data_5YH1
#
_model_server_result.job_id            Unfu5LOWz7L-gth5PSP5Zg 
_model_server_result.datetime_utc      '2024-11-22 17:44:57' 
_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          5yh1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":801}' 
#
_entry.id    5YH1 
#
_exptl.entry_id    5YH1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          2 
_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         120 
_cell.entry_id            5YH1 
_cell.length_a            132.5 
_cell.length_b            132.5 
_cell.length_c            212.245 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YH1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        182 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 63 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 132.5 0 0 
3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 66.25 114.748366 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 B N N 
? 2 C N N 
? 2 D N N 
? 2 E N 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
covale ? covale1 A C HIS 4 A HIS 303 1_555 A N MSE 5 A MSE 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale2 A C MSE 5 A MSE 304 1_555 A N ALA 6 A ALA 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale3 A C ILE 41 A ILE 340 1_555 A N MSE 42 A MSE 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale4 A C MSE 42 A MSE 341 1_555 A N LYS 43 A LYS 342 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? 
covale ? covale5 A C PHE 46 A PHE 345 1_555 A N MSE 47 A MSE 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale6 A C MSE 47 A MSE 346 1_555 A N ILE 48 A ILE 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale7 A C PHE 118 A PHE 417 1_555 A N MSE 119 A MSE 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale8 A C MSE 119 A MSE 418 1_555 A N MSE 120 A MSE 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale9 A C MSE 120 A MSE 419 1_555 A N GLU 121 A GLU 420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale10 A C HIS 123 A HIS 422 1_555 A N MSE 124 A MSE 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale11 A C MSE 124 A MSE 423 1_555 A N ARG 125 A ARG 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? 
covale ? covale12 A C GLY 200 A GLY 499 1_555 A N MSE 201 A MSE 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale13 A C MSE 201 A MSE 500 1_555 A N LEU 202 A LEU 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale14 A C PHE 269 A PHE 568 1_555 A N MSE 270 A MSE 569 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale15 A C MSE 270 A MSE 569 1_555 A N ASP 271 A ASP 570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale16 A C ARG 290 A ARG 589 1_555 A N MSE 291 A MSE 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? 
covale ? covale17 A C MSE 291 A MSE 590 1_555 A N LEU 292 A LEU 591 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale18 A C GLY 381 A GLY 680 1_555 A N MSE 382 A MSE 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale19 A C MSE 382 A MSE 681 1_555 A N ALA 383 A ALA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
metalc ? metalc1 A OD2 ASP 67 A ASP 366 1_555 F MN MN . A MN 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? 
metalc ? metalc2 A OD1 ASP 137 A ASP 436 1_555 F MN MN . A MN 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc3 A NE2 HIS 163 A HIS 462 1_555 F MN MN . A MN 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? 
metalc ? metalc4 A OD2 ASP 229 A ASP 528 1_555 F MN MN . A MN 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? 
metalc ? metalc5 F MN MN . A MN 805 1_555 G O HOH . A HOH 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? 
metalc ? metalc6 F MN MN . A MN 805 1_555 G O HOH . A HOH 929 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? 
#
_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 116 n n 
C1 C2 GOL sing 117 n n 
C1 H11 GOL sing 118 n n 
C1 H12 GOL sing 119 n n 
O1 HO1 GOL sing 120 n n 
C2 O2 GOL sing 121 n n 
C2 C3 GOL sing 122 n n 
C2 H2 GOL sing 123 n n 
O2 HO2 GOL sing 124 n n 
C3 O3 GOL sing 125 n n 
C3 H31 GOL sing 126 n n 
C3 H32 GOL sing 127 n n 
O3 HO3 GOL sing 128 n n 
#
_atom_sites.entry_id                     5YH1 
_atom_sites.fract_transf_matrix[1][1]    0.007547 
_atom_sites.fract_transf_matrix[1][2]    0.004357 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008715 
_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]    0.004712 
_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
B 2 GOL A 1 801 801 GOL GOL . 
C 2 GOL A 1 802 802 GOL GOL . 
D 2 GOL A 1 803 803 GOL GOL . 
E 2 GOL A 1 804 804 GOL GOL . 
F 3 MN A 1 805 805 MN MN . 
G 4 HOH A 1 901 901 HOH HOH . 
G 4 HOH A 2 902 902 HOH HOH . 
G 4 HOH A 3 903 903 HOH HOH . 
G 4 HOH A 4 904 904 HOH HOH . 
G 4 HOH A 5 905 905 HOH HOH . 
G 4 HOH A 6 906 906 HOH HOH . 
G 4 HOH A 7 907 907 HOH HOH . 
G 4 HOH A 8 908 908 HOH HOH . 
G 4 HOH A 9 909 909 HOH HOH . 
G 4 HOH A 10 910 910 HOH HOH . 
G 4 HOH A 11 911 911 HOH HOH . 
G 4 HOH A 12 912 912 HOH HOH . 
G 4 HOH A 13 913 913 HOH HOH . 
G 4 HOH A 14 914 914 HOH HOH . 
G 4 HOH A 15 915 915 HOH HOH . 
G 4 HOH A 16 916 916 HOH HOH . 
G 4 HOH A 17 917 917 HOH HOH . 
G 4 HOH A 18 918 918 HOH HOH . 
G 4 HOH A 19 919 919 HOH HOH . 
G 4 HOH A 20 920 920 HOH HOH . 
G 4 HOH A 21 921 921 HOH HOH . 
G 4 HOH A 22 922 922 HOH HOH . 
G 4 HOH A 23 923 923 HOH HOH . 
G 4 HOH A 24 924 924 HOH HOH . 
G 4 HOH A 25 925 925 HOH HOH . 
G 4 HOH A 26 926 926 HOH HOH . 
G 4 HOH A 27 927 927 HOH HOH . 
G 4 HOH A 28 928 928 HOH HOH . 
G 4 HOH A 29 929 929 HOH HOH . 
G 4 HOH A 30 930 930 HOH HOH . 
G 4 HOH A 31 931 931 HOH HOH . 
G 4 HOH A 32 932 932 HOH HOH . 
G 4 HOH A 33 933 933 HOH HOH . 
G 4 HOH A 34 934 934 HOH HOH . 
G 4 HOH A 35 935 935 HOH HOH . 
G 4 HOH A 36 936 936 HOH HOH . 
G 4 HOH A 37 937 937 HOH HOH . 
G 4 HOH A 38 938 938 HOH HOH . 
G 4 HOH A 39 939 939 HOH HOH . 
G 4 HOH A 40 940 940 HOH HOH . 
G 4 HOH A 41 941 941 HOH HOH . 
G 4 HOH A 42 942 942 HOH HOH . 
G 4 HOH A 43 943 943 HOH HOH . 
G 4 HOH A 44 944 944 HOH HOH . 
G 4 HOH A 45 945 945 HOH HOH . 
G 4 HOH A 46 946 946 HOH HOH . 
G 4 HOH A 47 947 947 HOH HOH . 
G 4 HOH A 48 948 948 HOH HOH . 
G 4 HOH A 49 949 949 HOH HOH . 
G 4 HOH A 50 950 950 HOH HOH . 
G 4 HOH A 51 951 951 HOH HOH . 
G 4 HOH A 52 952 952 HOH HOH . 
G 4 HOH A 53 953 953 HOH HOH . 
G 4 HOH A 54 954 954 HOH HOH . 
G 4 HOH A 55 955 955 HOH HOH . 
G 4 HOH A 56 956 956 HOH HOH . 
G 4 HOH A 57 957 957 HOH HOH . 
G 4 HOH A 58 958 958 HOH HOH . 
G 4 HOH A 59 959 959 HOH HOH . 
G 4 HOH A 60 960 960 HOH HOH . 
G 4 HOH A 61 961 961 HOH HOH . 
G 4 HOH A 62 962 962 HOH HOH . 
G 4 HOH A 63 963 963 HOH HOH . 
G 4 HOH A 64 964 964 HOH HOH . 
G 4 HOH A 65 965 965 HOH HOH . 
G 4 HOH A 66 966 966 HOH HOH . 
G 4 HOH A 67 967 967 HOH HOH . 
G 4 HOH A 68 968 968 HOH HOH . 
G 4 HOH A 69 969 969 HOH HOH . 
G 4 HOH A 70 970 970 HOH HOH . 
G 4 HOH A 71 971 971 HOH HOH . 
G 4 HOH A 72 972 972 HOH HOH . 
G 4 HOH A 73 973 973 HOH HOH . 
G 4 HOH A 74 974 974 HOH HOH . 
G 4 HOH A 75 975 975 HOH HOH . 
G 4 HOH A 76 976 976 HOH HOH . 
G 4 HOH A 77 977 977 HOH HOH . 
G 4 HOH A 78 978 978 HOH HOH . 
G 4 HOH A 79 979 979 HOH HOH . 
G 4 HOH A 80 980 980 HOH HOH . 
G 4 HOH A 81 981 981 HOH HOH . 
G 4 HOH A 82 982 982 HOH HOH . 
G 4 HOH A 83 983 983 HOH HOH . 
G 4 HOH A 84 984 984 HOH HOH . 
G 4 HOH A 85 985 985 HOH HOH . 
G 4 HOH A 86 986 986 HOH HOH . 
G 4 HOH A 87 987 987 HOH HOH . 
G 4 HOH A 88 988 988 HOH HOH . 
G 4 HOH A 89 989 989 HOH HOH . 
G 4 HOH A 90 990 990 HOH HOH . 
G 4 HOH A 91 991 991 HOH HOH . 
G 4 HOH A 92 992 992 HOH HOH . 
G 4 HOH A 93 993 993 HOH HOH . 
G 4 HOH A 94 994 994 HOH HOH . 
G 4 HOH A 95 995 995 HOH HOH . 
G 4 HOH A 96 996 996 HOH HOH . 
G 4 HOH A 97 997 997 HOH HOH . 
G 4 HOH A 98 998 998 HOH HOH . 
G 4 HOH A 99 999 999 HOH HOH . 
G 4 HOH A 100 1000 1000 HOH HOH . 
G 4 HOH A 101 1001 1001 HOH HOH . 
G 4 HOH A 102 1002 1002 HOH HOH . 
G 4 HOH A 103 1003 1003 HOH HOH . 
G 4 HOH A 104 1004 1004 HOH HOH . 
G 4 HOH A 105 1005 1005 HOH HOH . 
G 4 HOH A 106 1006 1006 HOH HOH . 
G 4 HOH A 107 1007 1007 HOH HOH . 
G 4 HOH A 108 1008 1008 HOH HOH . 
G 4 HOH A 109 1009 1009 HOH HOH . 
G 4 HOH A 110 1010 1010 HOH HOH . 
G 4 HOH A 111 1011 1011 HOH HOH . 
G 4 HOH A 112 1012 1012 HOH HOH . 
G 4 HOH A 113 1013 1013 HOH HOH . 
G 4 HOH A 114 1014 1014 HOH HOH . 
G 4 HOH A 115 1015 1015 HOH HOH . 
G 4 HOH A 116 1016 1016 HOH HOH . 
G 4 HOH A 117 1017 1017 HOH HOH . 
G 4 HOH A 118 1018 1018 HOH HOH . 
G 4 HOH A 119 1019 1019 HOH HOH . 
G 4 HOH A 120 1020 1020 HOH HOH . 
G 4 HOH A 121 1021 1021 HOH HOH . 
G 4 HOH A 122 1022 1022 HOH HOH . 
G 4 HOH A 123 1023 1023 HOH HOH . 
G 4 HOH A 124 1024 1024 HOH HOH . 
G 4 HOH A 125 1025 1025 HOH HOH . 
G 4 HOH A 126 1026 1026 HOH HOH . 
G 4 HOH A 127 1027 1027 HOH HOH . 
G 4 HOH A 128 1028 1028 HOH HOH . 
G 4 HOH A 129 1029 1029 HOH HOH . 
G 4 HOH A 130 1030 1030 HOH HOH . 
G 4 HOH A 131 1031 1031 HOH HOH . 
G 4 HOH A 132 1032 1032 HOH HOH . 
G 4 HOH A 133 1033 1033 HOH HOH . 
G 4 HOH A 134 1034 1034 HOH HOH . 
G 4 HOH A 135 1035 1035 HOH HOH . 
G 4 HOH A 136 1036 1036 HOH HOH . 
G 4 HOH A 137 1037 1037 HOH HOH . 
G 4 HOH A 138 1038 1038 HOH HOH . 
G 4 HOH A 139 1039 1039 HOH HOH . 
G 4 HOH A 140 1040 1040 HOH HOH . 
G 4 HOH A 141 1041 1041 HOH HOH . 
G 4 HOH A 142 1042 1042 HOH HOH . 
G 4 HOH A 143 1043 1043 HOH HOH . 
G 4 HOH A 144 1044 1044 HOH HOH . 
G 4 HOH A 145 1045 1045 HOH HOH . 
G 4 HOH A 146 1046 1046 HOH HOH . 
G 4 HOH A 147 1047 1047 HOH HOH . 
G 4 HOH A 148 1048 1048 HOH HOH . 
G 4 HOH A 149 1049 1049 HOH HOH . 
G 4 HOH A 150 1050 1050 HOH HOH . 
G 4 HOH A 151 1051 1051 HOH HOH . 
G 4 HOH A 152 1052 1052 HOH HOH . 
G 4 HOH A 153 1053 1053 HOH HOH . 
G 4 HOH A 154 1054 1054 HOH HOH . 
G 4 HOH A 155 1055 1055 HOH HOH . 
G 4 HOH A 156 1056 1056 HOH HOH . 
G 4 HOH A 157 1057 1057 HOH HOH . 
G 4 HOH A 158 1058 1058 HOH HOH . 
G 4 HOH A 159 1059 1059 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 . . . B 2 47.348 75.902 66.172 1 71.41 ? C1 GOL 801 A 1 
HETATM 2 O O1 GOL . . . B 2 47.231 74.562 65.679 1 72.48 ? O1 GOL 801 A 1 
HETATM 3 C C2 GOL . . . B 2 47.351 75.885 67.699 1 69.41 ? C2 GOL 801 A 1 
HETATM 4 O O2 GOL . . . B 2 46.69 74.707 68.159 1 68.84 ? O2 GOL 801 A 1 
HETATM 5 C C3 GOL . . . B 2 46.633 77.104 68.275 1 70.46 ? C3 GOL 801 A 1 
HETATM 6 O O3 GOL . . . B 2 47.562 77.863 69.052 1 70.55 ? O3 GOL 801 A 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           6 
#