data_8CLD # _model_server_result.job_id UOgmgtbz60TZQHjvoTUEgw _model_server_result.datetime_utc '2024-11-05 10:40:30' _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 8cld # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":501}' # _entry.id 8CLD # _exptl.entry_id 8CLD _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 8CLD _cell.length_a 106.06 _cell.length_b 159.61 _cell.length_c 180.61 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CLD _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 _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 O 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.17 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? metalc ? metalc7 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.712 ? metalc ? metalc8 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.855 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? metalc ? metalc10 J O1A GDP . B GDP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc11 C OD1 ASP 39 C ASP 39 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc12 C OD2 ASP 39 C ASP 39 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc13 C O THR 41 C THR 41 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.588 ? metalc ? metalc14 C OG1 THR 41 C THR 41 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc15 C O GLY 44 C GLY 44 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.99 ? metalc ? metalc16 C OE1 GLU 55 C GLU 55 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc17 C OE2 GLU 55 C GLU 55 1_555 N CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc18 C OE1 GLU 71 C GLU 71 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.868 ? metalc ? metalc19 L O1G GTP . C GTP 501 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc20 L O1B GTP . C GTP 501 1_555 M MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.943 ? # _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 224 n n PB O2B GDP sing 225 n n PB O3B GDP sing 226 n n PB O3A GDP sing 227 n n O2B HOB2 GDP sing 228 n n O3B HOB3 GDP sing 229 n n O3A PA GDP sing 230 n n PA O1A GDP doub 231 n n PA O2A GDP sing 232 n n PA O5' GDP sing 233 n n O2A HOA2 GDP sing 234 n n O5' C5' GDP sing 235 n n C5' C4' GDP sing 236 n n C5' H5' GDP sing 237 n n C5' "H5''" GDP sing 238 n n C4' O4' GDP sing 239 n n C4' C3' GDP sing 240 n n C4' H4' GDP sing 241 n n O4' C1' GDP sing 242 n n C3' O3' GDP sing 243 n n C3' C2' GDP sing 244 n n C3' H3' GDP sing 245 n n O3' HO3' GDP sing 246 n n C2' O2' GDP sing 247 n n C2' C1' GDP sing 248 n n C2' H2' GDP sing 249 n n O2' HO2' GDP sing 250 n n C1' N9 GDP sing 251 n n C1' H1' GDP sing 252 n n N9 C8 GDP sing 253 n y N9 C4 GDP sing 254 n y C8 N7 GDP doub 255 n y C8 H8 GDP sing 256 n n N7 C5 GDP sing 257 n y C5 C6 GDP sing 258 n n C5 C4 GDP doub 259 n y C6 O6 GDP doub 260 n n C6 N1 GDP sing 261 n n N1 C2 GDP sing 262 n n N1 HN1 GDP sing 263 n n C2 N2 GDP sing 264 n n C2 N3 GDP doub 265 n n N2 HN21 GDP sing 266 n n N2 HN22 GDP sing 267 n n N3 C4 GDP sing 268 n n # _atom_sites.entry_id 8CLD _atom_sites.fract_transf_matrix[1][1] 0.009429 _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] 0.006265 _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] 0.005537 _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 5 GTP C 1 501 506 GTP GTP . M 6 MG C 1 502 507 MG MG . N 7 CA C 1 503 508 CA CA . O 8 GDP D 1 501 509 GDP GTP . P 9 BKF D 1 502 510 BKF ANS . Q 10 ACP F 1 401 511 ACP ACP . R 11 HOH A 1 601 5 HOH HOH . S 11 HOH C 1 601 3 HOH HOH . T 11 HOH E 1 201 6 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 . . . O 8 25.448 -9.708 -42.981 1 69.55 ? PB GDP 501 D 1 HETATM 2 O O1B GDP . . . O 8 25.394 -8.552 -43.906 1 48.5 ? O1B GDP 501 D 1 HETATM 3 O O2B GDP . . . O 8 25.669 -9.475 -41.528 1 68.24 ? O2B GDP 501 D 1 HETATM 4 O O3B GDP . . . O 8 26.564 -10.691 -43.57 1 65.18 ? O3B GDP 501 D 1 HETATM 5 O O3A GDP . . . O 8 24.16 -10.638 -43.157 1 78.63 ? O3A GDP 501 D 1 HETATM 6 P PA GDP . . . O 8 22.68 -10.69 -42.549 1 72.72 ? PA GDP 501 D 1 HETATM 7 O O1A GDP . . . O 8 21.816 -11.396 -43.537 1 84.72 ? O1A GDP 501 D 1 HETATM 8 O O2A GDP . . . O 8 22.303 -9.318 -42.122 1 60.67 ? O2A GDP 501 D 1 HETATM 9 O O5' GDP . . . O 8 22.861 -11.611 -41.251 1 53.55 ? O5' GDP 501 D 1 HETATM 10 C C5' GDP . . . O 8 22.002 -12.768 -41.088 1 55.36 ? C5' GDP 501 D 1 HETATM 11 C C4' GDP . . . O 8 20.942 -12.468 -40.057 1 55.67 ? C4' GDP 501 D 1 HETATM 12 O O4' GDP . . . O 8 20.375 -11.166 -40.342 1 58.22 ? O4' GDP 501 D 1 HETATM 13 C C3' GDP . . . O 8 19.756 -13.445 -39.997 1 60 ? C3' GDP 501 D 1 HETATM 14 O O3' GDP . . . O 8 19.42 -13.783 -38.659 1 52.45 ? O3' GDP 501 D 1 HETATM 15 C C2' GDP . . . O 8 18.606 -12.676 -40.644 1 57.06 ? C2' GDP 501 D 1 HETATM 16 O O2' GDP . . . O 8 17.351 -13.018 -40.1 1 65.87 ? O2' GDP 501 D 1 HETATM 17 C C1' GDP . . . O 8 18.972 -11.239 -40.313 1 60.14 ? C1' GDP 501 D 1 HETATM 18 N N9 GDP . . . O 8 18.441 -10.3 -41.284 1 62.38 ? N9 GDP 501 D 1 HETATM 19 C C8 GDP . . . O 8 18.986 -9.967 -42.496 1 68.2 ? C8 GDP 501 D 1 HETATM 20 N N7 GDP . . . O 8 18.269 -9.101 -43.165 1 59.44 ? N7 GDP 501 D 1 HETATM 21 C C5 GDP . . . O 8 17.177 -8.866 -42.342 1 56.68 ? C5 GDP 501 D 1 HETATM 22 C C6 GDP . . . O 8 16.069 -8.017 -42.533 1 61.72 ? C6 GDP 501 D 1 HETATM 23 O O6 GDP . . . O 8 15.813 -7.3 -43.507 1 61.16 ? O6 GDP 501 D 1 HETATM 24 N N1 GDP . . . O 8 15.192 -8.087 -41.456 1 68.33 ? N1 GDP 501 D 1 HETATM 25 C C2 GDP . . . O 8 15.359 -8.855 -40.332 1 61.29 ? C2 GDP 501 D 1 HETATM 26 N N2 GDP . . . O 8 14.403 -8.777 -39.398 1 55.92 ? N2 GDP 501 D 1 HETATM 27 N N3 GDP . . . O 8 16.406 -9.651 -40.143 1 53.14 ? N3 GDP 501 D 1 HETATM 28 C C4 GDP . . . O 8 17.267 -9.604 -41.185 1 57.69 ? C4 GDP 501 D 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 33 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #