data_5K33 # _model_server_result.job_id VAFasVqXdBm00zj0khQfzQ _model_server_result.datetime_utc '2025-03-09 03:45:12' _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 5k33 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":506}' # _entry.id 5K33 # _exptl.entry_id 5K33 _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 1 _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 5K33 _cell.length_a 108.62 _cell.length_b 108.62 _cell.length_c 174.34 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5K33 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G 1 1 A,B,C,D,E,F,G 1 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 3 5 3 MAN BMA C1 O1 . O6 HO6 . sing 5 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 7 ? 4 4 3 MAN BMA C1 O1 . O3 HO3 . 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 3 n C NAG 1 B 1 NAG A 500 NAG 3 n C NAG 2 B 2 NAG A 501 NAG 3 n C BMA 3 B 3 BMA A 502 BMA 3 n C MAN 4 B 4 MAN A 506 MAN 3 n C MAN 5 B 5 MAN A 503 MAN 4 n D NAG 1 D 1 NAG C 583 NAG 4 n D NAG 2 D 2 NAG C 584 NAG 4 n D BMA 3 D 3 BMA C 585 BMA 4 n D MAN 4 D 4 MAN C 586 MAN # 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 37 A CYS 261 1_555 A SG CYS 97 A CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 143 A CYS 367 1_555 A SG CYS 206 A CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 B SG CYS 4 C CYS 4 1_555 B SG CYS 31 C CYS 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf4 B SG CYS 140 C CYS 140 1_555 B SG CYS 170 C CYS 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf5 B SG CYS 173 C CYS 173 1_555 B SG CYS 182 C CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 B SG CYS 177 C CYS 177 1_555 B SG CYS 190 C CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf7 B SG CYS 198 C CYS 198 1_555 B SG CYS 205 C CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf8 B SG CYS 202 C CYS 202 1_555 B SG CYS 213 C CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 B SG CYS 214 C CYS 214 1_555 B SG CYS 222 C CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf10 B SG CYS 218 C CYS 218 1_555 B SG CYS 230 C CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 B SG CYS 233 C CYS 233 1_555 B SG CYS 242 C CYS 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf12 B SG CYS 246 C CYS 246 1_555 B SG CYS 273 C CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf13 B SG CYS 277 C CYS 277 1_555 B SG CYS 289 C CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf14 B SG CYS 293 C CYS 293 1_555 B SG CYS 309 C CYS 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf15 B SG CYS 312 C CYS 312 1_555 B SG CYS 316 C CYS 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf16 B SG CYS 320 C CYS 320 1_555 B SG CYS 345 C CYS 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf17 B SG CYS 453 C CYS 453 1_555 B SG CYS 482 C CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf18 B SG CYS 489 C CYS 489 1_555 B SG CYS 498 C CYS 498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf19 B SG CYS 493 C CYS 493 1_555 B SG CYS 506 C CYS 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf20 B SG CYS 509 C CYS 509 1_555 B SG CYS 518 C CYS 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf21 B SG CYS 522 C CYS 522 1_555 B SG CYS 538 C CYS 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf22 B SG CYS 541 C CYS 541 1_555 B SG CYS 554 C CYS 554 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf23 B SG CYS 545 C CYS 545 1_555 B SG CYS 562 C CYS 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf24 B SG CYS 565 C CYS 565 1_555 B SG CYS 574 C CYS 574 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 73 A ASN 297 1_555 C C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale2 B ND2 ASN 165 C ASN 165 1_555 G C1 NAG . C NAG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 B ND2 ASN 237 C ASN 237 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale4 B ND2 ASN 549 C ASN 549 1_555 F C1 NAG . C NAG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 C O4 NAG . B NAG 1 1_555 C C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 C O4 NAG . B NAG 2 1_555 C C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale7 C O3 BMA . B BMA 3 1_555 C C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale8 C O6 BMA . B BMA 3 1_555 C C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale10 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale11 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? # _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 153 n n C1 C2 GOL sing 154 n n C1 H11 GOL sing 155 n n C1 H12 GOL sing 156 n n O1 HO1 GOL sing 157 n n C2 O2 GOL sing 158 n n C2 C3 GOL sing 159 n n C2 H2 GOL sing 160 n n O2 HO2 GOL sing 161 n n C3 O3 GOL sing 162 n n C3 H31 GOL sing 163 n n C3 H32 GOL sing 164 n n O3 HO3 GOL sing 165 n n # _atom_sites.entry_id 5K33 _atom_sites.fract_transf_matrix[1][1] 0.009206 _atom_sites.fract_transf_matrix[1][2] 0.005315 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010631 _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] 0.005736 _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 GOL A 1 506 5 GOL GOL . F 6 NAG C 1 705 587 NAG NAG . G 6 NAG C 1 706 588 NAG NAG . # 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 . . . E 5 -22.551 -33.681 4.942 1 147.12 ? C1 GOL 506 A 1 HETATM 2 O O1 GOL . . . E 5 -23.612 -33.769 4.016 1 145.45 ? O1 GOL 506 A 1 HETATM 3 C C2 GOL . . . E 5 -22.035 -32.247 5.004 1 148.52 ? C2 GOL 506 A 1 HETATM 4 O O2 GOL . . . E 5 -21.176 -32.006 3.911 1 150.8 ? O2 GOL 506 A 1 HETATM 5 C C3 GOL . . . E 5 -21.292 -32.005 6.316 1 146.12 ? C3 GOL 506 A 1 HETATM 6 O O3 GOL . . . E 5 -21.082 -30.622 6.507 1 144.15 ? O3 GOL 506 A 1 HETATM 7 H H11 GOL . . . E 5 -22.897 -33.991 5.928 1 176.54 ? H11 GOL 506 A 1 HETATM 8 H H12 GOL . . . E 5 -21.744 -34.349 4.64 1 176.54 ? H12 GOL 506 A 1 HETATM 9 H HO1 GOL . . . E 5 -23.896 -34.703 3.931 1 174.54 ? HO1 GOL 506 A 1 HETATM 10 H H2 GOL . . . E 5 -22.887 -31.569 4.958 1 178.22 ? H2 GOL 506 A 1 HETATM 11 H HO2 GOL . . . E 5 -20.855 -31.081 3.945 1 180.96 ? HO2 GOL 506 A 1 HETATM 12 H H31 GOL . . . E 5 -21.874 -32.406 7.146 1 175.34 ? H31 GOL 506 A 1 HETATM 13 H H32 GOL . . . E 5 -20.333 -32.522 6.295 1 175.34 ? H32 GOL 506 A 1 HETATM 14 H HO3 GOL . . . E 5 -20.733 -30.228 5.68 1 172.98 ? HO3 GOL 506 A 1 # _model_server_stats.io_time_ms 77 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #