data_5YLS # _model_server_result.job_id h-k-QXBxJDpoiQ3FEbyrfA _model_server_result.datetime_utc '2024-11-22 08:01:40' _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 5yls # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":504}' # _entry.id 5YLS # _exptl.entry_id 5YLS _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 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5YLS _cell.length_a 105.767 _cell.length_b 159.054 _cell.length_c 183.151 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YLS _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,P,Q,R,S,T,U,V,W,X,Y _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 # _struct_asym.details ? _struct_asym.entity_id 8 _struct_asym.id J _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # 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 metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.15 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc7 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc8 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc9 H MG MG . A MG 502 1_555 V O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc10 H MG MG . A MG 502 1_555 V O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc11 H MG MG . A MG 502 1_555 V O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc12 H MG MG . A MG 502 1_555 V O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc13 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc14 K O1A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc15 L MG MG . B MG 502 1_555 W O HOH . B HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.831 ? metalc ? metalc16 L MG MG . B MG 502 1_555 W O HOH . B HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc17 L MG MG . B MG 502 1_555 W O HOH . B HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc18 L MG MG . B MG 502 1_555 X O HOH . C HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc19 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc20 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc21 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? metalc ? metalc22 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? metalc ? metalc23 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc24 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? metalc ? metalc25 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.677 ? metalc ? metalc26 O O1G GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc27 O O1B GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc28 P MG MG . C MG 502 1_555 X O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc29 P MG MG . C MG 502 1_555 X O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc30 P MG MG . C MG 502 1_555 X O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc31 P MG MG . C MG 502 1_555 X O HOH . C HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? # _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 225 n n C1 C2 GOL sing 226 n n C1 H11 GOL sing 227 n n C1 H12 GOL sing 228 n n O1 HO1 GOL sing 229 n n C2 O2 GOL sing 230 n n C2 C3 GOL sing 231 n n C2 H2 GOL sing 232 n n O2 HO2 GOL sing 233 n n C3 O3 GOL sing 234 n n C3 H31 GOL sing 235 n n C3 H32 GOL sing 236 n n O3 HO3 GOL sing 237 n n # _atom_sites.entry_id 5YLS _atom_sites.fract_transf_matrix[1][1] 0.009455 _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] 0.006287 _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] 0.00546 _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 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 GOL A 1 504 601 GOL GOL . K 9 GDP B 1 501 501 GDP GDP . L 6 MG B 1 502 502 MG MG . M 10 MES B 1 503 505 MES MES . N 11 Y50 B 1 504 1 Y50 Y50 . O 5 GTP C 1 501 501 GTP GTP . P 6 MG C 1 502 502 MG MG . Q 7 CA C 1 503 504 CA CA . R 5 GTP D 1 501 501 GTP GTP . S 6 MG D 1 502 502 MG MG . T 11 Y50 D 1 503 2 Y50 Y50 . U 12 ACP F 1 401 401 ACP ACP . V 13 HOH A 1 601 11 HOH HOH . V 13 HOH A 2 602 2 HOH HOH . V 13 HOH A 3 603 1 HOH HOH . V 13 HOH A 4 604 3 HOH HOH . V 13 HOH A 5 605 4 HOH HOH . W 13 HOH B 1 601 17 HOH HOH . W 13 HOH B 2 602 18 HOH HOH . W 13 HOH B 3 603 10 HOH HOH . W 13 HOH B 4 604 12 HOH HOH . W 13 HOH B 5 605 15 HOH HOH . W 13 HOH B 6 606 16 HOH HOH . W 13 HOH B 7 607 13 HOH HOH . X 13 HOH C 1 601 5 HOH HOH . X 13 HOH C 2 602 6 HOH HOH . X 13 HOH C 3 603 7 HOH HOH . X 13 HOH C 4 604 8 HOH HOH . X 13 HOH C 5 605 14 HOH HOH . Y 13 HOH D 1 601 9 HOH HOH . Y 13 HOH D 2 602 19 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 8 5.486 247.321 69.157 1 64.4 ? C1 GOL 504 A 1 HETATM 2 O O1 GOL . . . J 8 4.947 247.168 67.841 1 63.77 ? O1 GOL 504 A 1 HETATM 3 C C2 GOL . . . J 8 6.711 246.429 69.311 1 64.26 ? C2 GOL 504 A 1 HETATM 4 O O2 GOL . . . J 8 7.702 246.775 68.338 1 62.76 ? O2 GOL 504 A 1 HETATM 5 C C3 GOL . . . J 8 7.291 246.637 70.701 1 65.82 ? C3 GOL 504 A 1 HETATM 6 O O3 GOL . . . J 8 6.899 245.548 71.546 1 68.6 ? O3 GOL 504 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 6 #