data_2IEY # _model_server_result.job_id U3-jq5PbjEReB4HlpPplHQ _model_server_result.datetime_utc '2024-11-22 20:48:58' _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 2iey # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1200}' # _entry.id 2IEY # _exptl.entry_id 2IEY _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 90 _cell.angle_gamma 120 _cell.entry_id 2IEY _cell.length_a 66.061 _cell.length_b 66.061 _cell.length_c 379.988 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2IEY _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA tetrameric 4 software_defined_assembly 3 PISA dimeric 2 software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 2 1 A,B,C,D,E,F 3 1,2 A,B,C,D,E,F 4 1 # 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' 12_544 x,x-y-1,-z-1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 33.0305 -57.210504 -63.331333 # 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 D 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 covale ? covale1 A C ALA 94 A ALA 92 1_555 A N MSE 95 A MSE 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C MSE 95 A MSE 93 1_555 A N GLY 96 A GLY 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C LEU 99 A LEU 97 1_555 A N MSE 100 A MSE 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale4 A C MSE 100 A MSE 98 1_555 A N PHE 101 A PHE 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 A C TRP 115 A TRP 113 1_555 A N MSE 116 A MSE 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 A C MSE 116 A MSE 114 1_555 A N SER 117 A SER 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 A C ILE 183 A ILE 181 1_555 A N MSE 184 A MSE 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale8 A C MSE 184 A MSE 182 1_555 A N LYS 185 A LYS 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale9 A C ARG 186 A ARG 184 1_555 A N MSE 187 A MSE 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale10 B C ALA 94 B ALA 92 1_555 B N MSE 95 B MSE 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale11 B C MSE 95 B MSE 93 1_555 B N GLY 96 B GLY 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale12 B C LEU 99 B LEU 97 1_555 B N MSE 100 B MSE 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale13 B C MSE 100 B MSE 98 1_555 B N PHE 101 B PHE 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale14 B C TRP 115 B TRP 113 1_555 B N MSE 116 B MSE 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale15 B C MSE 116 B MSE 114 1_555 B N SER 117 B SER 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale16 B C ILE 183 B ILE 181 1_555 B N MSE 184 B MSE 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale17 B C MSE 184 B MSE 182 1_555 B N LYS 185 B LYS 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? # _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 2IEY _atom_sites.fract_transf_matrix[1][1] 0.015138 _atom_sites.fract_transf_matrix[1][2] 0.00874 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017479 _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] 0.002632 _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 1 200 200 GDP GDP . D 2 GDP B 1 1200 1200 GDP GDP . E 3 HOH A 1 205 205 HOH HOH . E 3 HOH A 2 206 206 HOH HOH . E 3 HOH A 3 207 208 HOH HOH . E 3 HOH A 4 208 212 HOH HOH . E 3 HOH A 5 209 220 HOH HOH . E 3 HOH A 6 210 222 HOH HOH . E 3 HOH A 7 211 1 HOH HOH . F 3 HOH B 1 201 201 HOH HOH . F 3 HOH B 2 202 202 HOH HOH . F 3 HOH B 3 204 204 HOH HOH . F 3 HOH B 4 209 209 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 2 56.129 -10.397 -15.873 1 48.94 ? PB GDP 1200 B 1 HETATM 2 O O1B GDP . . . D 2 54.895 -9.803 -16.522 1 48.95 ? O1B GDP 1200 B 1 HETATM 3 O O2B GDP . . . D 2 55.88 -10.722 -14.424 1 48.79 ? O2B GDP 1200 B 1 HETATM 4 O O3B GDP . . . D 2 56.536 -11.69 -16.53 1 48.95 ? O3B GDP 1200 B 1 HETATM 5 O O3A GDP . . . D 2 57.328 -9.342 -16.032 1 48.09 ? O3A GDP 1200 B 1 HETATM 6 P PA GDP . . . D 2 57.985 -9.235 -17.493 1 47.81 ? PA GDP 1200 B 1 HETATM 7 O O1A GDP . . . D 2 58.87 -10.438 -17.753 1 46.62 ? O1A GDP 1200 B 1 HETATM 8 O O2A GDP . . . D 2 56.88 -9.097 -18.519 1 47.24 ? O2A GDP 1200 B 1 HETATM 9 O O5' GDP . . . D 2 58.852 -7.885 -17.429 1 46.41 ? O5' GDP 1200 B 1 HETATM 10 C C5' GDP . . . D 2 58.313 -6.713 -18.035 1 45.49 ? C5' GDP 1200 B 1 HETATM 11 C C4' GDP . . . D 2 59.355 -5.606 -18.031 1 44.56 ? C4' GDP 1200 B 1 HETATM 12 O O4' GDP . . . D 2 60.216 -5.813 -16.914 1 43.9 ? O4' GDP 1200 B 1 HETATM 13 C C3' GDP . . . D 2 60.22 -5.582 -19.289 1 44.16 ? C3' GDP 1200 B 1 HETATM 14 O O3' GDP . . . D 2 60.229 -4.283 -19.892 1 43.77 ? O3' GDP 1200 B 1 HETATM 15 C C2' GDP . . . D 2 61.619 -5.894 -18.833 1 43.93 ? C2' GDP 1200 B 1 HETATM 16 O O2' GDP . . . D 2 62.523 -5.003 -19.498 1 44.56 ? O2' GDP 1200 B 1 HETATM 17 C C1' GDP . . . D 2 61.574 -5.668 -17.325 1 42.75 ? C1' GDP 1200 B 1 HETATM 18 N N9 GDP . . . D 2 62.424 -6.601 -16.536 1 42.23 ? N9 GDP 1200 B 1 HETATM 19 C C8 GDP . . . D 2 62.191 -7.889 -16.204 1 42.02 ? C8 GDP 1200 B 1 HETATM 20 N N7 GDP . . . D 2 63.216 -8.387 -15.454 1 41.76 ? N7 GDP 1200 B 1 HETATM 21 C C5 GDP . . . D 2 64.119 -7.399 -15.298 1 41.97 ? C5 GDP 1200 B 1 HETATM 22 C C6 GDP . . . D 2 65.429 -7.202 -14.623 1 42.12 ? C6 GDP 1200 B 1 HETATM 23 O O6 GDP . . . D 2 65.984 -8.122 -13.983 1 42.06 ? O6 GDP 1200 B 1 HETATM 24 N N1 GDP . . . D 2 66.011 -5.996 -14.723 1 41.89 ? N1 GDP 1200 B 1 HETATM 25 C C2 GDP . . . D 2 65.454 -4.975 -15.399 1 41.8 ? C2 GDP 1200 B 1 HETATM 26 N N2 GDP . . . D 2 66.087 -3.785 -15.461 1 41.96 ? N2 GDP 1200 B 1 HETATM 27 N N3 GDP . . . D 2 64.267 -5.076 -16.033 1 41.64 ? N3 GDP 1200 B 1 HETATM 28 C C4 GDP . . . D 2 63.579 -6.233 -16.013 1 41.84 ? C4 GDP 1200 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #