data_3LBI # _model_server_result.job_id Y8fSEa9dOKSJ0soOhs_ACA _model_server_result.datetime_utc '2024-11-02 10:25:35' _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 3lbi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":528}' # _entry.id 3LBI # _exptl.entry_id 3LBI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _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 120 _cell.entry_id 3LBI _cell.length_a 88.716 _cell.length_b 88.716 _cell.length_c 134.583 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LBI _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA trimeric 3 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,B,C,D,E,F,G,H 1 1 A,B,C,D,E,F,G,H 2 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_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 44.358 76.83031 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -44.358 76.83031 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 OG SER 17 A SER 17 1_555 D MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc2 A O PHE 28 A PHE 28 1_555 C CA CA . A CA 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc3 A OD1 ASP 30 A ASP 30 1_555 C CA CA . A CA 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? metalc ? metalc4 A OG1 THR 35 A THR 35 1_555 D MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc5 A O ASP 107 A ASP 107 1_555 E CA CA . A CA 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? metalc ? metalc6 A O TYR 137 A TYR 137 1_555 E CA CA . A CA 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc7 C CA CA . A CA 167 1_555 H O HOH . A HOH 244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? metalc ? metalc8 C CA CA . A CA 167 1_555 H O HOH . A HOH 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? metalc ? metalc9 D MG MG . A MG 168 1_555 H O HOH . A HOH 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc10 D MG MG . A MG 168 1_555 H O HOH . A HOH 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc11 D MG MG . A MG 168 1_555 B O2G GNP . A GNP 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc12 D MG MG . A MG 168 1_555 B O2B GNP . A GNP 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc13 E CA CA . A CA 169 1_555 H O HOH . A HOH 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? metalc ? metalc14 E CA CA . A CA 169 1_555 H O HOH . A HOH 293 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc15 E CA CA . A CA 169 1_555 G O ACT . A ACT 719 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? metalc ? metalc16 E CA CA . A CA 169 1_555 G OXT ACT . A ACT 719 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? metalc ? metalc17 F MG MG . A MG 170 1_555 H O HOH . A HOH 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc18 F MG MG . A MG 170 1_555 H O HOH . A HOH 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? # _chem_comp.formula 'C10 H17 N6 O13 P3' _chem_comp.formula_weight 522.196 _chem_comp.id GNP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 PG O1G GNP doub 135 n n PG O2G GNP sing 136 n n PG O3G GNP sing 137 n n PG N3B GNP sing 138 n n O2G HOG2 GNP sing 139 n n O3G HOG3 GNP sing 140 n n N3B PB GNP sing 141 n n N3B HNB3 GNP sing 142 n n PB O1B GNP doub 143 n n PB O2B GNP sing 144 n n PB O3A GNP sing 145 n n O2B HOB2 GNP sing 146 n n O3A PA GNP sing 147 n n PA O1A GNP doub 148 n n PA O2A GNP sing 149 n n PA O5' GNP sing 150 n n O2A HOA2 GNP sing 151 n n O5' C5' GNP sing 152 n n C5' C4' GNP sing 153 n n C5' "H5'2" GNP sing 154 n n C5' "H5'1" GNP sing 155 n n C4' O4' GNP sing 156 n n C4' C3' GNP sing 157 n n C4' H4' GNP sing 158 n n O4' C1' GNP sing 159 n n C3' O3' GNP sing 160 n n C3' C2' GNP sing 161 n n C3' H3' GNP sing 162 n n O3' HO3' GNP sing 163 n n C2' O2' GNP sing 164 n n C2' C1' GNP sing 165 n n C2' H2' GNP sing 166 n n O2' HO2' GNP sing 167 n n C1' N9 GNP sing 168 n n C1' H1' GNP sing 169 n n N9 C8 GNP sing 170 n y N9 C4 GNP sing 171 n y C8 N7 GNP doub 172 n y C8 H8 GNP sing 173 n n N7 C5 GNP sing 174 n y C5 C6 GNP sing 175 n y C5 C4 GNP doub 176 n y C6 O6 GNP doub 177 n n C6 N1 GNP sing 178 n y N1 C2 GNP sing 179 n y N1 HN1 GNP sing 180 n n C2 N2 GNP sing 181 n n C2 N3 GNP doub 182 n y N2 HN21 GNP sing 183 n n N2 HN22 GNP sing 184 n n N3 C4 GNP sing 185 n y # _atom_sites.entry_id 3LBI _atom_sites.fract_transf_matrix[1][1] 0.011272 _atom_sites.fract_transf_matrix[1][2] 0.006508 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013016 _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] 0.00743 _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 GNP A 1 528 528 GNP GNP . C 3 CA A 1 167 1 CA CA . D 4 MG A 1 168 2 MG MG . E 3 CA A 1 169 3 CA CA . F 4 MG A 1 170 4 MG MG . G 5 ACT A 1 719 719 ACT ACT . H 6 HOH A 1 200 50 HOH HOH . H 6 HOH A 2 201 1 HOH HOH . H 6 HOH A 3 202 2 HOH HOH . H 6 HOH A 4 203 3 HOH HOH . H 6 HOH A 5 204 4 HOH HOH . H 6 HOH A 6 205 5 HOH HOH . H 6 HOH A 7 206 6 HOH HOH . H 6 HOH A 8 207 7 HOH HOH . H 6 HOH A 9 208 8 HOH HOH . H 6 HOH A 10 209 9 HOH HOH . H 6 HOH A 11 210 10 HOH HOH . H 6 HOH A 12 211 11 HOH HOH . H 6 HOH A 13 212 12 HOH HOH . H 6 HOH A 14 213 14 HOH HOH . H 6 HOH A 15 214 15 HOH HOH . H 6 HOH A 16 215 16 HOH HOH . H 6 HOH A 17 216 816 HOH HOH . H 6 HOH A 18 217 17 HOH HOH . H 6 HOH A 19 218 18 HOH HOH . H 6 HOH A 20 219 19 HOH HOH . H 6 HOH A 21 220 20 HOH HOH . H 6 HOH A 22 221 21 HOH HOH . H 6 HOH A 23 222 22 HOH HOH . H 6 HOH A 24 223 23 HOH HOH . H 6 HOH A 25 224 25 HOH HOH . H 6 HOH A 26 225 26 HOH HOH . H 6 HOH A 27 226 29 HOH HOH . H 6 HOH A 28 227 30 HOH HOH . H 6 HOH A 29 228 31 HOH HOH . H 6 HOH A 30 229 32 HOH HOH . H 6 HOH A 31 230 33 HOH HOH . H 6 HOH A 32 231 34 HOH HOH . H 6 HOH A 33 232 36 HOH HOH . H 6 HOH A 34 233 836 HOH HOH . H 6 HOH A 35 234 38 HOH HOH . H 6 HOH A 36 235 39 HOH HOH . H 6 HOH A 37 236 40 HOH HOH . H 6 HOH A 38 237 42 HOH HOH . H 6 HOH A 39 238 43 HOH HOH . H 6 HOH A 40 239 44 HOH HOH . H 6 HOH A 41 240 45 HOH HOH . H 6 HOH A 42 241 47 HOH HOH . H 6 HOH A 43 242 48 HOH HOH . H 6 HOH A 44 243 49 HOH HOH . H 6 HOH A 45 244 51 HOH HOH . H 6 HOH A 46 245 52 HOH HOH . H 6 HOH A 47 246 54 HOH HOH . H 6 HOH A 48 247 57 HOH HOH . H 6 HOH A 49 248 58 HOH HOH . H 6 HOH A 50 249 59 HOH HOH . H 6 HOH A 51 250 60 HOH HOH . H 6 HOH A 52 251 63 HOH HOH . H 6 HOH A 53 252 65 HOH HOH . H 6 HOH A 54 253 66 HOH HOH . H 6 HOH A 55 254 69 HOH HOH . H 6 HOH A 56 255 72 HOH HOH . H 6 HOH A 57 256 73 HOH HOH . H 6 HOH A 58 257 74 HOH HOH . H 6 HOH A 59 258 76 HOH HOH . H 6 HOH A 60 259 77 HOH HOH . H 6 HOH A 61 260 78 HOH HOH . H 6 HOH A 62 261 79 HOH HOH . H 6 HOH A 63 262 82 HOH HOH . H 6 HOH A 64 263 84 HOH HOH . H 6 HOH A 65 264 86 HOH HOH . H 6 HOH A 66 265 89 HOH HOH . H 6 HOH A 67 266 96 HOH HOH . H 6 HOH A 68 267 97 HOH HOH . H 6 HOH A 69 268 100 HOH HOH . H 6 HOH A 70 269 111 HOH HOH . H 6 HOH A 71 270 115 HOH HOH . H 6 HOH A 72 271 120 HOH HOH . H 6 HOH A 73 272 122 HOH HOH . H 6 HOH A 74 273 126 HOH HOH . H 6 HOH A 75 274 128 HOH HOH . H 6 HOH A 76 275 129 HOH HOH . H 6 HOH A 77 276 140 HOH HOH . H 6 HOH A 78 277 143 HOH HOH . H 6 HOH A 79 278 152 HOH HOH . H 6 HOH A 80 279 156 HOH HOH . H 6 HOH A 81 280 158 HOH HOH . H 6 HOH A 82 281 160 HOH HOH . H 6 HOH A 83 282 162 HOH HOH . H 6 HOH A 84 283 175 HOH HOH . H 6 HOH A 85 284 176 HOH HOH . H 6 HOH A 86 285 183 HOH HOH . H 6 HOH A 87 286 188 HOH HOH . H 6 HOH A 88 287 189 HOH HOH . H 6 HOH A 89 288 197 HOH HOH . H 6 HOH A 90 289 225 HOH HOH . H 6 HOH A 91 290 226 HOH HOH . H 6 HOH A 92 291 230 HOH HOH . H 6 HOH A 93 292 254 HOH HOH . H 6 HOH A 94 293 366 HOH HOH . H 6 HOH A 95 294 367 HOH HOH . H 6 HOH A 96 295 372 HOH HOH . H 6 HOH A 97 296 373 HOH HOH . H 6 HOH A 98 297 376 HOH HOH . H 6 HOH A 99 298 384 HOH HOH . H 6 HOH A 100 299 385 HOH HOH . H 6 HOH A 101 300 394 HOH HOH . H 6 HOH A 102 301 1024 HOH HOH . H 6 HOH A 103 302 1025 HOH HOH . H 6 HOH A 104 303 1026 HOH HOH . H 6 HOH A 105 304 1027 HOH HOH . H 6 HOH A 106 305 1028 HOH HOH . H 6 HOH A 107 306 1029 HOH HOH . H 6 HOH A 108 307 1030 HOH HOH . H 6 HOH A 109 308 1031 HOH HOH . H 6 HOH A 110 309 1032 HOH HOH . H 6 HOH A 111 310 1033 HOH HOH . H 6 HOH A 112 311 1034 HOH HOH . H 6 HOH A 113 312 1035 HOH HOH . H 6 HOH A 114 313 1036 HOH HOH . H 6 HOH A 115 314 1037 HOH HOH . H 6 HOH A 116 315 1038 HOH HOH . H 6 HOH A 117 316 1039 HOH HOH . H 6 HOH A 118 317 1040 HOH HOH . H 6 HOH A 119 318 1041 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 P PG GNP . . . B 2 -9.594 64.679 -67.354 1 26.71 ? PG GNP 528 A 1 HETATM 2 O O1G GNP . . . B 2 -8.705 64.206 -66.221 1 25.7 ? O1G GNP 528 A 1 HETATM 3 O O2G GNP . . . B 2 -10.585 65.684 -66.863 1 23.38 ? O2G GNP 528 A 1 HETATM 4 O O3G GNP . . . B 2 -10.245 63.434 -67.905 1 25.07 ? O3G GNP 528 A 1 HETATM 5 N N3B GNP . . . B 2 -8.703 65.333 -68.547 1 27.4 ? N3B GNP 528 A 1 HETATM 6 P PB GNP . . . B 2 -9.157 65.891 -69.998 1 21.4 ? PB GNP 528 A 1 HETATM 7 O O1B GNP . . . B 2 -9.549 64.794 -70.905 1 24.85 ? O1B GNP 528 A 1 HETATM 8 O O2B GNP . . . B 2 -10.178 66.946 -69.853 1 18.98 ? O2B GNP 528 A 1 HETATM 9 O O3A GNP . . . B 2 -7.948 66.576 -70.643 1 23.53 ? O3A GNP 528 A 1 HETATM 10 P PA GNP . . . B 2 -7.619 68.092 -70.6 1 22.34 ? PA GNP 528 A 1 HETATM 11 O O1A GNP . . . B 2 -8.576 68.847 -71.444 1 22.38 ? O1A GNP 528 A 1 HETATM 12 O O2A GNP . . . B 2 -7.424 68.595 -69.22 1 19.82 ? O2A GNP 528 A 1 HETATM 13 O O5' GNP . . . B 2 -6.231 68.243 -71.325 1 22.57 ? O5' GNP 528 A 1 HETATM 14 C C5' GNP . . . B 2 -5.066 67.562 -70.806 1 24.44 ? C5' GNP 528 A 1 HETATM 15 C C4' GNP . . . B 2 -3.803 68.184 -71.365 1 21.57 ? C4' GNP 528 A 1 HETATM 16 O O4' GNP . . . B 2 -3.761 67.963 -72.8 1 24.75 ? O4' GNP 528 A 1 HETATM 17 C C3' GNP . . . B 2 -3.7 69.696 -71.16 1 23.44 ? C3' GNP 528 A 1 HETATM 18 O O3' GNP . . . B 2 -2.366 70.065 -70.836 1 22.07 ? O3' GNP 528 A 1 HETATM 19 C C2' GNP . . . B 2 -4.106 70.269 -72.519 1 22.41 ? C2' GNP 528 A 1 HETATM 20 O O2' GNP . . . B 2 -3.513 71.527 -72.773 1 20.08 ? O2' GNP 528 A 1 HETATM 21 C C1' GNP . . . B 2 -3.583 69.196 -73.474 1 21.31 ? C1' GNP 528 A 1 HETATM 22 N N9 GNP . . . B 2 -4.392 69.177 -74.68 1 22.62 ? N9 GNP 528 A 1 HETATM 23 C C8 GNP . . . B 2 -5.755 69.005 -74.741 1 20.44 ? C8 GNP 528 A 1 HETATM 24 N N7 GNP . . . B 2 -6.215 69.058 -75.955 1 23.46 ? N7 GNP 528 A 1 HETATM 25 C C5 GNP . . . B 2 -5.101 69.286 -76.748 1 19.8 ? C5 GNP 528 A 1 HETATM 26 C C6 GNP . . . B 2 -4.991 69.438 -78.151 1 22.32 ? C6 GNP 528 A 1 HETATM 27 O O6 GNP . . . B 2 -5.897 69.39 -78.995 1 23.44 ? O6 GNP 528 A 1 HETATM 28 N N1 GNP . . . B 2 -3.674 69.658 -78.553 1 22.21 ? N1 GNP 528 A 1 HETATM 29 C C2 GNP . . . B 2 -2.608 69.726 -77.683 1 24.89 ? C2 GNP 528 A 1 HETATM 30 N N2 GNP . . . B 2 -1.398 69.946 -78.208 1 27.24 ? N2 GNP 528 A 1 HETATM 31 N N3 GNP . . . B 2 -2.702 69.584 -76.37 1 24.06 ? N3 GNP 528 A 1 HETATM 32 C C4 GNP . . . B 2 -3.972 69.358 -75.977 1 21.19 ? C4 GNP 528 A 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #