data_5FNV # _model_server_result.job_id S1ee_vHBMUu_za0USp8Y7Q _model_server_result.datetime_utc '2024-12-01 12:14:50' _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 5fnv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1429}' # _entry.id 5FNV # _exptl.entry_id 5FNV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 5FNV _cell.length_a 106.16 _cell.length_b 157.2 _cell.length_c 181.68 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5FNV _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 PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,Y,Z _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 8 _struct_asym.id J _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 covale ? covale1 C SG CYS 316 C CYS 316 1_555 R C03 X3H . C X3H 1443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.821 ? metalc ? metalc1 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 1440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc2 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 1440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc3 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 1440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc4 A O THR 41 A THR 41 1_555 I CA CA . A CA 1440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 1440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 1440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.859 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 1440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc8 G O1G GTP . A GTP 1438 1_555 H MG MG . A MG 1439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? metalc ? metalc9 G O2B GTP . A GTP 1438 1_555 H MG MG . A MG 1439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? metalc ? metalc10 H MG MG . A MG 1439 1_555 V O HOH . A HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc11 H MG MG . A MG 1439 1_555 V O HOH . A HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc12 H MG MG . A MG 1439 1_555 V O HOH . A HOH 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc13 H MG MG . A MG 1439 1_555 V O HOH . A HOH 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc14 B OE1 GLN 11 B GLN 11 1_555 K MG MG . B MG 1430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc15 B OE1 GLU 111 B GLU 111 1_555 L CA CA . B CA 1431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc16 J O1A GDP . B GDP 1429 1_555 K MG MG . B MG 1430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc17 K MG MG . B MG 1430 1_555 W O HOH . B HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.678 ? metalc ? metalc18 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 1442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc19 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 1442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc20 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 1442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc21 C O THR 41 C THR 41 1_555 Q CA CA . C CA 1442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc22 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 1442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc23 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 1442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.876 ? metalc ? metalc24 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 1442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc25 O O1B GTP . C GTP 1440 1_555 P MG MG . C MG 1441 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? metalc ? metalc26 O O1G GTP . C GTP 1440 1_555 P MG MG . C MG 1441 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? metalc ? metalc27 P MG MG . C MG 1441 1_555 X O HOH . C HOH 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc28 P MG MG . C MG 1441 1_555 X O HOH . C HOH 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc29 P MG MG . C MG 1441 1_555 X O HOH . C HOH 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc30 P MG MG . C MG 1441 1_555 X O HOH . C HOH 2008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc31 S O1B GTP . D GTP 1431 1_555 T MG MG . D MG 1432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.889 ? metalc ? metalc32 S O3G GTP . D GTP 1431 1_555 T MG MG . D MG 1432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.928 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 134 n n PB O2B GDP sing 135 n n PB O3B GDP sing 136 n n PB O3A GDP sing 137 n n O2B HOB2 GDP sing 138 n n O3B HOB3 GDP sing 139 n n O3A PA GDP sing 140 n n PA O1A GDP doub 141 n n PA O2A GDP sing 142 n n PA O5' GDP sing 143 n n O2A HOA2 GDP sing 144 n n O5' C5' GDP sing 145 n n C5' C4' GDP sing 146 n n C5' H5' GDP sing 147 n n C5' "H5''" GDP sing 148 n n C4' O4' GDP sing 149 n n C4' C3' GDP sing 150 n n C4' H4' GDP sing 151 n n O4' C1' GDP sing 152 n n C3' O3' GDP sing 153 n n C3' C2' GDP sing 154 n n C3' H3' GDP sing 155 n n O3' HO3' GDP sing 156 n n C2' O2' GDP sing 157 n n C2' C1' GDP sing 158 n n C2' H2' GDP sing 159 n n O2' HO2' GDP sing 160 n n C1' N9 GDP sing 161 n n C1' H1' GDP sing 162 n n N9 C8 GDP sing 163 n y N9 C4 GDP sing 164 n y C8 N7 GDP doub 165 n y C8 H8 GDP sing 166 n n N7 C5 GDP sing 167 n y C5 C6 GDP sing 168 n n C5 C4 GDP doub 169 n y C6 O6 GDP doub 170 n n C6 N1 GDP sing 171 n n N1 C2 GDP sing 172 n n N1 HN1 GDP sing 173 n n C2 N2 GDP sing 174 n n C2 N3 GDP doub 175 n n N2 HN21 GDP sing 176 n n N2 HN22 GDP sing 177 n n N3 C4 GDP sing 178 n n # _atom_sites.entry_id 5FNV _atom_sites.fract_transf_matrix[1][1] 0.00942 _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] 0.006361 _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] 0.005504 _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 1438 1438 GTP GTP . H 6 MG A 1 1439 1439 MG MG . I 7 CA A 1 1440 1440 CA CA . J 8 GDP B 1 1429 1429 GDP GDP . K 6 MG B 1 1430 1430 MG MG . L 7 CA B 1 1431 1431 CA CA . M 9 MES B 1 1432 1432 MES MES . N 9 MES B 1 1433 1433 MES MES . O 5 GTP C 1 1440 1440 GTP GTP . P 6 MG C 1 1441 1441 MG MG . Q 7 CA C 1 1442 1442 CA CA . R 10 X3H C 1 1443 1443 X3H X3H . S 5 GTP D 1 1431 1431 GTP GTP . T 6 MG D 1 1432 1432 MG MG . U 11 ACP F 1 1385 1385 ACP ACP . V 12 HOH A 1 2001 2001 HOH HOH . V 12 HOH A 2 2002 2002 HOH HOH . V 12 HOH A 3 2003 2003 HOH HOH . V 12 HOH A 4 2004 2004 HOH HOH . V 12 HOH A 5 2005 2005 HOH HOH . V 12 HOH A 6 2006 2006 HOH HOH . V 12 HOH A 7 2007 2007 HOH HOH . V 12 HOH A 8 2008 2008 HOH HOH . V 12 HOH A 9 2009 2009 HOH HOH . V 12 HOH A 10 2010 2010 HOH HOH . V 12 HOH A 11 2011 2011 HOH HOH . V 12 HOH A 12 2012 2012 HOH HOH . V 12 HOH A 13 2013 2013 HOH HOH . V 12 HOH A 14 2014 2014 HOH HOH . V 12 HOH A 15 2015 2015 HOH HOH . V 12 HOH A 16 2016 2016 HOH HOH . W 12 HOH B 1 2001 2001 HOH HOH . W 12 HOH B 2 2002 2002 HOH HOH . W 12 HOH B 3 2003 2003 HOH HOH . W 12 HOH B 4 2004 2004 HOH HOH . W 12 HOH B 5 2005 2005 HOH HOH . W 12 HOH B 6 2006 2006 HOH HOH . W 12 HOH B 7 2007 2007 HOH HOH . W 12 HOH B 8 2008 2008 HOH HOH . W 12 HOH B 9 2009 2009 HOH HOH . W 12 HOH B 10 2010 2010 HOH HOH . W 12 HOH B 11 2011 2011 HOH HOH . W 12 HOH B 12 2012 2012 HOH HOH . W 12 HOH B 13 2013 2013 HOH HOH . W 12 HOH B 14 2014 2014 HOH HOH . W 12 HOH B 15 2015 2015 HOH HOH . W 12 HOH B 16 2016 2016 HOH HOH . X 12 HOH C 1 2001 2001 HOH HOH . X 12 HOH C 2 2002 2002 HOH HOH . X 12 HOH C 3 2003 2003 HOH HOH . X 12 HOH C 4 2004 2004 HOH HOH . X 12 HOH C 5 2005 2005 HOH HOH . X 12 HOH C 6 2006 2006 HOH HOH . X 12 HOH C 7 2007 2007 HOH HOH . X 12 HOH C 8 2008 2008 HOH HOH . X 12 HOH C 9 2009 2009 HOH HOH . X 12 HOH C 10 2010 2010 HOH HOH . X 12 HOH C 11 2011 2011 HOH HOH . X 12 HOH C 12 2012 2012 HOH HOH . X 12 HOH C 13 2013 2013 HOH HOH . X 12 HOH C 14 2014 2014 HOH HOH . X 12 HOH C 15 2015 2015 HOH HOH . X 12 HOH C 16 2016 2016 HOH HOH . X 12 HOH C 17 2017 2017 HOH HOH . X 12 HOH C 18 2018 2018 HOH HOH . X 12 HOH C 19 2019 2019 HOH HOH . X 12 HOH C 20 2020 2020 HOH HOH . X 12 HOH C 21 2021 2021 HOH HOH . X 12 HOH C 22 2022 2022 HOH HOH . X 12 HOH C 23 2023 2023 HOH HOH . X 12 HOH C 24 2024 2024 HOH HOH . X 12 HOH C 25 2025 2025 HOH HOH . X 12 HOH C 26 2026 2026 HOH HOH . X 12 HOH C 27 2027 2027 HOH HOH . X 12 HOH C 28 2028 2028 HOH HOH . X 12 HOH C 29 2029 2029 HOH HOH . X 12 HOH C 30 2030 2030 HOH HOH . X 12 HOH C 31 2031 2031 HOH HOH . Y 12 HOH D 1 2001 2001 HOH HOH . Y 12 HOH D 2 2002 2002 HOH HOH . Y 12 HOH D 3 2003 2003 HOH HOH . Z 12 HOH F 1 2001 2001 HOH HOH . Z 12 HOH F 2 2002 2002 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 PB GDP . . . J 8 19.357 50.033 15.939 1 53.69 ? PB GDP 1429 B 1 HETATM 2 O O1B GDP . . . J 8 19.888 50.84 17.111 1 58.54 ? O1B GDP 1429 B 1 HETATM 3 O O2B GDP . . . J 8 18.864 51.007 14.915 1 50.88 ? O2B GDP 1429 B 1 HETATM 4 O O3B GDP . . . J 8 20.325 48.987 15.439 1 57.45 ? O3B GDP 1429 B 1 HETATM 5 O O3A GDP . . . J 8 18.118 49.099 16.448 1 52.06 ? O3A GDP 1429 B 1 HETATM 6 P PA GDP . . . J 8 16.646 49.629 16.941 1 51.91 ? PA GDP 1429 B 1 HETATM 7 O O1A GDP . . . J 8 15.643 49.451 15.79 1 66.89 ? O1A GDP 1429 B 1 HETATM 8 O O2A GDP . . . J 8 16.887 51.007 17.537 1 47.89 ? O2A GDP 1429 B 1 HETATM 9 O O5' GDP . . . J 8 16.396 48.574 18.146 1 48.74 ? O5' GDP 1429 B 1 HETATM 10 C C5' GDP . . . J 8 15.39 47.588 18.297 1 51.01 ? C5' GDP 1429 B 1 HETATM 11 C C4' GDP . . . J 8 14.83 47.649 19.722 1 54.65 ? C4' GDP 1429 B 1 HETATM 12 O O4' GDP . . . J 8 14.368 48.967 19.964 1 52.64 ? O4' GDP 1429 B 1 HETATM 13 C C3' GDP . . . J 8 13.619 46.756 19.952 1 56.73 ? C3' GDP 1429 B 1 HETATM 14 O O3' GDP . . . J 8 13.516 46.331 21.319 1 57.54 ? O3' GDP 1429 B 1 HETATM 15 C C2' GDP . . . J 8 12.436 47.624 19.594 1 55.81 ? C2' GDP 1429 B 1 HETATM 16 O O2' GDP . . . J 8 11.269 47.232 20.329 1 64.11 ? O2' GDP 1429 B 1 HETATM 17 C C1' GDP . . . J 8 12.933 48.967 20.027 1 55.18 ? C1' GDP 1429 B 1 HETATM 18 N N9 GDP . . . J 8 12.539 50.158 19.251 1 55.15 ? N9 GDP 1429 B 1 HETATM 19 C C8 GDP . . . J 8 12.9 50.505 18.01 1 55.84 ? C8 GDP 1429 B 1 HETATM 20 N N7 GDP . . . J 8 12.423 51.731 17.683 1 53.78 ? N7 GDP 1429 B 1 HETATM 21 C C5 GDP . . . J 8 11.756 52.186 18.75 1 54.47 ? C5 GDP 1429 B 1 HETATM 22 C C6 GDP . . . J 8 11.004 53.402 19.108 1 55.64 ? C6 GDP 1429 B 1 HETATM 23 O O6 GDP . . . J 8 10.866 54.339 18.304 1 56.94 ? O6 GDP 1429 B 1 HETATM 24 N N1 GDP . . . J 8 10.489 53.476 20.345 1 57.67 ? N1 GDP 1429 B 1 HETATM 25 C C2 GDP . . . J 8 10.619 52.489 21.26 1 55.8 ? C2 GDP 1429 B 1 HETATM 26 N N2 GDP . . . J 8 10.054 52.657 22.472 1 58.29 ? N2 GDP 1429 B 1 HETATM 27 N N3 GDP . . . J 8 11.285 51.336 21.013 1 51.81 ? N3 GDP 1429 B 1 HETATM 28 C C4 GDP . . . J 8 11.859 51.153 19.792 1 55.95 ? C4 GDP 1429 B 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 43 _model_server_stats.query_time_ms 520 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 28 #