data_6JK3 # _model_server_result.job_id jVNdUMrpYpxMP0XpBEBIkg _model_server_result.datetime_utc '2025-03-06 06:37:08' _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 6jk3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":104}' # _entry.id 6JK3 # _exptl.entry_id 6JK3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 3 _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 90 _cell.entry_id 6JK3 _cell.length_a 61.295 _cell.length_b 61.295 _cell.length_c 67.916 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JK3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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,L,M _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 ? 3 G N N ? 3 H N N ? 3 I N N ? 3 J N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 1 FUC NAG C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n D NAG 1 D 1 NAG A 102 NAG 2 n D NAG 2 D 2 NAG A 103 NAG 2 n D FUC 3 D 3 FUC A 101 FUC 2 n E NAG 1 E 1 NAG B 102 NAG 2 n E NAG 2 E 2 NAG B 103 NAG 2 n E FUC 3 E 3 FUC B 101 FUC 2 n F NAG 1 F 1 NAG C 102 NAG 2 n F NAG 2 F 2 NAG C 103 NAG 2 n F FUC 3 F 3 FUC C 101 FUC # 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 10 A CYS 10 1_555 A SG CYS 17 A CYS 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf2 B SG CYS 10 B CYS 10 1_555 B SG CYS 17 B CYS 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf3 C SG CYS 10 C CYS 10 1_555 C SG CYS 17 C CYS 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? covale ? covale1 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale2 D O6 NAG . D NAG 1 1_555 D C1 FUC . D FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale3 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? covale ? covale4 E O6 NAG . E NAG 1 1_555 E C1 FUC . E FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale5 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale6 F O6 NAG . F NAG 1 1_555 F C1 FUC . F FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? # _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 134 n n C1 C2 GOL sing 135 n n C1 H11 GOL sing 136 n n C1 H12 GOL sing 137 n n O1 HO1 GOL sing 138 n n C2 O2 GOL sing 139 n n C2 C3 GOL sing 140 n n C2 H2 GOL sing 141 n n O2 HO2 GOL sing 142 n n C3 O3 GOL sing 143 n n C3 H31 GOL sing 144 n n C3 H32 GOL sing 145 n n O3 HO3 GOL sing 146 n n # _atom_sites.entry_id 6JK3 _atom_sites.fract_transf_matrix[1][1] 0.016315 _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] 0.016315 _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] 0.014724 _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 3 GOL A 1 104 3 GOL GOL . H 3 GOL B 1 104 1 GOL GOL . I 3 GOL B 1 105 4 GOL GOL . J 3 GOL C 1 104 2 GOL GOL . K 4 HOH A 1 201 51 HOH HOH . K 4 HOH A 2 202 176 HOH HOH . K 4 HOH A 3 203 89 HOH HOH . K 4 HOH A 4 204 158 HOH HOH . K 4 HOH A 5 205 77 HOH HOH . K 4 HOH A 6 206 32 HOH HOH . K 4 HOH A 7 207 86 HOH HOH . K 4 HOH A 8 208 45 HOH HOH . K 4 HOH A 9 209 53 HOH HOH . K 4 HOH A 10 210 52 HOH HOH . K 4 HOH A 11 211 65 HOH HOH . K 4 HOH A 12 212 175 HOH HOH . K 4 HOH A 13 213 15 HOH HOH . K 4 HOH A 14 214 40 HOH HOH . K 4 HOH A 15 215 148 HOH HOH . K 4 HOH A 16 216 171 HOH HOH . K 4 HOH A 17 217 26 HOH HOH . K 4 HOH A 18 218 129 HOH HOH . K 4 HOH A 19 219 31 HOH HOH . K 4 HOH A 20 220 13 HOH HOH . K 4 HOH A 21 221 2 HOH HOH . K 4 HOH A 22 222 18 HOH HOH . K 4 HOH A 23 223 6 HOH HOH . K 4 HOH A 24 224 59 HOH HOH . K 4 HOH A 25 225 25 HOH HOH . K 4 HOH A 26 226 91 HOH HOH . K 4 HOH A 27 227 17 HOH HOH . K 4 HOH A 28 228 87 HOH HOH . K 4 HOH A 29 229 29 HOH HOH . K 4 HOH A 30 230 36 HOH HOH . K 4 HOH A 31 231 138 HOH HOH . K 4 HOH A 32 232 137 HOH HOH . K 4 HOH A 33 233 11 HOH HOH . K 4 HOH A 34 234 37 HOH HOH . K 4 HOH A 35 235 159 HOH HOH . K 4 HOH A 36 236 46 HOH HOH . K 4 HOH A 37 237 128 HOH HOH . K 4 HOH A 38 238 123 HOH HOH . K 4 HOH A 39 239 157 HOH HOH . K 4 HOH A 40 240 16 HOH HOH . K 4 HOH A 41 241 79 HOH HOH . K 4 HOH A 42 242 68 HOH HOH . K 4 HOH A 43 243 150 HOH HOH . K 4 HOH A 44 244 193 HOH HOH . K 4 HOH A 45 245 113 HOH HOH . K 4 HOH A 46 246 125 HOH HOH . K 4 HOH A 47 247 39 HOH HOH . K 4 HOH A 48 248 187 HOH HOH . K 4 HOH A 49 249 135 HOH HOH . K 4 HOH A 50 250 56 HOH HOH . K 4 HOH A 51 251 111 HOH HOH . K 4 HOH A 52 252 169 HOH HOH . K 4 HOH A 53 253 185 HOH HOH . K 4 HOH A 54 254 105 HOH HOH . K 4 HOH A 55 255 69 HOH HOH . K 4 HOH A 56 256 170 HOH HOH . K 4 HOH A 57 257 134 HOH HOH . K 4 HOH A 58 258 122 HOH HOH . K 4 HOH A 59 259 162 HOH HOH . K 4 HOH A 60 260 43 HOH HOH . L 4 HOH B 1 201 63 HOH HOH . L 4 HOH B 2 202 98 HOH HOH . L 4 HOH B 3 203 126 HOH HOH . L 4 HOH B 4 204 58 HOH HOH . L 4 HOH B 5 205 34 HOH HOH . L 4 HOH B 6 206 71 HOH HOH . L 4 HOH B 7 207 3 HOH HOH . L 4 HOH B 8 208 27 HOH HOH . L 4 HOH B 9 209 97 HOH HOH . L 4 HOH B 10 210 54 HOH HOH . L 4 HOH B 11 211 109 HOH HOH . L 4 HOH B 12 212 80 HOH HOH . L 4 HOH B 13 213 12 HOH HOH . L 4 HOH B 14 214 94 HOH HOH . L 4 HOH B 15 215 4 HOH HOH . L 4 HOH B 16 216 99 HOH HOH . L 4 HOH B 17 217 49 HOH HOH . L 4 HOH B 18 218 110 HOH HOH . L 4 HOH B 19 219 19 HOH HOH . L 4 HOH B 20 220 9 HOH HOH . L 4 HOH B 21 221 156 HOH HOH . L 4 HOH B 22 222 64 HOH HOH . L 4 HOH B 23 223 107 HOH HOH . L 4 HOH B 24 224 83 HOH HOH . L 4 HOH B 25 225 124 HOH HOH . L 4 HOH B 26 226 131 HOH HOH . L 4 HOH B 27 227 22 HOH HOH . L 4 HOH B 28 228 100 HOH HOH . L 4 HOH B 29 229 165 HOH HOH . L 4 HOH B 30 230 139 HOH HOH . L 4 HOH B 31 231 101 HOH HOH . L 4 HOH B 32 232 20 HOH HOH . L 4 HOH B 33 233 73 HOH HOH . L 4 HOH B 34 234 10 HOH HOH . L 4 HOH B 35 235 23 HOH HOH . L 4 HOH B 36 236 146 HOH HOH . L 4 HOH B 37 237 78 HOH HOH . L 4 HOH B 38 238 154 HOH HOH . L 4 HOH B 39 239 44 HOH HOH . L 4 HOH B 40 240 104 HOH HOH . L 4 HOH B 41 241 155 HOH HOH . L 4 HOH B 42 242 172 HOH HOH . L 4 HOH B 43 243 181 HOH HOH . L 4 HOH B 44 244 178 HOH HOH . L 4 HOH B 45 245 180 HOH HOH . L 4 HOH B 46 246 186 HOH HOH . L 4 HOH B 47 247 196 HOH HOH . L 4 HOH B 48 248 147 HOH HOH . L 4 HOH B 49 249 72 HOH HOH . L 4 HOH B 50 250 173 HOH HOH . M 4 HOH C 1 201 28 HOH HOH . M 4 HOH C 2 202 24 HOH HOH . M 4 HOH C 3 203 48 HOH HOH . M 4 HOH C 4 204 136 HOH HOH . M 4 HOH C 5 205 60 HOH HOH . M 4 HOH C 6 206 74 HOH HOH . M 4 HOH C 7 207 57 HOH HOH . M 4 HOH C 8 208 160 HOH HOH . M 4 HOH C 9 209 112 HOH HOH . M 4 HOH C 10 210 82 HOH HOH . M 4 HOH C 11 211 55 HOH HOH . M 4 HOH C 12 212 8 HOH HOH . M 4 HOH C 13 213 5 HOH HOH . M 4 HOH C 14 214 90 HOH HOH . M 4 HOH C 15 215 47 HOH HOH . M 4 HOH C 16 216 66 HOH HOH . M 4 HOH C 17 217 33 HOH HOH . M 4 HOH C 18 218 14 HOH HOH . M 4 HOH C 19 219 92 HOH HOH . M 4 HOH C 20 220 1 HOH HOH . M 4 HOH C 21 221 30 HOH HOH . M 4 HOH C 22 222 21 HOH HOH . M 4 HOH C 23 223 50 HOH HOH . M 4 HOH C 24 224 174 HOH HOH . M 4 HOH C 25 225 61 HOH HOH . M 4 HOH C 26 226 93 HOH HOH . M 4 HOH C 27 227 95 HOH HOH . M 4 HOH C 28 228 85 HOH HOH . M 4 HOH C 29 229 35 HOH HOH . M 4 HOH C 30 230 88 HOH HOH . M 4 HOH C 31 231 38 HOH HOH . M 4 HOH C 32 232 81 HOH HOH . M 4 HOH C 33 233 70 HOH HOH . M 4 HOH C 34 234 42 HOH HOH . M 4 HOH C 35 235 96 HOH HOH . M 4 HOH C 36 236 118 HOH HOH . M 4 HOH C 37 237 76 HOH HOH . M 4 HOH C 38 238 184 HOH HOH . M 4 HOH C 39 239 127 HOH HOH . M 4 HOH C 40 240 7 HOH HOH . M 4 HOH C 41 241 62 HOH HOH . M 4 HOH C 42 242 67 HOH HOH . M 4 HOH C 43 243 177 HOH HOH . M 4 HOH C 44 244 167 HOH HOH . M 4 HOH C 45 245 41 HOH HOH . M 4 HOH C 46 246 103 HOH HOH . M 4 HOH C 47 247 183 HOH HOH . M 4 HOH C 48 248 168 HOH HOH . M 4 HOH C 49 249 161 HOH HOH . M 4 HOH C 50 250 117 HOH HOH . M 4 HOH C 51 251 102 HOH HOH . M 4 HOH C 52 252 75 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 3 -15.526 -3.405 -0.49 1 25.22 ? C1 GOL 104 B 1 HETATM 2 O O1 GOL . . . H 3 -15.248 -4.629 -1.153 1 27.11 ? O1 GOL 104 B 1 HETATM 3 C C2 GOL . . . H 3 -16.291 -3.62 0.785 1 26.73 ? C2 GOL 104 B 1 HETATM 4 O O2 GOL . . . H 3 -17.467 -4.369 0.506 1 34.09 ? O2 GOL 104 B 1 HETATM 5 C C3 GOL . . . H 3 -16.599 -2.306 1.449 1 27.5 ? C3 GOL 104 B 1 HETATM 6 O O3 GOL . . . H 3 -17.388 -2.476 2.613 1 33.99 ? O3 GOL 104 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 240 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 6 #