data_8JNR # _model_server_result.job_id t8V4UvQPaT3DNKelm3nQRA _model_server_result.datetime_utc '2024-11-26 12:56:00' _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 8jnr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":1003}' # _entry.id 8JNR # _exptl.entry_id 8JNR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 322.232 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3S,5R)-5-(4-azanyl-3-methyl-2-oxo-pyrimidin-3-ium-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen 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 113.07 _cell.angle_gamma 90 _cell.entry_id 8JNR _cell.length_a 108.615 _cell.length_b 142.171 _cell.length_c 130.11 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8JNR _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetradecameric _pdbx_struct_assembly.oligomeric_count 14 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id T _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 disulf ? disulf1 G SG CYS 22 G CYS 22 1_555 G SG CYS 96 G CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 G SG CYS 140 G CYS 140 1_555 G SG CYS 196 G CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 H SG CYS 22 H CYS 22 1_555 H SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf4 H SG CYS 140 H CYS 140 1_555 H SG CYS 196 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 I SG CYS 22 I CYS 22 1_555 I SG CYS 96 I CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf6 I SG CYS 140 I CYS 140 1_555 I SG CYS 196 I CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf7 J SG CYS 22 J CYS 22 1_555 J SG CYS 96 J CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf8 J SG CYS 140 J CYS 140 1_555 J SG CYS 196 J CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf9 K SG CYS 24 K CYS 24 1_555 K SG CYS 89 K CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf10 K SG CYS 137 K CYS 137 1_555 K SG CYS 197 K CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf11 L SG CYS 24 L CYS 24 1_555 L SG CYS 89 L CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf12 L SG CYS 137 L CYS 137 1_555 L SG CYS 197 L CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf13 M SG CYS 24 M CYS 24 1_555 M SG CYS 89 M CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf14 M SG CYS 137 M CYS 137 1_555 M SG CYS 197 M CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf15 N SG CYS 24 N CYS 24 1_555 N SG CYS 89 N CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? disulf ? disulf16 N SG CYS 137 N CYS 137 1_555 N SG CYS 197 N CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 B O3' DT 1 B DT 4 1_555 B P ME6 2 B ME6 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.543 ? covale ? covale2 B O3' ME6 2 B ME6 5 1_555 B P DT 3 B DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.53 ? covale ? covale3 F O3' ME6 2 F ME6 5 1_555 F P DT 3 F DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.682 ? metalc ? metalc1 A NE2 HIS 143 A HIS 191 1_555 P MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc2 A OD2 ASP 145 A ASP 193 1_555 P MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc3 A NE2 HIS 209 A HIS 257 1_555 P MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc4 O O1 OGA . A OGA 1001 1_555 P MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? metalc ? metalc5 O O2' OGA . A OGA 1001 1_555 P MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc6 C NE2 HIS 143 C HIS 191 1_555 Q MN MN . C MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? metalc ? metalc7 C OD1 ASP 145 C ASP 193 1_555 Q MN MN . C MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc8 C NE2 HIS 209 C HIS 257 1_555 Q MN MN . C MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc9 D NE2 HIS 143 D HIS 191 1_555 S MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc10 D OD2 ASP 145 D ASP 193 1_555 S MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc11 D NE2 HIS 209 D HIS 257 1_555 S MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc12 R O2 OGA . D OGA 1001 1_555 S MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc13 R O2' OGA . D OGA 1001 1_555 S MN MN . D MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc14 E NE2 HIS 143 E HIS 191 1_555 U MN MN . E MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc15 E OD2 ASP 145 E ASP 193 1_555 U MN MN . E MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? metalc ? metalc16 E NE2 HIS 209 E HIS 257 1_555 U MN MN . E MN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? # _chem_comp.formula 'C10 H17 N3 O7 P 1' _chem_comp.formula_weight 322.232 _chem_comp.id ME6 _chem_comp.mon_nstd_flag n _chem_comp.name '[(2R,3S,5R)-5-(4-azanyl-3-methyl-2-oxo-pyrimidin-3-ium-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate' _chem_comp.type 'dna linking' _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 O2 C2 ME6 doub 253 n n C2 N1 ME6 sing 254 n n C2 N3 ME6 sing 255 n n N3 C4 ME6 doub 256 n n C20 N3 ME6 sing 257 n n C20 H20 ME6 sing 258 n n C20 H20A ME6 sing 259 n n C20 H20B ME6 sing 260 n n C4 N4 ME6 sing 261 n n C4 C5 ME6 sing 262 n n N4 HN4 ME6 sing 263 n n C5 H5 ME6 sing 264 n n C6 C5 ME6 doub 265 n n C6 H6 ME6 sing 266 n n N1 C6 ME6 sing 267 n n C1' N1 ME6 sing 268 n n C1' H1' ME6 sing 269 n n O4' C1' ME6 sing 270 n n C2' C1' ME6 sing 271 n n C2' H2' ME6 sing 272 n n C2' "H2'A" ME6 sing 273 n n C3' C2' ME6 sing 274 n n C3' O3' ME6 sing 275 n n C3' H3' ME6 sing 276 n n O3' HO3' ME6 sing 277 n n C4' O4' ME6 sing 278 n n C4' C3' ME6 sing 279 n n C4' H4' ME6 sing 280 n n C5' C4' ME6 sing 281 n n C5' H5' ME6 sing 282 n n C5' "H5'A" ME6 sing 283 n n O5' C5' ME6 sing 284 n n P O5' ME6 sing 285 n n P O3P ME6 sing 286 n n P O1P ME6 doub 287 n n O3P HO3P ME6 sing 288 n n O2P P ME6 sing 289 n n O2P HO2P ME6 sing 290 n n N4 H17 ME6 sing 291 n n # _atom_sites.entry_id 8JNR _atom_sites.fract_transf_matrix[1][1] 0.009207 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003922 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007034 _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] 0.008354 _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 O 5 OGA A 1 1001 1001 OGA OGA . P 6 MN A 1 1002 1002 MN MN . Q 6 MN C 1 1001 1001 MN MN . R 5 OGA D 1 1001 1001 OGA OGA . S 6 MN D 1 1002 1002 MN MN . T 7 ME6 D 1 1003 1003 ME6 ME6 . U 6 MN E 1 1001 1001 MN MN . # 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 O2 ME6 . . . T 7 25.004 -13.17 44.549 1 110.77 ? O2 ME6 1003 D 1 HETATM 2 C C2 ME6 . . . T 7 25.089 -12.373 45.423 1 103.81 ? C2 ME6 1003 D 1 HETATM 3 N N3 ME6 . . . T 7 24.032 -11.295 45.546 1 107.13 ? N3 ME6 1003 D 1 HETATM 4 C C20 ME6 . . . T 7 22.937 -11.286 44.544 1 104.72 ? C20 ME6 1003 D 1 HETATM 5 C C4 ME6 . . . T 7 24.103 -10.296 46.615 1 102.63 ? C4 ME6 1003 D 1 HETATM 6 N N4 ME6 . . . T 7 23.122 -9.221 46.799 1 97.88 ? N4 ME6 1003 D 1 HETATM 7 C C5 ME6 . . . T 7 25.219 -10.344 47.584 1 95.56 ? C5 ME6 1003 D 1 HETATM 8 C C6 ME6 . . . T 7 26.244 -11.405 47.454 1 100.43 ? C6 ME6 1003 D 1 HETATM 9 N N1 ME6 . . . T 7 26.222 -12.434 46.398 1 107.38 ? N1 ME6 1003 D 1 HETATM 10 C C1' ME6 . . . T 7 27.296 -13.502 46.325 1 123.8 ? C1' ME6 1003 D 1 HETATM 11 O O4' ME6 . . . T 7 27.334 -14.266 47.406 1 115.04 ? O4' ME6 1003 D 1 HETATM 12 C C2' ME6 . . . T 7 28.739 -12.879 46.198 1 124.45 ? C2' ME6 1003 D 1 HETATM 13 C C3' ME6 . . . T 7 29.627 -13.546 47.247 1 119.82 ? C3' ME6 1003 D 1 HETATM 14 O O3' ME6 . . . T 7 30.635 -14.446 46.638 1 118.83 ? O3' ME6 1003 D 1 HETATM 15 C C4' ME6 . . . T 7 28.809 -14.236 48.083 1 111.35 ? C4' ME6 1003 D 1 HETATM 16 C C5' ME6 . . . T 7 28.756 -13.626 49.443 1 105.17 ? C5' ME6 1003 D 1 HETATM 17 O O5' ME6 . . . T 7 28.288 -12.311 49.325 1 112.44 ? O5' ME6 1003 D 1 HETATM 18 P P ME6 . . . T 7 29.202 -10.93 49.673 1 121.06 ? P ME6 1003 D 1 HETATM 19 O O2P ME6 . . . T 7 30.541 -10.838 48.966 1 121.46 ? O2P ME6 1003 D 1 HETATM 20 O O1P ME6 . . . T 7 28.393 -9.653 49.489 1 114.55 ? O1P ME6 1003 D 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 20 #