' AR6 . . . Y 3 173.598 237.769 139.084 1 63.93 ? C2' AR6 501 H 1 HETATM 19 O O2' AR6 . . . Y 3 173.483 237.53 137.715 1 64.45 ? O2' AR6 501 H 1 HETATM 20 O O2A AR6 . . . Y 3 175.636 240.75 143.8 1 71.09 ? O2A AR6 501 H 1 HETATM 21 O O2B AR6 . . . Y 3 179.508 238.393 143.914 1 74.9 ? O2B AR6 501 H 1 HETATM 22 C C2D AR6 . . . Y 3 179.837 240.136 148.733 1 68.17 ? C2D AR6 501 H 1 HETATM 23 O O2D AR6 . . . Y 3 179.824 239.812 150.094 1 67.33 ? O2D AR6 501 H 1 HETATM 24 C C3' AR6 . . . Y 3 174.999 237.514 139.665 1 64.84 ? C3' AR6 501 H 1 HETATM 25 O O3' AR6 . . . Y 3 175.72 236.644 138.838 1 68.93 ? O3' AR6 501 H 1 HETATM 26 O O3A AR6 . . . Y 3 176.949 238.547 143.668 1 67.2 ? O3A AR6 501 H 1 HETATM 27 C C3D AR6 . . . Y 3 178.422 240.003 148.186 1 73.54 ? C3D AR6 501 H 1 HETATM 28 O O3D AR6 . . . Y 3 177.385 240.43 149.019 1 77.39 ? O3D AR6 501 H 1 HETATM 29 C C4' AR6 . . . Y 3 174.721 236.783 140.966 1 59.14 ? C4' AR6 501 H 1 HETATM 30 O O4' AR6 . . . Y 3 173.308 236.812 141.127 1 65.58 ? O4' AR6 501 H 1 HETATM 31 C C4D AR6 . . . Y 3 178.338 238.502 147.914 1 71.05 ? C4D AR6 501 H 1 HETATM 32 O O4D AR6 . . . Y 3 179.618 238.2 147.396 1 68.47 ? O4D AR6 501 H 1 HETATM 33 C C5' AR6 . . . Y 3 175.43 237.427 142.137 1 59.52 ? C5' AR6 501 H 1 HETATM 34 O O5' AR6 . . . Y 3 175.085 238.783 142.234 1 68.09 ? O5' AR6 501 H 1 HETATM 35 C C5D AR6 . . . Y 3 177.257 238.142 146.924 1 61.75 ? C5D AR6 501 H 1 HETATM 36 O O5D AR6 . . . Y 3 177.837 237.675 145.73 1 56.09 ? O5D AR6 501 H 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 340 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 36 #