data_3BGJ
#
_model_server_result.job_id            gZppE2_mIY49pdu5Rd9CCQ 
_model_server_result.datetime_utc      '2024-10-14 08:24:04' 
_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          3bgj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":1000}' 
#
_entry.id    3BGJ 
#
_exptl.entry_id    3BGJ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          3 
_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          111.66 
_cell.angle_gamma         90 
_cell.entry_id            3BGJ 
_cell.length_a            69.803 
_cell.length_b            61.821 
_cell.length_c            70.881 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3BGJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
#
_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                      3 
_struct_asym.id                             E 
_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
covale ? covale1 A NZ LYS 125 A LYS 125 1_555 C C6 U5P . A U5P 3000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.298 ? 
covale ? covale2 B NZ LYS 125 B LYS 125 1_555 D C6 U5P . B U5P 3000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? 
#
_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 129 n n 
C1 C2 GOL sing 130 n n 
C1 H11 GOL sing 131 n n 
C1 H12 GOL sing 132 n n 
O1 HO1 GOL sing 133 n n 
C2 O2 GOL sing 134 n n 
C2 C3 GOL sing 135 n n 
C2 H2 GOL sing 136 n n 
O2 HO2 GOL sing 137 n n 
C3 O3 GOL sing 138 n n 
C3 H31 GOL sing 139 n n 
C3 H32 GOL sing 140 n n 
O3 HO3 GOL sing 141 n n 
#
_atom_sites.entry_id                     3BGJ 
_atom_sites.fract_transf_matrix[1][1]    0.014326 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00569 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016176 
_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]    0.01518 
_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
C 2 U5P A 1 3000 3000 U5P U5P . 
D 2 U5P B 1 3000 3000 U5P U5P . 
E 3 GOL B 1 1000 1000 GOL GOL . 
F 4 HOH A 1 3001 2 HOH HOH . 
F 4 HOH A 2 3002 4 HOH HOH . 
F 4 HOH A 3 3003 8 HOH HOH . 
F 4 HOH A 4 3004 9 HOH HOH . 
F 4 HOH A 5 3005 10 HOH HOH . 
F 4 HOH A 6 3006 16 HOH HOH . 
F 4 HOH A 7 3007 19 HOH HOH . 
F 4 HOH A 8 3008 20 HOH HOH . 
F 4 HOH A 9 3009 21 HOH HOH . 
F 4 HOH A 10 3010 22 HOH HOH . 
F 4 HOH A 11 3011 27 HOH HOH . 
F 4 HOH A 12 3012 28 HOH HOH . 
F 4 HOH A 13 3013 30 HOH HOH . 
F 4 HOH A 14 3014 31 HOH HOH . 
F 4 HOH A 15 3015 33 HOH HOH . 
F 4 HOH A 16 3016 34 HOH HOH . 
F 4 HOH A 17 3017 35 HOH HOH . 
F 4 HOH A 18 3018 37 HOH HOH . 
F 4 HOH A 19 3019 38 HOH HOH . 
F 4 HOH A 20 3020 40 HOH HOH . 
F 4 HOH A 21 3021 41 HOH HOH . 
F 4 HOH A 22 3022 42 HOH HOH . 
F 4 HOH A 23 3023 43 HOH HOH . 
F 4 HOH A 24 3024 46 HOH HOH . 
F 4 HOH A 25 3025 49 HOH HOH . 
F 4 HOH A 26 3026 50 HOH HOH . 
F 4 HOH A 27 3027 52 HOH HOH . 
F 4 HOH A 28 3028 53 HOH HOH . 
F 4 HOH A 29 3029 54 HOH HOH . 
F 4 HOH A 30 3030 56 HOH HOH . 
F 4 HOH A 31 3031 57 HOH HOH . 
F 4 HOH A 32 3032 58 HOH HOH . 
F 4 HOH A 33 3033 60 HOH HOH . 
F 4 HOH A 34 3034 61 HOH HOH . 
F 4 HOH A 35 3035 63 HOH HOH . 
F 4 HOH A 36 3036 68 HOH HOH . 
F 4 HOH A 37 3037 69 HOH HOH . 
F 4 HOH A 38 3038 71 HOH HOH . 
F 4 HOH A 39 3039 73 HOH HOH . 
F 4 HOH A 40 3040 74 HOH HOH . 
F 4 HOH A 41 3041 77 HOH HOH . 
F 4 HOH A 42 3042 80 HOH HOH . 
F 4 HOH A 43 3043 81 HOH HOH . 
F 4 HOH A 44 3044 85 HOH HOH . 
F 4 HOH A 45 3045 86 HOH HOH . 
F 4 HOH A 46 3046 88 HOH HOH . 
F 4 HOH A 47 3047 89 HOH HOH . 
F 4 HOH A 48 3048 90 HOH HOH . 
F 4 HOH A 49 3049 91 HOH HOH . 
F 4 HOH A 50 3050 92 HOH HOH . 
F 4 HOH A 51 3051 93 HOH HOH . 
F 4 HOH A 52 3052 95 HOH HOH . 
F 4 HOH A 53 3053 101 HOH HOH . 
F 4 HOH A 54 3054 103 HOH HOH . 
F 4 HOH A 55 3055 105 HOH HOH . 
F 4 HOH A 56 3056 106 HOH HOH . 
F 4 HOH A 57 3057 107 HOH HOH . 
F 4 HOH A 58 3058 110 HOH HOH . 
F 4 HOH A 59 3059 112 HOH HOH . 
F 4 HOH A 60 3060 113 HOH HOH . 
F 4 HOH A 61 3061 116 HOH HOH . 
F 4 HOH A 62 3062 117 HOH HOH . 
F 4 HOH A 63 3063 118 HOH HOH . 
F 4 HOH A 64 3064 123 HOH HOH . 
F 4 HOH A 65 3065 128 HOH HOH . 
F 4 HOH A 66 3066 129 HOH HOH . 
F 4 HOH A 67 3067 130 HOH HOH . 
F 4 HOH A 68 3068 132 HOH HOH . 
F 4 HOH A 69 3069 136 HOH HOH . 
F 4 HOH A 70 3070 139 HOH HOH . 
F 4 HOH A 71 3071 142 HOH HOH . 
F 4 HOH A 72 3072 143 HOH HOH . 
F 4 HOH A 73 3073 146 HOH HOH . 
F 4 HOH A 74 3074 148 HOH HOH . 
F 4 HOH A 75 3075 153 HOH HOH . 
F 4 HOH A 76 3076 156 HOH HOH . 
F 4 HOH A 77 3077 157 HOH HOH . 
F 4 HOH A 78 3078 160 HOH HOH . 
F 4 HOH A 79 3079 161 HOH HOH . 
F 4 HOH A 80 3080 162 HOH HOH . 
F 4 HOH A 81 3081 163 HOH HOH . 
F 4 HOH A 82 3082 167 HOH HOH . 
F 4 HOH A 83 3083 168 HOH HOH . 
F 4 HOH A 84 3084 170 HOH HOH . 
F 4 HOH A 85 3085 178 HOH HOH . 
F 4 HOH A 86 3086 179 HOH HOH . 
F 4 HOH A 87 3087 180 HOH HOH . 
F 4 HOH A 88 3088 181 HOH HOH . 
F 4 HOH A 89 3089 182 HOH HOH . 
F 4 HOH A 90 3090 183 HOH HOH . 
F 4 HOH A 91 3091 186 HOH HOH . 
F 4 HOH A 92 3092 188 HOH HOH . 
F 4 HOH A 93 3093 190 HOH HOH . 
F 4 HOH A 94 3094 192 HOH HOH . 
F 4 HOH A 95 3095 194 HOH HOH . 
F 4 HOH A 96 3096 195 HOH HOH . 
F 4 HOH A 97 3097 196 HOH HOH . 
F 4 HOH A 98 3098 199 HOH HOH . 
F 4 HOH A 99 3099 201 HOH HOH . 
F 4 HOH A 100 3100 203 HOH HOH . 
F 4 HOH A 101 3101 210 HOH HOH . 
F 4 HOH A 102 3102 211 HOH HOH . 
F 4 HOH A 103 3103 213 HOH HOH . 
F 4 HOH A 104 3104 217 HOH HOH . 
F 4 HOH A 105 3105 218 HOH HOH . 
F 4 HOH A 106 3106 220 HOH HOH . 
F 4 HOH A 107 3107 221 HOH HOH . 
F 4 HOH A 108 3108 222 HOH HOH . 
F 4 HOH A 109 3109 224 HOH HOH . 
F 4 HOH A 110 3110 227 HOH HOH . 
F 4 HOH A 111 3111 229 HOH HOH . 
F 4 HOH A 112 3112 230 HOH HOH . 
F 4 HOH A 113 3113 232 HOH HOH . 
F 4 HOH A 114 3114 235 HOH HOH . 
F 4 HOH A 115 3115 236 HOH HOH . 
F 4 HOH A 116 3116 238 HOH HOH . 
F 4 HOH A 117 3117 239 HOH HOH . 
G 4 HOH B 1 3001 1 HOH HOH . 
G 4 HOH B 2 3002 3 HOH HOH . 
G 4 HOH B 3 3003 5 HOH HOH . 
G 4 HOH B 4 3004 6 HOH HOH . 
G 4 HOH B 5 3005 7 HOH HOH . 
G 4 HOH B 6 3006 11 HOH HOH . 
G 4 HOH B 7 3007 12 HOH HOH . 
G 4 HOH B 8 3008 13 HOH HOH . 
G 4 HOH B 9 3009 14 HOH HOH . 
G 4 HOH B 10 3010 15 HOH HOH . 
G 4 HOH B 11 3011 17 HOH HOH . 
G 4 HOH B 12 3012 18 HOH HOH . 
G 4 HOH B 13 3013 23 HOH HOH . 
G 4 HOH B 14 3014 24 HOH HOH . 
G 4 HOH B 15 3015 25 HOH HOH . 
G 4 HOH B 16 3016 26 HOH HOH . 
G 4 HOH B 17 3017 29 HOH HOH . 
G 4 HOH B 18 3018 32 HOH HOH . 
G 4 HOH B 19 3019 36 HOH HOH . 
G 4 HOH B 20 3020 39 HOH HOH . 
G 4 HOH B 21 3021 44 HOH HOH . 
G 4 HOH B 22 3022 47 HOH HOH . 
G 4 HOH B 23 3023 48 HOH HOH . 
G 4 HOH B 24 3024 55 HOH HOH . 
G 4 HOH B 25 3025 59 HOH HOH . 
G 4 HOH B 26 3026 62 HOH HOH . 
G 4 HOH B 27 3027 64 HOH HOH . 
G 4 HOH B 28 3028 65 HOH HOH . 
G 4 HOH B 29 3029 66 HOH HOH . 
G 4 HOH B 30 3030 67 HOH HOH . 
G 4 HOH B 31 3031 70 HOH HOH . 
G 4 HOH B 32 3032 72 HOH HOH . 
G 4 HOH B 33 3033 75 HOH HOH . 
G 4 HOH B 34 3034 76 HOH HOH . 
G 4 HOH B 35 3035 78 HOH HOH . 
G 4 HOH B 36 3036 79 HOH HOH . 
G 4 HOH B 37 3037 82 HOH HOH . 
G 4 HOH B 38 3038 83 HOH HOH . 
G 4 HOH B 39 3039 84 HOH HOH . 
G 4 HOH B 40 3040 87 HOH HOH . 
G 4 HOH B 41 3041 94 HOH HOH . 
G 4 HOH B 42 3042 96 HOH HOH . 
G 4 HOH B 43 3043 97 HOH HOH . 
G 4 HOH B 44 3044 98 HOH HOH . 
G 4 HOH B 45 3045 99 HOH HOH . 
G 4 HOH B 46 3046 100 HOH HOH . 
G 4 HOH B 47 3047 102 HOH HOH . 
G 4 HOH B 48 3048 104 HOH HOH . 
G 4 HOH B 49 3049 108 HOH HOH . 
G 4 HOH B 50 3050 109 HOH HOH . 
G 4 HOH B 51 3051 111 HOH HOH . 
G 4 HOH B 52 3052 114 HOH HOH . 
G 4 HOH B 53 3053 115 HOH HOH . 
G 4 HOH B 54 3054 119 HOH HOH . 
G 4 HOH B 55 3055 120 HOH HOH . 
G 4 HOH B 56 3056 121 HOH HOH . 
G 4 HOH B 57 3057 122 HOH HOH . 
G 4 HOH B 58 3058 124 HOH HOH . 
G 4 HOH B 59 3059 125 HOH HOH . 
G 4 HOH B 60 3060 126 HOH HOH . 
G 4 HOH B 61 3061 127 HOH HOH . 
G 4 HOH B 62 3062 131 HOH HOH . 
G 4 HOH B 63 3063 133 HOH HOH . 
G 4 HOH B 64 3064 134 HOH HOH . 
G 4 HOH B 65 3065 135 HOH HOH . 
G 4 HOH B 66 3066 137 HOH HOH . 
G 4 HOH B 67 3067 138 HOH HOH . 
G 4 HOH B 68 3068 140 HOH HOH . 
G 4 HOH B 69 3069 141 HOH HOH . 
G 4 HOH B 70 3070 144 HOH HOH . 
G 4 HOH B 71 3071 145 HOH HOH . 
G 4 HOH B 72 3072 147 HOH HOH . 
G 4 HOH B 73 3073 149 HOH HOH . 
G 4 HOH B 74 3074 151 HOH HOH . 
G 4 HOH B 75 3075 152 HOH HOH . 
G 4 HOH B 76 3076 154 HOH HOH . 
G 4 HOH B 77 3077 155 HOH HOH . 
G 4 HOH B 78 3078 158 HOH HOH . 
G 4 HOH B 79 3079 159 HOH HOH . 
G 4 HOH B 80 3080 164 HOH HOH . 
G 4 HOH B 81 3081 165 HOH HOH . 
G 4 HOH B 82 3082 169 HOH HOH . 
G 4 HOH B 83 3083 171 HOH HOH . 
G 4 HOH B 84 3084 172 HOH HOH . 
G 4 HOH B 85 3085 173 HOH HOH . 
G 4 HOH B 86 3086 174 HOH HOH . 
G 4 HOH B 87 3087 175 HOH HOH . 
G 4 HOH B 88 3088 176 HOH HOH . 
G 4 HOH B 89 3089 177 HOH HOH . 
G 4 HOH B 90 3090 184 HOH HOH . 
G 4 HOH B 91 3091 185 HOH HOH . 
G 4 HOH B 92 3092 187 HOH HOH . 
G 4 HOH B 93 3093 189 HOH HOH . 
G 4 HOH B 94 3094 191 HOH HOH . 
G 4 HOH B 95 3095 193 HOH HOH . 
G 4 HOH B 96 3096 197 HOH HOH . 
G 4 HOH B 97 3097 198 HOH HOH . 
G 4 HOH B 98 3098 200 HOH HOH . 
G 4 HOH B 99 3099 202 HOH HOH . 
G 4 HOH B 100 3100 204 HOH HOH . 
G 4 HOH B 101 3101 206 HOH HOH . 
G 4 HOH B 102 3102 207 HOH HOH . 
G 4 HOH B 103 3103 208 HOH HOH . 
G 4 HOH B 104 3104 209 HOH HOH . 
G 4 HOH B 105 3105 212 HOH HOH . 
G 4 HOH B 106 3106 214 HOH HOH . 
G 4 HOH B 107 3107 223 HOH HOH . 
G 4 HOH B 108 3108 225 HOH HOH . 
G 4 HOH B 109 3109 226 HOH HOH . 
G 4 HOH B 110 3110 228 HOH HOH . 
G 4 HOH B 111 3111 233 HOH HOH . 
G 4 HOH B 112 3112 240 HOH HOH . 
G 4 HOH B 113 3113 241 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 . . . E 3 -6.02 -15.097 32.783 1 59.21 ? C1 GOL 1000 B 1 
HETATM 2 O O1 GOL . . . E 3 -6.889 -14.133 32.195 1 58.29 ? O1 GOL 1000 B 1 
HETATM 3 C C2 GOL . . . E 3 -6.534 -16.527 32.588 1 59.46 ? C2 GOL 1000 B 1 
HETATM 4 O O2 GOL . . . E 3 -6.162 -17.304 33.708 1 59.82 ? O2 GOL 1000 B 1 
HETATM 5 C C3 GOL . . . E 3 -5.887 -17.192 31.373 1 59.73 ? C3 GOL 1000 B 1 
HETATM 6 O O3 GOL . . . E 3 -6.883 -17.586 30.45 1 59.81 ? O3 GOL 1000 B 1 
#
_model_server_stats.io_time_ms              52 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           314 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           6 
#