data_4QTN # _model_server_result.job_id vgqAw_ojF3VefnMYKKgBPw _model_server_result.datetime_utc '2024-11-24 01:05:32' _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 4qtn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":301}' # _entry.id 4QTN # _exptl.entry_id 4QTN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 255.247 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'Nicotinamide riboside' _entity.pdbx_number_of_molecules 3 _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 4QTN _cell.length_a 93.32 _cell.length_b 112.93 _cell.length_c 120.37 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4QTN _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 ? 2 D N N ? 2 F N N ? 2 I 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 covale ? covale1 A C LEU 24 A LEU 24 1_555 A N MSE 25 A MSE 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale2 A C MSE 25 A MSE 25 1_555 A N PHE 26 A PHE 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale3 A C GLU 87 A GLU 87 1_555 A N MSE 88 A MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 A C MSE 88 A MSE 88 1_555 A N MSE 89 A MSE 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale5 A C MSE 89 A MSE 89 1_555 A N LEU 90 A LEU 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 A C ALA 104 A ALA 104 1_555 A N MSE 105 A MSE 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? covale ? covale7 A C MSE 105 A MSE 105 1_555 A N TRP 106 A TRP 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale8 A C HIS 109 A HIS 109 1_555 A N MSE 110 A MSE 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.312 ? covale ? covale9 A C MSE 110 A MSE 110 1_555 A N ALA 111 A ALA 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale10 A C LEU 173 A LEU 173 1_555 A N MSE 174 A MSE 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale11 A C MSE 174 A MSE 174 1_555 A N ILE 175 A ILE 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale12 A C LEU 212 A LEU 212 1_555 A N MSE 213 A MSE 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale13 A C MSE 213 A MSE 213 1_555 A N TYR 214 A TYR 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale14 A C VAL 215 A VAL 215 1_555 A N MSE 216 A MSE 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale15 A C MSE 216 A MSE 216 1_555 A N TYR 217 A TYR 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale16 B C LEU 24 B LEU 24 1_555 B N MSE 25 B MSE 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale17 B C MSE 25 B MSE 25 1_555 B N PHE 26 B PHE 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale18 B C GLU 87 B GLU 87 1_555 B N MSE 88 B MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale19 B C MSE 88 B MSE 88 1_555 B N MSE 89 B MSE 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale20 B C MSE 89 B MSE 89 1_555 B N LEU 90 B LEU 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale21 B C ALA 104 B ALA 104 1_555 B N MSE 105 B MSE 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale22 B C MSE 105 B MSE 105 1_555 B N TRP 106 B TRP 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale23 B C HIS 109 B HIS 109 1_555 B N MSE 110 B MSE 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? covale ? covale24 B C MSE 110 B MSE 110 1_555 B N ALA 111 B ALA 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale25 B C LEU 173 B LEU 173 1_555 B N MSE 174 B MSE 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale26 B C MSE 174 B MSE 174 1_555 B N ILE 175 B ILE 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale27 B C LEU 212 B LEU 212 1_555 B N MSE 213 B MSE 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale28 B C MSE 213 B MSE 213 1_555 B N TYR 214 B TYR 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale29 B C VAL 215 B VAL 215 1_555 B N MSE 216 B MSE 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale30 B C MSE 216 B MSE 216 1_555 B N TYR 217 B TYR 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale31 C C LEU 24 C LEU 24 1_555 C N MSE 25 C MSE 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale32 C C MSE 25 C MSE 25 1_555 C N PHE 26 C PHE 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale33 C C GLU 87 C GLU 87 1_555 C N MSE 88 C MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale34 C C MSE 88 C MSE 88 1_555 C N MSE 89 C MSE 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale35 C C MSE 89 C MSE 89 1_555 C N LEU 90 C LEU 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale36 C C ALA 104 C ALA 104 1_555 C N MSE 105 C MSE 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale37 C C MSE 105 C MSE 105 1_555 C N TRP 106 C TRP 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale38 C C HIS 109 C HIS 109 1_555 C N MSE 110 C MSE 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale39 C C MSE 110 C MSE 110 1_555 C N ALA 111 C ALA 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale40 C C LEU 173 C LEU 173 1_555 C N MSE 174 C MSE 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale41 C C MSE 174 C MSE 174 1_555 C N ILE 175 C ILE 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale42 C C LEU 212 C LEU 212 1_555 C N MSE 213 C MSE 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale43 C C MSE 213 C MSE 213 1_555 C N TYR 214 C TYR 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale44 C C VAL 215 C VAL 215 1_555 C N MSE 216 C MSE 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale45 C C MSE 216 C MSE 216 1_555 C N TYR 217 C TYR 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? # _chem_comp.formula 'C11 H15 N2 O5 1' _chem_comp.formula_weight 255.247 _chem_comp.id NNR _chem_comp.mon_nstd_flag . _chem_comp.name 'Nicotinamide riboside' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 3-(aminocarbonyl)-1-beta-D-ribofuranosylpyridinium # 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 C5 C6 NNR doub 283 n y C5 C4 NNR sing 284 n y C6 N1 NNR sing 285 n y C4 C3 NNR doub 286 n y O2R C2R NNR sing 287 n n N1 C1R NNR sing 288 n n N1 C2 NNR doub 289 n y C3 C2 NNR sing 290 n y C3 C7 NNR sing 291 n n C1R C2R NNR sing 292 n n C1R O4R NNR sing 293 n n C2R C3R NNR sing 294 n n C7 O7 NNR doub 295 n n C7 N7 NNR sing 296 n n O3R C3R NNR sing 297 n n O4R C4R NNR sing 298 n n C3R C4R NNR sing 299 n n C4R C5R NNR sing 300 n n C5R O5R NNR sing 301 n n O2R HO2R NNR sing 302 n n C2R H2R NNR sing 303 n n C3R H3R NNR sing 304 n n O3R HO3R NNR sing 305 n n C4R H4R NNR sing 306 n n C5R H5R1 NNR sing 307 n n C5R H5R2 NNR sing 308 n n O5R HO5R NNR sing 309 n n C1R H1R NNR sing 310 n n C2 H2 NNR sing 311 n n C6 H6 NNR sing 312 n n C5 H5 NNR sing 313 n n C4 H4 NNR sing 314 n n N7 HN71 NNR sing 315 n n N7 HN72 NNR sing 316 n n # _atom_sites.entry_id 4QTN _atom_sites.fract_transf_matrix[1][1] 0.010716 _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] 0.008855 _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] 0.008308 _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 D 2 NNR A 1 301 1 NNR NNR . E 3 BOG A 1 302 1 BOG BOG . F 2 NNR B 1 301 2 NNR NNR . G 3 BOG B 1 302 2 BOG BOG . H 3 BOG B 1 303 3 BOG BOG . I 2 NNR C 1 301 3 NNR NNR . J 3 BOG C 1 302 4 BOG BOG . # 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 O2R NNR . . . I 2 68.463 41.514 59.085 1 105.58 ? O2R NNR 301 C 1 HETATM 2 C C2R NNR . . . I 2 68.453 42.155 57.693 1 103.59 ? C2R NNR 301 C 1 HETATM 3 C C3R NNR . . . I 2 68.404 41.065 56.616 1 104.16 ? C3R NNR 301 C 1 HETATM 4 O O3R NNR . . . I 2 68.987 39.936 57.093 1 125.38 ? O3R NNR 301 C 1 HETATM 5 C C4R NNR . . . I 2 69.233 41.603 55.469 1 105.77 ? C4R NNR 301 C 1 HETATM 6 C C5R NNR . . . I 2 68.35 42.346 54.382 1 111.39 ? C5R NNR 301 C 1 HETATM 7 O O5R NNR . . . I 2 69.235 43.146 53.528 1 117.91 ? O5R NNR 301 C 1 HETATM 8 O O4R NNR . . . I 2 70.083 42.428 56.013 1 103.24 ? O4R NNR 301 C 1 HETATM 9 C C1R NNR . . . I 2 69.534 42.839 57.467 1 99.6 ? C1R NNR 301 C 1 HETATM 10 N N1 NNR . . . I 2 69.287 44.293 57.515 1 99.32 ? N1 NNR 301 C 1 HETATM 11 C C2 NNR . . . I 2 69.207 45.052 56.338 1 83.42 ? C2 NNR 301 C 1 HETATM 12 C C6 NNR . . . I 2 69.125 44.919 58.729 1 95.62 ? C6 NNR 301 C 1 HETATM 13 C C5 NNR . . . I 2 68.873 46.312 58.773 1 95.41 ? C5 NNR 301 C 1 HETATM 14 C C4 NNR . . . I 2 68.813 47.052 57.612 1 77.23 ? C4 NNR 301 C 1 HETATM 15 C C3 NNR . . . I 2 68.96 46.442 56.403 1 77.25 ? C3 NNR 301 C 1 HETATM 16 C C7 NNR . . . I 2 68.844 47.285 55.145 1 88.53 ? C7 NNR 301 C 1 HETATM 17 O O7 NNR . . . I 2 69.362 46.936 54.126 1 99.16 ? O7 NNR 301 C 1 HETATM 18 N N7 NNR . . . I 2 68.09 48.509 55.18 1 102.1 ? N7 NNR 301 C 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 18 #