data_3NRT # _model_server_result.job_id 2hjADB4tHEhBoLos0NkflA _model_server_result.datetime_utc '2024-12-21 11:36:50' _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 3nrt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":101}' # _entry.id 3NRT # _exptl.entry_id 3NRT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 7 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 110.99 _cell.angle_gamma 90 _cell.entry_id 3NRT _cell.length_a 74.642 _cell.length_b 89.272 _cell.length_c 74.697 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NRT _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,H,I,J,O,P 1 1 C,D,K,L,Q,R 2 1 E,F,M,N,S,T 3 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 G N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L N N ? 2 M N N ? 2 N 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 PRO 15 A PRO 12 1_555 A N MSE 16 A MSE 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C MSE 16 A MSE 13 1_555 A N ASP 17 A ASP 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 A C ALA 85 A ALA 82 1_555 A N MSE 86 A MSE 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale4 A C MSE 86 A MSE 83 1_555 A N ASN 87 A ASN 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale5 A C LYS 90 A LYS 87 1_555 A N MSE 91 A MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale6 A C MSE 91 A MSE 88 1_555 A N VAL 92 A VAL 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale7 B C PRO 15 B PRO 12 1_555 B N MSE 16 B MSE 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale8 B C MSE 16 B MSE 13 1_555 B N ASP 17 B ASP 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale9 B C ALA 85 B ALA 82 1_555 B N MSE 86 B MSE 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale10 B C MSE 86 B MSE 83 1_555 B N ASN 87 B ASN 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale11 B C LYS 90 B LYS 87 1_555 B N MSE 91 B MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale12 B C MSE 91 B MSE 88 1_555 B N VAL 92 B VAL 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale13 C C PRO 15 C PRO 12 1_555 C N MSE 16 C MSE 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale14 C C MSE 16 C MSE 13 1_555 C N ASP 17 C ASP 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale15 C C ALA 85 C ALA 82 1_555 C N MSE 86 C MSE 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale16 C C MSE 86 C MSE 83 1_555 C N ASN 87 C ASN 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale17 C C LYS 90 C LYS 87 1_555 C N MSE 91 C MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale18 C C MSE 91 C MSE 88 1_555 C N VAL 92 C VAL 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale19 D C PRO 15 D PRO 12 1_555 D N MSE 16 D MSE 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale20 D C MSE 16 D MSE 13 1_555 D N ASP 17 D ASP 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale21 D C ALA 85 D ALA 82 1_555 D N MSE 86 D MSE 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale22 D C MSE 86 D MSE 83 1_555 D N ASN 87 D ASN 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale23 D C LYS 90 D LYS 87 1_555 D N MSE 91 D MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale24 D C MSE 91 D MSE 88 1_555 D N VAL 92 D VAL 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale25 E C PRO 15 E PRO 12 1_555 E N MSE 16 E MSE 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale26 E C MSE 16 E MSE 13 1_555 E N ASP 17 E ASP 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale27 E C ALA 85 E ALA 82 1_555 E N MSE 86 E MSE 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale28 E C MSE 86 E MSE 83 1_555 E N ASN 87 E ASN 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale29 E C LYS 90 E LYS 87 1_555 E N MSE 91 E MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale30 E C MSE 91 E MSE 88 1_555 E N VAL 92 E VAL 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale31 F C PRO 15 F PRO 12 1_555 F N MSE 16 F MSE 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale32 F C MSE 16 F MSE 13 1_555 F N ASP 17 F ASP 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale33 F C ALA 85 F ALA 82 1_555 F N MSE 86 F MSE 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale34 F C MSE 86 F MSE 83 1_555 F N ASN 87 F ASN 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale35 F C LYS 90 F LYS 87 1_555 F N MSE 91 F MSE 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale36 F C MSE 91 F MSE 88 1_555 F N VAL 92 F VAL 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? metalc ? metalc1 A OD2 ASP 59 A ASP 56 1_555 H MG MG . A MG 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? metalc ? metalc2 H MG MG . A MG 102 1_555 B OD2 ASP 59 B ASP 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.69 ? # _chem_comp.formula 'C3 H8 O3' _chem_comp.formula_weight 92.094 _chem_comp.id GOL _chem_comp.mon_nstd_flag . _chem_comp.name GLYCEROL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms GLYCERIN;PROPANE-1,2,3-TRIOL # 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 C1 O1 GOL sing 129 n n C1 C2 GOL sing 130 n n C1 H11 GOL sing 131 n n C1 H12 GOL sing 132 n n O1 HO1 GOL sing 133 n n C2 O2 GOL sing 134 n n C2 C3 GOL sing 135 n n C2 H2 GOL sing 136 n n O2 HO2 GOL sing 137 n n C3 O3 GOL sing 138 n n C3 H31 GOL sing 139 n n C3 H32 GOL sing 140 n n O3 HO3 GOL sing 141 n n # _atom_sites.entry_id 3NRT _atom_sites.fract_transf_matrix[1][1] 0.013397 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00514 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011202 _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] 0.014339 _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 2 GOL A 1 101 1 GOL GOL . H 3 MG A 1 102 1 MG MG . I 2 GOL A 1 103 1 GOL GOL . J 2 GOL B 1 101 1 GOL GOL . K 2 GOL C 1 101 1 GOL GOL . L 2 GOL D 1 101 1 GOL GOL . M 2 GOL E 1 101 1 GOL GOL . N 2 GOL F 1 101 1 GOL GOL . O 4 HOH A 1 104 9 HOH HOH . O 4 HOH A 2 105 105 HOH HOH . O 4 HOH A 3 106 106 HOH HOH . O 4 HOH A 4 107 12 HOH HOH . O 4 HOH A 5 108 14 HOH HOH . O 4 HOH A 6 109 23 HOH HOH . O 4 HOH A 7 110 31 HOH HOH . O 4 HOH A 8 111 49 HOH HOH . O 4 HOH A 9 112 64 HOH HOH . O 4 HOH A 10 113 67 HOH HOH . O 4 HOH A 11 114 68 HOH HOH . O 4 HOH A 12 115 72 HOH HOH . O 4 HOH A 13 116 78 HOH HOH . O 4 HOH A 14 117 90 HOH HOH . O 4 HOH A 15 118 118 HOH HOH . O 4 HOH A 16 119 96 HOH HOH . O 4 HOH A 17 120 98 HOH HOH . O 4 HOH A 18 122 122 HOH HOH . O 4 HOH A 19 138 138 HOH HOH . O 4 HOH A 20 140 140 HOH HOH . O 4 HOH A 21 156 156 HOH HOH . O 4 HOH A 22 181 181 HOH HOH . O 4 HOH A 23 183 183 HOH HOH . O 4 HOH A 24 189 189 HOH HOH . P 4 HOH B 1 102 5 HOH HOH . P 4 HOH B 2 103 18 HOH HOH . P 4 HOH B 3 104 28 HOH HOH . P 4 HOH B 4 105 30 HOH HOH . P 4 HOH B 5 106 51 HOH HOH . P 4 HOH B 6 107 56 HOH HOH . P 4 HOH B 7 108 59 HOH HOH . P 4 HOH B 8 109 69 HOH HOH . P 4 HOH B 9 110 100 HOH HOH . P 4 HOH B 10 116 116 HOH HOH . P 4 HOH B 11 120 120 HOH HOH . P 4 HOH B 12 128 128 HOH HOH . P 4 HOH B 13 172 172 HOH HOH . P 4 HOH B 14 180 180 HOH HOH . P 4 HOH B 15 187 187 HOH HOH . Q 4 HOH C 1 102 102 HOH HOH . Q 4 HOH C 2 103 8 HOH HOH . Q 4 HOH C 3 104 32 HOH HOH . Q 4 HOH C 4 105 41 HOH HOH . Q 4 HOH C 5 106 42 HOH HOH . Q 4 HOH C 6 107 70 HOH HOH . Q 4 HOH C 7 108 95 HOH HOH . Q 4 HOH C 8 109 101 HOH HOH . Q 4 HOH C 9 119 119 HOH HOH . Q 4 HOH C 10 127 127 HOH HOH . Q 4 HOH C 11 144 144 HOH HOH . R 4 HOH D 1 102 35 HOH HOH . R 4 HOH D 2 103 83 HOH HOH . R 4 HOH D 3 104 87 HOH HOH . R 4 HOH D 4 105 99 HOH HOH . R 4 HOH D 5 165 165 HOH HOH . R 4 HOH D 6 178 178 HOH HOH . R 4 HOH D 7 179 179 HOH HOH . R 4 HOH D 8 186 186 HOH HOH . R 4 HOH D 9 190 190 HOH HOH . R 4 HOH D 10 191 191 HOH HOH . S 4 HOH E 1 102 16 HOH HOH . S 4 HOH E 2 103 17 HOH HOH . S 4 HOH E 3 104 20 HOH HOH . S 4 HOH E 4 105 21 HOH HOH . S 4 HOH E 5 106 37 HOH HOH . S 4 HOH E 6 107 52 HOH HOH . S 4 HOH E 7 108 89 HOH HOH . S 4 HOH E 8 109 91 HOH HOH . S 4 HOH E 9 115 115 HOH HOH . S 4 HOH E 10 129 129 HOH HOH . S 4 HOH E 11 167 167 HOH HOH . S 4 HOH E 12 168 168 HOH HOH . S 4 HOH E 13 184 184 HOH HOH . S 4 HOH E 14 188 188 HOH HOH . T 4 HOH F 1 102 10 HOH HOH . T 4 HOH F 2 103 11 HOH HOH . T 4 HOH F 3 104 19 HOH HOH . T 4 HOH F 4 105 24 HOH HOH . T 4 HOH F 5 106 36 HOH HOH . T 4 HOH F 6 107 63 HOH HOH . T 4 HOH F 7 108 75 HOH HOH . T 4 HOH F 8 113 113 HOH HOH . T 4 HOH F 9 121 121 HOH HOH . T 4 HOH F 10 147 147 HOH HOH . T 4 HOH F 11 185 185 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 C C1 GOL . . . L 2 -23.963 5.238 -6.472 1 51.02 ? C1 GOL 101 D 1 HETATM 2 O O1 GOL . . . L 2 -23.069 6.177 -5.902 1 44.42 ? O1 GOL 101 D 1 HETATM 3 C C2 GOL . . . L 2 -25.377 5.826 -6.464 1 72.97 ? C2 GOL 101 D 1 HETATM 4 O O2 GOL . . . L 2 -26.219 5.049 -7.285 1 84.12 ? O2 GOL 101 D 1 HETATM 5 C C3 GOL . . . L 2 -25.948 5.822 -5.042 1 70.77 ? C3 GOL 101 D 1 HETATM 6 O O3 GOL . . . L 2 -26.34 4.505 -4.703 1 65.52 ? O3 GOL 101 D 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #