data_5VL3 # _model_server_result.job_id IyG3OqFX3vgb0n7AA7yXOg _model_server_result.datetime_utc '2025-08-13 10:36:14' _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 5vl3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":1006}' # _entry.id 5VL3 # _exptl.entry_id 5VL3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 8 _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 70.83 _cell.angle_beta 80.81 _cell.angle_gamma 80.99 _cell.entry_id 5VL3 _cell.length_a 87.11 _cell.length_b 90.22 _cell.length_c 136.632 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VL3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 PISA trimeric 3 author_and_software_defined_assembly 3 PISA trimeric 3 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,H,L,M,N 1 1 B,E,I,O,P 2 1 C,F,J,Q,R,U 3 1 D,G,K,S,T 4 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 # _struct_asym.details ? _struct_asym.entity_id 8 _struct_asym.id U _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 oligosaccharide 6 oligosaccharide 7 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 5 4 3 MAN BMA C1 O1 . O3 HO3 . sing 5 ? 5 5 3 MAN BMA C1 O1 . O6 HO6 . sing 6 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 7 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 8 ? 6 4 3 MAN BMA C1 O1 . O3 HO3 . sing 9 ? 7 2 1 NAG NAG C1 O1 . O4 HO4 . sing 10 ? 7 3 2 BMA NAG C1 O1 . O4 HO4 . 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 M NAG 1 G 1 NAG Q 1001 NAG 4 n M NAG 2 G 2 NAG Q 1002 NAG 5 n N NAG 1 I 1 NAG Q 1010 NAG 5 n N NAG 2 I 2 NAG Q 1011 NAG 5 n N BMA 3 I 3 BMA Q 1012 BMA 5 n N MAN 4 I 4 MAN Q 1014 MAN 5 n N MAN 5 I 5 MAN Q 1013 MAN 4 n O NAG 1 J 1 NAG R 1001 NAG 4 n O NAG 2 J 2 NAG R 1002 NAG 6 n P NAG 1 K 1 NAG R 1010 NAG 6 n P NAG 2 K 2 NAG R 1011 NAG 6 n P BMA 3 K 3 BMA R 1012 BMA 6 n P MAN 4 K 4 MAN R 1014 MAN 4 n Q NAG 1 M 1 NAG S 1001 NAG 4 n Q NAG 2 M 2 NAG S 1002 NAG 7 n R NAG 1 N 1 NAG S 1010 NAG 7 n R NAG 2 N 2 NAG S 1011 NAG 7 n R BMA 3 N 3 BMA S 1012 BMA 4 n S NAG 1 O 1 NAG T 1001 NAG 4 n S NAG 2 O 2 NAG T 1002 NAG 6 n T NAG 1 P 1 NAG T 1010 NAG 6 n T NAG 2 P 2 NAG T 1011 NAG 6 n T BMA 3 P 3 BMA T 1012 BMA 6 n T MAN 4 P 4 MAN T 1014 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 22 Q CYS 39 1_555 A SG CYS 150 Q CYS 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 A SG CYS 27 Q CYS 44 1_555 A SG CYS 85 Q CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 144 Q CYS 161 1_555 A SG CYS 202 Q CYS 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 248 Q CYS 265 1_555 A SG CYS 292 Q CYS 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 B SG CYS 22 R CYS 39 1_555 B SG CYS 150 R CYS 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 B SG CYS 27 R CYS 44 1_555 B SG CYS 85 R CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf7 B SG CYS 144 R CYS 161 1_555 B SG CYS 202 R CYS 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf8 B SG CYS 248 R CYS 265 1_555 B SG CYS 292 R CYS 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 C SG CYS 22 S CYS 39 1_555 C SG CYS 150 S CYS 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 C SG CYS 27 S CYS 44 1_555 C SG CYS 85 S CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf11 C SG CYS 144 S CYS 161 1_555 C SG CYS 202 S CYS 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf12 C SG CYS 248 S CYS 265 1_555 C SG CYS 292 S CYS 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf13 D SG CYS 22 T CYS 39 1_555 D SG CYS 150 T CYS 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf14 D SG CYS 27 T CYS 44 1_555 D SG CYS 85 T CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf15 D SG CYS 144 T CYS 161 1_555 D SG CYS 202 T CYS 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf16 D SG CYS 248 T CYS 265 1_555 D SG CYS 292 T CYS 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf17 E SG CYS 25 A CYS 22 1_555 E SG CYS 99 A CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf18 E SG CYS 146 A CYS 141 1_555 E SG CYS 202 A CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf19 F SG CYS 25 C CYS 22 1_555 F SG CYS 99 C CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf20 F SG CYS 146 C CYS 141 1_555 F SG CYS 202 C CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf21 G SG CYS 25 E CYS 22 1_555 G SG CYS 99 E CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf22 G SG CYS 146 E CYS 141 1_555 G SG CYS 202 E CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf23 H SG CYS 25 H CYS 22 1_555 H SG CYS 99 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf24 H SG CYS 146 H CYS 141 1_555 H SG CYS 202 H CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf25 I SG CYS 26 B CYS 23 1_555 I SG CYS 97 B CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf26 I SG CYS 142 B CYS 135 1_555 I SG CYS 202 B CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf27 J SG CYS 26 D CYS 23 1_555 J SG CYS 97 D CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf28 J SG CYS 142 D CYS 135 1_555 J SG CYS 202 D CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf29 K SG CYS 26 F CYS 23 1_555 K SG CYS 97 F CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf30 K SG CYS 142 F CYS 135 1_555 K SG CYS 202 F CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf31 L SG CYS 26 L CYS 23 1_555 L SG CYS 97 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf32 L SG CYS 142 L CYS 135 1_555 L SG CYS 202 L CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 84 Q ASN 101 1_555 N C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale2 A ND2 ASN 214 Q ASN 231 1_555 M C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 B ND2 ASN 84 R ASN 101 1_555 P C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 B ND2 ASN 214 R ASN 231 1_555 O C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale5 C ND2 ASN 84 S ASN 101 1_555 R C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale6 C ND2 ASN 214 S ASN 231 1_555 Q C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale7 D ND2 ASN 84 T ASN 101 1_555 T C1 NAG . P NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale8 D ND2 ASN 214 T ASN 231 1_555 S C1 NAG . O NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale9 M O4 NAG . G NAG 1 1_555 M C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale10 N O4 NAG . I NAG 1 1_555 N C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale11 N O4 NAG . I NAG 2 1_555 N C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale12 N O3 BMA . I BMA 3 1_555 N C1 MAN . I MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale13 N O6 BMA . I BMA 3 1_555 N C1 MAN . I MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale14 O O4 NAG . J NAG 1 1_555 O C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale15 P O4 NAG . K NAG 1 1_555 P C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale16 P O4 NAG . K NAG 2 1_555 P C1 BMA . K BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale17 P O3 BMA . K BMA 3 1_555 P C1 MAN . K MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale18 Q O4 NAG . M NAG 1 1_555 Q C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale19 R O4 NAG . N NAG 1 1_555 R C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale20 R O4 NAG . N NAG 2 1_555 R C1 BMA . N BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale21 S O4 NAG . O NAG 1 1_555 S C1 NAG . O NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale22 T O4 NAG . P NAG 1 1_555 T C1 NAG . P NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale23 T O4 NAG . P NAG 2 1_555 T C1 BMA . P BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale24 T O3 BMA . P BMA 3 1_555 T C1 MAN . P MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _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 5VL3 _atom_sites.fract_transf_matrix[1][1] 0.01148 _atom_sites.fract_transf_matrix[1][2] -0.001819 _atom_sites.fract_transf_matrix[1][3] -0.001359 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011222 _atom_sites.fract_transf_matrix[2][3] -0.003673 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.007801 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id U _pdbx_nonpoly_scheme.entity_id 8 _pdbx_nonpoly_scheme.mon_id GOL _pdbx_nonpoly_scheme.pdb_strand_id S _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 1006 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id GOL _pdbx_nonpoly_scheme.auth_mon_id GOL _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . U 8 67.138 73.447 -10.375 1 82.21 ? C1 GOL 1006 S 1 HETATM 2 O O1 GOL . . . U 8 67.429 73.255 -9.027 1 82.21 ? O1 GOL 1006 S 1 HETATM 3 C C2 GOL . . . U 8 68.32 74.239 -10.981 1 82.21 ? C2 GOL 1006 S 1 HETATM 4 O O2 GOL . . . U 8 69.326 73.403 -11.442 1 82.21 ? O2 GOL 1006 S 1 HETATM 5 C C3 GOL . . . U 8 67.699 75.087 -12.112 1 82.21 ? C3 GOL 1006 S 1 HETATM 6 O O3 GOL . . . U 8 67.652 76.4 -11.655 1 82.21 ? O3 GOL 1006 S 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 53 _model_server_stats.create_model_time_ms 256 _model_server_stats.query_time_ms 377 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 6 #