data_3V2B # _model_server_result.job_id qUds5RoBMKtgi6olMDmRXg _model_server_result.datetime_utc '2025-06-30 11:07:36' _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 3v2b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":800}' # _entry.id 3V2B # _exptl.entry_id 3V2B _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 1 _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 3V2B _cell.length_a 68.102 _cell.length_b 91.187 _cell.length_c 62.851 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3V2B _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 3V2B _atom_sites.fract_transf_matrix[1][1] 0.014684 _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] 0.010966 _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] 0.015911 _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 B 2 AR6 A 1 800 800 AR6 AR6 . C 3 HOH A 1 1 1 HOH HOH . C 3 HOH A 2 2 2 HOH HOH . C 3 HOH A 3 3 3 HOH HOH . C 3 HOH A 4 4 4 HOH HOH . C 3 HOH A 5 5 5 HOH HOH . C 3 HOH A 6 6 6 HOH HOH . C 3 HOH A 7 7 7 HOH HOH . C 3 HOH A 8 8 8 HOH HOH . C 3 HOH A 9 9 9 HOH HOH . C 3 HOH A 10 10 10 HOH HOH . C 3 HOH A 11 11 11 HOH HOH . C 3 HOH A 12 12 12 HOH HOH . C 3 HOH A 13 13 13 HOH HOH . C 3 HOH A 14 14 14 HOH HOH . C 3 HOH A 15 15 15 HOH HOH . C 3 HOH A 16 16 16 HOH HOH . C 3 HOH A 17 17 17 HOH HOH . C 3 HOH A 18 18 18 HOH HOH . C 3 HOH A 19 19 19 HOH HOH . C 3 HOH A 20 20 20 HOH HOH . C 3 HOH A 21 21 21 HOH HOH . C 3 HOH A 22 22 22 HOH HOH . C 3 HOH A 23 23 23 HOH HOH . C 3 HOH A 24 24 24 HOH HOH . C 3 HOH A 25 25 25 HOH HOH . C 3 HOH A 26 26 26 HOH HOH . C 3 HOH A 27 27 27 HOH HOH . C 3 HOH A 28 28 28 HOH HOH . C 3 HOH A 29 29 29 HOH HOH . C 3 HOH A 30 30 30 HOH HOH . C 3 HOH A 31 31 31 HOH HOH . C 3 HOH A 32 32 32 HOH HOH . C 3 HOH A 33 33 33 HOH HOH . C 3 HOH A 34 34 34 HOH HOH . C 3 HOH A 35 35 35 HOH HOH . C 3 HOH A 36 36 36 HOH HOH . C 3 HOH A 37 37 37 HOH HOH . C 3 HOH A 38 38 38 HOH HOH . C 3 HOH A 39 39 39 HOH HOH . C 3 HOH A 40 40 40 HOH HOH . C 3 HOH A 41 41 41 HOH HOH . C 3 HOH A 42 42 42 HOH HOH . C 3 HOH A 43 43 43 HOH HOH . C 3 HOH A 44 44 44 HOH HOH . C 3 HOH A 45 45 45 HOH HOH . C 3 HOH A 46 46 46 HOH HOH . C 3 HOH A 47 47 47 HOH HOH . C 3 HOH A 48 48 48 HOH HOH . C 3 HOH A 49 49 49 HOH HOH . C 3 HOH A 50 50 50 HOH HOH . C 3 HOH A 51 51 51 HOH HOH . C 3 HOH A 52 52 52 HOH HOH . C 3 HOH A 53 53 53 HOH HOH . C 3 HOH A 54 54 54 HOH HOH . C 3 HOH A 55 55 55 HOH HOH . C 3 HOH A 56 56 56 HOH HOH . C 3 HOH A 57 57 57 HOH HOH . C 3 HOH A 58 58 58 HOH HOH . C 3 HOH A 59 59 59 HOH HOH . C 3 HOH A 60 60 60 HOH HOH . C 3 HOH A 61 61 61 HOH HOH . C 3 HOH A 62 62 62 HOH HOH . C 3 HOH A 63 63 63 HOH HOH . C 3 HOH A 64 64 64 HOH HOH . C 3 HOH A 65 65 65 HOH HOH . C 3 HOH A 66 66 66 HOH HOH . C 3 HOH A 67 67 67 HOH HOH . C 3 HOH A 68 68 68 HOH HOH . C 3 HOH A 69 69 69 HOH HOH . C 3 HOH A 70 70 70 HOH HOH . C 3 HOH A 71 71 71 HOH HOH . C 3 HOH A 72 72 72 HOH HOH . C 3 HOH A 73 73 73 HOH HOH . C 3 HOH A 74 74 74 HOH HOH . C 3 HOH A 75 75 75 HOH HOH . C 3 HOH A 76 76 76 HOH HOH . C 3 HOH A 77 77 77 HOH HOH . C 3 HOH A 78 78 78 HOH HOH . C 3 HOH A 79 79 79 HOH HOH . C 3 HOH A 80 80 80 HOH HOH . C 3 HOH A 81 81 81 HOH HOH . C 3 HOH A 82 82 82 HOH HOH . C 3 HOH A 83 83 83 HOH HOH . C 3 HOH A 84 84 84 HOH HOH . C 3 HOH A 85 85 85 HOH HOH . C 3 HOH A 86 86 86 HOH HOH . C 3 HOH A 87 87 87 HOH HOH . C 3 HOH A 88 88 88 HOH HOH . C 3 HOH A 89 89 89 HOH HOH . C 3 HOH A 90 90 90 HOH HOH . C 3 HOH A 91 91 91 HOH HOH . C 3 HOH A 92 92 92 HOH HOH . C 3 HOH A 93 93 93 HOH HOH . C 3 HOH A 94 94 94 HOH HOH . C 3 HOH A 95 95 95 HOH HOH . C 3 HOH A 96 96 96 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 . . . B 2 15.079 17.291 -0.134 1 16.41 ? N1 AR6 800 A 1 HETATM 2 C C2 AR6 . . . B 2 14.151 16.816 -0.925 1 13.23 ? C2 AR6 800 A 1 HETATM 3 N N3 AR6 . . . B 2 13.016 17.473 -1.156 1 16.44 ? N3 AR6 800 A 1 HETATM 4 C C4 AR6 . . . B 2 12.799 18.647 -0.565 1 13.99 ? C4 AR6 800 A 1 HETATM 5 C C5 AR6 . . . B 2 13.751 19.195 0.293 1 15.02 ? C5 AR6 800 A 1 HETATM 6 C C6 AR6 . . . B 2 14.912 18.481 0.496 1 14.37 ? C6 AR6 800 A 1 HETATM 7 N N6 AR6 . . . B 2 15.871 18.911 1.268 1 12.51 ? N6 AR6 800 A 1 HETATM 8 N N7 AR6 . . . B 2 13.276 20.354 0.728 1 15.32 ? N7 AR6 800 A 1 HETATM 9 C C8 AR6 . . . B 2 12.059 20.523 0.222 1 15.26 ? C8 AR6 800 A 1 HETATM 10 N N9 AR6 . . . B 2 11.777 19.469 -0.579 1 17.2 ? N9 AR6 800 A 1 HETATM 11 P PA AR6 . . . B 2 10.016 23.62 -3.864 1 17.06 ? PA AR6 800 A 1 HETATM 12 P PB AR6 . . . B 2 8.871 23.544 -6.508 1 19.07 ? PB AR6 800 A 1 HETATM 13 C C1' AR6 . . . B 2 10.537 19.269 -1.357 1 17.09 ? C1' AR6 800 A 1 HETATM 14 O O1A AR6 . . . B 2 11.436 23.638 -3.532 1 19.92 ? O1A AR6 800 A 1 HETATM 15 O O1B AR6 . . . B 2 9.381 22.691 -7.653 1 18.06 ? O1B AR6 800 A 1 HETATM 16 C C1D AR6 . . . B 2 7.975 27.053 -9.943 1 30.86 ? C1D AR6 800 A 1 HETATM 17 O O1D AR6 . . . B 2 8.303 27.892 -11.047 1 35.08 ? O1D AR6 800 A 1 HETATM 18 C C2' AR6 . . . B 2 9.417 20.168 -0.938 1 20.97 ? C2' AR6 800 A 1 HETATM 19 O O2' AR6 . . . B 2 8.858 19.726 0.308 1 23.91 ? O2' AR6 800 A 1 HETATM 20 O O2A AR6 . . . B 2 9.041 24.637 -3.369 1 17.16 ? O2A AR6 800 A 1 HETATM 21 O O2B AR6 . . . B 2 7.558 23.35 -5.924 1 16.12 ? O2B AR6 800 A 1 HETATM 22 C C2D AR6 . . . B 2 7.64 27.994 -8.802 1 31.49 ? C2D AR6 800 A 1 HETATM 23 O O2D AR6 . . . B 2 7.89 29.306 -9.255 1 35.81 ? O2D AR6 800 A 1 HETATM 24 C C3' AR6 . . . B 2 8.465 19.924 -2.097 1 19.28 ? C3' AR6 800 A 1 HETATM 25 O O3' AR6 . . . B 2 7.755 18.702 -1.895 1 21.79 ? O3' AR6 800 A 1 HETATM 26 O O3A AR6 . . . B 2 10.078 23.496 -5.477 1 16.43 ? O3A AR6 800 A 1 HETATM 27 C C3D AR6 . . . B 2 8.646 27.639 -7.716 1 28.92 ? C3D AR6 800 A 1 HETATM 28 O O3D AR6 . . . B 2 9.196 28.83 -7.186 1 29.83 ? O3D AR6 800 A 1 HETATM 29 C C4' AR6 . . . B 2 9.434 19.775 -3.259 1 17.51 ? C4' AR6 800 A 1 HETATM 30 O O4' AR6 . . . B 2 10.757 19.755 -2.666 1 17.37 ? O4' AR6 800 A 1 HETATM 31 C C4D AR6 . . . B 2 9.742 26.853 -8.418 1 24.8 ? C4D AR6 800 A 1 HETATM 32 O O4D AR6 . . . B 2 9.143 26.316 -9.568 1 25.94 ? O4D AR6 800 A 1 HETATM 33 C C5' AR6 . . . B 2 9.452 20.999 -4.202 1 18.04 ? C5' AR6 800 A 1 HETATM 34 O O5' AR6 . . . B 2 9.376 22.193 -3.429 1 20.07 ? O5' AR6 800 A 1 HETATM 35 C C5D AR6 . . . B 2 10.123 25.619 -7.533 1 22.08 ? C5D AR6 800 A 1 HETATM 36 O O5D AR6 . . . B 2 8.942 25.04 -7.032 1 18.51 ? O5D AR6 800 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 36 #