data_5ZSL # _model_server_result.job_id tE-4R4E8vhQ24tCXNuOwmg _model_server_result.datetime_utc '2024-11-15 09:49:50' _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 5zsl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":917}' # _entry.id 5ZSL # _exptl.entry_id 5ZSL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 345.205 _entity.id 6 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description 2-amino-9-[(2S,3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxotetrahydro-2H-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]-3,9-dihydro-6H-purin-6-one _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 90 _cell.entry_id 5ZSL _cell.length_a 99.63 _cell.length_b 139.424 _cell.length_c 150.893 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZSL _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 ? 6 T N N ? 6 U N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n E NAG 1 C 1 NAG B 838 NAG 3 n E NAG 2 C 2 NAG B 839 NAG 3 n F NAG 1 F 1 NAG B 845 NAG 3 n F NAG 2 F 2 NAG B 846 NAG 3 n G NAG 1 G 1 NAG A 838 NAG 3 n G NAG 2 G 2 NAG A 839 NAG 3 n H NAG 1 H 1 NAG A 840 NAG 3 n H NAG 2 H 2 NAG A 841 NAG # 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 disulf ? disulf1 A SG CYS 14 B CYS 36 1_555 A SG CYS 29 B CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf2 A SG CYS 76 B CYS 98 1_555 A SG CYS 453 B CYS 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf3 A SG CYS 78 B CYS 100 1_555 A SG CYS 90 B CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? disulf ? disulf4 A SG CYS 161 B CYS 183 1_555 A SG CYS 167 B CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? disulf ? disulf5 A SG CYS 238 B CYS 260 1_555 A SG CYS 251 B CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf6 A SG CYS 241 B CYS 263 1_555 A SG CYS 248 B CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? disulf ? disulf7 A SG CYS 469 B CYS 491 1_555 A SG CYS 499 B CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf8 A SG CYS 765 B CYS 787 1_555 A SG CYS 792 B CYS 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? disulf ? disulf9 A SG CYS 767 B CYS 789 1_555 A SG CYS 811 B CYS 833 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf10 B SG CYS 14 A CYS 36 1_555 B SG CYS 29 A CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? disulf ? disulf11 B SG CYS 76 A CYS 98 1_555 B SG CYS 453 A CYS 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf12 B SG CYS 78 A CYS 100 1_555 B SG CYS 90 A CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? disulf ? disulf13 B SG CYS 161 A CYS 183 1_555 B SG CYS 167 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf14 B SG CYS 238 A CYS 260 1_555 B SG CYS 251 A CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? disulf ? disulf15 B SG CYS 241 A CYS 263 1_555 B SG CYS 248 A CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf16 B SG CYS 469 A CYS 491 1_555 B SG CYS 499 A CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf17 B SG CYS 765 A CYS 787 1_555 B SG CYS 792 A CYS 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf18 B SG CYS 767 A CYS 789 1_555 B SG CYS 811 A CYS 833 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? covale ? covale1 A ND2 ASN 47 B ASN 69 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 193 B ASN 215 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale3 A ND2 ASN 339 B ASN 361 1_555 M C1 NAG . B NAG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale4 A ND2 ASN 391 B ASN 413 1_555 L C1 NAG . B NAG 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale5 A ND2 ASN 501 B ASN 523 1_555 I C1 NAG . B NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale6 A ND2 ASN 512 B ASN 534 1_555 N C1 NAG . B NAG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale7 A ND2 ASN 568 B ASN 590 1_555 J C1 NAG . B NAG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale8 A ND2 ASN 657 B ASN 679 1_555 O C1 NAG . B NAG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale9 A ND2 ASN 698 B ASN 720 1_555 K C1 NAG . B NAG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale10 B ND2 ASN 47 A ASN 69 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale11 B ND2 ASN 193 A ASN 215 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale12 B ND2 ASN 391 A ASN 413 1_555 Y C1 NAG . A NAG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale13 B ND2 ASN 501 A ASN 523 1_555 V C1 NAG . A NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale14 B ND2 ASN 512 A ASN 534 1_555 X C1 NAG . A NAG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale15 B ND2 ASN 568 A ASN 590 1_555 W C1 NAG . A NAG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale16 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale17 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale18 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale19 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? # _chem_comp.formula 'C10 H12 N5 O7 P' _chem_comp.formula_weight 345.205 _chem_comp.id 9K9 _chem_comp.mon_nstd_flag . _chem_comp.name 2-amino-9-[(2S,3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxotetrahydro-2H-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]-3,9-dihydro-6H-purin-6-one _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 O C2 9K9 doub 1 n n N3 C 9K9 sing 2 n y N3 C4 9K9 doub 3 n y C2 C 9K9 sing 4 n n C2 N1 9K9 sing 5 n n C C1 9K9 doub 6 n y N1 C3 9K9 doub 7 n n C4 N2 9K9 sing 8 n y C1 N2 9K9 sing 9 n y C1 N 9K9 sing 10 n n N2 C5 9K9 sing 11 n n C3 N 9K9 sing 12 n n C3 N4 9K9 sing 13 n n O1 C5 9K9 sing 14 n n O1 C8 9K9 sing 15 n n C5 C6 9K9 sing 16 n n O2 C9 9K9 sing 17 n n C9 C8 9K9 sing 18 n n C8 C7 9K9 sing 19 n n C6 O3 9K9 sing 20 n n C6 C7 9K9 sing 21 n n O3 P 9K9 sing 22 n n C7 O4 9K9 sing 23 n n O4 P 9K9 sing 24 n n P O5 9K9 doub 25 n n P O6 9K9 sing 26 n n C4 H1 9K9 sing 27 n n N4 H2 9K9 sing 28 n n N4 H3 9K9 sing 29 n n N H4 9K9 sing 30 n n C5 H5 9K9 sing 31 n n C6 H6 9K9 sing 32 n n C8 H7 9K9 sing 33 n n C9 H8 9K9 sing 34 n n C9 H9 9K9 sing 35 n n O2 H10 9K9 sing 36 n n C7 H11 9K9 sing 37 n n O6 H12 9K9 sing 38 n n # _atom_sites.entry_id 5ZSL _atom_sites.fract_transf_matrix[1][1] 0.010037 _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] 0.007172 _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] 0.006627 _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 4 NAG B 1 901 836 NAG NAG . J 4 NAG B 1 902 837 NAG NAG . K 4 NAG B 1 905 840 NAG NAG . L 4 NAG B 1 906 841 NAG NAG . M 4 NAG B 1 907 842 NAG NAG . N 4 NAG B 1 908 843 NAG NAG . O 4 NAG B 1 909 844 NAG NAG . P 5 SO4 B 1 912 1 SO4 SO4 . Q 5 SO4 B 1 913 4 SO4 SO4 . R 5 SO4 B 1 914 5 SO4 SO4 . S 5 SO4 B 1 915 7 SO4 SO4 . T 6 9K9 B 1 916 1 9K9 sdf . U 6 9K9 B 1 917 2 9K9 sdf . V 4 NAG A 1 901 836 NAG NAG . W 4 NAG A 1 902 837 NAG NAG . X 4 NAG A 1 907 842 NAG NAG . Y 4 NAG A 1 908 843 NAG NAG . Z 5 SO4 A 1 909 2 SO4 SO4 . AA 5 SO4 A 1 910 3 SO4 SO4 . BA 5 SO4 A 1 911 6 SO4 SO4 . CA 7 HOH B 1 1001 6 HOH HOH . CA 7 HOH B 2 1002 15 HOH HOH . CA 7 HOH B 3 1003 3 HOH HOH . CA 7 HOH B 4 1004 12 HOH HOH . CA 7 HOH B 5 1005 7 HOH HOH . CA 7 HOH B 6 1006 14 HOH HOH . CA 7 HOH B 7 1007 1 HOH HOH . CA 7 HOH B 8 1008 10 HOH HOH . DA 7 HOH A 1 1001 9 HOH HOH . DA 7 HOH A 2 1002 4 HOH HOH . DA 7 HOH A 3 1003 11 HOH HOH . DA 7 HOH A 4 1004 13 HOH HOH . DA 7 HOH A 5 1005 8 HOH HOH . DA 7 HOH A 6 1006 5 HOH HOH . DA 7 HOH A 7 1007 2 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 O O 9K9 . . . U 6 -44.188 -18.686 -37.55 1 37.82 ? O 9K9 917 B 1 HETATM 2 C C2 9K9 . . . U 6 -43.563 -17.717 -38.039 1 37.24 ? C2 9K9 917 B 1 HETATM 3 C C 9K9 . . . U 6 -42.411 -17.929 -38.932 1 40.76 ? C 9K9 917 B 1 HETATM 4 N N3 9K9 . . . U 6 -41.738 -18.979 -39.442 1 39.56 ? N3 9K9 917 B 1 HETATM 5 C C4 9K9 . . . U 6 -40.737 -18.482 -40.216 1 37.13 ? C4 9K9 917 B 1 HETATM 6 N N1 9K9 . . . U 6 -43.894 -16.44 -37.759 1 35.96 ? N1 9K9 917 B 1 HETATM 7 C C3 9K9 . . . U 6 -43.254 -15.36 -38.229 1 33.88 ? C3 9K9 917 B 1 HETATM 8 N N4 9K9 . . . U 6 -43.711 -14.128 -37.896 1 32.14 ? N4 9K9 917 B 1 HETATM 9 N N 9K9 . . . U 6 -42.175 -15.488 -39.027 1 35.45 ? N 9K9 917 B 1 HETATM 10 C C1 9K9 . . . U 6 -41.738 -16.713 -39.401 1 41.25 ? C1 9K9 917 B 1 HETATM 11 N N2 9K9 . . . U 6 -40.742 -17.144 -40.195 1 41.84 ? N2 9K9 917 B 1 HETATM 12 C C5 9K9 . . . U 6 -39.818 -16.218 -40.871 1 41.14 ? C5 9K9 917 B 1 HETATM 13 C C6 9K9 . . . U 6 -40.592 -15.199 -41.697 1 41.96 ? C6 9K9 917 B 1 HETATM 14 O O3 9K9 . . . U 6 -40.395 -15.389 -43.08 1 47.27 ? O3 9K9 917 B 1 HETATM 15 O O1 9K9 . . . U 6 -39.064 -15.486 -39.89 1 42.72 ? O1 9K9 917 B 1 HETATM 16 C C8 9K9 . . . U 6 -38.88 -14.128 -40.331 1 45.71 ? C8 9K9 917 B 1 HETATM 17 C C9 9K9 . . . U 6 -38.864 -13.132 -39.145 1 41.63 ? C9 9K9 917 B 1 HETATM 18 O O2 9K9 . . . U 6 -40.187 -12.96 -38.604 1 37.19 ? O2 9K9 917 B 1 HETATM 19 C C7 9K9 . . . U 6 -40.02 -13.856 -41.305 1 44.63 ? C7 9K9 917 B 1 HETATM 20 O O4 9K9 . . . U 6 -39.557 -13.199 -42.451 1 53.1 ? O4 9K9 917 B 1 HETATM 21 P P 9K9 . . . U 6 -39.639 -14.149 -43.734 1 50.57 ? P 9K9 917 B 1 HETATM 22 O O6 9K9 . . . U 6 -38.241 -14.579 -44.011 1 49.21 ? O6 9K9 917 B 1 HETATM 23 O O5 9K9 . . . U 6 -40.462 -13.448 -44.8 1 49.31 ? O5 9K9 917 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 321 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #