data_4KB6 # _model_server_result.job_id -NmDgje2Ie0QJNxRe1RQcg _model_server_result.datetime_utc '2024-12-24 17:16:31' _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 4kb6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":502}' # _entry.id 4KB6 # _exptl.entry_id 4KB6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-TRIPHOSPHATE" _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 4KB6 _cell.length_a 86.28 _cell.length_b 111.89 _cell.length_c 117.78 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KB6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 4 _struct_asym.id E _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 OG SER 57 A SER 188 1_555 G MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.76 ? metalc ? metalc2 A OE1 GLN 69 A GLN 200 1_555 G MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc3 A OD1 ASN 71 A ASN 202 1_555 G MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc4 A SG CYS 242 A CYS 373 1_555 D ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc5 A SG CYS 243 A CYS 374 1_555 D ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc6 A SG CYS 250 A CYS 381 1_555 D ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc7 F O3B ATP . A ATP 503 1_555 G MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc8 F O3A ATP . A ATP 503 1_555 G MG MG . A MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? hydrog 'DC-DG PAIR' hydrog1 B N4 DC 1 B DC 1 1_555 C O6 DG 14 C DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N1 DG 2 B DG 2 1_555 C N3 DC 13 C DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N2 DG 2 B DG 2 1_555 C O2 DC 13 C DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B O6 DG 2 B DG 2 1_555 C N4 DC 13 C DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DG MISPAIR' hydrog5 B N6 DA 3 B DA 3 1_555 C O6 DG 11 C DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 DA 3 B DA 3 1_555 C N3 DT 12 C DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N6 DA 3 B DA 3 1_555 C O4 DT 12 C DT 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 DC 4 B DC 4 1_555 C N1 DG 11 C DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N4 DC 4 B DC 4 1_555 C O6 DG 11 C DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O2 DC 4 B DC 4 1_555 C N2 DG 11 C DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N1 DG 5 B DG 5 1_555 C N3 DC 10 C DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N2 DG 5 B DG 5 1_555 C O2 DC 10 C DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O6 DG 5 B DG 5 1_555 C N4 DC 10 C DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N3 DC 6 B DC 6 1_555 C N1 DG 9 C DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N4 DC 6 B DC 6 1_555 C O6 DG 9 C DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O2 DC 6 B DC 6 1_555 C N2 DG 9 C DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N3 DT 7 B DT 7 1_555 C N1 DA 8 C DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O4 DT 7 B DT 7 1_555 C N6 DA 8 C DA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N1 DA 8 B DA 8 1_555 C N3 DT 7 C DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N6 DA 8 B DA 8 1_555 C O4 DT 7 C DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog21 B N1 DG 9 B DG 9 1_555 C N3 DC 6 C DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog22 B N3 DC 10 B DC 10 1_555 C N2 DG 5 C DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'REVERSED WATSON-CRICK' hydrog23 B O2 DC 10 B DC 10 1_555 C N1 DG 5 C DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N1 DG 11 B DG 11 1_555 C N3 DC 4 C DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N2 DG 11 B DG 11 1_555 C O2 DC 4 C DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B O6 DG 11 B DG 11 1_555 C N4 DC 4 C DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N3 DT 12 B DT 12 1_555 C N1 DA 3 C DA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B O4 DT 12 B DT 12 1_555 C N6 DA 3 C DA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog29 B O2 DC 13 B DC 13 1_555 C N1 DG 2 C DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 327 n n PG O2G GTP sing 328 n n PG O3G GTP sing 329 n n PG O3B GTP sing 330 n n O2G HOG2 GTP sing 331 n n O3G HOG3 GTP sing 332 n n O3B PB GTP sing 333 n n PB O1B GTP doub 334 n n PB O2B GTP sing 335 n n PB O3A GTP sing 336 n n O2B HOB2 GTP sing 337 n n O3A PA GTP sing 338 n n PA O1A GTP doub 339 n n PA O2A GTP sing 340 n n PA O5' GTP sing 341 n n O2A HOA2 GTP sing 342 n n O5' C5' GTP sing 343 n n C5' C4' GTP sing 344 n n C5' H5' GTP sing 345 n n C5' "H5''" GTP sing 346 n n C4' O4' GTP sing 347 n n C4' C3' GTP sing 348 n n C4' H4' GTP sing 349 n n O4' C1' GTP sing 350 n n C3' O3' GTP sing 351 n n C3' C2' GTP sing 352 n n C3' H3' GTP sing 353 n n O3' HO3' GTP sing 354 n n C2' O2' GTP sing 355 n n C2' C1' GTP sing 356 n n C2' H2' GTP sing 357 n n O2' HO2' GTP sing 358 n n C1' N9 GTP sing 359 n n C1' H1' GTP sing 360 n n N9 C8 GTP sing 361 n y N9 C4 GTP sing 362 n y C8 N7 GTP doub 363 n y C8 H8 GTP sing 364 n n N7 C5 GTP sing 365 n y C5 C6 GTP sing 366 n n C5 C4 GTP doub 367 n y C6 O6 GTP doub 368 n n C6 N1 GTP sing 369 n n N1 C2 GTP sing 370 n n N1 HN1 GTP sing 371 n n C2 N2 GTP sing 372 n n C2 N3 GTP doub 373 n n N2 HN21 GTP sing 374 n n N2 HN22 GTP sing 375 n n N3 C4 GTP sing 376 n n # _atom_sites.entry_id 4KB6 _atom_sites.fract_transf_matrix[1][1] 0.01159 _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] 0.008937 _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] 0.00849 _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 D 3 ZN A 1 501 1 ZN ZN . E 4 GTP A 1 502 1 GTP GTP . F 5 ATP A 1 503 1 ATP ATP . G 6 MG A 1 504 1 MG MG . H 7 HOH A 1 601 1 HOH HOH . H 7 HOH A 2 602 2 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 . . . E 4 -28.328 -32.556 -11.625 1 157.15 ? PG GTP 502 A 1 HETATM 2 O O1G GTP . . . E 4 -27.138 -31.869 -11.065 1 148.19 ? O1G GTP 502 A 1 HETATM 3 O O2G GTP . . . E 4 -29.136 -32.932 -10.439 1 150.85 ? O2G GTP 502 A 1 HETATM 4 O O3G GTP . . . E 4 -27.802 -33.846 -12.122 1 132.35 ? O3G GTP 502 A 1 HETATM 5 O O3B GTP . . . E 4 -29.103 -31.699 -12.711 1 154.4 ? O3B GTP 502 A 1 HETATM 6 P PB GTP . . . E 4 -28.387 -30.724 -13.736 1 147.27 ? PB GTP 502 A 1 HETATM 7 O O1B GTP . . . E 4 -29.371 -29.979 -14.547 1 138.4 ? O1B GTP 502 A 1 HETATM 8 O O2B GTP . . . E 4 -27.698 -29.614 -13.032 1 149.85 ? O2B GTP 502 A 1 HETATM 9 O O3A GTP . . . E 4 -27.401 -31.532 -14.676 1 141.37 ? O3A GTP 502 A 1 HETATM 10 P PA GTP . . . E 4 -25.841 -31.689 -14.445 1 130.84 ? PA GTP 502 A 1 HETATM 11 O O1A GTP . . . E 4 -25.161 -32.052 -15.703 1 118.36 ? O1A GTP 502 A 1 HETATM 12 O O2A GTP . . . E 4 -25.19 -30.394 -14.149 1 138.27 ? O2A GTP 502 A 1 HETATM 13 O O5' GTP . . . E 4 -25.559 -32.75 -13.306 1 123.37 ? O5' GTP 502 A 1 HETATM 14 C C5' GTP . . . E 4 -24.563 -32.463 -12.346 1 123.51 ? C5' GTP 502 A 1 HETATM 15 C C4' GTP . . . E 4 -23.379 -33.293 -12.622 1 117.28 ? C4' GTP 502 A 1 HETATM 16 O O4' GTP . . . E 4 -23.358 -33.692 -14.074 1 113.12 ? O4' GTP 502 A 1 HETATM 17 C C3' GTP . . . E 4 -22.15 -32.526 -12.352 1 118.35 ? C3' GTP 502 A 1 HETATM 18 O O3' GTP . . . E 4 -21.558 -32.989 -11.106 1 113.33 ? O3' GTP 502 A 1 HETATM 19 C C2' GTP . . . E 4 -21.233 -32.769 -13.452 1 114.37 ? C2' GTP 502 A 1 HETATM 20 O O2' GTP . . . E 4 -19.997 -33.334 -12.941 1 111.28 ? O2' GTP 502 A 1 HETATM 21 C C1' GTP . . . E 4 -21.879 -33.745 -14.344 1 110.93 ? C1' GTP 502 A 1 HETATM 22 N N9 GTP . . . E 4 -21.6 -33.43 -15.669 1 109.56 ? N9 GTP 502 A 1 HETATM 23 C C8 GTP . . . E 4 -22.509 -33.141 -16.669 1 110.09 ? C8 GTP 502 A 1 HETATM 24 N N7 GTP . . . E 4 -21.846 -32.891 -17.816 1 104.84 ? N7 GTP 502 A 1 HETATM 25 C C5 GTP . . . E 4 -20.49 -33.009 -17.6 1 100.4 ? C5 GTP 502 A 1 HETATM 26 C C6 GTP . . . E 4 -19.288 -32.861 -18.453 1 99.34 ? C6 GTP 502 A 1 HETATM 27 O O6 GTP . . . E 4 -19.432 -32.518 -19.807 1 101.16 ? O6 GTP 502 A 1 HETATM 28 N N1 GTP . . . E 4 -18.04 -33.049 -17.915 1 102.76 ? N1 GTP 502 A 1 HETATM 29 C C2 GTP . . . E 4 -17.911 -33.392 -16.558 1 96.52 ? C2 GTP 502 A 1 HETATM 30 N N2 GTP . . . E 4 -16.62 -33.586 -16.003 1 97.02 ? N2 GTP 502 A 1 HETATM 31 N N3 GTP . . . E 4 -19.023 -33.54 -15.734 1 98.37 ? N3 GTP 502 A 1 HETATM 32 C C4 GTP . . . E 4 -20.307 -33.355 -16.231 1 102.69 ? C4 GTP 502 A 1 HETATM 33 H HO3' GTP . . . E 4 -20.687 -32.749 -11.078 1 136 ? HO3' GTP 502 A 1 HETATM 34 H HO2' GTP . . . E 4 -20.181 -34.046 -12.443 1 133.54 ? HO2' GTP 502 A 1 HETATM 35 H HN21 GTP . . . E 4 -16.528 -33.998 -15.187 1 116.42 ? HN21 GTP 502 A 1 HETATM 36 H HN22 GTP . . . E 4 -15.884 -33.303 -16.455 1 116.42 ? HN22 GTP 502 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 36 #