data_4B8W # _model_server_result.job_id dG-lTbBYmIOYeWXijN2x0A _model_server_result.datetime_utc '2024-11-24 01:35:35' _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 4b8w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":901}' # _entry.id 4B8W # _exptl.entry_id 4B8W _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 90 _cell.angle_gamma 90 _cell.entry_id 4B8W _cell.length_a 111.47 _cell.length_b 111.47 _cell.length_c 46.92 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4B8W _symmetry.cell_setting ? _symmetry.Int_Tables_number 77 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 42' # _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 ? 3 D N N ? 3 F N N # _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 4B8W _atom_sites.fract_transf_matrix[1][1] 0.008971 _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] 0.008971 _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] 0.021313 _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 NAP A 1 900 900 NAP NAP . D 3 GDP A 1 901 901 GDP GDP . E 2 NAP B 1 900 900 NAP NAP . F 3 GDP B 1 901 901 GDP GDP . 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 . 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 . # 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 . . . D 3 35.799 45.805 4.466 1 89.58 ? PB GDP 901 A 1 HETATM 2 O O1B GDP . . . D 3 34.711 46.234 3.554 1 90.18 ? O1B GDP 901 A 1 HETATM 3 O O2B GDP . . . D 3 35.414 44.6 5.344 1 91.57 ? O2B GDP 901 A 1 HETATM 4 O O3B GDP . . . D 3 37.129 45.505 3.766 1 89.55 ? O3B GDP 901 A 1 HETATM 5 O O3A GDP . . . D 3 36.112 46.859 5.579 1 85.1 ? O3A GDP 901 A 1 HETATM 6 P PA GDP . . . D 3 36.448 48.057 6.511 1 80.74 ? PA GDP 901 A 1 HETATM 7 O O1A GDP . . . D 3 35.313 48.98 6.716 1 79.65 ? O1A GDP 901 A 1 HETATM 8 O O2A GDP . . . D 3 37.024 47.433 7.766 1 78.22 ? O2A GDP 901 A 1 HETATM 9 O O5' GDP . . . D 3 37.777 48.558 5.701 1 79.67 ? O5' GDP 901 A 1 HETATM 10 C C5' GDP . . . D 3 38.888 47.779 5.197 1 74.52 ? C5' GDP 901 A 1 HETATM 11 C C4' GDP . . . D 3 39.345 48.213 3.819 1 69.2 ? C4' GDP 901 A 1 HETATM 12 O O4' GDP . . . D 3 39.798 49.586 3.852 1 66.19 ? O4' GDP 901 A 1 HETATM 13 C C3' GDP . . . D 3 40.517 47.417 3.246 1 66.82 ? C3' GDP 901 A 1 HETATM 14 O O3' GDP . . . D 3 40.449 47.24 1.834 1 64.5 ? O3' GDP 901 A 1 HETATM 15 C C2' GDP . . . D 3 41.73 48.231 3.705 1 65.68 ? C2' GDP 901 A 1 HETATM 16 O O2' GDP . . . D 3 42.86 48.034 2.865 1 67.3 ? O2' GDP 901 A 1 HETATM 17 C C1' GDP . . . D 3 41.192 49.658 3.599 1 63.44 ? C1' GDP 901 A 1 HETATM 18 N N9 GDP . . . D 3 41.794 50.599 4.564 1 59.3 ? N9 GDP 901 A 1 HETATM 19 C C8 GDP . . . D 3 42.719 51.566 4.285 1 57.34 ? C8 GDP 901 A 1 HETATM 20 N N7 GDP . . . D 3 43.04 52.296 5.326 1 56.3 ? N7 GDP 901 A 1 HETATM 21 C C5 GDP . . . D 3 42.28 51.78 6.366 1 55.83 ? C5 GDP 901 A 1 HETATM 22 C C6 GDP . . . D 3 42.167 52.175 7.78 1 55.05 ? C6 GDP 901 A 1 HETATM 23 O O6 GDP . . . D 3 42.847 53.066 8.295 1 54.59 ? O6 GDP 901 A 1 HETATM 24 N N1 GDP . . . D 3 41.256 51.451 8.532 1 55.1 ? N1 GDP 901 A 1 HETATM 25 C C2 GDP . . . D 3 40.541 50.451 8.018 1 55.54 ? C2 GDP 901 A 1 HETATM 26 N N2 GDP . . . D 3 39.671 49.792 8.787 1 55.37 ? N2 GDP 901 A 1 HETATM 27 N N3 GDP . . . D 3 40.642 50.052 6.714 1 56.56 ? N3 GDP 901 A 1 HETATM 28 C C4 GDP . . . D 3 41.512 50.732 5.898 1 57.3 ? C4 GDP 901 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 456 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #