data_5Z4P # _model_server_result.job_id I5BjS-CtzYTHfTLvLoMCuw _model_server_result.datetime_utc '2024-12-22 05:57:18' _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 5z4p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":503}' # _entry.id 5Z4P # _exptl.entry_id 5Z4P _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 5Z4P _cell.length_a 103.832 _cell.length_b 154.843 _cell.length_c 181.024 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Z4P _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,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA _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 U 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 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 K CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.908 ? metalc ? metalc8 G O3G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc9 G O2B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc10 B OE1 GLN 11 B GLN 11 1_555 N MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc11 B OE2 GLU 108 B GLU 110 1_555 P CA CA . B CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.198 ? metalc ? metalc12 B OE1 GLU 111 B GLU 113 1_555 P CA CA . B CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.833 ? metalc ? metalc13 B OE1 GLU 111 B GLU 113 1_555 Z CA CA . C CA 508 4_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.821 ? metalc ? metalc14 B OD2 ASP 177 B ASP 179 1_555 N MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc15 M O2A GDP . B GDP 501 1_555 N MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc16 N MG MG . B MG 502 1_555 JA O HOH . B HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc17 C OE1 GLU 71 C GLU 71 1_555 V MG MG . C MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.938 ? metalc ? metalc18 U O3G GTP . C GTP 503 1_555 V MG MG . C MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc19 U O2B GTP . C GTP 503 1_555 V MG MG . C MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc20 V MG MG . C MG 504 1_555 KA O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.882 ? metalc ? metalc21 DA O2B GDP . D GDP 501 1_555 EA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? # _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 290 n n PG O2G GTP sing 291 n n PG O3G GTP sing 292 n n PG O3B GTP sing 293 n n O2G HOG2 GTP sing 294 n n O3G HOG3 GTP sing 295 n n O3B PB GTP sing 296 n n PB O1B GTP doub 297 n n PB O2B GTP sing 298 n n PB O3A GTP sing 299 n n O2B HOB2 GTP sing 300 n n O3A PA GTP sing 301 n n PA O1A GTP doub 302 n n PA O2A GTP sing 303 n n PA O5' GTP sing 304 n n O2A HOA2 GTP sing 305 n n O5' C5' GTP sing 306 n n C5' C4' GTP sing 307 n n C5' H5' GTP sing 308 n n C5' "H5''" GTP sing 309 n n C4' O4' GTP sing 310 n n C4' C3' GTP sing 311 n n C4' H4' GTP sing 312 n n O4' C1' GTP sing 313 n n C3' O3' GTP sing 314 n n C3' C2' GTP sing 315 n n C3' H3' GTP sing 316 n n O3' HO3' GTP sing 317 n n C2' O2' GTP sing 318 n n C2' C1' GTP sing 319 n n C2' H2' GTP sing 320 n n O2' HO2' GTP sing 321 n n C1' N9 GTP sing 322 n n C1' H1' GTP sing 323 n n N9 C8 GTP sing 324 n y N9 C4 GTP sing 325 n y C8 N7 GTP doub 326 n y C8 H8 GTP sing 327 n n N7 C5 GTP sing 328 n y C5 C6 GTP sing 329 n n C5 C4 GTP doub 330 n y C6 O6 GTP doub 331 n n C6 N1 GTP sing 332 n n N1 C2 GTP sing 333 n n N1 HN1 GTP sing 334 n n C2 N2 GTP sing 335 n n C2 N3 GTP doub 336 n n N2 HN21 GTP sing 337 n n N2 HN22 GTP sing 338 n n N3 C4 GTP sing 339 n n # _atom_sites.entry_id 5Z4P _atom_sites.fract_transf_matrix[1][1] 0.009631 _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] 0.006458 _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] 0.005524 _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 GOL A 1 503 504 GOL GOL . J 7 GOL A 1 504 505 GOL GOL . K 8 CA A 1 505 506 CA CA . L 7 GOL A 1 506 201 GOL GOL . M 9 GDP B 1 501 501 GDP GDP . N 6 MG B 1 502 502 MG MG . O 7 GOL B 1 503 506 GOL GOL . P 8 CA B 1 504 508 CA CA . Q 10 MES B 1 505 509 MES MES . R 11 97O B 1 506 999 97O UNK . S 7 GOL C 1 501 504 GOL GOL . T 7 GOL C 1 502 505 GOL GOL . U 5 GTP C 1 503 501 GTP GTP . V 6 MG C 1 504 502 MG MG . W 7 GOL C 1 505 503 GOL GOL . X 7 GOL C 1 506 504 GOL GOL . Y 7 GOL C 1 507 505 GOL GOL . Z 8 CA C 1 508 508 CA CA . AA 12 IMD C 1 509 509 IMD IMD . BA 12 IMD C 1 510 510 IMD IMD . CA 12 IMD C 1 511 511 IMD IMD . DA 9 GDP D 1 501 501 GDP GDP . EA 6 MG D 1 502 502 MG MG . FA 7 GOL D 1 503 504 GOL GOL . GA 7 GOL D 1 504 505 GOL GOL . HA 13 ACP F 1 401 402 ACP ACP . IA 14 HOH A 1 601 32 HOH HOH . IA 14 HOH A 2 602 46 HOH HOH . IA 14 HOH A 3 603 34 HOH HOH . IA 14 HOH A 4 604 28 HOH HOH . IA 14 HOH A 5 605 16 HOH HOH . IA 14 HOH A 6 606 30 HOH HOH . IA 14 HOH A 7 607 36 HOH HOH . IA 14 HOH A 8 608 31 HOH HOH . IA 14 HOH A 9 609 10 HOH HOH . IA 14 HOH A 10 610 6 HOH HOH . IA 14 HOH A 11 611 21 HOH HOH . JA 14 HOH B 1 601 17 HOH HOH . JA 14 HOH B 2 602 37 HOH HOH . JA 14 HOH B 3 603 41 HOH HOH . JA 14 HOH B 4 604 40 HOH HOH . JA 14 HOH B 5 605 19 HOH HOH . JA 14 HOH B 6 606 38 HOH HOH . JA 14 HOH B 7 607 42 HOH HOH . JA 14 HOH B 8 608 39 HOH HOH . JA 14 HOH B 9 609 3 HOH HOH . JA 14 HOH B 10 610 7 HOH HOH . JA 14 HOH B 11 611 20 HOH HOH . JA 14 HOH B 12 612 18 HOH HOH . JA 14 HOH B 13 613 44 HOH HOH . KA 14 HOH C 1 601 8 HOH HOH . KA 14 HOH C 2 602 49 HOH HOH . KA 14 HOH C 3 603 14 HOH HOH . KA 14 HOH C 4 604 50 HOH HOH . KA 14 HOH C 5 605 11 HOH HOH . KA 14 HOH C 6 606 45 HOH HOH . KA 14 HOH C 7 607 48 HOH HOH . KA 14 HOH C 8 608 47 HOH HOH . KA 14 HOH C 9 609 4 HOH HOH . KA 14 HOH C 10 610 51 HOH HOH . KA 14 HOH C 11 611 15 HOH HOH . KA 14 HOH C 12 612 1 HOH HOH . KA 14 HOH C 13 613 2 HOH HOH . KA 14 HOH C 14 614 9 HOH HOH . KA 14 HOH C 15 615 5 HOH HOH . KA 14 HOH C 16 616 12 HOH HOH . KA 14 HOH C 17 617 43 HOH HOH . LA 14 HOH D 1 601 52 HOH HOH . LA 14 HOH D 2 602 23 HOH HOH . LA 14 HOH D 3 603 22 HOH HOH . LA 14 HOH D 4 604 25 HOH HOH . MA 14 HOH F 1 501 13 HOH HOH . MA 14 HOH F 2 502 26 HOH HOH . MA 14 HOH F 3 503 27 HOH HOH . MA 14 HOH F 4 504 35 HOH HOH . MA 14 HOH F 5 505 33 HOH HOH . MA 14 HOH F 6 506 24 HOH HOH . MA 14 HOH F 7 507 29 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 . . . U 5 20.07 -18.113 16.805 1 43.87 ? PG GTP 503 C 1 HETATM 2 O O1G GTP . . . U 5 20.24 -16.634 16.544 1 42.45 ? O1G GTP 503 C 1 HETATM 3 O O2G GTP . . . U 5 21.427 -18.663 17.213 1 47.26 ? O2G GTP 503 C 1 HETATM 4 O O3G GTP . . . U 5 19.042 -18.349 17.894 1 46.73 ? O3G GTP 503 C 1 HETATM 5 O O3B GTP . . . U 5 19.661 -18.915 15.474 1 47.1 ? O3B GTP 503 C 1 HETATM 6 P PB GTP . . . U 5 18.403 -19.92 15.37 1 40.98 ? PB GTP 503 C 1 HETATM 7 O O1B GTP . . . U 5 18.686 -21.044 14.414 1 47.96 ? O1B GTP 503 C 1 HETATM 8 O O2B GTP . . . U 5 17.858 -20.412 16.689 1 51.51 ? O2B GTP 503 C 1 HETATM 9 O O3A GTP . . . U 5 17.381 -18.89 14.699 1 50.19 ? O3A GTP 503 C 1 HETATM 10 P PA GTP . . . U 5 15.864 -19.272 14.365 1 44.88 ? PA GTP 503 C 1 HETATM 11 O O1A GTP . . . U 5 15.759 -20.745 14.053 1 47.64 ? O1A GTP 503 C 1 HETATM 12 O O2A GTP . . . U 5 14.964 -18.844 15.523 1 46.87 ? O2A GTP 503 C 1 HETATM 13 O O5' GTP . . . U 5 15.713 -18.35 13.053 1 46.9 ? O5' GTP 503 C 1 HETATM 14 C C5' GTP . . . U 5 14.829 -17.253 12.984 1 44.85 ? C5' GTP 503 C 1 HETATM 15 C C4' GTP . . . U 5 13.861 -17.521 11.847 1 42.94 ? C4' GTP 503 C 1 HETATM 16 O O4' GTP . . . U 5 13.355 -18.833 11.964 1 43.67 ? O4' GTP 503 C 1 HETATM 17 C C3' GTP . . . U 5 12.672 -16.616 11.891 1 48.41 ? C3' GTP 503 C 1 HETATM 18 O O3' GTP . . . U 5 12.43 -16.285 10.552 1 43.08 ? O3' GTP 503 C 1 HETATM 19 C C2' GTP . . . U 5 11.56 -17.49 12.422 1 47.79 ? C2' GTP 503 C 1 HETATM 20 O O2' GTP . . . U 5 10.321 -17.102 11.885 1 57.16 ? O2' GTP 503 C 1 HETATM 21 C C1' GTP . . . U 5 11.946 -18.871 11.948 1 40.71 ? C1' GTP 503 C 1 HETATM 22 N N9 GTP . . . U 5 11.544 -19.934 12.888 1 44.64 ? N9 GTP 503 C 1 HETATM 23 C C8 GTP . . . U 5 12.012 -20.107 14.171 1 43.86 ? C8 GTP 503 C 1 HETATM 24 N N7 GTP . . . U 5 11.407 -21.202 14.69 1 46.86 ? N7 GTP 503 C 1 HETATM 25 C C5 GTP . . . U 5 10.569 -21.747 13.757 1 45.11 ? C5 GTP 503 C 1 HETATM 26 C C6 GTP . . . U 5 9.716 -22.861 13.753 1 43.42 ? C6 GTP 503 C 1 HETATM 27 O O6 GTP . . . U 5 9.597 -23.615 14.725 1 44.74 ? O6 GTP 503 C 1 HETATM 28 N N1 GTP . . . U 5 8.978 -23.146 12.63 1 43.26 ? N1 GTP 503 C 1 HETATM 29 C C2 GTP . . . U 5 9.067 -22.341 11.507 1 43.2 ? C2 GTP 503 C 1 HETATM 30 N N2 GTP . . . U 5 8.35 -22.63 10.414 1 35.82 ? N2 GTP 503 C 1 HETATM 31 N N3 GTP . . . U 5 9.911 -21.242 11.527 1 43.2 ? N3 GTP 503 C 1 HETATM 32 C C4 GTP . . . U 5 10.649 -20.95 12.622 1 42.34 ? C4 GTP 503 C 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #