data_3LBN # _model_server_result.job_id jCWKhb8VZ344m1EhIAyf5w _model_server_result.datetime_utc '2024-10-18 16:22:47' _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 3lbn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":528}' # _entry.id 3LBN # _exptl.entry_id 3LBN _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 3LBN _cell.length_a 88.502 _cell.length_b 88.502 _cell.length_c 135.005 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LBN _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 1 1 A,B,C,D,E,F,G 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 44.251 76.64498 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 -44.251 76.64498 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc2 A O PHE 28 A PHE 28 1_555 C CA CA . A CA 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? metalc ? metalc3 A OD1 ASP 30 A ASP 30 1_555 C CA CA . A CA 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc4 A OG1 THR 35 A THR 35 1_555 D MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc5 C CA CA . A CA 167 1_555 G O HOH . A HOH 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc6 C CA CA . A CA 167 1_555 G O HOH . A HOH 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc7 D MG MG . A MG 168 1_555 G O HOH . A HOH 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc8 D MG MG . A MG 168 1_555 G O HOH . A HOH 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc9 D MG MG . A MG 168 1_555 B O2B GNP . A GNP 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc10 D MG MG . A MG 168 1_555 B O2G GNP . A GNP 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc11 E MG MG . A MG 169 1_555 G O HOH . A HOH 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc12 E MG MG . A MG 169 1_555 G O HOH . A HOH 259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc13 F MG MG . A MG 170 1_555 G O HOH . A HOH 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc14 F MG MG . A MG 170 1_555 G O HOH . A HOH 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc15 F MG MG . A MG 170 1_555 G O HOH . A HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? # _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 129 n n PG O2G GNP sing 130 n n PG O3G GNP sing 131 n n PG N3B GNP sing 132 n n O2G HOG2 GNP sing 133 n n O3G HOG3 GNP sing 134 n n N3B PB GNP sing 135 n n N3B HNB3 GNP sing 136 n n PB O1B GNP doub 137 n n PB O2B GNP sing 138 n n PB O3A GNP sing 139 n n O2B HOB2 GNP sing 140 n n O3A PA GNP sing 141 n n PA O1A GNP doub 142 n n PA O2A GNP sing 143 n n PA O5' GNP sing 144 n n O2A HOA2 GNP sing 145 n n O5' C5' GNP sing 146 n n C5' C4' GNP sing 147 n n C5' "H5'2" GNP sing 148 n n C5' "H5'1" GNP sing 149 n n C4' O4' GNP sing 150 n n C4' C3' GNP sing 151 n n C4' H4' GNP sing 152 n n O4' C1' GNP sing 153 n n C3' O3' GNP sing 154 n n C3' C2' GNP sing 155 n n C3' H3' GNP sing 156 n n O3' HO3' GNP sing 157 n n C2' O2' GNP sing 158 n n C2' C1' GNP sing 159 n n C2' H2' GNP sing 160 n n O2' HO2' GNP sing 161 n n C1' N9 GNP sing 162 n n C1' H1' GNP sing 163 n n N9 C8 GNP sing 164 n y N9 C4 GNP sing 165 n y C8 N7 GNP doub 166 n y C8 H8 GNP sing 167 n n N7 C5 GNP sing 168 n y C5 C6 GNP sing 169 n y C5 C4 GNP doub 170 n y C6 O6 GNP doub 171 n n C6 N1 GNP sing 172 n y N1 C2 GNP sing 173 n y N1 HN1 GNP sing 174 n n C2 N2 GNP sing 175 n n C2 N3 GNP doub 176 n y N2 HN21 GNP sing 177 n n N2 HN22 GNP sing 178 n n N3 C4 GNP sing 179 n y # _atom_sites.entry_id 3LBN _atom_sites.fract_transf_matrix[1][1] 0.011299 _atom_sites.fract_transf_matrix[1][2] 0.006524 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013047 _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] 0.007407 _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 4 MG A 1 169 4 MG MG . F 4 MG A 1 170 3 MG MG . G 5 HOH A 1 200 50 HOH HOH . G 5 HOH A 2 201 1 HOH HOH . G 5 HOH A 3 202 2 HOH HOH . G 5 HOH A 4 203 3 HOH HOH . G 5 HOH A 5 204 4 HOH HOH . G 5 HOH A 6 205 5 HOH HOH . G 5 HOH A 7 206 6 HOH HOH . G 5 HOH A 8 207 7 HOH HOH . G 5 HOH A 9 208 8 HOH HOH . G 5 HOH A 10 209 9 HOH HOH . G 5 HOH A 11 210 10 HOH HOH . G 5 HOH A 12 211 11 HOH HOH . G 5 HOH A 13 212 12 HOH HOH . G 5 HOH A 14 213 14 HOH HOH . G 5 HOH A 15 214 15 HOH HOH . G 5 HOH A 16 215 16 HOH HOH . G 5 HOH A 17 216 17 HOH HOH . G 5 HOH A 18 217 18 HOH HOH . G 5 HOH A 19 218 19 HOH HOH . G 5 HOH A 20 219 20 HOH HOH . G 5 HOH A 21 220 21 HOH HOH . G 5 HOH A 22 221 22 HOH HOH . G 5 HOH A 23 222 23 HOH HOH . G 5 HOH A 24 223 24 HOH HOH . G 5 HOH A 25 224 25 HOH HOH . G 5 HOH A 26 225 26 HOH HOH . G 5 HOH A 27 226 27 HOH HOH . G 5 HOH A 28 227 28 HOH HOH . G 5 HOH A 29 228 29 HOH HOH . G 5 HOH A 30 229 30 HOH HOH . G 5 HOH A 31 230 31 HOH HOH . G 5 HOH A 32 231 32 HOH HOH . G 5 HOH A 33 232 33 HOH HOH . G 5 HOH A 34 233 34 HOH HOH . G 5 HOH A 35 234 35 HOH HOH . G 5 HOH A 36 235 36 HOH HOH . G 5 HOH A 37 236 37 HOH HOH . G 5 HOH A 38 237 38 HOH HOH . G 5 HOH A 39 238 39 HOH HOH . G 5 HOH A 40 239 839 HOH HOH . G 5 HOH A 41 240 40 HOH HOH . G 5 HOH A 42 241 42 HOH HOH . G 5 HOH A 43 242 43 HOH HOH . G 5 HOH A 44 243 44 HOH HOH . G 5 HOH A 45 244 45 HOH HOH . G 5 HOH A 46 245 47 HOH HOH . G 5 HOH A 47 246 48 HOH HOH . G 5 HOH A 48 247 49 HOH HOH . G 5 HOH A 49 248 51 HOH HOH . G 5 HOH A 50 249 52 HOH HOH . G 5 HOH A 51 250 852 HOH HOH . G 5 HOH A 52 251 53 HOH HOH . G 5 HOH A 53 252 54 HOH HOH . G 5 HOH A 54 253 57 HOH HOH . G 5 HOH A 55 254 58 HOH HOH . G 5 HOH A 56 255 59 HOH HOH . G 5 HOH A 57 256 60 HOH HOH . G 5 HOH A 58 257 63 HOH HOH . G 5 HOH A 59 258 65 HOH HOH . G 5 HOH A 60 259 66 HOH HOH . G 5 HOH A 61 260 69 HOH HOH . G 5 HOH A 62 261 71 HOH HOH . G 5 HOH A 63 262 72 HOH HOH . G 5 HOH A 64 263 73 HOH HOH . G 5 HOH A 65 264 76 HOH HOH . G 5 HOH A 66 265 77 HOH HOH . G 5 HOH A 67 266 78 HOH HOH . G 5 HOH A 68 267 79 HOH HOH . G 5 HOH A 69 268 80 HOH HOH . G 5 HOH A 70 269 86 HOH HOH . G 5 HOH A 71 270 87 HOH HOH . G 5 HOH A 72 271 89 HOH HOH . G 5 HOH A 73 272 91 HOH HOH . G 5 HOH A 74 273 97 HOH HOH . G 5 HOH A 75 274 101 HOH HOH . G 5 HOH A 76 275 104 HOH HOH . G 5 HOH A 77 276 111 HOH HOH . G 5 HOH A 78 277 115 HOH HOH . G 5 HOH A 79 278 815 HOH HOH . G 5 HOH A 80 279 120 HOH HOH . G 5 HOH A 81 280 126 HOH HOH . G 5 HOH A 82 281 128 HOH HOH . G 5 HOH A 83 282 129 HOH HOH . G 5 HOH A 84 283 137 HOH HOH . G 5 HOH A 85 284 140 HOH HOH . G 5 HOH A 86 285 143 HOH HOH . G 5 HOH A 87 286 147 HOH HOH . G 5 HOH A 88 287 149 HOH HOH . G 5 HOH A 89 