data_8CLF # _model_server_result.job_id DrIpSjdSg45Hm2Z38UCu1Q _model_server_result.datetime_utc '2025-08-03 16:11:06' _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 8clf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":501}' # _entry.id 8CLF # _exptl.entry_id 8CLF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-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 90 _cell.entry_id 8CLF _cell.length_a 106.65 _cell.length_b 160.33 _cell.length_c 180.95 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CLF _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _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 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 8 J N N ? 8 P 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 metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? metalc ? metalc8 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.872 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc10 H MG MG . A MG 502 1_555 S O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.875 ? metalc ? metalc11 J O1A GDP . B GDP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc12 K MG MG . B MG 502 1_555 T O HOH . B HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? metalc ? metalc13 C OD1 ASP 39 C ASP 39 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.603 ? metalc ? metalc14 C OD2 ASP 39 C ASP 39 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc15 C O THR 41 C THR 41 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc16 C OG1 THR 41 C THR 41 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc17 C O GLY 44 C GLY 44 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc18 C OE1 GLU 55 C GLU 55 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc19 C OE2 GLU 55 C GLU 55 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc20 C OD2 ASP 69 C ASP 69 1_555 N MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc21 N MG MG . C MG 502 1_555 U O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc22 N MG MG . C MG 502 1_555 U O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? metalc ? metalc23 N MG MG . C MG 502 1_555 U O HOH . C HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc24 D OE1 GLN 11 D GLN 11 1_555 Q MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.964 ? metalc ? metalc25 D OD2 ASP 177 D ASP 179 1_555 Q MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? metalc ? metalc26 P O1A GDP . D GDP 501 1_555 Q MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? # _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 134 n n PB O2B GDP sing 135 n n PB O3B GDP sing 136 n n PB O3A GDP sing 137 n n O2B HOB2 GDP sing 138 n n O3B HOB3 GDP sing 139 n n O3A PA GDP sing 140 n n PA O1A GDP doub 141 n n PA O2A GDP sing 142 n n PA O5' GDP sing 143 n n O2A HOA2 GDP sing 144 n n O5' C5' GDP sing 145 n n C5' C4' GDP sing 146 n n C5' H5' GDP sing 147 n n C5' "H5''" GDP sing 148 n n C4' O4' GDP sing 149 n n C4' C3' GDP sing 150 n n C4' H4' GDP sing 151 n n O4' C1' GDP sing 152 n n C3' O3' GDP sing 153 n n C3' C2' GDP sing 154 n n C3' H3' GDP sing 155 n n O3' HO3' GDP sing 156 n n C2' O2' GDP sing 157 n n C2' C1' GDP sing 158 n n C2' H2' GDP sing 159 n n O2' HO2' GDP sing 160 n n C1' N9 GDP sing 161 n n C1' H1' GDP sing 162 n n N9 C8 GDP sing 163 n y N9 C4 GDP sing 164 n y C8 N7 GDP doub 165 n y C8 H8 GDP sing 166 n n N7 C5 GDP sing 167 n y C5 C6 GDP sing 168 n n C5 C4 GDP doub 169 n y C6 O6 GDP doub 170 n n C6 N1 GDP sing 171 n n N1 C2 GDP sing 172 n n N1 HN1 GDP sing 173 n n C2 N2 GDP sing 174 n n C2 N3 GDP doub 175 n n N2 HN21 GDP sing 176 n n N2 HN22 GDP sing 177 n n N3 C4 GDP sing 178 n n # _atom_sites.entry_id 8CLF _atom_sites.fract_transf_matrix[1][1] 0.009376 _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] 0.006237 _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] 0.005526 _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 GDP B 1 501 504 GDP GDP . K 6 MG B 1 502 505 MG MG . L 9 V1O B 1 503 506 V1O SQB . M 5 GTP C 1 501 507 GTP GTP . N 6 MG C 1 502 508 MG MG . O 7 CA C 1 503 512 CA CA . P 8 GDP D 1 501 509 GDP GDP . Q 6 MG D 1 502 510 MG MG . R 10 ACP F 1 401 511 ACP ACP . S 11 HOH A 1 601 66 HOH HOH . S 11 HOH A 2 602 29 HOH HOH . S 11 HOH A 3 603 42 HOH HOH . S 11 HOH A 4 604 8 HOH HOH . T 11 HOH B 1 601 65 HOH HOH . T 11 HOH B 2 602 3 HOH HOH . T 11 HOH B 3 603 14 HOH HOH . T 11 HOH B 4 604 1 HOH HOH . T 11 HOH B 5 605 5 HOH HOH . T 11 HOH B 6 606 30 HOH HOH . U 11 HOH C 1 601 13 HOH HOH . U 11 HOH C 2 602 27 HOH HOH . U 11 HOH C 3 603 48 HOH HOH . U 11 HOH C 4 604 11 HOH HOH . U 11 HOH C 5 605 68 HOH HOH . U 11 HOH C 6 606 36 HOH HOH . U 11 HOH C 7 607 43 HOH HOH . U 11 HOH C 8 608 25 HOH HOH . U 11 HOH C 9 609 44 HOH HOH . U 11 HOH C 10 610 63 HOH HOH . U 11 HOH C 11 611 17 HOH HOH . U 11 HOH C 12 612 2 HOH HOH . U 11 HOH C 13 613 28 HOH HOH . U 11 HOH C 14 614 46 HOH HOH . U 11 HOH C 15 615 49 HOH HOH . U 11 HOH C 16 616 72 HOH HOH . U 11 HOH C 17 617 4 HOH HOH . U 11 HOH C 18 618 45 HOH HOH . V 11 HOH D 1 601 58 HOH HOH . W 11 HOH F 1 501 19 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 8 25.598 -9.435 -43.32 1 96.77 ? PB GDP 501 D 1 HETATM 2 O O1B GDP . . . P 8 25.273 -8.517 -44.465 1 71.49 ? O1B GDP 501 D 1 HETATM 3 O O2B GDP . . . P 8 25.559 -8.74 -41.989 1 112.05 ? O2B GDP 501 D 1 HETATM 4 O O3B GDP . . . P 8 26.867 -10.214 -43.531 1 88.99 ? O3B GDP 501 D 1 HETATM 5 O O3A GDP . . . P 8 24.414 -10.518 -43.29 1 104.09 ? O3A GDP 501 D 1 HETATM 6 P PA GDP . . . P 8 22.864 -10.383 -42.917 1 88.85 ? PA GDP 501 D 1 HETATM 7 O O1A GDP . . . P 8 22.064 -11.198 -43.875 1 121.84 ? O1A GDP 501 D 1 HETATM 8 O O2A GDP . . . P 8 22.533 -8.937 -42.77 1 93.67 ? O2A GDP 501 D 1 HETATM 9 O O5' GDP . . . P 8 22.858 -11.088 -41.481 1 88.78 ? O5' GDP 501 D 1 HETATM 10 C C5' GDP . . . P 8 22.143 -12.337 -41.326 1 95.69 ? C5' GDP 501 D 1 HETATM 11 C C4' GDP . . . P 8 21.059 -12.156 -40.293 1 92.07 ? C4' GDP 501 D 1 HETATM 12 O O4' GDP . . . P 8 20.338 -10.931 -40.58 1 96.65 ? O4' GDP 501 D 1 HETATM 13 C C3' GDP . . . P 8 19.994 -13.258 -40.23 1 97.29 ? C3' GDP 501 D 1 HETATM 14 O O3' GDP . . . P 8 19.605 -13.52 -38.889 1 82.53 ? O3' GDP 501 D 1 HETATM 15 C C2' GDP . . . P 8 18.834 -12.666 -41.028 1 91.27 ? C2' GDP 501 D 1 HETATM 16 O O2' GDP . . . P 8 17.587 -13.187 -40.627 1 93.63 ? O2' GDP 501 D 1 HETATM 17 C C1' GDP . . . P 8 18.959 -11.194 -40.668 1 84.12 ? C1' GDP 501 D 1 HETATM 18 N N9 GDP . . . P 8 18.389 -10.301 -41.664 1 76.8 ? N9 GDP 501 D 1 HETATM 19 C C8 GDP . . . P 8 18.866 -10.059 -42.925 1 85.61 ? C8 GDP 501 D 1 HETATM 20 N N7 GDP . . . P 8 18.14 -9.197 -43.593 1 88.43 ? N7 GDP 501 D 1 HETATM 21 C C5 GDP . . . P 8 17.124 -8.853 -42.713 1 77.87 ? C5 GDP 501 D 1 HETATM 22 C C6 GDP . . . P 8 16.04 -7.959 -42.879 1 83.49 ? C6 GDP 501 D 1 HETATM 23 O O6 GDP . . . P 8 15.753 -7.276 -43.87 1 81.22 ? O6 GDP 501 D 1 HETATM 24 N N1 GDP . . . P 8 15.246 -7.909 -41.735 1 86.94 ? N1 GDP 501 D 1 HETATM 25 C C2 GDP . . . P 8 15.465 -8.62 -40.582 1 83.44 ? C2 GDP 501 D 1 HETATM 26 N N2 GDP . . . P 8 14.588 -8.434 -39.588 1 83.43 ? N2 GDP 501 D 1 HETATM 27 N N3 GDP . . . P 8 16.483 -9.461 -40.42 1 75.04 ? N3 GDP 501 D 1 HETATM 28 C C4 GDP . . . P 8 17.265 -9.526 -41.522 1 80.36 ? C4 GDP 501 D 1 HETATM 29 H H5' GDP . . . P 8 22.752 -13.04 -41.053 1 95.69 ? H5' GDP 501 D 1 HETATM 30 H "H5''" GDP . . . P 8 21.757 -12.609 -42.173 1 95.69 ? "H5''" GDP 501 D 1 HETATM 31 H H4' GDP . . . P 8 21.534 -12.162 -39.447 1 92.07 ? H4' GDP 501 D 1 HETATM 32 H H3' GDP . . . P 8 20.306 -14.107 -40.58 1 97.29 ? H3' GDP 501 D 1 HETATM 33 H HO3' GDP . . . P 8 20.112 -14.102 -38.559 1 82.53 ? HO3' GDP 501 D 1 HETATM 34 H H2' GDP . . . P 8 18.873 -12.858 -41.978 1 91.27 ? H2' GDP 501 D 1 HETATM 35 H HO2' GDP . . . P 8 17.261 -13.646 -41.251 1 93.63 ? HO2' GDP 501 D 1 HETATM 36 H H1' GDP . . . P 8 18.473 -11.034 -39.844 1 84.12 ? H1' GDP 501 D 1 HETATM 37 H H8 GDP . . . P 8 19.66 -10.483 -43.286 1 85.61 ? H8 GDP 501 D 1 HETATM 38 H HN1 GDP . . . P 8 14.561 -7.389 -41.753 1 86.94 ? HN1 GDP 501 D 1 HETATM 39 H HN21 GDP . . . P 8 13.929 -7.891 -39.692 1 83.43 ? HN21 GDP 501 D 1 HETATM 40 H HN22 GDP . . . P 8 14.683 -8.858 -38.846 1 83.43 ? HN22 GDP 501 D 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 71 _model_server_stats.create_model_time_ms 186 _model_server_stats.query_time_ms 1364 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 40 #