data_9GRO # _model_server_result.job_id BlmU8tLxQaIVtsCCeKbn_g _model_server_result.datetime_utc '2025-07-27 12:21:50' _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":"Q","auth_seq_id":1215}' # _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 . . . Q 7 22.914 4.673 -0.446 1 75.81 ? C1 I8P 1215 A 1 HETATM 2 C C2 I8P . . . Q 7 22.257 4.073 -1.689 1 82.38 ? C2 I8P 1215 A 1 HETATM 3 C C3 I8P . . . Q 7 22.833 4.712 -2.959 1 75.33 ? C3 I8P 1215 A 1 HETATM 4 C C4 I8P . . . Q 7 24.353 4.493 -3.022 1 66.43 ? C4 I8P 1215 A 1 HETATM 5 C C5 I8P . . . Q 7 25.084 5.038 -1.792 1 77.96 ? C5 I8P 1215 A 1 HETATM 6 C C6 I8P . . . Q 7 24.436 4.572 -0.473 1 77.75 ? C6 I8P 1215 A 1 HETATM 7 O O11 I8P . . . Q 7 22.421 3.949 0.657 1 89.38 ? O11 I8P 1215 A 1 HETATM 8 O O12 I8P . . . Q 7 22.526 2.698 -1.731 1 86.69 ? O12 I8P 1215 A 1 HETATM 9 O O13 I8P . . . Q 7 22.214 4.134 -4.072 1 82.77 ? O13 I8P 1215 A 1 HETATM 10 O O14 I8P . . . Q 7 24.819 5.149 -4.177 1 79.34 ? O14 I8P 1215 A 1 HETATM 11 O O15 I8P . . . Q 7 26.407 4.557 -1.762 1 76.4 ? O15 I8P 1215 A 1 HETATM 12 O O16 I8P . . . Q 7 24.931 5.367 0.575 1 82.85 ? O16 I8P 1215 A 1 HETATM 13 O O21 I8P . . . Q 7 21.746 4.098 3.154 1 97.43 ? O21 I8P 1215 A 1 HETATM 14 O O22 I8P . . . Q 7 21.247 0.637 -2.551 1 89.21 -1 O22 I8P 1215 A 1 HETATM 15 O O23 I8P . . . Q 7 20.276 5.818 -3.798 1 96.04 -1 O23 I8P 1215 A 1 HETATM 16 O O24 I8P . . . Q 7 24.293 2.941 -5.446 1 76.31 -1 O24 I8P 1215 A 1 HETATM 17 O O25 I8P . . . Q 7 28.277 4.869 -3.502 1 80.4 ? O25 I8P 1215 A 1 HETATM 18 O O26 I8P . . . Q 7 24.655 3.364 2.166 1 73.5 -1 O26 I8P 1215 A 1 HETATM 19 O O31 I8P . . . Q 7 22.094 6.196 1.864 1 87.15 -1 O31 I8P 1215 A 1 HETATM 20 O O32 I8P . . . Q 7 21.679 0.874 -0.128 1 90.86 ? O32 I8P 1215 A 1 HETATM 21 O O33 I8P . . . Q 7 21.658 5.914 -5.843 1 76.83 ? O33 I8P 1215 A 1 HETATM 22 O O34 I8P . . . Q 7 24.356 5.063 -6.708 1 73.88 ? O34 I8P 1215 A 1 HETATM 23 O O35 I8P . . . Q 7 28.703 5.582 -1.198 1 95.03 -1 O35 I8P 1215 A 1 HETATM 24 O O36 I8P . . . Q 7 26.928 4.191 1.708 1 74.8 -1 O36 I8P 1215 A 1 HETATM 25 O O41 I8P . . . Q 7 20 4.795 1.399 1 100.18 ? O41 I8P 1215 A 1 HETATM 26 O O42 I8P . . . Q 7 20.006 2.316 -1.238 1 90.19 -1 O42 I8P 1215 A 1 HETATM 27 O O43 I8P . . . Q 7 20.067 4.042 -5.502 1 82.13 -1 O43 I8P 1215 A 1 HETATM 28 O O44 I8P . . . Q 7 26.449 4.069 -5.834 1 67.61 -1 O44 I8P 1215 A 1 HETATM 29 O O45 I8P . . . Q 7 27.034 6.957 -2.694 1 98.09 ? O45 I8P 1215 A 1 HETATM 30 O O46 I8P . . . Q 7 25.38 5.547 3.086 1 81.16 ? O46 I8P 1215 A 1 HETATM 31 O O51 I8P . . . Q 7 18.549 6.929 1.561 1 100.61 -1 O51 I8P 1215 A 1 HETATM 32 O O55 I8P . . . Q 7 28.176 8.797 -1.363 1 91.7 ? O55 I8P 1215 A 1 HETATM 33 O O61 I8P . . . Q 7 20.467 6.898 0.013 1 101.69 ? O61 I8P 1215 A 1 HETATM 34 O O65 I8P . . . Q 7 26.12 7.773 -0.443 1 91.34 -1 O65 I8P 1215 A 1 HETATM 35 O O71 I8P . . . Q 7 18.456 5.543 -0.498 1 105.93 -1 O71 I8P 1215 A 1 HETATM 36 O O75 I8P . . . Q 7 25.98 9.308 -2.363 1 112.64 -1 O75 I8P 1215 A 1 HETATM 37 P PA1 I8P . . . Q 7 21.59 4.773 1.814 1 125.64 ? PA1 I8P 1215 A 1 HETATM 38 P PA2 I8P . . . Q 7 21.333 1.612 -1.402 1 122.03 ? PA2 I8P 1215 A 1 HETATM 39 P PA3 I8P . . . Q 7 21.024 4.996 -4.823 1 101.48 ? PA3 I8P 1215 A 1 HETATM 40 P PA4 I8P . . . Q 7 24.978 4.282 -5.572 1 71.98 ? PA4 I8P 1215 A 1 HETATM 41 P PA5 I8P . . . Q 7 27.652 5.49 -2.279 1 100.44 ? PA5 I8P 1215 A 1 HETATM 42 P PA6 I8P . . . Q 7 25.489 4.598 1.915 1 103.03 ? PA6 I8P 1215 A 1 HETATM 43 P PB1 I8P . . . Q 7 19.343 6.076 0.598 1 170.08 ? PB1 I8P 1215 A 1 HETATM 44 P PB5 I8P . . . Q 7 26.818 8.24 -1.696 1 146.52 ? PB5 I8P 1215 A 1 HETATM 45 H H1 I8P . . . Q 7 22.661 5.723 -0.363 1 91.22 ? H1 I8P 1215 A 1 HETATM 46 H H2 I8P . . . Q 7 21.184 4.222 -1.641 1 99.12 ? H2 I8P 1215 A 1 HETATM 47 H H3 I8P . . . Q 7 22.627 5.775 -2.979 1 90.65 ? H3 I8P 1215 A 1 HETATM 48 H H4 I8P . . . Q 7 24.567 3.432 -3.083 1 79.97 ? H4 I8P 1215 A 1 HETATM 49 H H5 I8P . . . Q 7 25.073 6.116 -1.871 1 93.81 ? H5 I8P 1215 A 1 HETATM 50 H H6 I8P . . . Q 7 24.707 3.531 -0.337 1 93.56 ? H6 I8P 1215 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 50 #