data_4KGJ # _model_server_result.job_id pGwXYMYFixZw39knxMgQzA _model_server_result.datetime_utc '2024-11-08 08:35:49' _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 4kgj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":916}' # _entry.id 4KGJ # _exptl.entry_id 4KGJ _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 7 _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 120 _cell.entry_id 4KGJ _cell.length_a 259.343 _cell.length_b 259.343 _cell.length_c 71.379 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KGJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # 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 monomeric 1 software_defined_assembly 1 PISA monomeric 1 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G,H,I,J,U 1 1 B,E,F,K,L,M,N,O,P,Q,R,S,T,V 2 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 H N N ? 6 I N N ? 6 L N N ? 6 M N N ? 6 N N N ? 6 O N N ? 6 P N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 5 ? 3 5 3 MAN BMA C1 O1 . O6 HO6 . sing 6 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 7 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 8 ? 4 4 3 MAN BMA C1 O1 . O6 HO6 . sing 9 ? 4 5 4 MAN MAN C1 O1 . O6 HO6 . sing 10 ? 4 6 5 MAN MAN C1 O1 . O2 HO2 . sing 11 ? 4 7 4 MAN MAN C1 O1 . O3 HO3 . sing 12 ? 4 8 3 MAN BMA C1 O1 . O3 HO3 . sing 13 ? 4 9 8 MAN MAN C1 O1 . O2 HO2 . 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 2 n C NAG 1 C 1 NAG C 951 NAG 2 n C NAG 2 C 2 NAG C 952 NAG 3 n D NAG 1 D 1 NAG C 991 NAG 3 n D NAG 2 D 2 NAG C 992 NAG 3 n D BMA 3 D 3 BMA C 993 BMA 3 n D MAN 4 D 4 MAN C 995 MAN 3 n D MAN 5 D 5 MAN C 994 MAN 2 n E NAG 1 E 1 NAG D 951 NAG 2 n E NAG 2 E 2 NAG D 952 NAG 4 n F NAG 1 F 1 NAG D 991 NAG 4 n F NAG 2 F 2 NAG D 992 NAG 4 n F BMA 3 F 3 BMA D 993 BMA 4 n F MAN 4 F 4 MAN D 994 MAN 4 n F MAN 5 F 5 MAN D 997 MAN 4 n F MAN 6 F 6 MAN D 998 MAN 4 n F MAN 7 F 7 MAN D 996 MAN 4 n F MAN 8 F 8 MAN D 995 MAN 4 n F MAN 9 F 9 MAN D 999 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 515 A CYS 541 1_555 A SG CYS 551 A CYS 577 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 B SG CYS 515 B CYS 541 1_555 B SG CYS 551 B CYS 577 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 84 A ASN 110 1_555 G C1 NAG . A NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale2 A ND2 ASN 346 A ASN 372 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 A ND2 ASN 389 A ASN 415 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale4 B ND2 ASN 84 B ASN 110 1_555 K C1 NAG . B NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 B ND2 ASN 346 B ASN 372 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 B ND2 ASN 389 B ASN 415 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale7 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale9 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale10 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale11 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale12 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale13 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale14 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale15 F O6 BMA . F BMA 3 1_555 F C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale16 F O3 BMA . F BMA 3 1_555 F C1 MAN . F MAN 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale17 F O6 MAN . F MAN 4 1_555 F C1 MAN . F MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale18 F O3 MAN . F MAN 4 1_555 F C1 MAN . F MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale19 F O2 MAN . F MAN 5 1_555 F C1 MAN . F MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale20 F O2 MAN . F MAN 8 1_555 F C1 MAN . F MAN 9 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 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 4KGJ _atom_sites.fract_transf_matrix[1][1] 0.003856 _atom_sites.fract_transf_matrix[1][2] 0.002226 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004452 _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] 0.01401 _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 NAG A 1 901 901 NAG NAG . H 6 GOL A 1 909 1 GOL GOL . I 6 GOL A 1 910 7 GOL GOL . J 7 IDF A 1 911 1 IDF IDF . K 5 NAG B 1 901 901 NAG NAG . L 6 GOL B 1 913 2 GOL GOL . M 6 GOL B 1 914 3 GOL GOL . N 6 GOL B 1 915 4 GOL GOL . O 6 GOL B 1 916 5 GOL GOL . P 6 GOL B 1 917 6 GOL GOL . Q 8 TLA B 1 918 1 TLA TLA . R 8 TLA B 1 919 2 TLA TLA . S 7 IDF B 1 920 2 IDF IDF . T 9 CL B 1 921 1 CL CL . U 10 HOH A 1 1001 2 HOH HOH . U 10 HOH A 2 1002 3 HOH HOH . U 10 HOH A 3 1003 8 HOH HOH . U 10 HOH A 4 1004 10 HOH HOH . U 10 HOH A 5 1005 13 HOH HOH . U 10 HOH A 6 1006 15 HOH HOH . U 10 HOH A 7 1007 16 HOH HOH . U 10 HOH A 8 1008 19 HOH HOH . U 10 HOH A 9 1009 20 HOH HOH . U 10 HOH A 10 1010 25 HOH HOH . U 10 HOH A 11 1011 31 HOH HOH . U 10 HOH A 12 1012 33 HOH HOH . U 10 HOH A 13 1013 39 HOH HOH . U 10 HOH A 14 1014 40 HOH HOH . U 10 HOH A 15 1015 44 HOH HOH . U 10 HOH A 16 1016 46 HOH HOH . U 10 HOH A 17 1017 49 HOH HOH . V 10 HOH B 1 1001 4 HOH HOH . V 10 HOH B 2 1002 5 HOH HOH . V 10 HOH B 3 1003 6 HOH HOH . V 10 HOH B 4 1004 7 HOH HOH . V 10 HOH B 5 1005 9 HOH HOH . V 10 HOH B 6 1006 11 HOH HOH . V 10 HOH B 7 1007 12 HOH HOH . V 10 HOH B 8 1008 14 HOH HOH . V 10 HOH B 9 1009 17 HOH HOH . V 10 HOH B 10 1010 18 HOH HOH . V 10 HOH B 11 1011 21 HOH HOH . V 10 HOH B 12 1012 22 HOH HOH . V 10 HOH B 13 1013 23 HOH HOH . V 10 HOH B 14 1014 24 HOH HOH . V 10 HOH B 15 1015 26 HOH HOH . V 10 HOH B 16 1016 27 HOH HOH . V 10 HOH B 17 1017 28 HOH HOH . V 10 HOH B 18 1018 29 HOH HOH . V 10 HOH B 19 1019 30 HOH HOH . V 10 HOH B 20 1020 32 HOH HOH . V 10 HOH B 21 1021 34 HOH HOH . V 10 HOH B 22 1022 35 HOH HOH . V 10 HOH B 23 1023 36 HOH HOH . V 10 HOH B 24 1024 37 HOH HOH . V 10 HOH B 25 1025 38 HOH HOH . V 10 HOH B 26 1026 41 HOH HOH . V 10 HOH B 27 1027 42 HOH HOH . V 10 HOH B 28 1028 43 HOH HOH . V 10 HOH B 29 1029 45 HOH HOH . V 10 HOH B 30 1030 47 HOH HOH . V 10 HOH B 31 1031 48 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 . . . O 6 281.492 -38.456 1.911 1 53.27 ? C1 GOL 916 B 1 HETATM 2 O O1 GOL . . . O 6 280.498 -37.426 1.892 1 53.45 ? O1 GOL 916 B 1 HETATM 3 C C2 GOL . . . O 6 281.187 -39.421 0.772 1 53.82 ? C2 GOL 916 B 1 HETATM 4 O O2 GOL . . . O 6 281.914 -39.028 -0.4 1 51.46 ? O2 GOL 916 B 1 HETATM 5 C C3 GOL . . . O 6 281.555 -40.845 1.186 1 54.1 ? C3 GOL 916 B 1 HETATM 6 O O3 GOL . . . O 6 282.974 -41.017 1.133 1 55.53 ? O3 GOL 916 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 6 #