data_9IM5 # _model_server_result.job_id YE9xCyDcYbe9rNk7wcYSuw _model_server_result.datetime_utc '2025-03-07 00:06:43' _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 9im5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":506}' # _entry.id 9IM5 # _exptl.entry_id 9IM5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 11 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 90 _cell.entry_id 9IM5 _cell.length_a 107.35 _cell.length_b 160.78 _cell.length_c 184.54 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9IM5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # 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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,X,Y 1 1 F,W 1 2 # 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' 3_545 -x,y-1/2,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 -80.39 92.27 # _struct_asym.details ? _struct_asym.entity_id 11 _struct_asym.id P _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 OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc8 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc10 B OE1 GLU 111 B GLU 111 1_555 L CA CA . B CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.005 ? metalc ? metalc11 B OE2 GLU 111 B GLU 111 1_555 L CA CA . B CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? metalc ? metalc12 K MG MG . B MG 501 1_555 P O1A GDP . B GDP 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc13 C OD1 ASP 39 C ASP 39 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc14 C OD2 ASP 39 C ASP 39 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc15 C O THR 41 C THR 41 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc16 C OG1 THR 41 C THR 41 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc17 C O GLY 44 C GLY 44 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc18 C OE1 GLU 55 C GLU 55 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.724 ? metalc ? metalc19 C OE2 GLU 55 C GLU 55 1_555 S CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc20 Q O1G GTP . C GTP 501 1_555 R MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc21 Q O1B GTP . C GTP 501 1_555 R MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 182 n n PB O2B GDP sing 183 n n PB O3B GDP sing 184 n n PB O3A GDP sing 185 n n O2B HOB2 GDP sing 186 n n O3B HOB3 GDP sing 187 n n O3A PA GDP sing 188 n n PA O1A GDP doub 189 n n PA O2A GDP sing 190 n n PA O5' GDP sing 191 n n O2A HOA2 GDP sing 192 n n O5' C5' GDP sing 193 n n C5' C4' GDP sing 194 n n C5' H5' GDP sing 195 n n C5' "H5''" GDP sing 196 n n C4' O4' GDP sing 197 n n C4' C3' GDP sing 198 n n C4' H4' GDP sing 199 n n O4' C1' GDP sing 200 n n C3' O3' GDP sing 201 n n C3' C2' GDP sing 202 n n C3' H3' GDP sing 203 n n O3' HO3' GDP sing 204 n n C2' O2' GDP sing 205 n n C2' C1' GDP sing 206 n n C2' H2' GDP sing 207 n n O2' HO2' GDP sing 208 n n C1' N9 GDP sing 209 n n C1' H1' GDP sing 210 n n N9 C8 GDP sing 211 n y N9 C4 GDP sing 212 n y C8 N7 GDP doub 213 n y C8 H8 GDP sing 214 n n N7 C5 GDP sing 215 n y C5 C6 GDP sing 216 n n C5 C4 GDP doub 217 n y C6 O6 GDP doub 218 n n C6 N1 GDP sing 219 n n N1 C2 GDP sing 220 n n N1 HN1 GDP sing 221 n n C2 N2 GDP sing 222 n n C2 N3 GDP doub 223 n n N2 HN21 GDP sing 224 n n N2 HN22 GDP sing 225 n n N3 C4 GDP sing 226 n n # _atom_sites.entry_id 9IM5 _atom_sites.fract_transf_matrix[1][1] 0.009315 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00622 _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] 0.005419 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 CL A 1 504 504 CL CL . K 6 MG B 1 501 502 MG MG . L 7 CA B 1 502 503 CA CA . M 9 MES B 1 503 504 MES MES . N 9 MES B 1 504 505 MES MES . O 10 A1L2T B 1 505 601 A1L2T LIG . P 11 GDP B 1 506 501 GDP GDP . Q 5 GTP C 1 501 501 GTP GTP . R 6 MG C 1 502 502 MG MG . S 7 CA C 1 503 503 CA CA . T 5 GTP D 1 501 501 GTP GTP . U 6 MG D 1 502 502 MG MG . V 10 A1L2T D 1 503 601 A1L2T LIG . W 12 ACP F 1 401 401 ACP ACP . X 13 HOH A 1 601 2 HOH HOH . Y 13 HOH B 1 601 4 HOH HOH . Y 13 HOH B 2 602 1 HOH HOH . Y 13 HOH B 3 603 5 HOH HOH . Y 13 HOH B 4 604 6 HOH HOH . Y 13 HOH B 5 605 3 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 PB GDP . . . P 11 19.264 50.629 15.978 1 30.8 ? PB GDP 506 B 1 HETATM 2 O O1B GDP . . . P 11 18.72 51.498 14.874 1 37.14 ? O1B GDP 506 B 1 HETATM 3 O O2B GDP . . . P 11 19.862 51.488 17.065 1 33.19 ? O2B GDP 506 B 1 HETATM 4 O O3B GDP . . . P 11 20.339 49.706 15.452 1 29.69 ? O3B GDP 506 B 1 HETATM 5 O O3A GDP . . . P 11 18.13 49.659 16.588 1 32.63 ? O3A GDP 506 B 1 HETATM 6 P PA GDP . . . P 11 16.637 50.081 17.035 1 26.59 ? PA GDP 506 B 1 HETATM 7 O O1A GDP . . . P 11 15.614 49.841 15.952 1 37.39 ? O1A GDP 506 B 1 HETATM 8 O O2A GDP . . . P 11 16.582 51.507 17.533 1 31.19 ? O2A GDP 506 B 1 HETATM 9 O O5' GDP . . . P 11 16.485 49.027 18.246 1 26.74 ? O5' GDP 506 B 1 HETATM 10 C C5' GDP . . . P 11 15.371 48.154 18.37 1 36.19 ? C5' GDP 506 B 1 HETATM 11 C C4' GDP . . . P 11 14.864 48.162 19.808 1 38.65 ? C4' GDP 506 B 1 HETATM 12 O O4' GDP . . . P 11 14.321 49.448 20.104 1 30.76 ? O4' GDP 506 B 1 HETATM 13 C C3' GDP . . . P 11 13.707 47.21 19.966 1 37.58 ? C3' GDP 506 B 1 HETATM 14 O O3' GDP . . . P 11 13.568 46.938 21.359 1 45.5 ? O3' GDP 506 B 1 HETATM 15 C C2' GDP . . . P 11 12.527 48.04 19.526 1 38.99 ? C2' GDP 506 B 1 HETATM 16 O O2' GDP . . . P 11 11.339 47.519 20.124 1 45.71 ? O2' GDP 506 B 1 HETATM 17 C C1' GDP . . . P 11 12.89 49.403 20.082 1 32.17 ? C1' GDP 506 B 1 HETATM 18 N N9 GDP . . . P 11 12.452 50.598 19.314 1 33.9 ? N9 GDP 506 B 1 HETATM 19 C C8 GDP . . . P 11 12.752 50.921 18.039 1 34.05 ? C8 GDP 506 B 1 HETATM 20 N N7 GDP . . . P 11 12.217 52.131 17.701 1 32.84 ? N7 GDP 506 B 1 HETATM 21 C C5 GDP . . . P 11 11.584 52.612 18.791 1 30.98 ? C5 GDP 506 B 1 HETATM 22 C C6 GDP . . . P 11 10.812 53.828 19.148 1 32.71 ? C6 GDP 506 B 1 HETATM 23 O O6 GDP . . . P 11 10.616 54.737 18.318 1 34.61 ? O6 GDP 506 B 1 HETATM 24 N N1 GDP . . . P 11 10.319 53.939 20.388 1 32.29 ? N1 GDP 506 B 1 HETATM 25 C C2 GDP . . . P 11 10.507 52.986 21.315 1 33.13 ? C2 GDP 506 B 1 HETATM 26 N N2 GDP . . . P 11 9.973 53.179 22.542 1 33.66 ? N2 GDP 506 B 1 HETATM 27 N N3 GDP . . . P 11 11.202 51.844 21.067 1 30.17 ? N3 GDP 506 B 1 HETATM 28 C C4 GDP . . . P 11 11.749 51.605 19.849 1 33.48 ? C4 GDP 506 B 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #