data_5GJE # _model_server_result.job_id 5IXgDmH4MBrj9hCU8ZXf0A _model_server_result.datetime_utc '2024-11-23 01:14:49' _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 5gje # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":1309}' # _entry.id 5GJE # _exptl.entry_id 5GJE _exptl.method 'ELECTRON MICROSCOPY' # _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 ? # _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,K,L,M,N,O _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 ? _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 N _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 # 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 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 D NAG 1 D 1 NAG A 701 NAG 4 n D NAG 2 D 2 NAG A 702 NAG 4 n E NAG 1 E 1 NAG A 703 NAG 4 n E NAG 2 E 2 NAG A 704 NAG 4 n F NAG 1 F 1 NAG A 705 NAG 4 n F NAG 2 F 2 NAG A 706 NAG 5 n G NAG 1 G 1 NAG B 2692 NAG 5 n G NAG 2 G 2 NAG B 2693 NAG 5 n G FUC 3 G 3 FUC B 2694 FUC 4 n H NAG 1 H 1 NAG B 3039 NAG 4 n H NAG 2 H 2 NAG B 3040 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 274 A CYS 274 1_555 A SG CYS 289 A CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.826 ? disulf ? disulf2 A SG CYS 291 A CYS 291 1_555 A SG CYS 304 A CYS 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? disulf ? disulf3 A SG CYS 573 A CYS 573 1_555 A SG CYS 584 A CYS 584 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? disulf ? disulf4 A SG CYS 580 A CYS 580 1_555 A SG CYS 593 A CYS 593 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? disulf ? disulf5 A SG CYS 595 A CYS 595 1_555 A SG CYS 608 A CYS 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? disulf ? disulf6 B SG CYS 263 B CYS 893 1_555 B SG CYS 274 B CYS 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 B SG CYS 270 B CYS 900 1_555 B SG CYS 284 B CYS 914 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 B SG CYS 286 B CYS 916 1_555 B SG CYS 299 B CYS 929 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf9 B SG CYS 577 B CYS 1207 1_555 B SG CYS 588 B CYS 1218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf10 B SG CYS 584 B CYS 1214 1_555 B SG CYS 598 B CYS 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf11 B SG CYS 600 B CYS 1230 1_555 B SG CYS 613 B CYS 1243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf12 C SG CYS 8 C CYS 189 1_555 C SG CYS 20 C CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf13 C SG CYS 14 C CYS 195 1_555 C SG CYS 29 C CYS 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf14 C SG CYS 19 C CYS 200 1_555 C SG CYS 56 C CYS 237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf15 C SG CYS 39 C CYS 220 1_555 C SG CYS 64 C CYS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf16 C SG CYS 58 C CYS 239 1_555 C SG CYS 82 C CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? covale ? covale1 A ND2 ASN 262 A ASN 262 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale2 A ND2 ASN 414 A ASN 414 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale3 A ND2 ASN 467 A ASN 467 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale4 B ND2 ASN 62 B ASN 692 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 B ND2 ASN 229 B ASN 859 1_555 K C1 NAG . B NAG 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 B ND2 ASN 235 B ASN 865 1_555 L C1 NAG . B NAG 1305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 B ND2 ASN 296 B ASN 926 1_555 M C1 NAG . B NAG 1306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale8 B ND2 ASN 409 B ASN 1039 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.392 ? covale ? covale10 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? covale ? covale11 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? covale ? covale12 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale13 G O6 NAG . G NAG 1 1_555 G C1 FUC . G FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale14 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 152 n n C1 C2 GOL sing 153 n n C1 H11 GOL sing 154 n n C1 H12 GOL sing 155 n n O1 HO1 GOL sing 156 n n C2 O2 GOL sing 157 n n C2 C3 GOL sing 158 n n C2 H2 GOL sing 159 n n O2 HO2 GOL sing 160 n n C3 O3 GOL sing 161 n n C3 H31 GOL sing 162 n n C3 H32 GOL sing 163 n n O3 HO3 GOL sing 164 n n # _atom_sites.entry_id 5GJE _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 I 6 PO4 A 1 707 707 PO4 PO4 . J 6 PO4 A 1 708 708 PO4 PO4 . K 7 NAG B 1 1304 2859 NAG NAG . L 7 NAG B 1 1305 2865 NAG NAG . M 7 NAG B 1 1306 2926 NAG NAG . N 8 GOL B 1 1309 102 GOL GOL . O 9 HOH A 1 801 808 HOH HOH . O 9 HOH A 2 802 805 HOH HOH . O 9 HOH A 3 803 809 HOH HOH . O 9 HOH A 4 804 807 HOH HOH . O 9 HOH A 5 805 802 HOH HOH . O 9 HOH A 6 806 803 HOH HOH . O 9 HOH A 7 807 811 HOH HOH . O 9 HOH A 8 808 812 HOH HOH . O 9 HOH A 9 809 801 HOH HOH . O 9 HOH A 10 810 813 HOH HOH . O 9 HOH A 11 811 810 HOH HOH . O 9 HOH A 12 812 806 HOH HOH . O 9 HOH A 13 813 804 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 . . . N 8 234.418 223.618 220.251 1 71.46 ? C1 GOL 1309 B 1 HETATM 2 O O1 GOL . . . N 8 234.394 222.25 219.908 1 77.76 ? O1 GOL 1309 B 1 HETATM 3 C C2 GOL . . . N 8 234.688 223.756 221.742 1 76.62 ? C2 GOL 1309 B 1 HETATM 4 O O2 GOL . . . N 8 233.479 223.621 222.451 1 88.41 ? O2 GOL 1309 B 1 HETATM 5 C C3 GOL . . . N 8 235.309 225.116 222.042 1 82.08 ? C3 GOL 1309 B 1 HETATM 6 O O3 GOL . . . N 8 236.671 225.106 221.683 1 84.67 ? O3 GOL 1309 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 141 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 6 #