data_2X77 # _model_server_result.job_id 4K-NRLgXYEvGSQcWiY71eg _model_server_result.datetime_utc '2025-03-04 22:27:18' _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 2x77 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":188}' # _entry.id 2X77 # _exptl.entry_id 2X77 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 93.1 _cell.angle_gamma 90 _cell.entry_id 2X77 _cell.length_a 35.286 _cell.length_b 78.944 _cell.length_c 58.034 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2X77 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 2 C N N ? 2 E 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 disulf ? disulf1 A SG CYS 85 A CYS 83 1_555 B SG CYS 85 B CYS 83 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc1 A OG1 THR 36 A THR 34 1_555 D MG MG . A MG 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc2 C O1B GDP . A GDP 188 1_555 D MG MG . A MG 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc3 D MG MG . A MG 189 1_555 G O HOH . A HOH 2013 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.879 ? metalc ? metalc4 D MG MG . A MG 189 1_555 G O HOH . A HOH 2017 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc5 D MG MG . A MG 189 1_555 G O HOH . A HOH 2049 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc6 D MG MG . A MG 189 1_555 G O HOH . A HOH 2050 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc7 B OG1 THR 36 B THR 34 1_555 F MG MG . B MG 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc8 B OE2 GLU 59 B GLU 57 1_555 F MG MG . B MG 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? metalc ? metalc9 E O1B GDP . B GDP 188 1_555 F MG MG . B MG 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc10 F MG MG . B MG 189 1_555 H O HOH . B HOH 2010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc11 F MG MG . B MG 189 1_555 H O HOH . B HOH 2015 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc12 F MG MG . B MG 189 1_555 H O HOH . B HOH 2029 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc13 F MG MG . B MG 189 1_555 H O HOH . B HOH 2030 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? # _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 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 2X77 _atom_sites.fract_transf_matrix[1][1] 0.02834 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001535 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012667 _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] 0.017257 _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 C 2 GDP A 1 188 188 GDP GDP . D 3 MG A 1 189 189 MG MG . E 2 GDP B 1 188 188 GDP GDP . F 3 MG B 1 189 189 MG MG . G 4 HOH A 1 2001 2001 HOH HOH . G 4 HOH A 2 2002 2002 HOH HOH . G 4 HOH A 3 2003 2003 HOH HOH . G 4 HOH A 4 2004 2004 HOH HOH . G 4 HOH A 5 2005 2005 HOH HOH . G 4 HOH A 6 2006 2006 HOH HOH . G 4 HOH A 7 2007 2007 HOH HOH . G 4 HOH A 8 2008 2008 HOH HOH . G 4 HOH A 9 2009 2009 HOH HOH . G 4 HOH A 10 2010 2010 HOH HOH . G 4 HOH A 11 2011 2011 HOH HOH . G 4 HOH A 12 2012 2012 HOH HOH . G 4 HOH A 13 2013 2013 HOH HOH . G 4 HOH A 14 2014 2014 HOH HOH . G 4 HOH A 15 2015 2015 HOH HOH . G 4 HOH A 16 2016 2016 HOH HOH . G 4 HOH A 17 2017 2017 HOH HOH . G 4 HOH A 18 2018 2018 HOH HOH . G 4 HOH A 19 2019 2019 HOH HOH . G 4 HOH A 20 2020 2020 HOH HOH . G 4 HOH A 21 2021 2021 HOH HOH . G 4 HOH A 22 2022 2022 HOH HOH . G 4 HOH A 23 2023 2023 HOH HOH . G 4 HOH A 24 2024 2024 HOH HOH . G 4 HOH A 25 2025 2025 HOH HOH . G 4 HOH A 26 2026 2026 HOH HOH . G 4 HOH A 27 2027 2027 HOH HOH . G 4 HOH A 28 2028 2028 HOH HOH . G 4 HOH A 29 2029 2029 HOH HOH . G 4 HOH A 30 2030 2030 HOH HOH . G 4 HOH A 31 2031 2031 HOH HOH . G 4 HOH A 32 2032 2032 HOH HOH . G 4 HOH A 33 2033 2033 HOH HOH . G 4 HOH A 34 2034 2034 HOH HOH . G 4 HOH A 35 2035 2035 HOH HOH . G 4 HOH A 36 2036 2036 HOH HOH . G 4 HOH A 37 2037 2037 HOH HOH . G 4 HOH A 38 2038 2038 HOH HOH . G 4 HOH A 39 2039 2039 HOH HOH . G 4 HOH A 40 2040 2040 HOH HOH . G 4 HOH A 41 2041 2041 HOH HOH . G 4 HOH A 42 2042 2042 HOH HOH . G 4 HOH A 43 2043 2043 HOH HOH . G 4 HOH A 44 2044 2044 HOH HOH . G 4 HOH A 45 2045 2045 HOH HOH . G 4 HOH A 46 2046 2046 HOH HOH . G 4 HOH A 47 2047 2047 HOH HOH . G 4 HOH A 48 2048 2048 HOH HOH . G 4 HOH A 49 2049 2049 HOH HOH . G 4 HOH A 50 2050 2050 HOH HOH . H 4 HOH B 1 2001 2001 HOH HOH . H 4 HOH B 2 2002 2002 HOH HOH . H 4 HOH B 3 2003 2003 HOH HOH . H 4 HOH B 4 2004 2004 HOH HOH . H 4 HOH B 5 2005 2005 HOH HOH . H 4 HOH B 6 2006 2006 HOH HOH . H 4 HOH B 7 2007 2007 HOH HOH . H 4 HOH B 8 2008 2008 HOH HOH . H 4 HOH B 9 2009 2009 HOH HOH . H 4 HOH B 10 2010 2010 HOH HOH . H 4 HOH B 11 2011 2011 HOH HOH . H 4 HOH B 12 2012 2012 HOH HOH . H 4 HOH B 13 2013 2013 HOH HOH . H 4 HOH B 14 2014 2014 HOH HOH . H 4 HOH B 15 2015 2015 HOH HOH . H 4 HOH B 16 2016 2016 HOH HOH . H 4 HOH B 17 2017 2017 HOH HOH . H 4 HOH B 18 2018 2018 HOH HOH . H 4 HOH B 19 2019 2019 HOH HOH . H 4 HOH B 20 2020 2020 HOH HOH . H 4 HOH B 21 2021 2021 HOH HOH . H 4 HOH B 22 2022 2022 HOH HOH . H 4 HOH B 23 2023 2023 HOH HOH . H 4 HOH B 24 2024 2024 HOH HOH . H 4 HOH B 25 2025 2025 HOH HOH . H 4 HOH B 26 2026 2026 HOH HOH . H 4 HOH B 27 2027 2027 HOH HOH . H 4 HOH B 28 2028 2028 HOH HOH . H 4 HOH B 29 2029 2029 HOH HOH . H 4 HOH B 30 2030 2030 HOH HOH . H 4 HOH B 31 2031 2031 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 . . . E 2 28.321 38.235 50.105 1 25.4 ? PB GDP 188 B 1 HETATM 2 O O1B GDP . . . E 2 28.749 36.737 50.254 1 21.46 ? O1B GDP 188 B 1 HETATM 3 O O2B GDP . . . E 2 26.805 38.158 50.519 1 24.96 ? O2B GDP 188 B 1 HETATM 4 O O3B GDP . . . E 2 28.308 38.685 48.641 1 27.39 ? O3B GDP 188 B 1 HETATM 5 O O3A GDP . . . E 2 29.064 39.29 51.01 1 26.56 ? O3A GDP 188 B 1 HETATM 6 P PA GDP . . . E 2 30.611 39.213 51.776 1 22.71 ? PA GDP 188 B 1 HETATM 7 O O1A GDP . . . E 2 31.519 38.502 50.824 1 26.98 ? O1A GDP 188 B 1 HETATM 8 O O2A GDP . . . E 2 30.52 38.572 53.096 1 23.45 ? O2A GDP 188 B 1 HETATM 9 O O5' GDP . . . E 2 30.833 40.759 52.01 1 22.5 ? O5' GDP 188 B 1 HETATM 10 C C5' GDP . . . E 2 30.785 41.781 51.077 1 28.83 ? C5' GDP 188 B 1 HETATM 11 C C4' GDP . . . E 2 31.718 42.975 51.613 1 31.22 ? C4' GDP 188 B 1 HETATM 12 O O4' GDP . . . E 2 31.072 43.502 52.805 1 31.05 ? O4' GDP 188 B 1 HETATM 13 C C3' GDP . . . E 2 33.162 42.583 51.999 1 32.14 ? C3' GDP 188 B 1 HETATM 14 O O3' GDP . . . E 2 34.036 43.695 51.686 1 34.46 ? O3' GDP 188 B 1 HETATM 15 C C2' GDP . . . E 2 33.018 42.465 53.502 1 32.98 ? C2' GDP 188 B 1 HETATM 16 O O2' GDP . . . E 2 34.206 42.782 54.181 1 33.24 ? O2' GDP 188 B 1 HETATM 17 C C1' GDP . . . E 2 32.054 43.601 53.843 1 31.28 ? C1' GDP 188 B 1 HETATM 18 N N9 GDP . . . E 2 31.205 43.316 54.999 1 28.01 ? N9 GDP 188 B 1 HETATM 19 C C8 GDP . . . E 2 30.581 42.153 55.226 1 27.73 ? C8 GDP 188 B 1 HETATM 20 N N7 GDP . . . E 2 29.866 42.246 56.352 1 28.11 ? N7 GDP 188 B 1 HETATM 21 C C5 GDP . . . E 2 30.054 43.483 56.84 1 28.09 ? C5 GDP 188 B 1 HETATM 22 C C6 GDP . . . E 2 29.579 44.138 57.968 1 28.21 ? C6 GDP 188 B 1 HETATM 23 O O6 GDP . . . E 2 28.815 43.558 58.742 1 25.6 ? O6 GDP 188 B 1 HETATM 24 N N1 GDP . . . E 2 29.969 45.477 58.204 1 26.65 ? N1 GDP 188 B 1 HETATM 25 C C2 GDP . . . E 2 30.839 46.084 57.311 1 28.7 ? C2 GDP 188 B 1 HETATM 26 N N2 GDP . . . E 2 31.193 47.356 57.523 1 28.87 ? N2 GDP 188 B 1 HETATM 27 N N3 GDP . . . E 2 31.268 45.423 56.209 1 27.24 ? N3 GDP 188 B 1 HETATM 28 C C4 GDP . . . E 2 30.906 44.158 55.969 1 27.79 ? C4 GDP 188 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #