data_5LCV # _model_server_result.job_id 3Qer-RyvZGf8E7FKDEnl8g _model_server_result.datetime_utc '2024-11-27 08:35:24' _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 5lcv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":505}' # _entry.id 5LCV # _exptl.entry_id 5LCV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 92.094 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description GLYCEROL _entity.pdbx_number_of_molecules 3 _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 5LCV _cell.length_a 204.288 _cell.length_b 207.317 _cell.length_c 124.576 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LCV _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details 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,N _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 G N N ? 6 H N N ? 6 J N N # _pdbx_entity_branch.entity_id 4 _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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 4 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 4 n E NAG 1 C 1 NAG B 1154 NAG 4 n E NAG 2 C 2 NAG B 1155 NAG 4 n E BMA 3 C 3 BMA B 1156 BMA 4 n E FUC 4 C 4 FUC B 1157 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 3 A CYS 3 1_555 A SG CYS 30 A CYS 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 60 A CYS 60 1_555 A SG CYS 121 A CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 A SG CYS 74 A CYS 74 1_555 A SG CYS 105 A CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 A SG CYS 92 A CYS 92 1_555 A SG CYS 116 A CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 A SG CYS 190 A CYS 190 1_555 A SG CYS 291 A CYS 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 A SG CYS 308 A CYS 308 1_555 A SG CYS 339 A CYS 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf7 B SG CYS 3 B CYS 3 1_555 B SG CYS 30 B CYS 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf8 B SG CYS 60 B CYS 60 1_555 B SG CYS 121 B CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf9 B SG CYS 74 B CYS 74 1_555 B SG CYS 105 B CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf10 B SG CYS 92 B CYS 92 1_555 B SG CYS 116 B CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf11 B SG CYS 190 B CYS 190 1_555 B SG CYS 291 B CYS 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf12 B SG CYS 308 B CYS 308 1_555 B SG CYS 339 B CYS 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf13 C SG CYS 22 H CYS 22 1_555 C SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf14 C SG CYS 160 H CYS 140 1_555 C SG CYS 216 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf15 D SG CYS 22 L CYS 23 1_555 D SG CYS 90 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf16 D SG CYS 138 L CYS 135 1_555 D SG CYS 197 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 A ND2 ASN 154 A ASN 154 1_555 F C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 B ND2 ASN 154 B ASN 154 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale4 E O6 NAG . C NAG 1 1_555 E C1 FUC . C FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? covale ? covale5 E O4 NAG . C NAG 2 1_555 E C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? # _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 180 n n C1 C2 GOL sing 181 n n C1 H11 GOL sing 182 n n C1 H12 GOL sing 183 n n O1 HO1 GOL sing 184 n n C2 O2 GOL sing 185 n n C2 C3 GOL sing 186 n n C2 H2 GOL sing 187 n n O2 HO2 GOL sing 188 n n C3 O3 GOL sing 189 n n C3 H31 GOL sing 190 n n C3 H32 GOL sing 191 n n O3 HO3 GOL sing 192 n n # _atom_sites.entry_id 5LCV _atom_sites.fract_transf_matrix[1][1] 0.004895 _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] 0.004824 _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] 0.008027 _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 F 5 NAG A 1 501 1154 NAG NAG . G 6 GOL A 1 502 1 GOL GOL . H 6 GOL A 1 503 2 GOL GOL . I 7 FMT A 1 504 1 FMT FMT . J 6 GOL B 1 505 3 GOL GOL . K 8 HOH A 1 601 7 HOH HOH . K 8 HOH A 2 602 34 HOH HOH . K 8 HOH A 3 603 20 HOH HOH . K 8 HOH A 4 604 32 HOH HOH . K 8 HOH A 5 605 28 HOH HOH . K 8 HOH A 6 606 42 HOH HOH . K 8 HOH A 7 607 37 HOH HOH . K 8 HOH A 8 608 3 HOH HOH . K 8 HOH A 9 609 2 HOH HOH . K 8 HOH A 10 610 29 HOH HOH . K 8 HOH A 11 611 5 HOH HOH . K 8 HOH A 12 612 11 HOH HOH . K 8 HOH A 13 613 23 HOH HOH . K 8 HOH A 14 614 46 HOH HOH . K 8 HOH A 15 615 14 HOH HOH . K 8 HOH A 16 616 41 HOH HOH . L 8 HOH B 1 601 33 HOH HOH . L 8 HOH B 2 602 30 HOH HOH . L 8 HOH B 3 603 44 HOH HOH . L 8 HOH B 4 604 9 HOH HOH . L 8 HOH B 5 605 38 HOH HOH . L 8 HOH B 6 606 35 HOH HOH . L 8 HOH B 7 607 8 HOH HOH . L 8 HOH B 8 608 6 HOH HOH . L 8 HOH B 9 609 17 HOH HOH . L 8 HOH B 10 610 4 HOH HOH . L 8 HOH B 11 611 22 HOH HOH . L 8 HOH B 12 612 19 HOH HOH . L 8 HOH B 13 613 13 HOH HOH . L 8 HOH B 14 614 31 HOH HOH . L 8 HOH B 15 615 16 HOH HOH . M 8 HOH H 1 301 1 HOH HOH . M 8 HOH H 2 302 43 HOH HOH . M 8 HOH H 3 303 45 HOH HOH . M 8 HOH H 4 304 26 HOH HOH . M 8 HOH H 5 305 27 HOH HOH . M 8 HOH H 6 306 12 HOH HOH . M 8 HOH H 7 307 24 HOH HOH . M 8 HOH H 8 308 25 HOH HOH . N 8 HOH L 1 301 39 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 . . . J 6 40.527 59.008 5.787 1 76.88 ? C1 GOL 505 B 1 HETATM 2 O O1 GOL . . . J 6 40.538 58.557 7.137 1 76.84 ? O1 GOL 505 B 1 HETATM 3 C C2 GOL . . . J 6 40.492 60.518 5.713 1 76.72 ? C2 GOL 505 B 1 HETATM 4 O O2 GOL . . . J 6 40.674 60.929 4.355 1 76.2 ? O2 GOL 505 B 1 HETATM 5 C C3 GOL . . . J 6 39.177 61.057 6.226 1 77.25 ? C3 GOL 505 B 1 HETATM 6 O O3 GOL . . . J 6 39.151 61.067 7.648 1 77.53 ? O3 GOL 505 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 6 #