data_5ZSM # _model_server_result.job_id ngnXfsbYtsvd84d8olJL7w _model_server_result.datetime_utc '2024-11-28 10:14:33' _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 5zsm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"DA","auth_seq_id":914}' # _entry.id 5ZSM # _exptl.entry_id 5ZSM _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 5ZSM _cell.length_a 99.655 _cell.length_b 139.173 _cell.length_c 150.794 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZSM _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 PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_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 _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 R N N ? 6 DA 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 A 838 NAG 3 n F NAG 2 F 2 NAG A 839 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? disulf ? disulf2 A SG CYS 76 B CYS 98 1_555 A SG CYS 453 B CYS 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf3 A SG CYS 78 B CYS 100 1_555 A SG CYS 90 B CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf4 A SG CYS 161 B CYS 183 1_555 A SG CYS 167 B CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf5 A SG CYS 238 B CYS 260 1_555 A SG CYS 251 B CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? disulf ? disulf6 A SG CYS 241 B CYS 263 1_555 A SG CYS 248 B CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf7 A SG CYS 469 B CYS 491 1_555 A SG CYS 499 B CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf8 A SG CYS 765 B CYS 787 1_555 A SG CYS 792 B CYS 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? disulf ? disulf9 A SG CYS 767 B CYS 789 1_555 A SG CYS 811 B CYS 833 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf10 B SG CYS 14 A CYS 36 1_555 B SG CYS 29 A CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? disulf ? disulf11 B SG CYS 76 A CYS 98 1_555 B SG CYS 453 A CYS 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf12 B SG CYS 78 A CYS 100 1_555 B SG CYS 90 A CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? disulf ? disulf13 B SG CYS 161 A CYS 183 1_555 B SG CYS 167 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf14 B SG CYS 238 A CYS 260 1_555 B SG CYS 251 A CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf15 B SG CYS 241 A CYS 263 1_555 B SG CYS 248 A CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf16 B SG CYS 469 A CYS 491 1_555 B SG CYS 499 A CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf17 B SG CYS 765 A CYS 787 1_555 B SG CYS 792 A CYS 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? disulf ? disulf18 B SG CYS 767 A CYS 789 1_555 B SG CYS 811 A CYS 833 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? covale ? covale1 A ND2 ASN 47 B ASN 69 1_555 M C1 NAG . B NAG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale2 A ND2 ASN 193 B ASN 215 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale3 A ND2 ASN 339 B ASN 361 1_555 K C1 NAG . B NAG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? covale ? covale4 A ND2 ASN 391 B ASN 413 1_555 I C1 NAG . B NAG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale5 A ND2 ASN 501 B ASN 523 1_555 H C1 NAG . B NAG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale6 A ND2 ASN 512 B ASN 534 1_555 L C1 NAG . B NAG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale7 A ND2 ASN 568 B ASN 590 1_555 G C1 NAG . B NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale8 A ND2 ASN 657 B ASN 679 1_555 N C1 NAG . B NAG 910 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? covale ? covale9 A ND2 ASN 698 B ASN 720 1_555 J C1 NAG . B NAG 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale10 B ND2 ASN 47 A ASN 69 1_555 U C1 NAG . A NAG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale11 B ND2 ASN 193 A ASN 215 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale12 B ND2 ASN 391 A ASN 413 1_555 V C1 NAG . A NAG 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale13 B ND2 ASN 501 A ASN 523 1_555 T C1 NAG . A NAG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? covale ? covale14 B ND2 ASN 512 A ASN 534 1_555 W C1 NAG . A NAG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale15 B ND2 ASN 568 A ASN 590 1_555 S C1 NAG . A NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale16 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale17 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? # _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 5ZSM _atom_sites.fract_transf_matrix[1][1] 0.010035 _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] 0.007185 _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] 0.006632 _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 G 4 NAG B 1 901 836 NAG NAG . H 4 NAG B 1 902 837 NAG NAG . I 4 NAG B 1 905 840 NAG NAG . J 4 NAG B 1 906 841 NAG NAG . K 4 NAG B 1 907 842 NAG NAG . L 4 NAG B 1 908 843 NAG NAG . M 4 NAG B 1 909 844 NAG NAG . N 4 NAG B 1 910 845 NAG NAG . O 5 SO4 B 1 911 2 SO4 SO4 . P 5 SO4 B 1 912 5 SO4 SO4 . Q 5 SO4 B 1 913 6 SO4 SO4 . R 6 9K9 B 1 914 2 9K9 sdf . S 4 NAG A 1 901 836 NAG NAG . T 4 NAG A 1 902 837 NAG NAG . U 4 NAG A 1 905 840 NAG NAG . V 4 NAG A 1 906 841 NAG NAG . W 4 NAG A 1 907 842 NAG NAG . X 5 SO4 A 1 908 1 SO4 SO4 . Y 5 SO4 A 1 909 3 SO4 SO4 . Z 5 SO4 A 1 910 4 SO4 SO4 . AA 5 SO4 A 1 911 7 SO4 SO4 . BA 5 SO4 A 1 912 8 SO4 SO4 . CA 5 SO4 A 1 913 9 SO4 SO4 . DA 6 9K9 A 1 914 1 9K9 sdf . EA 7 HOH B 1 1001 3 HOH HOH . EA 7 HOH B 2 1002 7 HOH HOH . EA 7 HOH B 3 1003 20 HOH HOH . EA 7 HOH B 4 1004 9 HOH HOH . EA 7 HOH B 5 1005 4 HOH HOH . EA 7 HOH B 6 1006 8 HOH HOH . EA 7 HOH B 7 1007 17 HOH HOH . EA 7 HOH B 8 1008 11 HOH HOH . EA 7 HOH B 9 1009 1 HOH HOH . EA 7 HOH B 10 1010 10 HOH HOH . EA 7 HOH B 11 1011 6 HOH HOH . EA 7 HOH B 12 1012 16 HOH HOH . EA 7 HOH B 13 1013 15 HOH HOH . EA 7 HOH B 14 1014 14 HOH HOH . EA 7 HOH B 15 1015 18 HOH HOH . EA 7 HOH B 16 1016 19 HOH HOH . EA 7 HOH B 17 1017 22 HOH HOH . EA 7 HOH B 18 1018 21 HOH HOH . FA 7 HOH A 1 1001 12 HOH HOH . FA 7 HOH A 2 1002 5 HOH HOH . FA 7 HOH A 3 1003 13 HOH HOH . FA 7 HOH A 4 1004 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 . . . DA 6 -10.632 -28.501 -16.373 1 35.54 ? O 9K9 914 A 1 HETATM 2 C C2 9K9 . . . DA 6 -11.268 -28.297 -15.325 1 35.34 ? C2 9K9 914 A 1 HETATM 3 C C 9K9 . . . DA 6 -12.42 -29.135 -14.906 1 39.26 ? C 9K9 914 A 1 HETATM 4 N N3 9K9 . . . DA 6 -13.059 -30.233 -15.37 1 38.58 ? N3 9K9 914 A 1 HETATM 5 C C4 9K9 . . . DA 6 -14.057 -30.486 -14.467 1 40.48 ? C4 9K9 914 A 1 HETATM 6 N N1 9K9 . . . DA 6 -10.951 -27.267 -14.56 1 34.44 ? N1 9K9 914 A 1 HETATM 7 C C3 9K9 . . . DA 6 -11.611 -26.949 -13.438 1 34.55 ? C3 9K9 914 A 1 HETATM 8 N N4 9K9 . . . DA 6 -11.182 -25.888 -12.717 1 33.43 ? N4 9K9 914 A 1 HETATM 9 N N 9K9 . . . DA 6 -12.676 -27.644 -12.987 1 34.9 ? N 9K9 914 A 1 HETATM 10 C C1 9K9 . . . DA 6 -13.117 -28.711 -13.677 1 37.59 ? C1 9K9 914 A 1 HETATM 11 N N2 9K9 . . . DA 6 -14.079 -29.59 -13.448 1 38.99 ? N2 9K9 914 A 1 HETATM 12 C C5 9K9 . . . DA 6 -15.028 -29.492 -12.293 1 39.71 ? C5 9K9 914 A 1 HETATM 13 C C6 9K9 . . . DA 6 -14.376 -29.366 -10.935 1 42.44 ? C6 9K9 914 A 1 HETATM 14 O O3 9K9 . . . DA 6 -14.463 -30.53 -10.177 1 44.15 ? O3 9K9 914 A 1 HETATM 15 O O1 9K9 . . . DA 6 -15.728 -28.239 -12.428 1 41.88 ? O1 9K9 914 A 1 HETATM 16 C C8 9K9 . . . DA 6 -16.124 -27.733 -11.146 1 41.13 ? C8 9K9 914 A 1 HETATM 17 C C9 9K9 . . . DA 6 -16.096 -26.218 -11.177 1 40.55 ? C9 9K9 914 A 1 HETATM 18 O O2 9K9 . . . DA 6 -14.815 -25.784 -11.702 1 39.99 ? O2 9K9 914 A 1 HETATM 19 C C7 9K9 . . . DA 6 -15.097 -28.275 -10.16 1 44.94 ? C7 9K9 914 A 1 HETATM 20 O O4 9K9 . . . DA 6 -15.611 -28.806 -8.928 1 46.59 ? O4 9K9 914 A 1 HETATM 21 P P 9K9 . . . DA 6 -15.256 -30.33 -8.847 1 41.89 ? P 9K9 914 A 1 HETATM 22 O O6 9K9 . . . DA 6 -14.354 -30.727 -7.738 1 43.2 ? O6 9K9 914 A 1 HETATM 23 O O5 9K9 . . . DA 6 -16.518 -31.106 -9.063 1 48.79 ? O5 9K9 914 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 246 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 23 #