data_3VHX # _model_server_result.job_id 2FERUvo7iSTCwrpK3eNknw _model_server_result.datetime_utc '2024-11-29 16:36:15' _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 3vhx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":184}' # _entry.id 3VHX # _exptl.entry_id 3VHX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 3 _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 98.74 _cell.angle_gamma 90 _cell.entry_id 3VHX _cell.length_a 45.743 _cell.length_b 174.573 _cell.length_c 76.814 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VHX _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,I,J,K,L,R,S,T,U 1 1 E,F,G,H,M,N,O,P,Q,V,W,X,Y 2 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 ? 3 I N N ? 3 K N N ? 3 M N N ? 3 P 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 OG1 THR 16 A THR 27 1_555 J MG MG . A MG 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.809 ? metalc ? metalc2 A OG1 THR 33 A THR 44 1_555 J MG MG . A MG 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc3 I O1B GTP . A GTP 184 1_555 J MG MG . A MG 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc4 I O1G GTP . A GTP 184 1_555 J MG MG . A MG 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc5 J MG MG . A MG 185 1_555 R O HOH . A HOH 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc6 C OG1 THR 16 C THR 27 1_555 L MG MG . C MG 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc7 C OG1 THR 33 C THR 44 1_555 L MG MG . C MG 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc8 K O1G GTP . C GTP 184 1_555 L MG MG . C MG 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc9 K O1B GTP . C GTP 184 1_555 L MG MG . C MG 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc10 L MG MG . C MG 185 1_555 T O HOH . C HOH 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.734 ? metalc ? metalc11 L MG MG . C MG 185 1_555 T O HOH . C HOH 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc12 E OG1 THR 16 E THR 27 1_555 N MG MG . E MG 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc13 E OG1 THR 33 E THR 44 1_555 N MG MG . E MG 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc14 M O1G GTP . E GTP 184 1_555 N MG MG . E MG 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc15 M O1B GTP . E GTP 184 1_555 N MG MG . E MG 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc16 N MG MG . E MG 185 1_555 V O HOH . E HOH 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc17 N MG MG . E MG 185 1_555 V O HOH . E HOH 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.725 ? metalc ? metalc18 G OG1 THR 16 G THR 27 1_555 Q MG MG . G MG 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc19 G OG1 THR 33 G THR 44 1_555 Q MG MG . G MG 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc20 P O1G GTP . G GTP 184 1_555 Q MG MG . G MG 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.85 ? metalc ? metalc21 P O1B GTP . G GTP 184 1_555 Q MG MG . G MG 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? # _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 142 n n PG O2G GTP sing 143 n n PG O3G GTP sing 144 n n PG O3B GTP sing 145 n n O2G HOG2 GTP sing 146 n n O3G HOG3 GTP sing 147 n n O3B PB GTP sing 148 n n PB O1B GTP doub 149 n n PB O2B GTP sing 150 n n PB O3A GTP sing 151 n n O2B HOB2 GTP sing 152 n n O3A PA GTP sing 153 n n PA O1A GTP doub 154 n n PA O2A GTP sing 155 n n PA O5' GTP sing 156 n n O2A HOA2 GTP sing 157 n n O5' C5' GTP sing 158 n n C5' C4' GTP sing 159 n n C5' H5' GTP sing 160 n n C5' "H5''" GTP sing 161 n n C4' O4' GTP sing 162 n n C4' C3' GTP sing 163 n n C4' H4' GTP sing 164 n n O4' C1' GTP sing 165 n n C3' O3' GTP sing 166 n n C3' C2' GTP sing 167 n n C3' H3' GTP sing 168 n n O3' HO3' GTP sing 169 n n C2' O2' GTP sing 170 n n C2' C1' GTP sing 171 n n C2' H2' GTP sing 172 n n O2' HO2' GTP sing 173 n n C1' N9 GTP sing 174 n n C1' H1' GTP sing 175 n n N9 C8 GTP sing 176 n y N9 C4 GTP sing 177 n y C8 N7 GTP doub 178 n y C8 H8 GTP sing 179 n n N7 C5 GTP sing 180 n y C5 C6 GTP sing 181 n n C5 C4 GTP doub 182 n y C6 O6 GTP doub 183 n n C6 N1 GTP sing 184 n n N1 C2 GTP sing 185 n n N1 HN1 GTP sing 186 n n C2 N2 GTP sing 187 n n C2 N3 GTP doub 188 n n N2 HN21 GTP sing 189 n n N2 HN22 GTP sing 190 n n N3 C4 GTP sing 191 n n # _atom_sites.entry_id 3VHX _atom_sites.fract_transf_matrix[1][1] 0.021861 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003361 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005728 _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] 0.013171 _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 I 3 GTP A 1 184 174 GTP GTP . J 4 MG A 1 185 175 MG MG . K 3 GTP C 1 184 174 GTP GTP . L 4 MG C 1 185 175 MG MG . M 3 GTP E 1 184 174 GTP GTP . N 4 MG E 1 185 175 MG MG . O 5 GOL F 1 1 1 GOL GOL . P 3 GTP G 1 184 174 GTP GTP . Q 4 MG G 1 185 175 MG MG . R 6 HOH A 1 186 20 HOH HOH . R 6 HOH A 2 187 24 HOH HOH . R 6 HOH A 3 188 37 HOH HOH . R 6 HOH A 4 189 51 HOH HOH . R 6 HOH A 5 190 63 HOH HOH . R 6 HOH A 6 191 65 HOH HOH . R 6 HOH A 7 192 78 HOH HOH . R 6 HOH A 8 193 92 HOH HOH . S 6 HOH B 1 808 6 HOH HOH . S 6 HOH B 2 809 17 HOH HOH . S 6 HOH B 3 810 25 HOH HOH . S 6 HOH B 4 811 53 HOH HOH . S 6 HOH B 5 812 58 HOH HOH . S 6 HOH B 6 813 85 HOH HOH . S 6 HOH B 7 814 96 HOH HOH . T 6 HOH C 1 186 3 HOH HOH . T 6 HOH C 2 187 12 HOH HOH . T 6 HOH C 3 188 16 HOH HOH . T 6 HOH C 4 189 19 HOH HOH . T 6 HOH C 5 190 21 HOH HOH . T 6 HOH C 6 191 22 HOH HOH . T 6 HOH C 7 192 30 HOH HOH . T 6 HOH C 8 193 31 HOH HOH . T 6 HOH C 9 194 34 HOH HOH . T 6 HOH C 10 195 35 HOH HOH . T 6 HOH C 11 196 38 HOH HOH . T 6 HOH C 12 197 39 HOH HOH . T 6 HOH C 13 198 41 HOH HOH . T 6 HOH C 14 199 42 HOH HOH . T 6 HOH C 15 200 46 HOH HOH . T 6 HOH C 16 201 47 HOH HOH . T 6 HOH C 17 202 48 HOH HOH . T 6 HOH C 18 203 49 HOH HOH . T 6 HOH C 19 204 57 HOH HOH . T 6 HOH C 20 205 66 HOH HOH . T 6 HOH C 21 206 79 HOH HOH . T 6 HOH C 22 207 82 HOH HOH . T 6 HOH C 23 208 89 HOH HOH . T 6 HOH C 24 209 90 HOH HOH . T 6 HOH C 25 210 93 HOH HOH . T 6 HOH C 26 211 101 HOH HOH . T 6 HOH C 27 212 102 HOH HOH . T 6 HOH C 28 213 105 HOH HOH . U 6 HOH D 1 808 4 HOH HOH . U 6 HOH D 2 809 5 HOH HOH . U 6 HOH D 3 810 7 HOH HOH . U 6 HOH D 4 811 11 HOH HOH . U 6 HOH D 5 812 18 HOH HOH . U 6 HOH D 6 813 33 HOH HOH . U 6 HOH D 7 814 62 HOH HOH . U 6 HOH D 8 815 69 HOH HOH . U 6 HOH D 9 816 81 HOH HOH . U 6 HOH D 10 817 84 HOH HOH . U 6 HOH D 11 818 87 HOH HOH . U 6 HOH D 12 819 88 HOH HOH . V 6 HOH E 1 186 2 HOH HOH . V 6 HOH E 2 187 14 HOH HOH . V 6 HOH E 3 188 27 HOH HOH . V 6 HOH E 4 189 28 HOH HOH . V 6 HOH E 5 190 29 HOH HOH . V 6 HOH E 6 191 32 HOH HOH . V 6 HOH E 7 192 45 HOH HOH . V 6 HOH E 8 193 50 HOH HOH . V 6 HOH E 9 194 52 HOH HOH . V 6 HOH E 10 195 54 HOH HOH . V 6 HOH E 11 196 64 HOH HOH . V 6 HOH E 12 197 67 HOH HOH . V 6 HOH E 13 198 70 HOH HOH . V 6 HOH E 14 199 71 HOH HOH . V 6 HOH E 15 200 72 HOH HOH . V 6 HOH E 16 201 83 HOH HOH . V 6 HOH E 17 202 86 HOH HOH . V 6 HOH E 18 203 91 HOH HOH . V 6 HOH E 19 204 94 HOH HOH . V 6 HOH E 20 205 98 HOH HOH . V 6 HOH E 21 206 100 HOH HOH . V 6 HOH E 22 207 104 HOH HOH . W 6 HOH F 1 808 8 HOH HOH . W 6 HOH F 2 809 9 HOH HOH . W 6 HOH F 3 810 10 HOH HOH . W 6 HOH F 4 811 15 HOH HOH . W 6 HOH F 5 812 23 HOH HOH . W 6 HOH F 6 813 36 HOH HOH . W 6 HOH F 7 814 40 HOH HOH . W 6 HOH F 8 815 56 HOH HOH . W 6 HOH F 9 816 59 HOH HOH . W 6 HOH F 10 817 61 HOH HOH . W 6 HOH F 11 818 74 HOH HOH . W 6 HOH F 12 819 75 HOH HOH . W 6 HOH F 13 820 76 HOH HOH . W 6 HOH F 14 821 77 HOH HOH . W 6 HOH F 15 822 95 HOH HOH . W 6 HOH F 16 823 103 HOH HOH . W 6 HOH F 17 824 1 HOH HOH . X 6 HOH G 1 186 44 HOH HOH . X 6 HOH G 2 187 68 HOH HOH . X 6 HOH G 3 188 73 HOH HOH . Y 6 HOH H 1 808 13 HOH HOH . Y 6 HOH H 2 809 26 HOH HOH . Y 6 HOH H 3 810 43 HOH HOH . Y 6 HOH H 4 811 55 HOH HOH . Y 6 HOH H 5 812 60 HOH HOH . Y 6 HOH H 6 813 80 HOH HOH . Y 6 HOH H 7 814 97 HOH HOH . Y 6 HOH H 8 815 99 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 . . . M 3 -22.564 -65.595 -59.334 1 36 ? PG GTP 184 E 1 HETATM 2 O O1G GTP . . . M 3 -21.587 -65.629 -60.478 1 35.38 ? O1G GTP 184 E 1 HETATM 3 O O2G GTP . . . M 3 -22.926 -66.999 -58.916 1 37.65 ? O2G GTP 184 E 1 HETATM 4 O O3G GTP . . . M 3 -22.011 -64.796 -58.18 1 34.95 ? O3G GTP 184 E 1 HETATM 5 O O3B GTP . . . M 3 -23.873 -64.832 -59.849 1 37.78 ? O3B GTP 184 E 1 HETATM 6 P PB GTP . . . M 3 -23.782 -63.307 -60.367 1 36.75 ? PB GTP 184 E 1 HETATM 7 O O1B GTP . . . M 3 -22.614 -63.139 -61.307 1 36.2 ? O1B GTP 184 E 1 HETATM 8 O O2B GTP . . . M 3 -23.687 -62.329 -59.224 1 35.01 ? O2B GTP 184 E 1 HETATM 9 O O3A GTP . . . M 3 -25.208 -63.156 -61.109 1 36.61 ? O3A GTP 184 E 1 HETATM 10 P PA GTP . . . M 3 -25.393 -63.235 -62.703 1 36.42 ? PA GTP 184 E 1 HETATM 11 O O1A GTP . . . M 3 -24.738 -64.45 -63.3 1 36.21 ? O1A GTP 184 E 1 HETATM 12 O O2A GTP . . . M 3 -24.898 -61.948 -63.326 1 34.9 ? O2A GTP 184 E 1 HETATM 13 O O5' GTP . . . M 3 -26.996 -63.342 -62.856 1 38.61 ? O5' GTP 184 E 1 HETATM 14 C C5' GTP . . . M 3 -27.738 -64.529 -62.709 1 39.53 ? C5' GTP 184 E 1 HETATM 15 C C4' GTP . . . M 3 -29.043 -64.393 -63.495 1 41.77 ? C4' GTP 184 E 1 HETATM 16 O O4' GTP . . . M 3 -29.756 -63.226 -63.106 1 41.47 ? O4' GTP 184 E 1 HETATM 17 C C3' GTP . . . M 3 -28.789 -64.272 -64.991 1 42.31 ? C3' GTP 184 E 1 HETATM 18 O O3' GTP . . . M 3 -29.729 -65.058 -65.687 1 44.69 ? O3' GTP 184 E 1 HETATM 19 C C2' GTP . . . M 3 -29.018 -62.797 -65.252 1 41.57 ? C2' GTP 184 E 1 HETATM 20 O O2' GTP . . . M 3 -29.399 -62.479 -66.569 1 43.91 ? O2' GTP 184 E 1 HETATM 21 C C1' GTP . . . M 3 -30.113 -62.485 -64.258 1 41.77 ? C1' GTP 184 E 1 HETATM 22 N N9 GTP . . . M 3 -30.135 -61.045 -64.005 1 40.09 ? N9 GTP 184 E 1 HETATM 23 C C8 GTP . . . M 3 -29.068 -60.265 -63.643 1 38.81 ? C8 GTP 184 E 1 HETATM 24 N N7 GTP . . . M 3 -29.493 -58.992 -63.502 1 38.65 ? N7 GTP 184 E 1 HETATM 25 C C5 GTP . . . M 3 -30.812 -58.956 -63.772 1 40.18 ? C5 GTP 184 E 1 HETATM 26 C C6 GTP . . . M 3 -31.725 -57.915 -63.779 1 41.56 ? C6 GTP 184 E 1 HETATM 27 O O6 GTP . . . M 3 -31.341 -56.78 -63.492 1 40.85 ? O6 GTP 184 E 1 HETATM 28 N N1 GTP . . . M 3 -33.048 -58.171 -64.097 1 43.93 ? N1 GTP 184 E 1 HETATM 29 C C2 GTP . . . M 3 -33.446 -59.458 -64.412 1 44.99 ? C2 GTP 184 E 1 HETATM 30 N N2 GTP . . . M 3 -34.711 -59.719 -64.726 1 48.03 ? N2 GTP 184 E 1 HETATM 31 N N3 GTP . . . M 3 -32.522 -60.483 -64.407 1 43.92 ? N3 GTP 184 E 1 HETATM 32 C C4 GTP . . . M 3 -31.229 -60.238 -64.091 1 41.19 ? C4 GTP 184 E 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #