data_8WD0 # _model_server_result.job_id f5v8BYHZSrIVzi0rIw09KA _model_server_result.datetime_utc '2024-10-11 02:20:56' _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 8wd0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":501}' # _entry.id 8WD0 # _exptl.entry_id 8WD0 _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 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 8WD0 _cell.length_a 156.56 _cell.length_b 181.54 _cell.length_c 104.74 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8WD0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _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,Y,Z,AA _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 O N N ? 5 R 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.595 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? metalc ? metalc8 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc10 K MG MG . B MG 501 1_555 N O1A GDP . B GDP 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc11 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? metalc ? metalc12 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc13 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc14 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc15 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc16 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc17 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc18 O O1G GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc19 O O1B GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc20 R O1G GTP . D GTP 501 1_555 S MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? metalc ? metalc21 R O2G GTP . D GTP 501 1_555 S MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc22 R O1B GTP . D GTP 501 1_555 S MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? # _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 238 n n PG O2G GTP sing 239 n n PG O3G GTP sing 240 n n PG O3B GTP sing 241 n n O2G HOG2 GTP sing 242 n n O3G HOG3 GTP sing 243 n n O3B PB GTP sing 244 n n PB O1B GTP doub 245 n n PB O2B GTP sing 246 n n PB O3A GTP sing 247 n n O2B HOB2 GTP sing 248 n n O3A PA GTP sing 249 n n PA O1A GTP doub 250 n n PA O2A GTP sing 251 n n PA O5' GTP sing 252 n n O2A HOA2 GTP sing 253 n n O5' C5' GTP sing 254 n n C5' C4' GTP sing 255 n n C5' H5' GTP sing 256 n n C5' "H5''" GTP sing 257 n n C4' O4' GTP sing 258 n n C4' C3' GTP sing 259 n n C4' H4' GTP sing 260 n n O4' C1' GTP sing 261 n n C3' O3' GTP sing 262 n n C3' C2' GTP sing 263 n n C3' H3' GTP sing 264 n n O3' HO3' GTP sing 265 n n C2' O2' GTP sing 266 n n C2' C1' GTP sing 267 n n C2' H2' GTP sing 268 n n O2' HO2' GTP sing 269 n n C1' N9 GTP sing 270 n n C1' H1' GTP sing 271 n n N9 C8 GTP sing 272 n y N9 C4 GTP sing 273 n y C8 N7 GTP doub 274 n y C8 H8 GTP sing 275 n n N7 C5 GTP sing 276 n y C5 C6 GTP sing 277 n n C5 C4 GTP doub 278 n y C6 O6 GTP doub 279 n n C6 N1 GTP sing 280 n n N1 C2 GTP sing 281 n n N1 HN1 GTP sing 282 n n C2 N2 GTP sing 283 n n C2 N3 GTP doub 284 n n N2 HN21 GTP sing 285 n n N2 HN22 GTP sing 286 n n N3 C4 GTP sing 287 n n # _atom_sites.entry_id 8WD0 _atom_sites.fract_transf_matrix[1][1] 0.006387 _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] 0.005508 _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] 0.009547 _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 GOL A 1 504 504 GOL GOL . K 6 MG B 1 501 502 MG MG . L 9 MES B 1 502 503 MES MES . M 10 W4F B 1 503 601 W4F LIG . N 11 GDP B 1 504 501 GDP GDP . O 5 GTP C 1 501 501 GTP GTP . P 6 MG C 1 502 502 MG MG . Q 7 CA C 1 503 503 CA CA . R 5 GTP D 1 501 501 GTP GTP . S 6 MG D 1 502 502 MG MG . T 10 W4F D 1 503 601 W4F LIG . U 12 ACP F 1 401 401 ACP ACP . V 13 HOH A 1 601 7 HOH HOH . V 13 HOH A 2 602 9 HOH HOH . V 13 HOH A 3 603 54 HOH HOH . V 13 HOH A 4 604 57 HOH HOH . V 13 HOH A 5 605 72 HOH HOH . V 13 HOH A 6 606 49 HOH HOH . V 13 HOH A 7 607 74 HOH HOH . V 13 HOH A 8 608 59 HOH HOH . V 13 HOH A 9 609 37 HOH HOH . V 13 HOH A 10 610 69 HOH HOH . V 13 HOH A 11 611 56 HOH HOH . W 13 HOH B 1 601 33 HOH HOH . W 13 HOH B 2 602 48 HOH HOH . W 13 HOH B 3 603 36 HOH HOH . W 13 HOH B 4 604 19 HOH HOH . W 13 HOH B 5 605 75 HOH HOH . W 13 HOH B 6 606 44 HOH HOH . W 13 HOH B 7 607 38 HOH HOH . W 13 HOH B 8 608 14 HOH HOH . W 13 HOH B 9 609 2 HOH HOH . W 13 HOH B 10 610 40 HOH HOH . W 13 HOH B 11 611 18 HOH HOH . W 13 HOH B 12 612 13 HOH HOH . W 13 HOH B 13 613 52 HOH HOH . W 13 HOH B 14 614 45 HOH HOH . W 13 HOH B 15 615 4 HOH HOH . X 13 HOH C 1 601 24 HOH HOH . X 13 HOH C 2 602 10 HOH HOH . X 13 HOH C 3 603 31 HOH HOH . X 13 HOH C 4 604 34 HOH HOH . X 13 HOH C 5 605 32 HOH HOH . X 13 HOH C 6 606 16 HOH HOH . X 13 HOH C 7 607 67 HOH HOH . X 13 HOH C 8 608 35 HOH HOH . X 13 HOH C 9 609 41 HOH HOH . X 13 HOH C 10 610 11 HOH HOH . X 13 HOH C 11 611 76 HOH HOH . X 13 HOH C 12 612 53 HOH HOH . X 13 HOH C 13 613 26 HOH HOH . X 13 HOH C 14 614 30 HOH HOH . X 13 HOH C 15 615 22 HOH HOH . X 13 HOH C 16 616 1 HOH HOH . X 13 HOH C 17 617 66 HOH HOH . X 13 HOH C 18 618 15 HOH HOH . X 13 HOH C 19 619 25 HOH HOH . X 13 HOH C 20 620 70 HOH HOH . X 13 HOH C 21 621 50 HOH HOH . X 13 HOH C 22 622 47 HOH HOH . X 13 HOH C 23 623 43 HOH HOH . X 13 HOH C 24 624 60 HOH HOH . X 13 HOH C 25 625 62 HOH HOH . X 13 HOH C 26 626 51 HOH HOH . X 13 HOH C 27 627 58 HOH HOH . X 13 HOH C 28 628 68 HOH HOH . Y 13 HOH D 1 601 6 HOH HOH . Y 13 HOH D 2 602 29 HOH HOH . Y 13 HOH D 3 603 46 HOH HOH . Y 13 HOH D 4 604 63 HOH HOH . Z 13 HOH E 1 201 71 HOH HOH . Z 13 HOH E 2 202 65 HOH HOH . Z 13 HOH E 3 203 27 HOH HOH . Z 13 HOH E 4 204 55 HOH HOH . AA 13 HOH F 1 501 8 HOH HOH . AA 13 HOH F 2 502 39 HOH HOH . AA 13 HOH F 3 503 12 HOH HOH . AA 13 HOH F 4 504 42 HOH HOH . AA 13 HOH F 5 505 20 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 . . . O 5 18.281 -16.841 20.301 0 46.68 ? PG GTP 501 C 1 HETATM 2 O O1G GTP . . . O 5 18.491 -17.825 19.176 0 48.06 ? O1G GTP 501 C 1 HETATM 3 O O2G GTP . . . O 5 18.518 -17.515 21.631 0 47.12 ? O2G GTP 501 C 1 HETATM 4 O O3G GTP . . . O 5 16.865 -16.32 20.263 0 47.56 ? O3G GTP 501 C 1 HETATM 5 O O3B GTP . . . O 5 19.318 -15.622 20.117 0 45.1 ? O3B GTP 501 C 1 HETATM 6 P PB GTP . . . O 5 20.192 -15.483 18.771 0 44.36 ? PB GTP 501 C 1 HETATM 7 O O1B GTP . . . O 5 20.983 -16.749 18.553 0 44.66 ? O1B GTP 501 C 1 HETATM 8 O O2B GTP . . . O 5 21.109 -14.288 18.863 0 43.89 ? O2B GTP 501 C 1 HETATM 9 O O3A GTP . . . O 5 19.121 -15.298 17.581 0 45.01 ? O3A GTP 501 C 1 HETATM 10 P PA GTP . . . O 5 19.514 -14.505 16.233 0 44.72 ? PA GTP 501 C 1 HETATM 11 O O1A GTP . . . O 5 19.403 -15.44 15.053 0 46.11 ? O1A GTP 501 C 1 HETATM 12 O O2A GTP . . . O 5 20.904 -13.925 16.327 0 43.49 ? O2A GTP 501 C 1 HETATM 13 O O5' GTP . . . O 5 18.41 -13.339 16.107 0 47.01 ? O5' GTP 501 C 1 HETATM 14 C C5' GTP . . . O 5 17.468 -13.305 15.057 0 50.71 ? C5' GTP 501 C 1 HETATM 15 C C4' GTP . . . O 5 17.805 -12.18 14.086 0 50.66 ? C4' GTP 501 C 1 HETATM 16 O O4' GTP . . . O 5 19.15 -12.304 13.669 0 48.39 ? O4' GTP 501 C 1 HETATM 17 C C3' GTP . . . O 5 16.938 -12.243 12.841 0 54.53 ? C3' GTP 501 C 1 HETATM 18 O O3' GTP . . . O 5 16.369 -10.976 12.607 0 55.67 ? O3' GTP 501 C 1 HETATM 19 C C2' GTP . . . O 5 17.893 -12.569 11.715 0 53.1 ? C2' GTP 501 C 1 HETATM 20 O O2' GTP . . . O 5 17.577 -11.832 10.558 0 54.58 ? O2' GTP 501 C 1 HETATM 21 C C1' GTP . . . O 5 19.254 -12.18 12.265 0 48.52 ? C1' GTP 501 C 1 HETATM 22 N N9 GTP . . . O 5 20.296 -13.094 11.774 0 46.87 ? N9 GTP 501 C 1 HETATM 23 C C8 GTP . . . O 5 20.486 -14.398 12.15 0 46.86 ? C8 GTP 501 C 1 HETATM 24 N N7 GTP . . . O 5 21.553 -14.886 11.478 0 45.89 ? N7 GTP 501 C 1 HETATM 25 C C5 GTP . . . O 5 22.051 -13.91 10.687 0 45.99 ? C5 GTP 501 C 1 HETATM 26 C C6 GTP . . . O 5 23.125 -13.875 9.806 0 45.53 ? C6 GTP 501 C 1 HETATM 27 O O6 GTP . . . O 5 23.819 -14.876 9.642 0 45.54 ? O6 GTP 501 C 1 HETATM 28 N N1 GTP . . . O 5 23.403 -12.712 9.117 0 45.61 ? N1 GTP 501 C 1 HETATM 29 C C2 GTP . . . O 5 22.616 -11.594 9.309 0 45.51 ? C2 GTP 501 C 1 HETATM 30 N N2 GTP . . . O 5 22.884 -10.472 8.646 0 45.92 ? N2 GTP 501 C 1 HETATM 31 N N3 GTP . . . O 5 21.552 -11.637 10.186 0 45.68 ? N3 GTP 501 C 1 HETATM 32 C C4 GTP . . . O 5 21.273 -12.777 10.865 0 46.26 ? C4 GTP 501 C 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 50 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #