data_4TO1 # _model_server_result.job_id g4oVwu-PCmVfXvP-zWRALQ _model_server_result.datetime_utc '2024-11-25 02:05:15' _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 4to1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":701}' # _entry.id 4TO1 # _exptl.entry_id 4TO1 _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 115.79 _cell.angle_gamma 90 _cell.entry_id 4TO1 _cell.length_a 86.204 _cell.length_b 141.586 _cell.length_c 98.187 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4TO1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,X _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 N N N ? 5 P N N ? 5 Q N N ? 5 T 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 F O3G DTP . A DTP 702 1_555 G MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.936 ? metalc ? metalc2 F O1B DTP . A DTP 702 1_555 G MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc3 G MG MG . A MG 703 1_555 P O2B GTP . C GTP 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc4 G MG MG . A MG 703 1_555 P O1A GTP . C GTP 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc5 G MG MG . A MG 703 1_555 P O3G GTP . C GTP 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.852 ? metalc ? metalc6 G MG MG . A MG 703 1_555 W O HOH . C HOH 808 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc7 H MG MG . A MG 704 1_555 U O HOH . A HOH 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc8 H MG MG . A MG 704 1_555 J O1B DTP . B DTP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc9 H MG MG . A MG 704 1_555 J O2G DTP . B DTP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.725 ? metalc ? metalc10 H MG MG . A MG 704 1_555 T O1G GTP . D GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.781 ? metalc ? metalc11 H MG MG . A MG 704 1_555 T O1B GTP . D GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc12 H MG MG . A MG 704 1_555 T O2A GTP . D GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc13 K O1B DCP . C DCP 701 1_555 L MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.849 ? metalc ? metalc14 K O2G DCP . C DCP 701 1_555 L MG MG . C MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc15 L MG MG . C MG 702 1_555 Q O3G GTP . D GTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc16 L MG MG . C MG 702 1_555 Q O2B GTP . D GTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? metalc ? metalc17 L MG MG . C MG 702 1_555 Q O1A GTP . D GTP 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc18 L MG MG . C MG 702 1_555 X O HOH . D HOH 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc19 M MG MG . C MG 703 1_555 N O1G GTP . C GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.835 ? metalc ? metalc20 M MG MG . C MG 703 1_555 N O1A GTP . C GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc21 M MG MG . C MG 703 1_555 N O1B GTP . C GTP 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc22 M MG MG . C MG 703 1_555 W O HOH . C HOH 821 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc23 M MG MG . C MG 703 1_555 R O2G DCP . D DCP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? metalc ? metalc24 M MG MG . C MG 703 1_555 R O1B DCP . D DCP 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.867 ? # _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 222 n n PG O2G GTP sing 223 n n PG O3G GTP sing 224 n n PG O3B GTP sing 225 n n O2G HOG2 GTP sing 226 n n O3G HOG3 GTP sing 227 n n O3B PB GTP sing 228 n n PB O1B GTP doub 229 n n PB O2B GTP sing 230 n n PB O3A GTP sing 231 n n O2B HOB2 GTP sing 232 n n O3A PA GTP sing 233 n n PA O1A GTP doub 234 n n PA O2A GTP sing 235 n n PA O5' GTP sing 236 n n O2A HOA2 GTP sing 237 n n O5' C5' GTP sing 238 n n C5' C4' GTP sing 239 n n C5' H5' GTP sing 240 n n C5' "H5''" GTP sing 241 n n C4' O4' GTP sing 242 n n C4' C3' GTP sing 243 n n C4' H4' GTP sing 244 n n O4' C1' GTP sing 245 n n C3' O3' GTP sing 246 n n C3' C2' GTP sing 247 n n C3' H3' GTP sing 248 n n O3' HO3' GTP sing 249 n n C2' O2' GTP sing 250 n n C2' C1' GTP sing 251 n n C2' H2' GTP sing 252 n n O2' HO2' GTP sing 253 n n C1' N9 GTP sing 254 n n C1' H1' GTP sing 255 n n N9 C8 GTP sing 256 n y N9 C4 GTP sing 257 n y C8 N7 GTP doub 258 n y C8 H8 GTP sing 259 n n N7 C5 GTP sing 260 n y C5 C6 GTP sing 261 n n C5 C4 GTP doub 262 n y C6 O6 GTP doub 263 n n C6 N1 GTP sing 264 n n N1 C2 GTP sing 265 n n N1 HN1 GTP sing 266 n n C2 N2 GTP sing 267 n n C2 N3 GTP doub 268 n n N2 HN21 GTP sing 269 n n N2 HN22 GTP sing 270 n n N3 C4 GTP sing 271 n n # _atom_sites.entry_id 4TO1 _atom_sites.fract_transf_matrix[1][1] 0.0116 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005605 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007063 _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] 0.011311 _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 E 2 DCP A 1 701 700 DCP DCP . F 3 DTP A 1 702 800 DTP DTP . G 4 MG A 1 703 850 MG MG . H 4 MG A 1 704 850 MG MG . I 2 DCP B 1 701 700 DCP DCP . J 3 DTP B 1 702 800 DTP DTP . K 2 DCP C 1 701 800 DCP DCP . L 4 MG C 1 702 850 MG MG . M 4 MG C 1 703 850 MG MG . N 5 GTP C 1 704 900 GTP GTP . O 2 DCP C 1 705 700 DCP DCP . P 5 GTP C 1 706 900 GTP GTP . Q 5 GTP D 1 701 900 GTP GTP . R 2 DCP D 1 702 800 DCP DCP . S 2 DCP D 1 703 700 DCP DCP . T 5 GTP D 1 704 900 GTP GTP . U 6 HOH A 1 801 11 HOH HOH . U 6 HOH A 2 802 18 HOH HOH . U 6 HOH A 3 803 22 HOH HOH . U 6 HOH A 4 804 31 HOH HOH . U 6 HOH A 5 805 32 HOH HOH . U 6 HOH A 6 806 44 HOH HOH . U 6 HOH A 7 807 46 HOH HOH . V 6 HOH B 1 801 15 HOH HOH . V 6 HOH B 2 802 34 HOH HOH . V 6 HOH B 3 803 38 HOH HOH . V 6 HOH B 4 804 48 HOH HOH . V 6 HOH B 5 805 51 HOH HOH . V 6 HOH B 6 806 52 HOH HOH . W 6 HOH C 1 801 25 HOH HOH . W 6 HOH C 2 802 1 HOH HOH . W 6 HOH C 3 803 3 HOH HOH . W 6 HOH C 4 804 4 HOH HOH . W 6 HOH C 5 805 9 HOH HOH . W 6 HOH C 6 806 10 HOH HOH . W 6 HOH C 7 807 12 HOH HOH . W 6 HOH C 8 808 14 HOH HOH . W 6 HOH C 9 809 17 HOH HOH . W 6 HOH C 10 810 19 HOH HOH . W 6 HOH C 11 811 20 HOH HOH . W 6 HOH C 12 812 21 HOH HOH . W 6 HOH C 13 813 27 HOH HOH . W 6 HOH C 14 814 33 HOH HOH . W 6 HOH C 15 815 47 HOH HOH . W 6 HOH C 16 816 49 HOH HOH . W 6 HOH C 17 817 50 HOH HOH . W 6 HOH C 18 818 53 HOH HOH . W 6 HOH C 19 819 54 HOH HOH . W 6 HOH C 20 820 58 HOH HOH . W 6 HOH C 21 821 59 HOH HOH . W 6 HOH C 22 822 60 HOH HOH . X 6 HOH D 1 801 55 HOH HOH . X 6 HOH D 2 802 56 HOH HOH . X 6 HOH D 3 803 57 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 . . . Q 5 -33.76 -33.909 117.633 1 24.09 ? PG GTP 701 D 1 HETATM 2 O O1G GTP . . . Q 5 -32.671 -34.782 118.156 1 23.4 ? O1G GTP 701 D 1 HETATM 3 O O2G GTP . . . Q 5 -35.136 -34.552 117.56 1 23.91 ? O2G GTP 701 D 1 HETATM 4 O O3G GTP . . . Q 5 -33.283 -33.244 116.382 1 22.92 ? O3G GTP 701 D 1 HETATM 5 O O3B GTP . . . Q 5 -33.981 -32.79 118.756 1 22.05 ? O3B GTP 701 D 1 HETATM 6 P PB GTP . . . Q 5 -34.358 -31.261 118.45 1 22.63 ? PB GTP 701 D 1 HETATM 7 O O1B GTP . . . Q 5 -35.519 -30.909 119.324 1 22.01 ? O1B GTP 701 D 1 HETATM 8 O O2B GTP . . . Q 5 -34.292 -31.006 116.988 1 23.83 ? O2B GTP 701 D 1 HETATM 9 O O3A GTP . . . Q 5 -33.139 -30.397 119.069 1 23.22 ? O3A GTP 701 D 1 HETATM 10 P PA GTP . . . Q 5 -31.605 -30.597 118.598 1 23.92 ? PA GTP 701 D 1 HETATM 11 O O1A GTP . . . Q 5 -31.588 -31.179 117.211 1 23.69 ? O1A GTP 701 D 1 HETATM 12 O O2A GTP . . . Q 5 -30.767 -31.293 119.66 1 22.81 ? O2A GTP 701 D 1 HETATM 13 O O5' GTP . . . Q 5 -31.258 -29.03 118.553 1 25.43 ? O5' GTP 701 D 1 HETATM 14 C C5' GTP . . . Q 5 -31.725 -28.146 117.542 1 27.59 ? C5' GTP 701 D 1 HETATM 15 C C4' GTP . . . Q 5 -30.511 -27.647 116.774 1 29.53 ? C4' GTP 701 D 1 HETATM 16 O O4' GTP . . . Q 5 -29.69 -26.844 117.643 1 30.42 ? O4' GTP 701 D 1 HETATM 17 C C3' GTP . . . Q 5 -29.565 -28.735 116.22 1 29 ? C3' GTP 701 D 1 HETATM 18 O O3' GTP . . . Q 5 -30.039 -29.139 114.916 1 28.1 ? O3' GTP 701 D 1 HETATM 19 C C2' GTP . . . Q 5 -28.193 -28.071 116.203 1 27.66 ? C2' GTP 701 D 1 HETATM 20 O O2' GTP . . . Q 5 -27.896 -27.542 114.913 1 26.57 ? O2' GTP 701 D 1 HETATM 21 C C1' GTP . . . Q 5 -28.342 -26.866 117.094 1 28.49 ? C1' GTP 701 D 1 HETATM 22 N N9 GTP . . . Q 5 -27.409 -26.852 118.233 1 28.98 ? N9 GTP 701 D 1 HETATM 23 C C8 GTP . . . Q 5 -26.682 -25.786 118.654 1 30.57 ? C8 GTP 701 D 1 HETATM 24 N N7 GTP . . . Q 5 -25.949 -26.098 119.735 1 27.99 ? N7 GTP 701 D 1 HETATM 25 C C5 GTP . . . Q 5 -26.222 -27.353 120.023 1 27 ? C5 GTP 701 D 1 HETATM 26 C C6 GTP . . . Q 5 -25.787 -28.281 121.056 1 26.59 ? C6 GTP 701 D 1 HETATM 27 O O6 GTP . . . Q 5 -24.994 -27.827 121.897 1 26.47 ? O6 GTP 701 D 1 HETATM 28 N N1 GTP . . . Q 5 -26.263 -29.546 121.027 1 26.67 ? N1 GTP 701 D 1 HETATM 29 C C2 GTP . . . Q 5 -27.16 -29.936 120.081 1 27.91 ? C2 GTP 701 D 1 HETATM 30 N N2 GTP . . . Q 5 -27.67 -31.172 120.034 1 29.24 ? N2 GTP 701 D 1 HETATM 31 N N3 GTP . . . Q 5 -27.628 -29.127 119.103 1 29.92 ? N3 GTP 701 D 1 HETATM 32 C C4 GTP . . . Q 5 -27.191 -27.847 119.039 1 28.45 ? C4 GTP 701 D 1 # _model_server_stats.io_time_ms 38 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 248 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #