data_8CLF # _model_server_result.job_id wRuJfntHwDesQ9yxOZ7TqA _model_server_result.datetime_utc '2024-11-05 11:03:10' _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":"G","auth_seq_id":501}' # _entry.id 8CLF # _exptl.entry_id 8CLF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-TRIPHOSPHATE" _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 ? 5 G N N ? 5 M 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 H16 N5 O14 P3' _chem_comp.formula_weight 523.18 _chem_comp.id GTP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _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 PG O1G GTP doub 225 n n PG O2G GTP sing 226 n n PG O3G GTP sing 227 n n PG O3B GTP sing 228 n n O2G HOG2 GTP sing 229 n n O3G HOG3 GTP sing 230 n n O3B PB GTP sing 231 n n PB O1B GTP doub 232 n n PB O2B GTP sing 233 n n PB O3A GTP sing 234 n n O2B HOB2 GTP sing 235 n n O3A PA GTP sing 236 n n PA O1A GTP doub 237 n n PA O2A GTP sing 238 n n PA O5' GTP sing 239 n n O2A HOA2 GTP sing 240 n n O5' C5' GTP sing 241 n n C5' C4' GTP sing 242 n n C5' H5' GTP sing 243 n n C5' "H5''" GTP sing 244 n n C4' O4' GTP sing 245 n n C4' C3' GTP sing 246 n n C4' H4' GTP sing 247 n n O4' C1' GTP sing 248 n n C3' O3' GTP sing 249 n n C3' C2' GTP sing 250 n n C3' H3' GTP sing 251 n n O3' HO3' GTP sing 252 n n C2' O2' GTP sing 253 n n C2' C1' GTP sing 254 n n C2' H2' GTP sing 255 n n O2' HO2' GTP sing 256 n n C1' N9 GTP sing 257 n n C1' H1' GTP sing 258 n n N9 C8 GTP sing 259 n y N9 C4 GTP sing 260 n y C8 N7 GTP doub 261 n y C8 H8 GTP sing 262 n n N7 C5 GTP sing 263 n y C5 C6 GTP sing 264 n n C5 C4 GTP doub 265 n y C6 O6 GTP doub 266 n n C6 N1 GTP sing 267 n n N1 C2 GTP sing 268 n n N1 HN1 GTP sing 269 n n C2 N2 GTP sing 270 n n C2 N3 GTP doub 271 n n N2 HN21 GTP sing 272 n n N2 HN22 GTP sing 273 n n N3 C4 GTP sing 274 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 PG GTP . . . G 5 27.742 75.186 45.88 1 70.83 ? PG GTP 501 A 1 HETATM 2 O O1G GTP . . . G 5 26.487 75.528 45.141 1 62.09 ? O1G GTP 501 A 1 HETATM 3 O O2G GTP . . . G 5 28.964 75.78 45.248 1 64.66 ? O2G GTP 501 A 1 HETATM 4 O O3G GTP . . . G 5 27.878 73.718 46.141 1 46.15 ? O3G GTP 501 A 1 HETATM 5 O O3B GTP . . . G 5 27.618 75.869 47.331 1 79.93 ? O3B GTP 501 A 1 HETATM 6 P PB GTP . . . G 5 26.98 77.241 47.845 1 54.04 ? PB GTP 501 A 1 HETATM 7 O O1B GTP . . . G 5 26.688 78.099 46.667 1 57.29 ? O1B GTP 501 A 1 HETATM 8 O O2B GTP . . . G 5 27.822 77.765 48.95 1 54.68 ? O2B GTP 501 A 1 HETATM 9 O O3A GTP . . . G 5 25.601 76.71 48.453 1 62.82 ? O3A GTP 501 A 1 HETATM 10 P PA GTP . . . G 5 24.41 77.398 49.268 1 54.11 ? PA GTP 501 A 1 HETATM 11 O O1A GTP . . . G 5 23.184 77.388 48.423 1 72.63 ? O1A GTP 501 A 1 HETATM 12 O O2A GTP . . . G 5 24.88 78.701 49.815 1 60.68 ? O2A GTP 501 A 1 HETATM 13 O O5' GTP . . . G 5 24.239 76.353 50.465 1 52.04 ? O5' GTP 501 A 1 HETATM 14 C C5' GTP . . . G 5 23.056 75.524 50.497 1 56.79 ? C5' GTP 501 A 1 HETATM 15 C C4' GTP . . . G 5 22.45 75.59 51.875 1 61.46 ? C4' GTP 501 A 1 HETATM 16 O O4' GTP . . . G 5 22.289 76.979 52.253 1 58.89 ? O4' GTP 501 A 1 HETATM 17 C C3' GTP . . . G 5 21.054 74.98 52.024 1 61.43 ? C3' GTP 501 A 1 HETATM 18 O O3' GTP . . . G 5 20.827 74.545 53.357 1 53.99 ? O3' GTP 501 A 1 HETATM 19 C C2' GTP . . . G 5 20.159 76.166 51.674 1 55.37 ? C2' GTP 501 A 1 HETATM 20 O O2' GTP . . . G 5 18.873 76.029 52.231 1 60.97 ? O2' GTP 501 A 1 HETATM 21 C C1' GTP . . . G 5 20.922 77.313 52.323 1 49.19 ? C1' GTP 501 A 1 HETATM 22 N N9 GTP . . . G 5 20.741 78.596 51.658 1 61.03 ? N9 GTP 501 A 1 HETATM 23 C C8 GTP . . . G 5 21.053 78.903 50.36 1 58.6 ? C8 GTP 501 A 1 HETATM 24 N N7 GTP . . . G 5 20.789 80.147 50.045 1 59.66 ? N7 GTP 501 A 1 HETATM 25 C C5 GTP . . . G 5 20.272 80.691 51.212 1 61.08 ? C5 GTP 501 A 1 HETATM 26 C C6 GTP . . . G 5 19.813 82.003 51.479 1 67.47 ? C6 GTP 501 A 1 HETATM 27 O O6 GTP . . . G 5 19.768 82.972 50.711 1 66.83 ? O6 GTP 501 A 1 HETATM 28 N N1 GTP . . . G 5 19.373 82.128 52.796 1 60.53 ? N1 GTP 501 A 1 HETATM 29 C C2 GTP . . . G 5 19.378 81.127 53.733 1 57.47 ? C2 GTP 501 A 1 HETATM 30 N N2 GTP . . . G 5 18.915 81.441 54.948 1 54.01 ? N2 GTP 501 A 1 HETATM 31 N N3 GTP . . . G 5 19.809 79.893 53.488 1 62.99 ? N3 GTP 501 A 1 HETATM 32 C C4 GTP . . . G 5 20.24 79.748 52.213 1 62.21 ? C4 GTP 501 A 1 HETATM 33 H H5' GTP . . . G 5 23.283 74.608 50.274 1 56.79 ? H5' GTP 501 A 1 HETATM 34 H "H5''" GTP . . . G 5 22.416 75.827 49.834 1 56.79 ? "H5''" GTP 501 A 1 HETATM 35 H H4' GTP . . . G 5 23.064 75.079 52.425 1 61.46 ? H4' GTP 501 A 1 HETATM 36 H H3' GTP . . . G 5 20.904 74.196 51.472 1 61.43 ? H3' GTP 501 A 1 HETATM 37 H HO3' GTP . . . G 5 20.047 74.24 53.424 1 53.99 ? HO3' GTP 501 A 1 HETATM 38 H H2' GTP . . . G 5 20.002 76.276 50.723 1 55.37 ? H2' GTP 501 A 1 HETATM 39 H HO2' GTP . . . G 5 18.932 75.994 53.068 1 60.97 ? HO2' GTP 501 A 1 HETATM 40 H H1' GTP . . . G 5 20.588 77.419 53.227 1 49.19 ? H1' GTP 501 A 1 HETATM 41 H H8 GTP . . . G 5 21.431 78.263 49.737 1 58.6 ? H8 GTP 501 A 1 HETATM 42 H HN1 GTP . . . G 5 19.074 82.896 53.041 1 60.53 ? HN1 GTP 501 A 1 HETATM 43 H HN21 GTP . . . G 5 18.634 82.238 55.108 1 54.01 ? HN21 GTP 501 A 1 HETATM 44 H HN22 GTP . . . G 5 18.898 80.846 55.569 1 54.01 ? HN22 GTP 501 A 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 44 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 44 #