data_3O47 # _model_server_result.job_id 8Tmvqx92i6Z8DQMCovbAPQ _model_server_result.datetime_utc '2024-12-21 11:58:33' _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 3o47 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 3O47 # _exptl.entry_id 3O47 _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 3O47 _cell.length_a 79.298 _cell.length_b 129.161 _cell.length_c 157.685 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3O47 _symmetry.cell_setting ? _symmetry.Int_Tables_number 24 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 21 21' # 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 dimeric 2 software_defined_assembly 1 PISA dimeric 2 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,C,D 1 1,2 B,E,F 2 1,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_545 -x,-y-1/2,z -1 0 0 0 -1 0 0 0 1 0 -64.5805 0 3 'crystal symmetry operation' 7_456 -x-1/2,y,-z+1 -1 0 0 0 1 0 0 0 -1 -39.649 0 157.685 # 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 # 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 SG CYS 40 A CYS 22 1_555 C ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc2 A SG CYS 43 A CYS 25 1_555 C ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc3 A SG CYS 60 A CYS 42 1_555 C ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc4 A SG CYS 63 A CYS 45 1_555 C ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc5 B SG CYS 40 B CYS 22 1_555 E ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc6 B SG CYS 43 B CYS 25 1_555 E ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc7 B SG CYS 60 B CYS 42 1_555 E ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc8 B SG CYS 63 B CYS 45 1_555 E ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? # _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 3O47 _atom_sites.fract_transf_matrix[1][1] 0.012611 _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] 0.007742 _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] 0.006342 _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 ZN A 1 501 501 ZN ZN . D 3 GDP A 1 502 502 GDP GDP . E 2 ZN B 1 501 501 ZN ZN . F 3 GDP B 1 502 502 GDP GDP . # 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 -18.455 -33.172 61.502 1 54.37 ? PB GDP 502 A 1 HETATM 2 O O1B GDP . . . D 3 -17.486 -32.733 60.509 1 56.24 ? O1B GDP 502 A 1 HETATM 3 O O2B GDP . . . D 3 -18.82 -31.844 62.42 1 55.99 ? O2B GDP 502 A 1 HETATM 4 O O3B GDP . . . D 3 -19.773 -33.848 60.873 1 55.74 ? O3B GDP 502 A 1 HETATM 5 O O3A GDP . . . D 3 -17.881 -34.369 62.427 1 56.2 ? O3A GDP 502 A 1 HETATM 6 P PA GDP . . . D 3 -16.263 -34.64 62.539 1 55.52 ? PA GDP 502 A 1 HETATM 7 O O1A GDP . . . D 3 -15.789 -35.321 61.313 1 56.9 ? O1A GDP 502 A 1 HETATM 8 O O2A GDP . . . D 3 -15.367 -33.344 62.878 1 57.55 ? O2A GDP 502 A 1 HETATM 9 O O5' GDP . . . D 3 -16.149 -35.754 63.631 1 56.32 ? O5' GDP 502 A 1 HETATM 10 C C5' GDP . . . D 3 -16.917 -35.411 64.789 1 55.99 ? C5' GDP 502 A 1 HETATM 11 C C4' GDP . . . D 3 -16.395 -36.245 65.949 1 56.74 ? C4' GDP 502 A 1 HETATM 12 O O4' GDP . . . D 3 -16.863 -37.597 65.775 1 56.42 ? O4' GDP 502 A 1 HETATM 13 C C3' GDP . . . D 3 -14.84 -36.351 66.056 1 57.56 ? C3' GDP 502 A 1 HETATM 14 O O3' GDP . . . D 3 -14.5 -36.474 67.428 1 61.81 ? O3' GDP 502 A 1 HETATM 15 C C2' GDP . . . D 3 -14.63 -37.667 65.319 1 57.86 ? C2' GDP 502 A 1 HETATM 16 O O2' GDP . . . D 3 -13.381 -38.285 65.368 1 59.9 ? O2' GDP 502 A 1 HETATM 17 C C1' GDP . . . D 3 -15.75 -38.507 65.851 1 56.33 ? C1' GDP 502 A 1 HETATM 18 N N9 GDP . . . D 3 -16.088 -39.487 64.87 1 55.41 ? N9 GDP 502 A 1 HETATM 19 C C8 GDP . . . D 3 -16.351 -39.299 63.524 1 55.21 ? C8 GDP 502 A 1 HETATM 20 N N7 GDP . . . D 3 -16.693 -40.416 62.985 1 55.36 ? N7 GDP 502 A 1 HETATM 21 C C5 GDP . . . D 3 -16.683 -41.384 63.943 1 54.29 ? C5 GDP 502 A 1 HETATM 22 C C6 GDP . . . D 3 -16.953 -42.82 63.956 1 55.47 ? C6 GDP 502 A 1 HETATM 23 O O6 GDP . . . D 3 -17.296 -43.423 62.931 1 55.57 ? O6 GDP 502 A 1 HETATM 24 N N1 GDP . . . D 3 -16.864 -43.486 65.168 1 55.13 ? N1 GDP 502 A 1 HETATM 25 C C2 GDP . . . D 3 -16.479 -42.818 66.348 1 55.26 ? C2 GDP 502 A 1 HETATM 26 N N2 GDP . . . D 3 -16.419 -43.556 67.51 1 57.3 ? N2 GDP 502 A 1 HETATM 27 N N3 GDP . . . D 3 -16.2 -41.488 66.354 1 55.49 ? N3 GDP 502 A 1 HETATM 28 C C4 GDP . . . D 3 -16.302 -40.769 65.186 1 54.97 ? C4 GDP 502 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #