data_6DF3 # _model_server_result.job_id 5MCQn8-gdUjaz9BikOhkww _model_server_result.datetime_utc '2025-07-01 19:00:24' _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 6df3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 6DF3 # _exptl.entry_id 6DF3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 2 _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 6DF3 _cell.length_a 77.702 _cell.length_b 77.702 _cell.length_c 124.785 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DF3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_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 ? 6 F N N ? 6 G N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 4 n D NAG 1 A 1 NAG L 301 NAG 4 n D NAG 2 A 2 NAG L 302 NAG # 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 105 L CYS 128 1_555 A SG CYS 194 L CYS 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? disulf ? disulf2 B SG CYS 8 C CYS 59 1_555 B SG CYS 55 C CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? disulf ? disulf3 C SG CYS 55 H CYS 89 1_555 C SG CYS 63 H CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 C SG CYS 168 H CYS 202 1_555 C SG CYS 189 H CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? covale ? covale1 A ND2 ASN 57 L ASN 80 1_555 D C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale2 A ND2 ASN 64 L ASN 87 1_555 E C1 NAG . L NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 D O4 NAG . A NAG 1 1_555 D C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? # _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 6DF3 _atom_sites.fract_transf_matrix[1][1] 0.01287 _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] 0.01287 _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] 0.008014 _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 E 5 NAG L 1 303 303 NAG NAG . F 6 GOL C 1 301 1 GOL GOL . G 6 GOL C 1 302 2 GOL GOL . H 7 HOH L 1 401 60 HOH HOH . H 7 HOH L 2 402 67 HOH HOH . H 7 HOH L 3 403 58 HOH HOH . H 7 HOH L 4 404 24 HOH HOH . H 7 HOH L 5 405 43 HOH HOH . H 7 HOH L 6 406 51 HOH HOH . H 7 HOH L 7 407 30 HOH HOH . H 7 HOH L 8 408 64 HOH HOH . H 7 HOH L 9 409 20 HOH HOH . H 7 HOH L 10 410 59 HOH HOH . H 7 HOH L 11 411 9 HOH HOH . H 7 HOH L 12 412 35 HOH HOH . H 7 HOH L 13 413 19 HOH HOH . H 7 HOH L 14 414 55 HOH HOH . I 7 HOH C 1 401 75 HOH HOH . I 7 HOH C 2 402 16 HOH HOH . I 7 HOH C 3 403 52 HOH HOH . I 7 HOH C 4 404 79 HOH HOH . I 7 HOH C 5 405 14 HOH HOH . I 7 HOH C 6 406 48 HOH HOH . I 7 HOH C 7 407 13 HOH HOH . I 7 HOH C 8 408 42 HOH HOH . I 7 HOH C 9 409 46 HOH HOH . I 7 HOH C 10 410 47 HOH HOH . I 7 HOH C 11 411 62 HOH HOH . I 7 HOH C 12 412 5 HOH HOH . I 7 HOH C 13 413 49 HOH HOH . I 7 HOH C 14 414 10 HOH HOH . I 7 HOH C 15 415 76 HOH HOH . I 7 HOH C 16 416 4 HOH HOH . I 7 HOH C 17 417 31 HOH HOH . I 7 HOH C 18 418 44 HOH HOH . I 7 HOH C 19 419 56 HOH HOH . I 7 HOH C 20 420 45 HOH HOH . I 7 HOH C 21 421 71 HOH HOH . I 7 HOH C 22 422 50 HOH HOH . I 7 HOH C 23 423 33 HOH HOH . I 7 HOH C 24 424 15 HOH HOH . I 7 HOH C 25 425 53 HOH HOH . I 7 HOH C 26 426 39 HOH HOH . I 7 HOH C 27 427 37 HOH HOH . I 7 HOH C 28 428 21 HOH HOH . J 7 HOH H 1 301 77 HOH HOH . J 7 HOH H 2 302 17 HOH HOH . J 7 HOH H 3 303 63 HOH HOH . J 7 HOH H 4 304 36 HOH HOH . J 7 HOH H 5 305 57 HOH HOH . J 7 HOH H 6 306 61 HOH HOH . J 7 HOH H 7 307 80 HOH HOH . J 7 HOH H 8 308 69 HOH HOH . J 7 HOH H 9 309 66 HOH HOH . J 7 HOH H 10 310 2 HOH HOH . J 7 HOH H 11 311 8 HOH HOH . J 7 HOH H 12 312 41 HOH HOH . J 7 HOH H 13 313 32 HOH HOH . J 7 HOH H 14 314 34 HOH HOH . J 7 HOH H 15 315 6 HOH HOH . J 7 HOH H 16 316 72 HOH HOH . J 7 HOH H 17 317 12 HOH HOH . J 7 HOH H 18 318 68 HOH HOH . J 7 HOH H 19 319 28 HOH HOH . J 7 HOH H 20 320 27 HOH HOH . J 7 HOH H 21 321 78 HOH HOH . J 7 HOH H 22 322 26 HOH HOH . J 7 HOH H 23 323 23 HOH HOH . J 7 HOH H 24 324 11 HOH HOH . J 7 HOH H 25 325 7 HOH HOH . J 7 HOH H 26 326 54 HOH HOH . J 7 HOH H 27 327 3 HOH HOH . J 7 HOH H 28 328 40 HOH HOH . J 7 HOH H 29 329 74 HOH HOH . J 7 HOH H 30 330 22 HOH HOH . J 7 HOH H 31 331 18 HOH HOH . J 7 HOH H 32 332 65 HOH HOH . J 7 HOH H 33 333 73 HOH HOH . J 7 HOH H 34 334 1 HOH HOH . J 7 HOH H 35 335 70 HOH HOH . J 7 HOH H 36 336 29 HOH HOH . J 7 HOH H 37 337 38 HOH HOH . J 7 HOH H 38 338 25 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 . . . F 6 10.099 8.286 60.514 1 78.25 ? C1 GOL 301 C 1 HETATM 2 O O1 GOL . . . F 6 11.384 8.919 60.384 1 79.98 ? O1 GOL 301 C 1 HETATM 3 C C2 GOL . . . F 6 9.393 8.247 59.154 1 87.61 ? C2 GOL 301 C 1 HETATM 4 O O2 GOL . . . F 6 10.26 7.738 58.12 1 91.04 ? O2 GOL 301 C 1 HETATM 5 C C3 GOL . . . F 6 8.113 7.407 59.243 1 91.47 ? C3 GOL 301 C 1 HETATM 6 O O3 GOL . . . F 6 7.715 6.954 57.939 1 88.34 ? O3 GOL 301 C 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 6 #