data_3RR8 # _model_server_result.job_id zem4GN8D20dwm1CGZUPbtg _model_server_result.datetime_utc '2025-01-10 12:50:10' _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 3rr8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1}' # _entry.id 3RR8 # _exptl.entry_id 3RR8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 4 _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 120 _cell.entry_id 3RR8 _cell.length_a 108.965 _cell.length_b 108.965 _cell.length_c 90.406 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RR8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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,K _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 ? 5 E N N ? 5 F N N ? 5 G N N ? 5 H 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 B O3' DC 11 B DC 111 1_555 B P DDG 12 B DDG 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? covale ? covale2 C O3' DA 3 C DA 203 1_555 C P 3DR 4 C 3DR 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.609 ? covale ? covale3 C O3' 3DR 4 C 3DR 204 1_555 C P DC 5 C DC 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.607 ? hydrog WATSON-CRICK hydrog1 B N1 DG 1 B DG 101 1_555 C N3 DC 16 C DC 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 DG 1 B DG 101 1_555 C O2 DC 16 C DC 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 DG 1 B DG 101 1_555 C N4 DC 16 C DC 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DA 2 B DA 102 1_555 C N3 DT 15 C DT 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N6 DA 2 B DA 102 1_555 C O4 DT 15 C DT 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DC 3 B DC 103 1_555 C N1 DG 14 C DG 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N4 DC 3 B DC 103 1_555 C O6 DG 14 C DG 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O2 DC 3 B DC 103 1_555 C N2 DG 14 C DG 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 DC 4 B DC 104 1_555 C N1 DG 13 C DG 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N4 DC 4 B DC 104 1_555 C O6 DG 13 C DG 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O2 DC 4 B DC 104 1_555 C N2 DG 13 C DG 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 DA 5 B DA 105 1_555 C N3 DT 12 C DT 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N6 DA 5 B DA 105 1_555 C O4 DT 12 C DT 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N3 DC 6 B DC 106 1_555 C N1 DG 11 C DG 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N4 DC 6 B DC 106 1_555 C O6 DG 11 C DG 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O2 DC 6 B DC 106 1_555 C N2 DG 11 C DG 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N1 DG 7 B DG 107 1_555 C N3 DC 10 C DC 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N2 DG 7 B DG 107 1_555 C O2 DC 10 C DC 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B O6 DG 7 B DG 107 1_555 C N4 DC 10 C DC 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N1 DG 8 B DG 108 1_555 C N3 DC 9 C DC 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N2 DG 8 B DG 108 1_555 C O2 DC 9 C DC 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B O6 DG 8 B DG 108 1_555 C N4 DC 9 C DC 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N3 DC 9 B DC 109 1_555 C N1 DG 8 C DG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N4 DC 9 B DC 109 1_555 C O6 DG 8 C DG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B O2 DC 9 B DC 109 1_555 C N2 DG 8 C DG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N1 DG 10 B DG 110 1_555 C N3 DC 7 C DC 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N2 DG 10 B DG 110 1_555 C O2 DC 7 C DC 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B O6 DG 10 B DG 110 1_555 C N4 DC 7 C DC 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 B N3 DC 11 B DC 111 1_555 C N1 DG 6 C DG 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B N4 DC 11 B DC 111 1_555 C O6 DG 6 C DG 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 B O2 DC 11 B DC 111 1_555 C N2 DG 6 C DG 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 374 n n C1 C2 GOL sing 375 n n C1 H11 GOL sing 376 n n C1 H12 GOL sing 377 n n O1 HO1 GOL sing 378 n n C2 O2 GOL sing 379 n n C2 C3 GOL sing 380 n n C2 H2 GOL sing 381 n n O2 HO2 GOL sing 382 n n C3 O3 GOL sing 383 n n C3 H31 GOL sing 384 n n C3 H32 GOL sing 385 n n O3 HO3 GOL sing 386 n n # _atom_sites.entry_id 3RR8 _atom_sites.fract_transf_matrix[1][1] 0.009177 _atom_sites.fract_transf_matrix[1][2] 0.005298 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010597 _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] 0.011061 _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 4 DG3 A 1 1 1 DG3 DG3 . E 5 GOL A 1 833 1 GOL GOL . F 5 GOL A 1 834 1 GOL GOL . G 5 GOL A 1 835 1 GOL GOL . H 5 GOL B 1 1 1 GOL GOL . I 6 HOH A 1 5 5 HOH HOH . I 6 HOH A 2 6 6 HOH HOH . I 6 HOH A 3 7 7 HOH HOH . I 6 HOH A 4 12 12 HOH HOH . I 6 HOH A 5 13 13 HOH HOH . I 6 HOH A 6 14 14 HOH HOH . I 6 HOH A 7 15 15 HOH HOH . I 6 HOH A 8 16 16 HOH HOH . I 6 HOH A 9 17 17 HOH HOH . I 6 HOH A 10 18 18 HOH HOH . I 6 HOH A 11 19 19 HOH HOH . I 6 HOH A 12 20 20 HOH HOH . I 6 HOH A 13 21 21 HOH HOH . I 6 HOH A 14 24 24 HOH HOH . I 6 HOH A 15 25 25 HOH HOH . I 6 HOH A 16 26 26 HOH HOH . I 6 HOH A 17 27 27 HOH HOH . I 6 HOH A 18 28 28 HOH HOH . I 6 HOH A 19 29 29 HOH HOH . I 6 HOH A 20 32 32 HOH HOH . I 6 HOH A 21 33 33 HOH HOH . I 6 HOH A 22 34 34 HOH HOH . I 6 HOH A 23 35 35 HOH HOH . I 6 HOH A 24 36 36 HOH HOH . I 6 HOH A 25 37 37 HOH HOH . I 6 HOH A 26 38 38 HOH HOH . I 6 HOH A 27 39 39 HOH HOH . I 6 HOH A 28 41 41 HOH HOH . I 6 HOH A 29 42 42 HOH HOH . I 6 HOH A 30 43 43 HOH HOH . I 6 HOH A 31 45 45 HOH HOH . I 6 HOH A 32 47 47 HOH HOH . I 6 HOH A 33 48 48 HOH HOH . I 6 HOH A 34 51 51 HOH HOH . I 6 HOH A 35 52 52 HOH HOH . I 6 HOH A 36 53 53 HOH HOH . I 6 HOH A 37 54 54 HOH HOH . I 6 HOH A 38 55 55 HOH HOH . I 6 HOH A 39 57 57 HOH HOH . I 6 HOH A 40 60 60 HOH HOH . I 6 HOH A 41 61 61 HOH HOH . I 6 HOH A 42 63 63 HOH HOH . I 6 HOH A 43 64 64 HOH HOH . I 6 HOH A 44 65 65 HOH HOH . I 6 HOH A 45 67 67 HOH HOH . I 6 HOH A 46 69 69 HOH HOH . I 6 HOH A 47 70 70 HOH HOH . I 6 HOH A 48 71 71 HOH HOH . I 6 HOH A 49 72 72 HOH HOH . I 6 HOH A 50 73 73 HOH HOH . I 6 HOH A 51 74 74 HOH HOH . I 6 HOH A 52 75 75 HOH HOH . I 6 HOH A 53 76 76 HOH HOH . I 6 HOH A 54 77 77 HOH HOH . I 6 HOH A 55 78 78 HOH HOH . I 6 HOH A 56 80 80 HOH HOH . I 6 HOH A 57 81 81 HOH HOH . I 6 HOH A 58 82 82 HOH HOH . I 6 HOH A 59 83 83 HOH HOH . I 6 HOH A 60 84 84 HOH HOH . I 6 HOH A 61 85 85 HOH HOH . I 6 HOH A 62 88 88 HOH HOH . I 6 HOH A 63 89 89 HOH HOH . I 6 HOH A 64 90 90 HOH HOH . I 6 HOH A 65 91 91 HOH HOH . I 6 HOH A 66 92 92 HOH HOH . I 6 HOH A 67 93 93 HOH HOH . I 6 HOH A 68 94 94 HOH HOH . I 6 HOH A 69 95 95 HOH HOH . I 6 HOH A 70 96 96 HOH HOH . I 6 HOH A 71 99 99 HOH HOH . I 6 HOH A 72 100 100 HOH HOH . I 6 HOH A 73 836 1 HOH HOH . I 6 HOH A 74 837 1 HOH HOH . I 6 HOH A 75 838 1 HOH HOH . I 6 HOH A 76 839 1 HOH HOH . I 6 HOH A 77 840 1 HOH HOH . J 6 HOH B 1 8 8 HOH HOH . J 6 HOH B 2 11 11 HOH HOH . J 6 HOH B 3 40 40 HOH HOH . J 6 HOH B 4 44 44 HOH HOH . J 6 HOH B 5 49 49 HOH HOH . J 6 HOH B 6 58 58 HOH HOH . J 6 HOH B 7 59 59 HOH HOH . J 6 HOH B 8 62 62 HOH HOH . J 6 HOH B 9 86 86 HOH HOH . J 6 HOH B 10 87 87 HOH HOH . J 6 HOH B 11 98 98 HOH HOH . K 6 HOH C 1 1 1 HOH HOH . K 6 HOH C 2 2 2 HOH HOH . K 6 HOH C 3 4 4 HOH HOH . K 6 HOH C 4 10 10 HOH HOH . K 6 HOH C 5 22 22 HOH HOH . K 6 HOH C 6 31 31 HOH HOH . K 6 HOH C 7 46 46 HOH HOH . K 6 HOH C 8 50 50 HOH HOH . K 6 HOH C 9 56 56 HOH HOH . K 6 HOH C 10 66 66 HOH HOH . K 6 HOH C 11 68 68 HOH HOH . K 6 HOH C 12 79 79 HOH HOH . K 6 HOH C 13 97 97 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 . . . H 5 31.017 -26.835 5.431 1 47.94 ? C1 GOL 1 B 1 HETATM 2 O O1 GOL . . . H 5 29.731 -26.267 5.309 1 49.03 ? O1 GOL 1 B 1 HETATM 3 C C2 GOL . . . H 5 32.059 -25.726 5.498 1 43.67 ? C2 GOL 1 B 1 HETATM 4 O O2 GOL . . . H 5 32.325 -25.408 6.845 1 39.92 ? O2 GOL 1 B 1 HETATM 5 C C3 GOL . . . H 5 33.341 -26.189 4.815 1 39.28 ? C3 GOL 1 B 1 HETATM 6 O O3 GOL . . . H 5 34.349 -25.217 4.992 1 22.9 ? O3 GOL 1 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 6 #