data_2VH5 # _model_server_result.job_id vu1jbJJA3EJLjV9JaJSH9w _model_server_result.datetime_utc '2025-07-02 23:40:17' _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 2vh5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1167}' # _entry.id 2VH5 # _exptl.entry_id 2VH5 _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 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 2VH5 _cell.length_a 75.863 _cell.length_b 85.403 _cell.length_c 63.084 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VH5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 5 _struct_asym.id G _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 OD2 ASP 62 H ASP 62 1_555 E ZN ZN . H ZN 1116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc2 A OD1 ASP 73 H ASP 73 1_555 D ZN ZN . H ZN 1115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc3 C OG SER 17 R SER 17 1_555 H MG MG . R MG 1168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.726 ? metalc ? metalc4 C OG1 THR 35 R THR 35 1_555 H MG MG . R MG 1168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.901 ? metalc ? metalc5 G O2G GTP . R GTP 1167 1_555 H MG MG . R MG 1168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.891 ? metalc ? metalc6 G O1B GTP . R GTP 1167 1_555 H MG MG . R MG 1168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.823 ? # _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 129 n n PG O2G GTP sing 130 n n PG O3G GTP sing 131 n n PG O3B GTP sing 132 n n O2G HOG2 GTP sing 133 n n O3G HOG3 GTP sing 134 n n O3B PB GTP sing 135 n n PB O1B GTP doub 136 n n PB O2B GTP sing 137 n n PB O3A GTP sing 138 n n O2B HOB2 GTP sing 139 n n O3A PA GTP sing 140 n n PA O1A GTP doub 141 n n PA O2A GTP sing 142 n n PA O5' GTP sing 143 n n O2A HOA2 GTP sing 144 n n O5' C5' GTP sing 145 n n C5' C4' GTP sing 146 n n C5' H5' GTP sing 147 n n C5' "H5''" GTP sing 148 n n C4' O4' GTP sing 149 n n C4' C3' GTP sing 150 n n C4' H4' GTP sing 151 n n O4' C1' GTP sing 152 n n C3' O3' GTP sing 153 n n C3' C2' GTP sing 154 n n C3' H3' GTP sing 155 n n O3' HO3' GTP sing 156 n n C2' O2' GTP sing 157 n n C2' C1' GTP sing 158 n n C2' H2' GTP sing 159 n n O2' HO2' GTP sing 160 n n C1' N9 GTP sing 161 n n C1' H1' GTP sing 162 n n N9 C8 GTP sing 163 n y N9 C4 GTP sing 164 n y C8 N7 GTP doub 165 n y C8 H8 GTP sing 166 n n N7 C5 GTP sing 167 n y C5 C6 GTP sing 168 n n C5 C4 GTP doub 169 n y C6 O6 GTP doub 170 n n C6 N1 GTP sing 171 n n N1 C2 GTP sing 172 n n N1 HN1 GTP sing 173 n n C2 N2 GTP sing 174 n n C2 N3 GTP doub 175 n n N2 HN21 GTP sing 176 n n N2 HN22 GTP sing 177 n n N3 C4 GTP sing 178 n n # _atom_sites.entry_id 2VH5 _atom_sites.fract_transf_matrix[1][1] 0.013182 _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] 0.011709 _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] 0.015852 _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 4 ZN H 1 1115 1115 ZN ZN . E 4 ZN H 1 1116 1116 ZN ZN . F 4 ZN R 1 1169 1169 ZN ZN . G 5 GTP R 1 1167 1167 GTP GTP . H 6 MG R 1 1168 1168 MG MG . I 7 HOH H 1 2001 2001 HOH HOH . I 7 HOH H 2 2002 2002 HOH HOH . I 7 HOH H 3 2003 2003 HOH HOH . I 7 HOH H 4 2004 2004 HOH HOH . I 7 HOH H 5 2005 2005 HOH HOH . I 7 HOH H 6 2006 2006 HOH HOH . I 7 HOH H 7 2007 2007 HOH HOH . I 7 HOH H 8 2008 2008 HOH HOH . I 7 HOH H 9 2009 2009 HOH HOH . I 7 HOH H 10 2010 2010 HOH HOH . J 7 HOH L 1 2001 2001 HOH HOH . J 7 HOH L 2 2002 2002 HOH HOH . J 7 HOH L 3 2003 2003 HOH HOH . J 7 HOH L 4 2004 2004 HOH HOH . J 7 HOH L 5 2005 2005 HOH HOH . J 7 HOH L 6 2006 2006 HOH HOH . J 7 HOH L 7 2007 2007 HOH HOH . J 7 HOH L 8 2008 2008 HOH HOH . J 7 HOH L 9 2009 2009 HOH HOH . K 7 HOH R 1 2001 2001 HOH HOH . K 7 HOH R 2 2002 2002 HOH HOH . K 7 HOH R 3 2003 2003 HOH HOH . K 7 HOH R 4 2004 2004 HOH HOH . K 7 HOH R 5 2005 2005 HOH HOH . K 7 HOH R 6 2006 2006 HOH HOH . K 7 HOH R 7 2007 2007 HOH HOH . K 7 HOH R 8 2008 2008 HOH HOH . K 7 HOH R 9 2009 2009 HOH HOH . K 7 HOH R 10 2010 2010 HOH HOH . K 7 HOH R 11 2011 2011 HOH HOH . K 7 HOH R 12 2012 2012 HOH HOH . K 7 HOH R 13 2013 2013 HOH HOH . K 7 HOH R 14 2014 2014 HOH HOH . K 7 HOH R 15 2015 2015 HOH HOH . K 7 HOH R 16 2016 2016 HOH HOH . K 7 HOH R 17 2017 2017 HOH HOH . K 7 HOH R 18 2018 2018 HOH HOH . K 7 HOH R 19 2019 2019 HOH HOH . K 7 HOH R 20 2020 2020 HOH HOH . K 7 HOH R 21 2021 2021 HOH HOH . K 7 HOH R 22 2022 2022 HOH HOH . K 7 HOH R 23 2023 2023 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 . . . G 5 1.522 22.286 22.231 1 34.7 ? PG GTP 1167 R 1 HETATM 2 O O1G GTP . . . G 5 1.078 22.901 20.936 1 34.9 ? O1G GTP 1167 R 1 HETATM 3 O O2G GTP . . . G 5 2.591 21.232 22.019 1 35.19 ? O2G GTP 1167 R 1 HETATM 4 O O3G GTP . . . G 5 0.318 21.667 22.876 1 35.91 ? O3G GTP 1167 R 1 HETATM 5 O O3B GTP . . . G 5 2.103 23.439 23.188 1 34.11 ? O3B GTP 1167 R 1 HETATM 6 P PB GTP . . . G 5 2.94 23.082 24.523 1 33.31 ? PB GTP 1167 R 1 HETATM 7 O O1B GTP . . . G 5 3.543 21.697 24.387 1 32.09 ? O1B GTP 1167 R 1 HETATM 8 O O2B GTP . . . G 5 2.034 23.244 25.723 1 33.09 ? O2B GTP 1167 R 1 HETATM 9 O O3A GTP . . . G 5 4.035 24.244 24.561 1 33.78 ? O3A GTP 1167 R 1 HETATM 10 P PA GTP . . . G 5 5.632 24.034 24.503 1 35.61 ? PA GTP 1167 R 1 HETATM 11 O O1A GTP . . . G 5 6.147 23.196 25.644 1 35.39 ? O1A GTP 1167 R 1 HETATM 12 O O2A GTP . . . G 5 6.132 23.497 23.173 1 36.28 ? O2A GTP 1167 R 1 HETATM 13 O O5' GTP . . . G 5 6.116 25.555 24.659 1 34.77 ? O5' GTP 1167 R 1 HETATM 14 C C5' GTP . . . G 5 5.702 26.566 23.772 1 35.1 ? C5' GTP 1167 R 1 HETATM 15 C C4' GTP . . . G 5 6.671 27.73 23.96 1 36.87 ? C4' GTP 1167 R 1 HETATM 16 O O4' GTP . . . G 5 6.67 28.152 25.321 1 37.37 ? O4' GTP 1167 R 1 HETATM 17 C C3' GTP . . . G 5 8.103 27.338 23.631 1 35.95 ? C3' GTP 1167 R 1 HETATM 18 O O3' GTP . . . G 5 8.715 28.419 22.98 1 34.89 ? O3' GTP 1167 R 1 HETATM 19 C C2' GTP . . . G 5 8.742 27.165 24.983 1 35.89 ? C2' GTP 1167 R 1 HETATM 20 O O2' GTP . . . G 5 10.097 27.506 24.911 1 38.05 ? O2' GTP 1167 R 1 HETATM 21 C C1' GTP . . . G 5 7.978 28.159 25.836 1 35.39 ? C1' GTP 1167 R 1 HETATM 22 N N9 GTP . . . G 5 7.955 27.814 27.26 1 35 ? N9 GTP 1167 R 1 HETATM 23 C C8 GTP . . . G 5 7.579 26.621 27.819 1 35.36 ? C8 GTP 1167 R 1 HETATM 24 N N7 GTP . . . G 5 7.713 26.71 29.165 1 35.53 ? N7 GTP 1167 R 1 HETATM 25 C C5 GTP . . . G 5 8.157 27.953 29.465 1 35.08 ? C5 GTP 1167 R 1 HETATM 26 C C6 GTP . . . G 5 8.455 28.565 30.67 1 34.4 ? C6 GTP 1167 R 1 HETATM 27 O O6 GTP . . . G 5 8.313 27.944 31.717 1 35.52 ? O6 GTP 1167 R 1 HETATM 28 N N1 GTP . . . G 5 8.911 29.863 30.677 1 34.58 ? N1 GTP 1167 R 1 HETATM 29 C C2 GTP . . . G 5 9.073 30.554 29.485 1 34.93 ? C2 GTP 1167 R 1 HETATM 30 N N2 GTP . . . G 5 9.504 31.81 29.489 1 34.9 ? N2 GTP 1167 R 1 HETATM 31 N N3 GTP . . . G 5 8.782 29.938 28.283 1 34.92 ? N3 GTP 1167 R 1 HETATM 32 C C4 GTP . . . G 5 8.324 28.656 28.275 1 35.2 ? C4 GTP 1167 R 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 32 #