data_3RY6 # _model_server_result.job_id nz8BYaRcnnM6jEZ2FYcjfQ _model_server_result.datetime_utc '2024-11-24 19:47:25' _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 3ry6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":603}' # _entry.id 3RY6 # _exptl.entry_id 3RY6 _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 4 _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 3RY6 _cell.length_a 153.38 _cell.length_b 255.55 _cell.length_c 58.44 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RY6 _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 ? _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 _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 I N N ? 6 J N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 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 ? 3 2 1 NAG NDG 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 4 NAG MAN C1 O1 . O2 HO2 . sing 5 ? 3 6 5 GAL NAG C1 O1 . O4 HO4 . sing 6 ? 3 7 6 SIA GAL C2 O2 . O6 HO6 . sing 7 ? 3 8 3 MAN BMA C1 O1 . O6 HO6 . sing 8 ? 3 9 8 NAG MAN C1 O1 . O2 HO2 . sing 9 ? 3 10 1 FUL NDG C1 O1 . O6 HO6 . sing 10 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 11 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 12 ? 4 4 3 MAN BMA C1 O1 . O3 HO3 . sing 13 ? 4 5 4 NAG MAN C1 O1 . O2 HO2 . sing 14 ? 4 6 5 GAL NAG C1 O1 . O4 HO4 . sing 15 ? 4 7 6 SIA GAL C2 O2 . O6 HO6 . sing 16 ? 4 8 3 MAN BMA C1 O1 . O6 HO6 . sing 17 ? 4 9 8 NAG MAN C1 O1 . O2 HO2 . sing 18 ? 4 10 9 GAL NAG C1 O1 . O4 HO4 . sing 19 ? 4 11 10 SIA GAL C2 O2 . O6 HO6 . sing 20 ? 4 12 1 FUL NAG C1 O1 . O6 HO6 . sing 21 ? 5 2 1 NAG NDG C1 O1 . O4 HO4 . sing 22 ? 5 3 2 MAN NAG C1 O1 . O4 HO4 . sing 23 ? 5 4 3 BMA MAN C1 O1 . O3 HO3 . sing 24 ? 5 5 3 MAN MAN C1 O1 . O6 HO6 . sing 25 ? 5 6 1 FUL NDG 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 3 n D NDG 1 D 1 NDG A 801 NDG 3 n D NAG 2 D 2 NAG A 803 NAG 3 n D BMA 3 D 3 BMA A 804 BMA 3 n D MAN 4 D 4 MAN A 808 MAN 3 n D NAG 5 D 5 NAG A 809 NAG 3 n D GAL 6 D 6 GAL A 810 GAL 3 n D SIA 7 D 7 SIA A 811 SIA 3 n D MAN 8 D 8 MAN A 805 MAN 3 n D NAG 9 D 9 NAG A 806 NAG 3 n D FUL 10 D 10 FUL A 802 FUL 4 n E NAG 1 E 1 NAG B 801 NAG 4 n E NAG 2 E 2 NAG B 803 NAG 4 n E BMA 3 E 3 BMA B 804 BMA 4 n E MAN 4 E 4 MAN B 808 MAN 4 n E NAG 5 E 5 NAG B 809 NAG 4 n E GAL 6 E 6 GAL B 810 GAL 4 n E SIA 7 E 7 SIA B 811 SIA 4 n E MAN 8 E 8 MAN B 805 MAN 4 n E NAG 9 E 9 NAG B 806 NAG 4 n E GAL 10 E 10 GAL B 807 GAL 4 n E SIA 11 E 11 SIA B 812 SIA 4 n E FUL 12 E 12 FUL B 802 FUL 5 n F NDG 1 F 1 NDG C 200 NDG 5 n F NAG 2 F 2 NAG C 201 NAG 5 n F MAN 3 F 3 MAN C 203 MAN 5 n F BMA 4 F 4 BMA C 205 BMA 5 n F MAN 5 F 5 MAN C 204 MAN 5 n F FUL 6 F 6 FUL C 202 FUL # 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 31 A CYS 261 1_555 A SG CYS 91 A CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 A SG CYS 137 A CYS 367 1_555 A SG CYS 195 A CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf3 B SG CYS 31 B CYS 261 1_555 B SG CYS 91 B CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf4 B SG CYS 137 B CYS 367 1_555 B SG CYS 195 B CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf5 C SG CYS 23 C CYS 29 1_555 C SG CYS 65 C CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf6 C SG CYS 104 C CYS 110 1_555 C SG CYS 148 C CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 B ND2 ASN 67 B ASN 297 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale2 C ND2 ASN 58 C ASN 64 1_555 K C1 NAG . C NAG 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale3 D O4 NDG . D NDG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale4 D O6 NDG . D NDG 1 1_555 D C1 FUL . D FUL 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? covale ? covale5 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.376 ? covale ? covale6 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 ? covale ? covale7 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale8 D O2 MAN . D MAN 4 1_555 D C1 NAG . D NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? covale ? covale9 D O4 NAG . D NAG 5 1_555 D C1 GAL . D GAL 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? covale ? covale10 D O6 GAL . D GAL 6 1_555 D C2 SIA . D SIA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? covale ? covale11 D O2 MAN . D MAN 8 1_555 D C1 NAG . D NAG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? covale ? covale12 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.387 ? covale ? covale13 E O6 NAG . E NAG 1 1_555 E C1 FUL . E FUL 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? covale ? covale14 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.392 ? covale ? covale15 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? covale ? covale16 E O6 BMA . E BMA 3 1_555 E C1 MAN . E MAN 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.397 ? covale ? covale17 E O2 MAN . E MAN 4 1_555 E C1 NAG . E NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.394 ? covale ? covale18 E O4 NAG . E NAG 5 1_555 E C1 GAL . E GAL 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.388 ? covale ? covale19 E O6 GAL . E GAL 6 1_555 E C2 SIA . E SIA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.406 ? covale ? covale20 E O2 MAN . E MAN 8 1_555 E C1 NAG . E NAG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.381 ? covale ? covale21 E O4 NAG . E NAG 9 1_555 E C1 GAL . E GAL 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? covale ? covale22 E O6 GAL . E GAL 10 1_555 E C2 SIA . E SIA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.407 ? covale ? covale23 F O4 NDG . F NDG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.404 ? covale ? covale24 F O6 NDG . F NDG 1 1_555 F C1 FUL . F FUL 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale25 F O4 NAG . F NAG 2 1_555 F C1 MAN . F MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.397 ? covale ? covale26 F O3 MAN . F MAN 3 1_555 F C1 BMA . F BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.404 ? covale ? covale27 F O6 MAN . F MAN 3 1_555 F C1 MAN . F MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? # _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 200 n n C1 C2 GOL sing 201 n n C1 H11 GOL sing 202 n n C1 H12 GOL sing 203 n n O1 HO1 GOL sing 204 n n C2 O2 GOL sing 205 n n C2 C3 GOL sing 206 n n C2 H2 GOL sing 207 n n O2 HO2 GOL sing 208 n n C3 O3 GOL sing 209 n n C3 H31 GOL sing 210 n n C3 H32 GOL sing 211 n n O3 HO3 GOL sing 212 n n # _atom_sites.entry_id 3RY6 _atom_sites.fract_transf_matrix[1][1] 0.00652 _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] 0.003913 _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] 0.017112 _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 G 6 GOL A 1 600 600 GOL GOL . H 6 GOL B 1 601 601 GOL GOL . I 6 GOL B 1 602 602 GOL GOL . J 6 GOL B 1 603 603 GOL GOL . K 7 NAG C 1 206 206 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 . . . J 6 83.475 94.923 69.671 1 27.2 ? C1 GOL 603 B 1 HETATM 2 O O1 GOL . . . J 6 84.623 94.327 70.646 1 26.88 ? O1 GOL 603 B 1 HETATM 3 C C2 GOL . . . J 6 82.148 94.455 69.689 1 27.84 ? C2 GOL 603 B 1 HETATM 4 O O2 GOL . . . J 6 81.629 94.286 70.925 1 23.05 ? O2 GOL 603 B 1 HETATM 5 C C3 GOL . . . J 6 81.776 94.315 68.542 1 31.1 ? C3 GOL 603 B 1 HETATM 6 O O3 GOL . . . J 6 82.248 94.47 67.062 1 23.65 ? O3 GOL 603 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 6 #