data_8UB0 # _model_server_result.job_id Dew2YfXtjDuyzYTbMIPgyg _model_server_result.datetime_utc '2024-12-11 22:30:43' _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 8ub0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":201}' # _entry.id 8UB0 # _exptl.entry_id 8UB0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.361 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S)-2-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]amino}-3-(1H-imidazol-4-yl)propanoic acid (non-preferred name)' _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 90.18 _cell.angle_gamma 90 _cell.entry_id 8UB0 _cell.length_a 100.829 _cell.length_b 32.807 _cell.length_c 74.156 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8UB0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,G 1 1 B,F,H 2 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 4 _struct_asym.id F _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 A SG CYS 26 A CYS 26 1_555 A SG CYS 84 A CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? disulf ? disulf2 A SG CYS 40 A CYS 40 1_555 A SG CYS 95 A CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? disulf ? disulf3 A SG CYS 58 A CYS 58 1_555 A SG CYS 110 A CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? disulf ? disulf4 A SG CYS 65 A CYS 65 1_555 A SG CYS 72 A CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf5 B SG CYS 26 B CYS 26 1_555 B SG CYS 84 B CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? disulf ? disulf6 B SG CYS 40 B CYS 40 1_555 B SG CYS 95 B CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? disulf ? disulf7 B SG CYS 58 B CYS 58 1_555 B SG CYS 110 B CYS 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? disulf ? disulf8 B SG CYS 65 B CYS 65 1_555 B SG CYS 72 B CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? # _chem_comp.formula 'C16 H21 N8 O8 P' _chem_comp.formula_weight 484.361 _chem_comp.id A1BA4 _chem_comp.mon_nstd_flag . _chem_comp.name '(2S)-2-{[(R)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]amino}-3-(1H-imidazol-4-yl)propanoic acid (non-preferred name)' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "Histidine-5'-O-adenosine phosphoramidate" # 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 N6 C6 A1BA4 sing 1 n n C6 N1 A1BA4 doub 2 n y C6 C5 A1BA4 sing 3 n y N1 C2 A1BA4 sing 4 n y C5 N7 A1BA4 sing 5 n y C5 C4 A1BA4 doub 6 n y N7 C8 A1BA4 doub 7 n y C2 N3 A1BA4 doub 8 n y C4 N3 A1BA4 sing 9 n y C4 N9 A1BA4 sing 10 n y C8 N9 A1BA4 sing 11 n y N9 C1' A1BA4 sing 12 n n O2' C2' A1BA4 sing 13 n n C2' C1' A1BA4 sing 14 n n C2' C3' A1BA4 sing 15 n n C1' O4' A1BA4 sing 16 n n C3' O3' A1BA4 sing 17 n n C3' C4' A1BA4 sing 18 n n O4' C4' A1BA4 sing 19 n n C4' C5' A1BA4 sing 20 n n C5' O5' A1BA4 sing 21 n n OP2 P A1BA4 doub 22 n n O5' P A1BA4 sing 23 n n OP1 P A1BA4 sing 24 n n P N A1BA4 sing 25 n n N CA A1BA4 sing 26 n n OXT C A1BA4 doub 27 n n C O A1BA4 sing 28 n n C CA A1BA4 sing 29 n n CA CB A1BA4 sing 30 n n CB CG A1BA4 sing 31 n n CD2 CG A1BA4 doub 32 n y CD2 NE2 A1BA4 sing 33 n y CG ND1 A1BA4 sing 34 n y NE2 CE1 A1BA4 sing 35 n y ND1 CE1 A1BA4 doub 36 n y C8 H1 A1BA4 sing 37 n n C2 H2 A1BA4 sing 38 n n CD2 H3 A1BA4 sing 39 n n NE2 H4 A1BA4 sing 40 n n CE1 H5 A1BA4 sing 41 n n CB H7 A1BA4 sing 42 n n CB H8 A1BA4 sing 43 n n CA H9 A1BA4 sing 44 n n O H10 A1BA4 sing 45 n n N H11 A1BA4 sing 46 n n OP1 H12 A1BA4 sing 47 n n C5' H13 A1BA4 sing 48 n n C5' H14 A1BA4 sing 49 n n C4' H15 A1BA4 sing 50 n n C3' H16 A1BA4 sing 51 n n O3' H17 A1BA4 sing 52 n n C2' H18 A1BA4 sing 53 n n O2' H19 A1BA4 sing 54 n n C1' H20 A1BA4 sing 55 n n N6 H21 A1BA4 sing 56 n n N6 H22 A1BA4 sing 57 n n # _atom_sites.entry_id 8UB0 _atom_sites.fract_transf_matrix[1][1] 0.009918 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000031 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.030481 _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] 0.013485 _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 AMP A 1 201 201 AMP AMP . D 3 PEG A 1 202 1 PEG PEG . E 3 PEG A 1 203 2 PEG PEG . F 4 A1BA4 B 1 201 201 A1BA4 AXV . G 5 HOH A 1 301 47 HOH HOH . G 5 HOH A 2 302 26 HOH HOH . G 5 HOH A 3 303 66 HOH HOH . G 5 HOH A 4 304 7 HOH HOH . G 5 HOH A 5 305 16 HOH HOH . G 5 HOH A 6 306 33 HOH HOH . G 5 HOH A 7 307 50 HOH HOH . G 5 HOH A 8 308 20 HOH HOH . G 5 HOH A 9 309 71 HOH HOH . G 5 HOH A 10 310 12 HOH HOH . G 5 HOH A 11 311 38 HOH HOH . G 5 HOH A 12 312 28 HOH HOH . G 5 HOH A 13 313 44 HOH HOH . G 5 HOH A 14 314 27 HOH HOH . G 5 HOH A 15 315 37 HOH HOH . G 5 HOH A 16 316 5 HOH HOH . G 5 HOH A 17 317 11 HOH HOH . G 5 HOH A 18 318 36 HOH HOH . G 5 HOH A 19 319 81 HOH HOH . G 5 HOH A 20 320 8 HOH HOH . G 5 HOH A 21 321 22 HOH HOH . G 5 HOH A 22 322 75 HOH HOH . G 5 HOH A 23 323 53 HOH HOH . G 5 HOH A 24 324 41 HOH HOH . G 5 HOH A 25 325 80 HOH HOH . G 5 HOH A 26 326 45 HOH HOH . G 5 HOH A 27 327 18 HOH HOH . G 5 HOH A 28 328 51 HOH HOH . G 5 HOH A 29 329 34 HOH HOH . G 5 HOH A 30 330 52 HOH HOH . G 5 HOH A 31 331 32 HOH HOH . G 5 HOH A 32 332 35 HOH HOH . G 5 HOH A 33 333 42 HOH HOH . G 5 HOH A 34 334 70 HOH HOH . G 5 HOH A 35 335 3 HOH HOH . G 5 HOH A 36 336 23 HOH HOH . G 5 HOH A 37 337 43 HOH HOH . G 5 HOH A 38 338 9 HOH HOH . G 5 HOH A 39 339 4 HOH HOH . G 5 HOH A 40 340 14 HOH HOH . G 5 HOH A 41 341 17 HOH HOH . G 5 HOH A 42 342 6 HOH HOH . G 5 HOH A 43 343 78 HOH HOH . G 5 HOH A 44 344 31 HOH HOH . G 5 HOH A 45 345 24 HOH HOH . G 5 HOH A 46 346 74 HOH HOH . G 5 HOH A 47 347 67 HOH HOH . G 5 HOH A 48 348 65 HOH HOH . G 5 HOH A 49 349 13 HOH HOH . G 5 HOH A 50 350 19 HOH HOH . G 5 HOH A 51 351 21 HOH HOH . G 5 HOH A 52 352 39 HOH HOH . H 5 HOH B 1 301 76 HOH HOH . H 5 HOH B 2 302 73 HOH HOH . H 5 HOH B 3 303 60 HOH HOH . H 5 HOH B 4 304 55 HOH HOH . H 5 HOH B 5 305 57 HOH HOH . H 5 HOH B 6 306 10 HOH HOH . H 5 HOH B 7 307 77 HOH HOH . H 5 HOH B 8 308 49 HOH HOH . H 5 HOH B 9 309 61 HOH HOH . H 5 HOH B 10 310 48 HOH HOH . H 5 HOH B 11 311 62 HOH HOH . H 5 HOH B 12 312 54 HOH HOH . H 5 HOH B 13 313 40 HOH HOH . H 5 HOH B 14 314 25 HOH HOH . H 5 HOH B 15 315 69 HOH HOH . H 5 HOH B 16 316 72 HOH HOH . H 5 HOH B 17 317 15 HOH HOH . H 5 HOH B 18 318 46 HOH HOH . H 5 HOH B 19 319 30 HOH HOH . H 5 HOH B 20 320 56 HOH HOH . H 5 HOH B 21 321 59 HOH HOH . H 5 HOH B 22 322 29 HOH HOH . H 5 HOH B 23 323 58 HOH HOH . H 5 HOH B 24 324 68 HOH HOH . H 5 HOH B 25 325 64 HOH HOH . H 5 HOH B 26 326 63 HOH HOH . H 5 HOH B 27 327 79 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 N N1 A1BA4 . . . F 4 35.893 -20.583 -23.303 1 35.85 ? N1 A1BA4 201 B 1 HETATM 2 N N3 A1BA4 . . . F 4 37.305 -21.099 -21.435 1 37.49 ? N3 A1BA4 201 B 1 HETATM 3 C C4 A1BA4 . . . F 4 37.825 -19.857 -21.542 1 49.66 ? C4 A1BA4 201 B 1 HETATM 4 C C5 A1BA4 . . . F 4 37.409 -19.002 -22.482 1 47.65 ? C5 A1BA4 201 B 1 HETATM 5 C C6 A1BA4 . . . F 4 36.465 -19.365 -23.343 1 38.97 ? C6 A1BA4 201 B 1 HETATM 6 C C8 A1BA4 . . . F 4 38.932 -18.001 -21.335 1 51 ? C8 A1BA4 201 B 1 HETATM 7 C C2 A1BA4 . . . F 4 36.318 -21.496 -22.332 1 35.39 ? C2 A1BA4 201 B 1 HETATM 8 C CD2 A1BA4 . . . F 4 42.1 -21.809 -11.522 1 102.48 ? CD2 A1BA4 201 B 1 HETATM 9 N NE2 A1BA4 . . . F 4 42.52 -22.405 -10.401 1 99.48 ? NE2 A1BA4 201 B 1 HETATM 10 C CE1 A1BA4 . . . F 4 42.576 -21.492 -9.43 1 98.23 ? CE1 A1BA4 201 B 1 HETATM 11 N ND1 A1BA4 . . . F 4 42.188 -20.325 -9.943 1 108.07 ? ND1 A1BA4 201 B 1 HETATM 12 C CG A1BA4 . . . F 4 41.89 -20.53 -11.227 1 106.78 ? CG A1BA4 201 B 1 HETATM 13 C CB A1BA4 . . . F 4 41.401 -19.43 -12.194 1 103.15 ? CB A1BA4 201 B 1 HETATM 14 C CA A1BA4 . . . F 4 39.894 -19.595 -12.516 1 104.6 ? CA A1BA4 201 B 1 HETATM 15 C C A1BA4 . . . F 4 39.275 -18.244 -12.949 1 111.62 ? C A1BA4 201 B 1 HETATM 16 O OXT A1BA4 . . . F 4 40.037 -17.402 -13.484 1 120.66 ? OXT A1BA4 201 B 1 HETATM 17 O O A1BA4 . . . F 4 38.048 -18.087 -12.736 1 98.27 ? O A1BA4 201 B 1 HETATM 18 N N A1BA4 . . . F 4 39.643 -20.607 -13.564 1 98.24 ? N A1BA4 201 B 1 HETATM 19 P P A1BA4 . . . F 4 39.366 -20.314 -15.175 1 101.94 ? P A1BA4 201 B 1 HETATM 20 O OP1 A1BA4 . . . F 4 38.168 -19.46 -15.38 1 77.12 ? OP1 A1BA4 201 B 1 HETATM 21 O OP2 A1BA4 . . . F 4 39.407 -21.629 -15.857 1 95.34 ? OP2 A1BA4 201 B 1 HETATM 22 O O5' A1BA4 . . . F 4 40.754 -19.475 -15.515 1 112.64 ? O5' A1BA4 201 B 1 HETATM 23 C C5' A1BA4 . . . F 4 40.865 -18.656 -16.672 1 101.36 ? C5' A1BA4 201 B 1 HETATM 24 C C4' A1BA4 . . . F 4 40.613 -19.555 -17.879 1 92.75 ? C4' A1BA4 201 B 1 HETATM 25 O O4' A1BA4 . . . F 4 39.582 -18.959 -18.645 1 85.31 ? O4' A1BA4 201 B 1 HETATM 26 C C3' A1BA4 . . . F 4 41.754 -19.66 -18.861 1 87.36 ? C3' A1BA4 201 B 1 HETATM 27 O O3' A1BA4 . . . F 4 42.667 -20.707 -18.472 1 81.5 ? O3' A1BA4 201 B 1 HETATM 28 C C2' A1BA4 . . . F 4 40.986 -20.081 -20.112 1 86.82 ? C2' A1BA4 201 B 1 HETATM 29 O O2' A1BA4 . . . F 4 41.217 -21.477 -20.408 1 86.36 ? O2' A1BA4 201 B 1 HETATM 30 C C1' A1BA4 . . . F 4 39.499 -19.846 -19.731 1 76.21 ? C1' A1BA4 201 B 1 HETATM 31 N N9 A1BA4 . . . F 4 38.764 -19.23 -20.845 1 59.4 ? N9 A1BA4 201 B 1 HETATM 32 N N7 A1BA4 . . . F 4 38.088 -17.852 -22.346 1 48.14 ? N7 A1BA4 201 B 1 HETATM 33 N N6 A1BA4 . . . F 4 36.124 -18.438 -24.236 1 37.96 ? N6 A1BA4 201 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 33 #