data_9GRO # _model_server_result.job_id YD8o9-UP_l2Uned8zknNyw _model_server_result.datetime_utc '2025-07-27 12:17:05' _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 9gro # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"DA","auth_seq_id":1210}' # _entry.id 9GRO # _exptl.entry_id 9GRO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 819.995 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)]' _entity.pdbx_number_of_molecules 2 _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 9GRO _cell.length_a 114.586 _cell.length_b 114.586 _cell.length_c 172.179 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9GRO _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # 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 ? monomeric 1 author_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,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,GA 1 1 B,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,HA 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 ? 7 Q N N ? 7 DA 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 disulf ? disulf1 A SG CYS 260 A CYS 793 1_555 B SG CYS 260 B CYS 793 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc1 A NE2 HIS 118 A HIS 651 1_555 C ZN ZN . A ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc2 A OE2 GLU 263 A GLU 796 1_555 C ZN ZN . A ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? metalc ? metalc3 A ND1 HIS 303 A HIS 836 1_555 C ZN ZN . A ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc4 A ND1 HIS 464 A HIS 1064 1_555 C ZN ZN . A ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc5 B NE2 HIS 118 B HIS 651 1_555 U ZN ZN . B ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc6 B OE2 GLU 263 B GLU 796 1_555 U ZN ZN . B ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc7 B ND1 HIS 303 B HIS 836 1_555 U ZN ZN . B ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc8 B ND1 HIS 464 B HIS 1064 1_555 U ZN ZN . B ZN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? # _chem_comp.formula 'C6 H20 O30 P8' _chem_comp.formula_weight 819.995 _chem_comp.id I8P _chem_comp.mon_nstd_flag . _chem_comp.name '(1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)]' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '1D-myo-inositol 1,5-bisdiphosphate 2,3,4,6-tetrakisphosphate' # 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 O11 C1 I8P sing 183 n n C2 C1 I8P sing 184 n n C1 C6 I8P sing 185 n n C1 H1 I8P sing 186 n n O12 C2 I8P sing 187 n n C2 C3 I8P sing 188 n n C2 H2 I8P sing 189 n n O13 C3 I8P sing 190 n n C3 C4 I8P sing 191 n n C3 H3 I8P sing 192 n n C4 C5 I8P sing 193 n n C4 O14 I8P sing 194 n n C4 H4 I8P sing 195 n n C6 C5 I8P sing 196 n n C5 O15 I8P sing 197 n n C5 H5 I8P sing 198 n n C6 