data_7DAD # _model_server_result.job_id 4j1m4mHsH2N_Kefc1eLbvQ _model_server_result.datetime_utc '2024-11-05 08:27:56' _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 7dad # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":501}' # _entry.id 7DAD # _exptl.entry_id 7DAD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 9 _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 7DAD _cell.length_a 105.163 _cell.length_b 158.506 _cell.length_c 181.605 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7DAD _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 ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_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,X _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 # _struct_asym.details ? _struct_asym.entity_id 9 _struct_asym.id L _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc8 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc10 B OE1 GLN 11 B GLN 11 1_555 M MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc11 B OE1 GLU 111 B GLU 111 1_555 N CA CA . B CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.102 ? metalc ? metalc12 B OE2 GLU 111 B GLU 111 1_555 N CA CA . B CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.581 ? metalc ? metalc13 L O1A GDP . B GDP 501 1_555 M MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? metalc ? metalc14 C OD1 ASP 39 C ASP 39 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc15 C OD2 ASP 39 C ASP 39 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc16 C O THR 41 C THR 41 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc17 C OG1 THR 41 C THR 41 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc18 C O GLY 44 C GLY 44 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc19 C OE1 GLU 55 C GLU 55 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? metalc ? metalc20 C OE2 GLU 55 C GLU 55 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc21 R O1G GTP . C GTP 501 1_555 S MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc22 R O1B GTP . C GTP 501 1_555 S MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc23 F OE1 GLU 331 F GLU 331 1_555 X MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.769 ? metalc ? metalc24 F OE2 GLU 331 F GLU 331 1_555 X MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? metalc ? metalc25 F OD1 ASN 333 F ASN 333 1_555 X MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.76 ? metalc ? metalc26 W O2G ACP . F ACP 401 1_555 X MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? metalc ? metalc27 W O2B ACP . F ACP 401 1_555 X MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? # _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 210 n n PB O2B GDP sing 211 n n PB O3B GDP sing 212 n n PB O3A GDP sing 213 n n O2B HOB2 GDP sing 214 n n O3B HOB3 GDP sing 215 n n O3A PA GDP sing 216 n n PA O1A GDP doub 217 n n PA O2A GDP sing 218 n n PA O5' GDP sing 219 n n O2A HOA2 GDP sing 220 n n O5' C5' GDP sing 221 n n C5' C4' GDP sing 222 n n C5' H5' GDP sing 223 n n C5' "H5''" GDP sing 224 n n C4' O4' GDP sing 225 n n C4' C3' GDP sing 226 n n C4' H4' GDP sing 227 n n O4' C1' GDP sing 228 n n C3' O3' GDP sing 229 n n C3' C2' GDP sing 230 n n C3' H3' GDP sing 231 n n O3' HO3' GDP sing 232 n n C2' O2' GDP sing 233 n n C2' C1' GDP sing 234 n n C2' H2' GDP sing 235 n n O2' HO2' GDP sing 236 n n C1' N9 GDP sing 237 n n C1' H1' GDP sing 238 n n N9 C8 GDP sing 239 n y N9 C4 GDP sing 240 n y C8 N7 GDP doub 241 n y C8 H8 GDP sing 242 n n N7 C5 GDP sing 243 n y C5 C6 GDP sing 244 n n C5 C4 GDP doub 245 n y C6 O6 GDP doub 246 n n C6 N1 GDP sing 247 n n N1 C2 GDP sing 248 n n N1 HN1 GDP sing 249 n n C2 N2 GDP sing 250 n n C2 N3 GDP doub 251 n n N2 HN21 GDP sing 252 n n N2 HN22 GDP sing 253 n n N3 C4 GDP sing 254 n n # _atom_sites.entry_id 7DAD _atom_sites.fract_transf_matrix[1][1] 0.009509 _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] 0.006309 _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] 0.005506 _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 7 CA A 1 505 505 CA CA . L 9 GDP B 1 501 499 GDP GDP . M 6 MG B 1 502 500 MG MG . N 7 CA B 1 503 501 CA CA . O 10 MES B 1 504 502 MES MES . P 10 MES B 1 505 503 MES MES . Q 6 MG B 1 506 504 MG MG . R 5 GTP C 1 501 501 GTP GTP . S 6 MG C 1 502 502 MG MG . T 7 CA C 1 503 503 CA CA . U 5 GTP D 1 501 499 GTP GTP . V 11 EPD D 1 502 1 EPD EPD . W 12 ACP F 1 401 703 ACP ACP . X 6 MG F 1 402 1 MG MG . # 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 . . . L 9 18.922 49.749 15.922 1 29.64 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . L 9 18.623 50.907 14.994 1 24.64 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . L 9 19.484 50.216 17.249 1 45.87 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . L 9 19.969 48.857 15.274 1 41.76 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . L 9 17.637 48.832 16.229 1 40.11 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . L 9 16.336 49.397 16.983 1 19.55 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . L 9 15.131 49.262 16.088 1 40.11 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . L 9 16.559 50.828 17.384 1 30.4 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . L 9 16.165 48.367 18.195 1 17.86 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . L 9 15.044 47.489 18.226 1 22.29 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . L 9 14.422 47.517 19.608 1 22.37 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . L 9 13.997 48.853 19.851 1 31.61 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . L 9 13.195 46.655 19.718 1 24.24 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . L 9 13.163 46.145 21.051 1 34.77 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . L 9 12.042 47.6 19.492 1 27.22 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . L 9 10.928 47.343 20.345 1 44.21 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . L 9 12.593 48.898 19.978 1 24.21 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . L 9 12.131 50.029 19.173 1 31.44 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . L 9 12.365 50.274 17.871 1 29.49 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . L 9 11.782 51.452 17.51 1 36.83 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . L 9 11.172 51.971 18.611 1 36.28 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . L 9 10.385 53.178 18.968 1 35.76 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . L 9 10.125 54.048 18.11 1 37.83 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . L 9 9.954 53.315 20.237 1 38.61 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . L 9 10.213 52.408 21.205 1 37.31 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . L 9 9.753 52.613 22.466 1 37.49 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . L 9 10.923 51.278 20.951 1 35.41 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . L 9 11.412 51.02 19.702 1 37.57 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 42 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #