data_4IRU # _model_server_result.job_id 5hoYyig31NMqVCaCZ4cMWQ _model_server_result.datetime_utc '2024-11-04 23:24:22' _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 4iru # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":202}' # _entry.id 4IRU # _exptl.entry_id 4IRU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 4IRU _cell.length_a 139.404 _cell.length_b 139.404 _cell.length_c 384.519 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4IRU _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 2 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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,PA,QA 1 1 C,D,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,RA,SA 2 1 E,F,MA,NA,OA,TA 3 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 T N N ? 7 IA N N ? 7 NA 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 covale ? covale1 A C LEU 8 A LEU 332 1_555 A N MSE 9 A MSE 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C MSE 9 A MSE 333 1_555 A N THR 10 A THR 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C ASP 30 A ASP 354 1_555 A N MSE 31 A MSE 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 A C MSE 31 A MSE 355 1_555 A N GLU 32 A GLU 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale5 A C LYS 224 A LYS 548 1_555 A N MSE 225 A MSE 549 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale6 A C MSE 225 A MSE 549 1_555 A N ASN 226 A ASN 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale7 B C PHE 172 B PHE 165 1_555 B N MSE 173 B MSE 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale8 B C MSE 173 B MSE 166 1_555 B N THR 174 B THR 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale9 B C THR 174 B THR 167 1_555 B N MSE 175 B MSE 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale10 B C MSE 175 B MSE 168 1_555 B N ALA 176 B ALA 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale11 B C ARG 182 B ARG 175 1_555 B N MSE 183 B MSE 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale12 C C LEU 8 C LEU 332 1_555 C N MSE 9 C MSE 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale13 C C MSE 9 C MSE 333 1_555 C N THR 10 C THR 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale14 C C ASP 30 C ASP 354 1_555 C N MSE 31 C MSE 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale15 C C MSE 31 C MSE 355 1_555 C N GLU 32 C GLU 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale16 C C LYS 224 C LYS 548 1_555 C N MSE 225 C MSE 549 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale17 C C MSE 225 C MSE 549 1_555 C N ASN 226 C ASN 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale18 D C PHE 172 D PHE 165 1_555 D N MSE 173 D MSE 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale19 D C MSE 173 D MSE 166 1_555 D N THR 174 D THR 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale20 D C THR 174 D THR 167 1_555 D N MSE 175 D MSE 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale21 D C MSE 175 D MSE 168 1_555 D N ALA 176 D ALA 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale22 D C ARG 182 D ARG 175 1_555 D N MSE 183 D MSE 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale23 E C LEU 8 E LEU 332 1_555 E N MSE 9 E MSE 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale24 E C MSE 9 E MSE 333 1_555 E N THR 10 E THR 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale25 E C ASP 30 E ASP 354 1_555 E N MSE 31 E MSE 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale26 E C MSE 31 E MSE 355 1_555 E N GLU 32 E GLU 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale27 E C LYS 224 E LYS 548 1_555 E N MSE 225 E MSE 549 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale28 E C MSE 225 E MSE 549 1_555 E N ASN 226 E ASN 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale29 F C PHE 172 F PHE 165 1_555 F N MSE 173 F MSE 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale30 F C MSE 173 F MSE 166 1_555 F N THR 174 F THR 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale31 F C THR 174 F THR 167 1_555 F N MSE 175 F MSE 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale32 F C MSE 175 F MSE 168 1_555 F N ALA 176 F ALA 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale33 F C ARG 182 F ARG 175 1_555 F N MSE 183 F MSE 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 HA MG MG . D MG 201 1_555 IA O3B GDP . D GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.855 ? metalc ? metalc2 S MG MG . B MG 201 1_555 T O3B GDP . B GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc3 D OG SER 32 D SER 25 1_555 HA MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc4 B OG SER 32 B SER 25 1_555 S MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc5 D OG1 THR 50 D THR 43 1_555 HA MG MG . D MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? metalc ? metalc6 MA MG MG . F MG 200 1_555 NA O1B GDP . F GDP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? metalc ? metalc7 B OG1 THR 50 B THR 43 1_555 S MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.687 ? metalc ? metalc8 C OE1 GLU 212 C GLU 536 1_555 GA K K . C K 708 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.025 ? metalc ? metalc9 A O ASN 39 A ASN 363 1_555 P K K . A K 910 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.262 ? metalc ? metalc10 A OE1 GLU 212 A GLU 536 1_555 O K K . A K 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.269 ? metalc ? metalc11 H OXT ACT . A ACT 902 1_555 P K K . A K 910 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.318 ? metalc ? metalc12 HA MG MG . D MG 201 1_555 SA O HOH . D HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.861 ? metalc ? metalc13 S MG MG . B MG 201 1_555 QA O HOH . B HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.862 ? metalc ? metalc14 HA MG MG . D MG 201 1_555 SA O HOH . D HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? # _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 ? # _atom_sites.entry_id 4IRU _atom_sites.fract_transf_matrix[1][1] 0.007173 _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] 0.007173 _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] 0.002601 _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 3 ACT A 1 901 901 ACT ACT . H 3 ACT A 1 902 902 ACT ACT . I 4 GOL A 1 903 920 GOL GOL . J 4 GOL A 1 904 921 GOL GOL . K 4 GOL A 1 905 922 GOL GOL . L 4 GOL A 1 906 923 GOL GOL . M 4 GOL A 1 907 924 GOL GOL . N 4 GOL A 1 908 925 GOL GOL . O 5 K A 1 909 930 K K . P 5 K A 1 910 931 K K . Q 5 K A 1 911 932 K K . R 5 K A 1 912 935 K K . S 6 MG B 1 201 200 MG MG . T 7 GDP B 1 202 201 GDP GDP . U 8 AF3 B 1 203 202 AF3 AF3 . V 3 ACT B 1 204 903 ACT ACT . W 3 ACT B 1 205 904 ACT ACT . X 4 GOL B 1 206 926 GOL GOL . Y 5 K B 1 207 933 K K . Z 3 ACT C 1 701 905 ACT ACT . AA 3 ACT C 1 702 906 ACT ACT . BA 3 ACT C 1 703 907 ACT ACT . CA 3 ACT C 1 704 908 ACT ACT . DA 3 ACT C 1 705 909 ACT ACT . EA 3 ACT C 1 706 911 ACT ACT . FA 4 GOL C 1 707 927 GOL GOL . GA 5 K C 1 708 934 K K . HA 6 MG D 1 201 200 MG MG . IA 7 GDP D 1 202 201 GDP GDP . JA 8 AF3 D 1 203 202 AF3 AF3 . KA 3 ACT D 1 204 910 ACT ACT . LA 3 ACT D 1 205 912 ACT ACT . MA 6 MG F 1 200 200 MG MG . NA 7 GDP F 1 201 201 GDP GDP . OA 8 AF3 F 1 202 202 AF3 AF3 . PA 9 HOH A 1 1001 950 HOH HOH . PA 9 HOH A 2 1002 951 HOH HOH . PA 9 HOH A 3 1003 952 HOH HOH . PA 9 HOH A 4 1004 953 HOH HOH . PA 9 HOH A 5 1005 954 HOH HOH . PA 9 HOH A 6 1006 955 HOH HOH . PA 9 HOH A 7 1007 957 HOH HOH . PA 9 HOH A 8 1008 958 HOH HOH . QA 9 HOH B 1 301 956 HOH HOH . QA 9 HOH B 2 302 959 HOH HOH . QA 9 HOH B 3 303 960 HOH HOH . QA 9 HOH B 4 304 961 HOH HOH . QA 9 HOH B 5 305 962 HOH HOH . QA 9 HOH B 6 306 963 HOH HOH . QA 9 HOH B 7 307 964 HOH HOH . QA 9 HOH B 8 308 965 HOH HOH . RA 9 HOH C 1 801 966 HOH HOH . RA 9 HOH C 2 802 967 HOH HOH . RA 9 HOH C 3 803 968 HOH HOH . RA 9 HOH C 4 804 969 HOH HOH . RA 9 HOH C 5 805 970 HOH HOH . RA 9 HOH C 6 806 971 HOH HOH . RA 9 HOH C 7 807 972 HOH HOH . RA 9 HOH C 8 808 973 HOH HOH . RA 9 HOH C 9 809 974 HOH HOH . RA 9 HOH C 10 810 975 HOH HOH . RA 9 HOH C 11 811 976 HOH HOH . RA 9 HOH C 12 812 977 HOH HOH . SA 9 HOH D 1 301 979 HOH HOH . SA 9 HOH D 2 302 980 HOH HOH . SA 9 HOH D 3 303 981 HOH HOH . TA 9 HOH F 1 301 978 HOH HOH . TA 9 HOH F 2 302 982 HOH HOH . TA 9 HOH F 3 303 983 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 . . . T 7 168.879 73.338 -13.853 1 19.15 ? PB GDP 202 B 1 HETATM 2 O O1B GDP . . . T 7 168.747 72.309 -12.785 1 19.85 ? O1B GDP 202 B 1 HETATM 3 O O2B GDP . . . T 7 170.184 74.026 -13.815 1 20.44 ? O2B GDP 202 B 1 HETATM 4 O O3B GDP . . . T 7 168.422 73.002 -15.238 1 20.25 ? O3B GDP 202 B 1 HETATM 5 O O3A GDP . . . T 7 167.909 74.501 -13.379 1 21.75 ? O3A GDP 202 B 1 HETATM 6 P PA GDP . . . T 7 166.366 74.707 -13.809 1 23.13 ? PA GDP 202 B 1 HETATM 7 O O1A GDP . . . T 7 165.53 73.531 -13.35 1 22.89 ? O1A GDP 202 B 1 HETATM 8 O O2A GDP . . . T 7 166.33 75.104 -15.255 1 23.55 ? O2A GDP 202 B 1 HETATM 9 O O5' GDP . . . T 7 166.027 75.978 -12.873 1 23.66 ? O5' GDP 202 B 1 HETATM 10 C C5' GDP . . . T 7 165.8 75.698 -11.498 1 26.38 ? C5' GDP 202 B 1 HETATM 11 C C4' GDP . . . T 7 164.791 76.642 -10.895 1 29.96 ? C4' GDP 202 B 1 HETATM 12 O O4' GDP . . . T 7 165.44 77.855 -10.482 1 32.79 ? O4' GDP 202 B 1 HETATM 13 C C3' GDP . . . T 7 163.683 77.059 -11.86 1 31.59 ? C3' GDP 202 B 1 HETATM 14 O O3' GDP . . . T 7 162.593 76.106 -11.981 1 30.84 ? O3' GDP 202 B 1 HETATM 15 C C2' GDP . . . T 7 163.31 78.425 -11.3 1 32.4 ? C2' GDP 202 B 1 HETATM 16 O O2' GDP . . . T 7 162.413 78.288 -10.191 1 33 ? O2' GDP 202 B 1 HETATM 17 C C1' GDP . . . T 7 164.62 78.996 -10.778 1 34.22 ? C1' GDP 202 B 1 HETATM 18 N N9 GDP . . . T 7 165.239 79.842 -11.844 1 37.7 ? N9 GDP 202 B 1 HETATM 19 C C8 GDP . . . T 7 165.864 79.37 -12.935 1 40.32 ? C8 GDP 202 B 1 HETATM 20 N N7 GDP . . . T 7 166.318 80.365 -13.733 1 41.32 ? N7 GDP 202 B 1 HETATM 21 C C5 GDP . . . T 7 165.985 81.526 -13.162 1 41.03 ? C5 GDP 202 B 1 HETATM 22 C C6 GDP . . . T 7 166.171 82.967 -13.491 1 42.63 ? C6 GDP 202 B 1 HETATM 23 O O6 GDP . . . T 7 166.764 83.352 -14.525 1 42.16 ? O6 GDP 202 B 1 HETATM 24 N N1 GDP . . . T 7 165.685 83.861 -12.633 1 43.43 ? N1 GDP 202 B 1 HETATM 25 C C2 GDP . . . T 7 165.038 83.481 -11.521 1 44.03 ? C2 GDP 202 B 1 HETATM 26 N N2 GDP . . . T 7 164.565 84.445 -10.704 1 47.42 ? N2 GDP 202 B 1 HETATM 27 N N3 GDP . . . T 7 164.838 82.187 -11.166 1 41.76 ? N3 GDP 202 B 1 HETATM 28 C C4 GDP . . . T 7 165.281 81.174 -11.923 1 39.23 ? C4 GDP 202 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 246 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #