data_5EY8 # _model_server_result.job_id WfRdG9PDj1fu7JnXd-_tYg _model_server_result.datetime_utc '2024-11-05 00:22:07' _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 5ey8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":701}' # _entry.id 5EY8 # _exptl.entry_id 5EY8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 627.753 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl hydrogen phosphate' _entity.pdbx_number_of_molecules 8 _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 5EY8 _cell.length_a 164.04 _cell.length_b 164.04 _cell.length_c 231.53 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EY8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 75 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 4' # 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 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 ? monomeric 1 author_defined_assembly 5 ? monomeric 1 author_defined_assembly 6 ? monomeric 1 author_defined_assembly 7 ? monomeric 1 author_defined_assembly 8 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,I 1 1 B,J 2 1 C,K 3 1 D,L 4 1 E,M,N 5 1 F,O,P 6 1 G,Q 7 1 H,R 8 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 I N N ? 2 J N N ? 2 K N N ? 2 L N N ? 2 M N N ? 2 O N N ? 2 Q N N ? 2 R N N # _chem_comp.formula 'C30 H54 N5 O7 P' _chem_comp.formula_weight 627.753 _chem_comp.id 5SV _chem_comp.mon_nstd_flag . _chem_comp.name '[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl icosyl hydrogen phosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C24 C23 5SV sing 1 n n C23 C22 5SV sing 2 n n C22 C21 5SV sing 3 n n C21 C20 5SV sing 4 n n C20 C19 5SV sing 5 n n C19 C18 5SV sing 6 n n C18 C17 5SV sing 7 n n C17 C16 5SV sing 8 n n C16 C15 5SV sing 9 n n C15 C14 5SV sing 10 n n C14 C13 5SV sing 11 n n C13 C12 5SV sing 12 n n C12 C11 5SV sing 13 n n C11 C10 5SV sing 14 n n N6 C6 5SV sing 15 n n C10 C9 5SV sing 16 n n C9 O3P 5SV sing 17 n n C6 C5 5SV doub 18 n y C6 N1 5SV sing 19 n y N7 C5 5SV sing 20 n y N7 C8 5SV doub 21 n y C5 C4 5SV sing 22 n y N1 C2 5SV doub 23 n y C8 N9 5SV sing 24 n y O3P P 5SV sing 25 n n C4 N9 5SV sing 26 n y C4 N3 5SV doub 27 n y C2 N3 5SV sing 28 n y O1P P 5SV doub 29 n n N9 C1' 5SV sing 30 n n P O5' 5SV sing 31 n n P O2P 5SV sing 32 n n C5' O5' 5SV sing 33 n n C5' C4' 5SV sing 34 n n C1' C2' 5SV sing 35 n n C1' O4' 5SV sing 36 n n C3' C2' 5SV sing 37 n n C3' C4' 5SV sing 38 n n C3' O3' 5SV sing 39 n n C2' O2' 5SV sing 40 n n O4' C4' 5SV sing 41 n n C2 H1 5SV sing 42 n n C8 H2 5SV sing 43 n n C9 H3 5SV sing 44 n n C9 H4 5SV sing 45 n n C10 H5 5SV sing 46 n n C10 H6 5SV sing 47 n n C11 H7 5SV sing 48 n n C11 H8 5SV sing 49 n n C12 H9 5SV sing 50 n n C12 H10 5SV sing 51 n n C13 H11 5SV sing 52 n n C13 H12 5SV sing 53 n n C14 H13 5SV sing 54 n n C14 H14 5SV sing 55 n n C15 H15 5SV sing 56 n n C15 H16 5SV sing 57 n n O2P H17 5SV sing 58 n n C5' H18 5SV sing 59 n n C5' H19 5SV sing 60 n n C4' H20 5SV sing 61 n n C3' H21 5SV sing 62 n n O3' H22 5SV sing 63 n n C2' H23 5SV sing 64 n n O2' H24 5SV sing 65 n n C1' H25 5SV sing 66 n n N6 H26 5SV sing 67 n n N6 H27 5SV sing 68 n n C16 H28 5SV sing 69 n n C16 H29 5SV sing 70 n n C17 H30 5SV sing 71 n n C17 H31 5SV sing 72 n n C18 H32 5SV sing 73 n n C18 H33 5SV sing 74 n n C19 H34 5SV sing 75 n n C19 H35 5SV sing 76 n n C20 H36 5SV sing 77 n n C20 H37 5SV sing 78 n n C21 H38 5SV sing 79 n n C21 H39 5SV sing 80 n n C22 H40 5SV sing 81 n n C22 H41 5SV sing 82 n n C23 H42 5SV sing 83 n n C24 H43 5SV sing 84 n n C24 H44 5SV sing 85 n n C24 C25 5SV sing 86 n n C25 C26 5SV sing 87 n n C26 C27 5SV sing 88 n n C27 C28 5SV sing 89 n n C23 H45 5SV sing 90 n n C25 H46 5SV sing 91 n n C25 H47 5SV sing 92 n n C26 H48 5SV sing 93 n n C26 H49 5SV sing 94 n n C27 H50 5SV sing 95 n n C27 H51 5SV sing 96 n n C28 H52 5SV sing 97 n n C28 H53 5SV sing 98 n n C28 H54 5SV sing 99 n n # _atom_sites.entry_id 5EY8 _atom_sites.fract_transf_matrix[1][1] 0.006096 _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] 0.006096 _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] 0.004319 _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 I 2 5SV A 1 701 631 5SV KK2 . J 2 5SV B 1 701 631 5SV KK2 . K 2 5SV C 1 701 631 5SV KK2 . L 2 5SV D 1 701 631 5SV KK2 . M 2 5SV E 1 701 631 5SV KK2 . N 3 GOL E 1 702 637 GOL GOL . O 2 5SV F 1 701 631 5SV KK2 . P 3 GOL F 1 702 637 GOL GOL . Q 2 5SV G 1 701 631 5SV KK2 . R 2 5SV H 1 701 631 5SV KK2 . # 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 C C2 5SV . . . J 2 43.622 62.354 111.707 1 39.14 ? C2 5SV 701 B 1 HETATM 2 C C4 5SV . . . J 2 44.828 60.452 111.574 1 39 ? C4 5SV 701 B 1 HETATM 3 C C6 5SV . . . J 2 44.541 61.853 109.638 1 39.12 ? C6 5SV 701 B 1 HETATM 4 C C5 5SV . . . J 2 45.084 60.685 110.204 1 39.03 ? C5 5SV 701 B 1 HETATM 5 N N1 5SV . . . J 2 43.789 62.708 110.403 1 39.18 ? N1 5SV 701 B 1 HETATM 6 N N3 5SV . . . J 2 44.087 61.275 112.386 1 39.05 ? N3 5SV 701 B 1 HETATM 7 C C8 5SV . . . J 2 46.105 58.83 110.685 1 38.9 ? C8 5SV 701 B 1 HETATM 8 C C9 5SV . . . J 2 49.89 56.276 109.364 1 38.84 ? C9 5SV 701 B 1 HETATM 9 C C10 5SV . . . J 2 48.995 56.897 108.256 1 38.85 ? C10 5SV 701 B 1 HETATM 10 C C11 5SV . . . J 2 49.712 56.844 106.908 1 38.88 ? C11 5SV 701 B 1 HETATM 11 C C12 5SV . . . J 2 48.959 57.602 105.818 1 38.9 ? C12 5SV 701 B 1 HETATM 12 C C13 5SV . . . J 2 48.814 56.771 104.541 1 38.83 ? C13 5SV 701 B 1 HETATM 13 C C14 5SV . . . J 2 49.618 57.333 103.351 1 38.91 ? C14 5SV 701 B 1 HETATM 14 C C15 5SV . . . J 2 51.077 56.835 103.311 1 38.93 ? C15 5SV 701 B 1 HETATM 15 O O2P 5SV . . . J 2 50.874 56.151 112.403 1 38.88 ? O2P 5SV 701 B 1 HETATM 16 P P 5SV . . . J 2 49.596 55.554 111.971 1 38.77 ? P 5SV 701 B 1 HETATM 17 O O1P 5SV . . . J 2 49.444 53.974 111.929 1 51.39 ? O1P 5SV 701 B 1 HETATM 18 O O5' 5SV . . . J 2 48.356 55.888 112.883 1 38.75 ? O5' 5SV 701 B 1 HETATM 19 C C5' 5SV . . . J 2 47.059 55.459 112.717 1 38.66 ? C5' 5SV 701 B 1 HETATM 20 C C4' 5SV . . . J 2 46.171 56.432 113.495 1 38.71 ? C4' 5SV 701 B 1 HETATM 21 O O4' 5SV . . . J 2 46.604 57.741 113.207 1 38.83 ? O4' 5SV 701 B 1 HETATM 22 C C3' 5SV . . . J 2 44.675 56.357 113.133 1 38.65 ? C3' 5SV 701 B 1 HETATM 23 O O3' 5SV . . . J 2 44.12 55.388 113.956 1 38.56 ? O3' 5SV 701 B 1 HETATM 24 C C2' 5SV . . . J 2 44.218 57.8 113.453 1 38.75 ? C2' 5SV 701 B 1 HETATM 25 O O2' 5SV . . . J 2 43.924 57.875 114.809 1 38.75 ? O2' 5SV 701 B 1 HETATM 26 C C1' 5SV . . . J 2 45.509 58.629 113.198 1 38.86 ? C1' 5SV 701 B 1 HETATM 27 N N9 5SV . . . J 2 45.487 59.261 111.876 1 38.92 ? N9 5SV 701 B 1 HETATM 28 N N7 5SV . . . J 2 45.879 59.665 109.664 1 38.97 ? N7 5SV 701 B 1 HETATM 29 N N6 5SV . . . J 2 44.772 62.175 108.35 1 68.17 ? N6 5SV 701 B 1 HETATM 30 O O3P 5SV . . . J 2 49.114 55.911 110.48 1 38.78 ? O3P 5SV 701 B 1 HETATM 31 C C16 5SV . . . J 2 51.524 56.51 101.871 1 38.93 ? C16 5SV 701 B 1 HETATM 32 C C17 5SV . . . J 2 53.047 56.547 101.637 1 39.01 ? C17 5SV 701 B 1 HETATM 33 C C18 5SV . . . J 2 53.442 56.968 100.195 1 39.06 ? C18 5SV 701 B 1 HETATM 34 C C19 5SV . . . J 2 54.968 57.168 100.072 1 39.16 ? C19 5SV 701 B 1 HETATM 35 C C20 5SV . . . J 2 55.373 57.816 98.745 1 39.24 ? C20 5SV 701 B 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 77 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 35 #