O16 I8P sing 199 n n C6 H6 I8P sing 200 n n PA1 O11 I8P sing 201 n n PA2 O12 I8P sing 202 n n O13 PA3 I8P sing 203 n n O14 PA4 I8P sing 204 n n O15 PA5 I8P sing 205 n n PA6 O16 I8P sing 206 n n O21 PA1 I8P doub 207 n n O22 PA2 I8P sing 208 n n O22 HO22 I8P sing 209 n n PA3 O23 I8P sing 210 n n O23 HO23 I8P sing 211 n n O24 PA4 I8P sing 212 n n O24 HO24 I8P sing 213 n n PA5 O25 I8P doub 214 n n PA6 O26 I8P sing 215 n n O26 HO26 I8P sing 216 n n O31 PA1 I8P sing 217 n n O31 HO31 I8P sing 218 n n O32 PA2 I8P doub 219 n n O33 PA3 I8P doub 220 n n O34 PA4 I8P doub 221 n n PA5 O35 I8P sing 222 n n O35 HO35 I8P sing 223 n n PA6 O36 I8P sing 224 n n O36 HO36 I8P sing 225 n n PA1 O41 I8P sing 226 n n O41 PB1 I8P sing 227 n n PA2 O42 I8P sing 228 n n O42 HO42 I8P sing 229 n n O43 PA3 I8P sing 230 n n O43 HO43 I8P sing 231 n n PA4 O44 I8P sing 232 n n O44 HO44 I8P sing 233 n n O45 PA5 I8P sing 234 n n O45 PB5 I8P sing 235 n n O46 PA6 I8P doub 236 n n O51 PB1 I8P sing 237 n n O51 HO51 I8P sing 238 n n O55 PB5 I8P doub 239 n n O61 PB1 I8P doub 240 n n O65 PB5 I8P sing 241 n n O65 HO65 I8P sing 242 n n PB1 O71 I8P sing 243 n n O71 HO71 I8P sing 244 n n PB5 O75 I8P sing 245 n n O75 HO75 I8P sing 246 n n # _atom_sites.entry_id 9GRO _atom_sites.fract_transf_matrix[1][1] 0.008727 _atom_sites.fract_transf_matrix[1][2] 0.005039 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010077 _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] 0.005808 _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 ZN A 1 1201 2000 ZN ZN . D 3 SPM A 1 1202 2001 SPM SPM . E 3 SPM A 1 1203 2002 SPM SPM . F 4 ORN A 1 1204 2003 ORN ORN . G 5 PUT A 1 1205 2004 PUT PUT . H 5 PUT A 1 1206 2005 PUT PUT . I 6 EDO A 1 1207 2006 EDO EDO . J 6 EDO A 1 1208 2007 EDO EDO . K 6 EDO A 1 1209 2008 EDO EDO . L 6 EDO A 1 1210 2009 EDO EDO . M 6 EDO A 1 1211 2010 EDO EDO . N 5 PUT A 1 1212 2011 PUT PUT . O 6 EDO A 1 1213 2012 EDO EDO . P 6 EDO A 1 1214 2013 EDO EDO . Q 7 I8P A 1 1215 3000 I8P I8P . R 6 EDO A 1 1216 3001 EDO EDO . S 6 EDO A 1 1217 3002 EDO EDO . T 5 PUT A 1 1218 3003 PUT PUT . U 2 ZN B 1 1201 2000 ZN ZN . V 8 1JW B 1 1202 2001 1JW 1JW . W 5 PUT B 1 1203 2002 PUT PUT . X 8 1JW B 1 1204 2003 1JW 1JW . Y 6 EDO B 1 1205 2004 EDO EDO . Z 6 EDO B 1 1206 2005 EDO EDO . AA 6 EDO B 1 1207 2006 EDO EDO . BA 5 PUT B 1 1208 2007 PUT PUT . CA 6 EDO B 1 1209 2008 EDO EDO . DA 7 I8P B 1 1210 3000 I8P I8P . EA 6 EDO B 1 1211 3001 EDO EDO . FA 6 EDO B 1 1212 3003 EDO EDO . GA 9 HOH A 1 1301 50 HOH HOH . GA 9 HOH A 2 1302 19 HOH HOH . GA 9 HOH A 3 1303 5 HOH HOH . GA 9 HOH A 4 1304 45 HOH HOH . GA 9 HOH A 5 1305 33 HOH HOH . GA 9 HOH A 6 1306 48 HOH HOH . GA 9 HOH A 7 1307 30 HOH HOH . GA 9 HOH A 8 1308 25 HOH HOH . GA 9 HOH A 9 1309 1 HOH HOH . GA 9 HOH A 10 1310 3 HOH HOH . GA 9 HOH A 11 1311 23 HOH HOH . GA 9 HOH A 12 1312 24 HOH HOH . GA 9 HOH A 13 1313 51 HOH HOH . GA 9 HOH A 14 1314 29 HOH HOH . GA 9 HOH A 15 1315 41 HOH HOH . GA 9 HOH A 16 1316 10 HOH HOH . GA 9 HOH A 17 1317 35 HOH HOH . GA 9 HOH A 18 1318 26 HOH HOH . GA 9 HOH A 19 1319 15 HOH HOH . GA 9 HOH A 20 1320 34 HOH HOH . GA 9 HOH A 21 1321 37 HOH HOH . GA 9 HOH A 22 1322 9 HOH HOH . GA 9 HOH A 23 1323 7 HOH HOH . GA 9 HOH A 24 1324 40 HOH HOH . GA 9 HOH A 25 1325 8 HOH HOH . GA 9 HOH A 26 1326 2 HOH HOH . GA 9 HOH A 27 1327 46 HOH HOH . HA 9 HOH B 1 1301 11 HOH HOH . HA 9 HOH B 2 1302 44 HOH HOH . HA 9 HOH B 3 1303 17 HOH HOH . HA 9 HOH B 4 1304 36 HOH HOH . HA 9 HOH B 5 1305 49 HOH HOH . HA 9 HOH B 6 1306 12 HOH HOH . HA 9 HOH B 7 1307 22 HOH HOH . HA 9 HOH B 8 1308 32 HOH HOH . HA 9 HOH B 9 1309 6 HOH HOH . HA 9 HOH B 10 1310 16 HOH HOH . HA 9 HOH B 11 1311 39 HOH HOH . HA 9 HOH B 12 1312 4 HOH HOH . HA 9 HOH B 13 1313 13 HOH HOH . HA 9 HOH B 14 1314 20 HOH HOH . HA 9 HOH B 15 1315 47 HOH HOH . HA 9 HOH B 16 1316 18 HOH HOH . HA 9 HOH B 17 1317 42 HOH HOH . HA 9 HOH B 18 1318 21 HOH HOH . HA 9 HOH B 19 1319 14 HOH HOH . HA 9 HOH B 20 1320 27 HOH HOH . HA 9 HOH B 21 1321 31 HOH HOH . HA 9 HOH B 22 1322 43 HOH HOH . HA 9 HOH B 23 1323 28 HOH HOH . HA 9 HOH B 24 1324 38 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 I8P . . . DA 7 68.164 -44.18 -22.728 1 116.43 ? C1 I8P 1210 B 1 HETATM 2 C C2 I8P . . . DA 7 67.078 -44.425 -21.668 1 114.99 ? C2 I8P 1210 B 1 HETATM 3 C C3 I8P . . . DA 7 67.444 -43.996 -20.239 1 118.97 ? C3 I8P 1210 B 1 HETATM 4 C C4 I8P . . . DA 7 68.064 -42.604 -20.203 1 116.66 ? C4 I8P 1210 B 1 HETATM 5 C C5 I8P . . . DA 7 69.312 -42.634 -21.078 1 118.69 ? C5 I8P 1210 B 1 HETATM 6 C C6 I8P . . . DA 7 68.926 -42.868 -22.543 1 119.64 ? C6 I8P 1210 B 1 HETATM 7 O O11 I8P . . . DA 7 67.486 -44.161 -23.969 1 125.78 ? O11 I8P 1210 B 1 HETATM 8 O O12 I8P . . . DA 7 65.944 -43.7 -22.081 1 121.05 ? O12 I8P 1210 B 1 HETATM 9 O O13 I8P . . . DA 7 66.283 -43.995 -19.458 1 124.75 ? O13 I8P 1210 B 1 HETATM 10 O O14 I8P . . . DA 7 68.436 -42.256 -18.903 1 115.72 ? O14 I8P 1210 B 1 HETATM 11 O O15 I8P . . . DA 7 69.969 -41.421 -20.933 1 124.35 ? O15 I8P 1210 B 1 HETATM 12 O O16 I8P . . . DA 7 70.109 -42.904 -23.296 1 123.85 ? O16 I8P 1210 B 1 HETATM 13 O O21 I8P . . . DA 7 69.457 -44.843 -25.458 1 123.09 ? O21 I8P 1210 B 1 HETATM 14 O O22 I8P . . . DA 7 63.442 -43.547 -22.668 1 126.39 -1 O22 I8P 1210 B 1 HETATM 15 O O23 I8P . . . DA 7 66.503 -46.278 -18.216 1 110.34 -1 O23 I8P 1210 B 1 HETATM 16 O O24 I8P . . . DA 7 66.055 -41.449 -18.375 1 104.23 -1 O24 I8P 1210 B 1 HETATM 17 O O25 I8P . . . DA 7 71.668 -41.821 -19.023 1 121.85 ? O25 I8P 1210 B 1 HETATM 18 O O26 I8P . . . DA 7 69.046 -41.9 -25.422 1 131.97 -1 O26 I8P 1210 B 1 HETATM 19 O O31 I8P . . . DA 7 67.809 -46.591 -24.839 1 131.28 -1 O31 I8P 1210 B 1 HETATM 20 O O32 I8P . . . DA 7 64.783 -45.39 -23.638 1 115.6 ? O32 I8P 1210 B 1 HETATM 21 O O33 I8P . . . DA 7 67.39 -44.232 -17.157 1 113.6 ? O33 I8P 1210 B 1 HETATM 22 O O34 I8P . . . DA 7 67.819 -41.154 -16.655 1 115.55 ? O34 I8P 1210 B 1 HETATM 23 O O35 I8P . . . DA 7 72.269 -40.332 -20.94 1 131.52 -1 O35 I8P 1210 B 1 HETATM 24 O O36 I8P . . . DA 7 70.443 -40.433 -24.021 1 114.83 -1 O36 I8P 1210 B 1 HETATM 25 O O41 I8P . . . DA 7 67.115 -44.806 -26.541 1 128.89 ? O41 I8P 1210 B 1 HETATM 26 O O42 I8P . . . DA 7 64.222 -45.407 -21.235 1 108.13 -1 O42 I8P 1210 B 1 HETATM 27 O O43 I8P . . . DA 7 64.94 -44.566 -17.36 1 102.06 -1 O43 I8P 1210 B 1 HETATM 28 O O44 I8P . . . DA 7 67.838 -39.764 -18.705 1 113.2 -1 O44 I8P 1210 B 1 HETATM 29 O O45 I8P . . . DA 7 72.137 -42.865 -21.291 1 126.8 ? O45 I8P 1210 B 1 HETATM 30 O O46 I8P . . . DA 7 71.499 -42.269 -25.315 1 126.1 ? O46 I8P 1210 B 1 HETATM 31 O O51 I8P . . . DA 7 68.352 -45.869 -28.54 1 123.04 -1 O51 I8P 1210 B 1 HETATM 32 O O55 I8P . . . DA 7 72.916 -41.43 -23.228 1 134.74 ? O55 I8P 1210 B 1 HETATM 33 O O61 I8P . . . DA 7 66.743 -44.026 -28.952 1 125.12 ? O61 I8P 1210 B 1 HETATM 34 O O65 I8P . . . DA 7 73.081 -43.909 -23.404 1 138.39 -1 O65 I8P 1210 B 1 HETATM 35 O O71 I8P . . . DA 7 68.929 -43.567 -27.875 1 133.12 -1 O71 I8P 1210 B 1 HETATM 36 O O75 I8P . . . DA 7 74.602 -42.657 -21.892 1 141.88 -1 O75 I8P 1210 B 1 HETATM 37 P PA1 I8P . . . DA 7 68.001 -45.134 -25.194 1 199.3 ? PA1 I8P 1210 B 1 HETATM 38 P PA2 I8P . . . DA 7 64.563 -44.527 -22.415 1 178.52 ? PA2 I8P 1210 B 1 HETATM 39 P PA3 I8P . . . DA 7 66.282 -44.795 -18.016 1 182.11 ? PA3 I8P 1210 B 1 HETATM 40 P PA4 I8P . . . DA 7 67.512 -41.125 -18.136 1 180.29 ? PA4 I8P 1210 B 1 HETATM 41 P PA5 I8P . . . DA 7 71.535 -41.568 -20.503 1 186.81 ? PA5 I8P 1210 B 1 HETATM 42 P PA6 I8P . . . DA 7 70.273 -41.843 -24.543 1 189.5 ? PA6 I8P 1210 B 1 HETATM 43 P PB1 I8P . . . DA 7 67.803 -44.561 -28.018 1 203.88 ? PB1 I8P 1210 B 1 HETATM 44 P PB5 I8P . . . DA 7 73.223 -42.712 -22.495 1 224 ? PB5 I8P 1210 B 1 HETATM 45 H H1 I8P . . . DA 7 68.906 -44.968 -22.687 1 139.97 ? H1 I8P 1210 B 1 HETATM 46 H H2 I8P . . . DA 7 66.886 -45.491 -21.62 1 138.24 ? H2 I8P 1210 B 1 HETATM 47 H H3 I8P . . . DA 7 68.151 -44.706 -19.827 1 143.02 ? H3 I8P 1210 B 1 HETATM 48 H H4 I8P . . . DA 7 67.345 -41.86 -20.527 1 140.24 ? H4 I8P 1210 B 1 HETATM 49 H H5 I8P . . . DA 7 69.988 -43.418 -20.768 1 142.69 ? H5 I8P 1210 B 1 HETATM 50 H H6 I8P . . . DA 7 68.298 -42.058 -22.895 1 143.82 ? H6 I8P 1210 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 50 #