288 152 HOH HOH . G 5 HOH A 90 289 156 HOH HOH . G 5 HOH A 91 290 158 HOH HOH . G 5 HOH A 92 291 162 HOH HOH . G 5 HOH A 93 292 175 HOH HOH . G 5 HOH A 94 293 176 HOH HOH . G 5 HOH A 95 294 183 HOH HOH . G 5 HOH A 96 295 189 HOH HOH . G 5 HOH A 97 296 194 HOH HOH . G 5 HOH A 98 297 216 HOH HOH . G 5 HOH A 99 298 223 HOH HOH . G 5 HOH A 100 299 226 HOH HOH . G 5 HOH A 101 300 230 HOH HOH . G 5 HOH A 102 301 324 HOH HOH . G 5 HOH A 103 302 373 HOH HOH . G 5 HOH A 104 303 384 HOH HOH . G 5 HOH A 105 304 394 HOH HOH . G 5 HOH A 106 305 700 HOH HOH . G 5 HOH A 107 306 1042 HOH HOH . G 5 HOH A 108 307 1043 HOH HOH . G 5 HOH A 109 308 1044 HOH HOH . G 5 HOH A 110 309 1045 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 -9.548 64.424 -67.64 1 27.28 ? PG GNP 528 A 1 HETATM 2 O O1G GNP . . . B 2 -8.629 64.072 -66.485 1 29.46 ? O1G GNP 528 A 1 HETATM 3 O O2G GNP . . . B 2 -10.586 65.388 -67.16 1 25.49 ? O2G GNP 528 A 1 HETATM 4 O O3G GNP . . . B 2 -10.146 63.134 -68.171 1 27.61 ? O3G GNP 528 A 1 HETATM 5 N N3B GNP . . . B 2 -8.651 65.108 -68.815 1 23.41 ? N3B GNP 528 A 1 HETATM 6 P PB GNP . . . B 2 -9.155 65.701 -70.224 1 23.91 ? PB GNP 528 A 1 HETATM 7 O O1B GNP . . . B 2 -9.577 64.636 -71.164 1 21.67 ? O1B GNP 528 A 1 HETATM 8 O O2B GNP . . . B 2 -10.21 66.7 -70.007 1 25.17 ? O2B GNP 528 A 1 HETATM 9 O O3A GNP . . . B 2 -7.966 66.433 -70.869 1 21.27 ? O3A GNP 528 A 1 HETATM 10 P PA GNP . . . B 2 -7.631 67.942 -70.835 1 23.33 ? PA GNP 528 A 1 HETATM 11 O O1A GNP . . . B 2 -8.581 68.67 -71.722 1 21.62 ? O1A GNP 528 A 1 HETATM 12 O O2A GNP . . . B 2 -7.493 68.435 -69.436 1 25.85 ? O2A GNP 528 A 1 HETATM 13 O O5' GNP . . . B 2 -6.225 68.059 -71.528 1 21.98 ? O5' GNP 528 A 1 HETATM 14 C C5' GNP . . . B 2 -5.068 67.338 -71.038 1 24.22 ? C5' GNP 528 A 1 HETATM 15 C C4' GNP . . . B 2 -3.794 67.959 -71.566 1 24.99 ? C4' GNP 528 A 1 HETATM 16 O O4' GNP . . . B 2 -3.779 67.771 -72.995 1 22.94 ? O4' GNP 528 A 1 HETATM 17 C C3' GNP . . . B 2 -3.663 69.464 -71.339 1 27.52 ? C3' GNP 528 A 1 HETATM 18 O O3' GNP . . . B 2 -2.305 69.832 -71.127 1 23.06 ? O3' GNP 528 A 1 HETATM 19 C C2' GNP . . . B 2 -4.178 70.064 -72.651 1 26.91 ? C2' GNP 528 A 1 HETATM 20 O O2' GNP . . . B 2 -3.614 71.333 -72.95 1 23.4 ? O2' GNP 528 A 1 HETATM 21 C C1' GNP . . . B 2 -3.671 69.025 -73.643 1 22.61 ? C1' GNP 528 A 1 HETATM 22 N N9 GNP . . . B 2 -4.48 68.995 -74.846 1 21.43 ? N9 GNP 528 A 1 HETATM 23 C C8 GNP . . . B 2 -5.843 68.809 -74.919 1 20.51 ? C8 GNP 528 A 1 HETATM 24 N N7 GNP . . . B 2 -6.293 68.855 -76.143 1 19.57 ? N7 GNP 528 A 1 HETATM 25 C C5 GNP . . . B 2 -5.176 69.1 -76.924 1 16.65 ? C5 GNP 528 A 1 HETATM 26 C C6 GNP . . . B 2 -5.053 69.244 -78.325 1 20.79 ? C6 GNP 528 A 1 HETATM 27 O O6 GNP . . . B 2 -5.947 69.192 -79.183 1 23.58 ? O6 GNP 528 A 1 HETATM 28 N N1 GNP . . . B 2 -3.732 69.474 -78.706 1 21.57 ? N1 GNP 528 A 1 HETATM 29 C C2 GNP . . . B 2 -2.671 69.547 -77.831 1 28.38 ? C2 GNP 528 A 1 HETATM 30 N N2 GNP . . . B 2 -1.465 69.791 -78.357 1 23.05 ? N2 GNP 528 A 1 HETATM 31 N N3 GNP . . . B 2 -2.776 69.412 -76.519 1 25.37 ? N3 GNP 528 A 1 HETATM 32 C C4 GNP . . . B 2 -4.052 69.186 -76.136 1 20.31 ? C4 GNP 528 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #