data_9NWN # _model_server_result.job_id 9kKiFvPzRE3TtsTV0j-OdQ _model_server_result.datetime_utc '2025-08-29 08:32:58' _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 9nwn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 9NWN # _exptl.entry_id 9NWN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine" _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 9NWN _cell.length_a 49.135 _cell.length_b 56.769 _cell.length_c 93.705 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9NWN _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall 'P 2 2ab' _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1,2 B,E,F,H 2 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' 2_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 56.769 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E 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 A OD1 ASP 6 B ASP 6 1_555 D MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? metalc ? metalc2 A O GLY 7 B GLY 7 1_555 D MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc3 A OD2 ASP 57 B ASP 57 1_555 D MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.874 ? metalc ? metalc4 C O1B ZAN . B ZAN 201 1_555 D MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? metalc ? metalc5 C O1G ZAN . B ZAN 201 1_555 D MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.807 ? metalc ? metalc6 C O2A ZAN . B ZAN 201 1_555 D MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc7 C O3B ZAN . B ZAN 201 1_555 D MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.709 ? metalc ? metalc8 B OD1 ASP 6 A ASP 6 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc9 B O GLY 7 A GLY 7 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc10 B OD2 ASP 57 A ASP 57 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.58 ? metalc ? metalc11 E O1B ZAN . A ZAN 201 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc12 E O1G ZAN . A ZAN 201 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc13 E O2A ZAN . A ZAN 201 1_555 F MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.841 ? # _chem_comp.formula 'C10 H17 N6 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id ZAN _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine" _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 C2 N1 ZAN doub 297 n y C2 N3 ZAN sing 298 n y O2' C2' ZAN sing 299 n n N1 C6 ZAN sing 300 n y N3 C4 ZAN doub 301 n y C2' C1' ZAN sing 302 n n C2' C3' ZAN sing 303 n n C6 N6 ZAN sing 304 n n C6 C5 ZAN doub 305 n y C4 C5 ZAN sing 306 n y C4 N9 ZAN sing 307 n y O3' C3' ZAN sing 308 n n C1' N9 ZAN sing 309 n n C1' O4' ZAN sing 310 n n C5 N7 ZAN sing 311 n y C3' C4' ZAN sing 312 n n N9 C8 ZAN sing 313 n y O2B PB ZAN doub 314 n n N7 C8 ZAN doub 315 n y C4' O4' ZAN sing 316 n n C4' C5' ZAN sing 317 n n PB O1B ZAN sing 318 n n PB N3A ZAN sing 319 n n PB O3B ZAN sing 320 n n N3A PA ZAN sing 321 n n O3B PG ZAN sing 322 n n C5' O5' ZAN sing 323 n n O5' PA ZAN sing 324 n n PA O2A ZAN doub 325 n n PA O1A ZAN sing 326 n n O3G PG ZAN doub 327 n n PG O1G ZAN sing 328 n n PG O2G ZAN sing 329 n n O1A H1 ZAN sing 330 n n O1B H2 ZAN sing 331 n n O1G H3 ZAN sing 332 n n O2G H4 ZAN sing 333 n n N3A H5 ZAN sing 334 n n C5' H6 ZAN sing 335 n n C5' H7 ZAN sing 336 n n C4' H8 ZAN sing 337 n n C3' H9 ZAN sing 338 n n O3' H10 ZAN sing 339 n n C2' H11 ZAN sing 340 n n O2' H12 ZAN sing 341 n n C1' H13 ZAN sing 342 n n C8 H14 ZAN sing 343 n n N6 H15 ZAN sing 344 n n N6 H16 ZAN sing 345 n n C2 H17 ZAN sing 346 n n # _atom_sites.entry_id 9NWN _atom_sites.fract_transf_matrix[1][1] 0.020352 _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] 0.017615 _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] 0.010672 _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 C 2 ZAN B 1 201 2 ZAN ZAN . D 3 MG B 1 202 2 MG MG . E 2 ZAN A 1 201 1 ZAN ZAN . F 3 MG A 1 202 1 MG MG . G 4 HOH B 1 301 33 HOH HOH . G 4 HOH B 2 302 31 HOH HOH . G 4 HOH B 3 303 58 HOH HOH . G 4 HOH B 4 304 19 HOH HOH . G 4 HOH B 5 305 29 HOH HOH . G 4 HOH B 6 306 54 HOH HOH . G 4 HOH B 7 307 20 HOH HOH . G 4 HOH B 8 308 69 HOH HOH . G 4 HOH B 9 309 61 HOH HOH . G 4 HOH B 10 310 11 HOH HOH . G 4 HOH B 11 311 56 HOH HOH . G 4 HOH B 12 312 3 HOH HOH . G 4 HOH B 13 313 51 HOH HOH . G 4 HOH B 14 314 9 HOH HOH . G 4 HOH B 15 315 4 HOH HOH . G 4 HOH B 16 316 13 HOH HOH . G 4 HOH B 17 317 59 HOH HOH . G 4 HOH B 18 318 22 HOH HOH . G 4 HOH B 19 319 14 HOH HOH . G 4 HOH B 20 320 12 HOH HOH . G 4 HOH B 21 321 24 HOH HOH . G 4 HOH B 22 322 53 HOH HOH . G 4 HOH B 23 323 23 HOH HOH . G 4 HOH B 24 324 45 HOH HOH . G 4 HOH B 25 325 48 HOH HOH . G 4 HOH B 26 326 42 HOH HOH . G 4 HOH B 27 327 27 HOH HOH . G 4 HOH B 28 328 71 HOH HOH . G 4 HOH B 29 329 15 HOH HOH . G 4 HOH B 30 330 62 HOH HOH . G 4 HOH B 31 331 36 HOH HOH . G 4 HOH B 32 332 65 HOH HOH . G 4 HOH B 33 333 41 HOH HOH . G 4 HOH B 34 334 30 HOH HOH . H 4 HOH A 1 301 32 HOH HOH . H 4 HOH A 2 302 35 HOH HOH . H 4 HOH A 3 303 55 HOH HOH . H 4 HOH A 4 304 63 HOH HOH . H 4 HOH A 5 305 47 HOH HOH . H 4 HOH A 6 306 1 HOH HOH . H 4 HOH A 7 307 37 HOH HOH . H 4 HOH A 8 308 34 HOH HOH . H 4 HOH A 9 309 18 HOH HOH . H 4 HOH A 10 310 52 HOH HOH . H 4 HOH A 11 311 16 HOH HOH . H 4 HOH A 12 312 46 HOH HOH . H 4 HOH A 13 313 6 HOH HOH . H 4 HOH A 14 314 64 HOH HOH . H 4 HOH A 15 315 43 HOH HOH . H 4 HOH A 16 316 25 HOH HOH . H 4 HOH A 17 317 26 HOH HOH . H 4 HOH A 18 318 7 HOH HOH . H 4 HOH A 19 319 40 HOH HOH . H 4 HOH A 20 320 21 HOH HOH . H 4 HOH A 21 321 17 HOH HOH . H 4 HOH A 22 322 8 HOH HOH . H 4 HOH A 23 323 57 HOH HOH . H 4 HOH A 24 324 49 HOH HOH . H 4 HOH A 25 325 39 HOH HOH . H 4 HOH A 26 326 66 HOH HOH . H 4 HOH A 27 327 70 HOH HOH . H 4 HOH A 28 328 5 HOH HOH . H 4 HOH A 29 329 38 HOH HOH . H 4 HOH A 30 330 67 HOH HOH . H 4 HOH A 31 331 60 HOH HOH . H 4 HOH A 32 332 10 HOH HOH . H 4 HOH A 33 333 2 HOH HOH . H 4 HOH A 34 334 28 HOH HOH . H 4 HOH A 35 335 50 HOH HOH . H 4 HOH A 36 336 68 HOH HOH . H 4 HOH A 37 337 44 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 P PA ZAN . . . E 2 3.215 27.667 -29.598 1 36.28 ? PA ZAN 201 A 1 HETATM 2 P PB ZAN . . . E 2 5.458 29.174 -28.514 1 32.39 ? PB ZAN 201 A 1 HETATM 3 P PG ZAN . . . E 2 6.777 26.848 -27.308 1 27.53 ? PG ZAN 201 A 1 HETATM 4 O O1A ZAN . . . E 2 1.907 26.981 -29.232 1 42.91 ? O1A ZAN 201 A 1 HETATM 5 O O1B ZAN . . . E 2 5.778 28.794 -29.943 1 33.32 ? O1B ZAN 201 A 1 HETATM 6 O O1G ZAN . . . E 2 6.258 26.11 -28.502 1 37.6 ? O1G ZAN 201 A 1 HETATM 7 O O2A ZAN . . . E 2 4.229 26.647 -30.103 1 33.82 ? O2A ZAN 201 A 1 HETATM 8 O O2B ZAN . . . E 2 5.396 30.609 -28.131 1 44.07 ? O2B ZAN 201 A 1 HETATM 9 O O2G ZAN . . . E 2 8.272 26.64 -27.284 1 30.44 ? O2G ZAN 201 A 1 HETATM 10 N N3A ZAN . . . E 2 3.911 28.61 -28.28 1 29.07 ? N3A ZAN 201 A 1 HETATM 11 O O3B ZAN . . . E 2 6.592 28.474 -27.521 1 40.8 ? O3B ZAN 201 A 1 HETATM 12 O O3G ZAN . . . E 2 6.113 26.295 -26.073 1 37.86 ? O3G ZAN 201 A 1 HETATM 13 O O5' ZAN . . . E 2 3.036 28.789 -30.747 1 44.04 ? O5' ZAN 201 A 1 HETATM 14 C C5' ZAN . . . E 2 1.818 29.21 -31.216 1 43.82 ? C5' ZAN 201 A 1 HETATM 15 C C4' ZAN . . . E 2 1.499 30.637 -31.139 1 36.55 ? C4' ZAN 201 A 1 HETATM 16 O O4' ZAN . . . E 2 2.179 31.289 -32.444 1 33.87 ? O4' ZAN 201 A 1 HETATM 17 C C3' ZAN . . . E 2 0.172 30.592 -31.298 1 38.37 ? C3' ZAN 201 A 1 HETATM 18 O O3' ZAN . . . E 2 -0.49 31.754 -30.722 1 43.06 ? O3' ZAN 201 A 1 HETATM 19 C C2' ZAN . . . E 2 -0.057 30.65 -32.848 1 38.77 ? C2' ZAN 201 A 1 HETATM 20 O O2' ZAN . . . E 2 -1.199 31.272 -33.102 1 43.01 ? O2' ZAN 201 A 1 HETATM 21 C C1' ZAN . . . E 2 1.179 31.534 -33.267 1 40.7 ? C1' ZAN 201 A 1 HETATM 22 N N9 ZAN . . . E 2 1.742 31.255 -34.599 1 33.75 ? N9 ZAN 201 A 1 HETATM 23 C C8 ZAN . . . E 2 2.363 30.085 -34.805 1 38.49 ? C8 ZAN 201 A 1 HETATM 24 N N7 ZAN . . . E 2 2.776 30.086 -36.107 1 37.38 ? N7 ZAN 201 A 1 HETATM 25 C C5 ZAN . . . E 2 2.418 31.243 -36.665 1 38.25 ? C5 ZAN 201 A 1 HETATM 26 C C6 ZAN . . . E 2 2.61 31.741 -37.952 1 37.95 ? C6 ZAN 201 A 1 HETATM 27 N N6 ZAN . . . E 2 3.279 31.198 -39.193 1 39.26 ? N6 ZAN 201 A 1 HETATM 28 N N1 ZAN . . . E 2 2.15 32.962 -38.256 1 34.77 ? N1 ZAN 201 A 1 HETATM 29 C C2 ZAN . . . E 2 1.498 33.697 -37.297 1 33.14 ? C2 ZAN 201 A 1 HETATM 30 N N3 ZAN . . . E 2 1.31 33.208 -36.04 1 37.27 ? N3 ZAN 201 A 1 HETATM 31 C C4 ZAN . . . E 2 1.774 31.988 -35.729 1 40.56 ? C4 ZAN 201 A 1 HETATM 32 H H5 ZAN . . . E 2 3.475 28.769 -27.556 1 34.92 ? H5 ZAN 201 A 1 HETATM 33 H H6 ZAN . . . E 2 1.766 28.954 -32.15 1 52.62 ? H6 ZAN 201 A 1 HETATM 34 H H7 ZAN . . . E 2 1.138 28.736 -30.712 1 52.62 ? H7 ZAN 201 A 1 HETATM 35 H H8 ZAN . . . E 2 1.766 31.157 -30.365 1 43.9 ? H8 ZAN 201 A 1 HETATM 36 H H9 ZAN . . . E 2 -0.151 29.77 -30.896 1 46.08 ? H9 ZAN 201 A 1 HETATM 37 H H10 ZAN . . . E 2 -0.109 32.454 -30.988 1 51.71 ? H10 ZAN 201 A 1 HETATM 38 H H11 ZAN . . . E 2 -0.069 29.784 -33.285 1 46.57 ? H11 ZAN 201 A 1 HETATM 39 H H13 ZAN . . . E 2 0.816 32.431 -33.2 1 48.87 ? H13 ZAN 201 A 1 HETATM 40 H H14 ZAN . . . E 2 2.495 29.376 -34.156 1 46.22 ? H14 ZAN 201 A 1 HETATM 41 H H15 ZAN . . . E 2 3.043 31.481 -39.97 1 47.15 ? H15 ZAN 201 A 1 HETATM 42 H H16 ZAN . . . E 2 3.888 30.595 -39.116 1 47.15 ? H16 ZAN 201 A 1 HETATM 43 H H17 ZAN . . . E 2 1.165 34.581 -37.519 1 39.8 ? H17 ZAN 201 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 352 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #