data_3CH5 # _model_server_result.job_id 7CAQWulUKZyuuUytR1ATIw _model_server_result.datetime_utc '2025-02-05 06:07:46' _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 3ch5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":220}' # _entry.id 3CH5 # _exptl.entry_id 3CH5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _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 3CH5 _cell.length_a 69.7 _cell.length_b 75.35 _cell.length_c 123.05 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CH5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 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 PISA octameric 8 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_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,B,C,D,E,F,G,H 1 1,2,3,4 A,B,C,D,E,F,G,H 2 1,2 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_554 -x,y,-z-1 -1 0 0 0 1 0 0 0 -1 0 0 -123.05 4 'crystal symmetry operation' 4_554 x,-y,-z-1 1 0 0 0 -1 0 0 0 -1 0 0 -123.05 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _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 metalc ? metalc1 A OG1 THR 24 A THR 24 1_555 C MG MG . A MG 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc2 E O1B GDP . A GDP 220 1_555 C MG MG . A MG 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc3 C MG MG . A MG 221 1_555 G O HOH . A HOH 236 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc4 C MG MG . A MG 221 1_555 G O HOH . A HOH 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc5 C MG MG . A MG 221 1_555 G O HOH . A HOH 269 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc6 C MG MG . A MG 221 1_555 G O HOH . A HOH 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc7 B SG CYS 25 B CYS 727 1_555 F ZN ZN . B ZN 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc8 B SG CYS 28 B CYS 730 1_555 F ZN ZN . B ZN 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc9 B SG CYS 39 B CYS 741 1_555 F ZN ZN . B ZN 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc10 B SG CYS 42 B CYS 744 1_555 F ZN ZN . B ZN 800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? # _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 3CH5 _atom_sites.fract_transf_matrix[1][1] 0.014347 _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] 0.013271 _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] 0.008127 _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 3 MG A 1 221 221 MG MG . D 4 SO4 A 1 222 222 SO4 SO4 . E 5 GDP A 1 220 220 GDP GDP . F 6 ZN B 1 800 800 ZN ZN . G 7 HOH A 1 223 223 HOH HOH . G 7 HOH A 2 224 224 HOH HOH . G 7 HOH A 3 225 225 HOH HOH . G 7 HOH A 4 226 226 HOH HOH . G 7 HOH A 5 227 227 HOH HOH . G 7 HOH A 6 228 228 HOH HOH . G 7 HOH A 7 229 229 HOH HOH . G 7 HOH A 8 230 230 HOH HOH . G 7 HOH A 9 231 231 HOH HOH . G 7 HOH A 10 232 232 HOH HOH . G 7 HOH A 11 233 233 HOH HOH . G 7 HOH A 12 234 234 HOH HOH . G 7 HOH A 13 235 235 HOH HOH . G 7 HOH A 14 236 236 HOH HOH . G 7 HOH A 15 237 237 HOH HOH . G 7 HOH A 16 238 238 HOH HOH . G 7 HOH A 17 239 239 HOH HOH . G 7 HOH A 18 240 240 HOH HOH . G 7 HOH A 19 241 241 HOH HOH . G 7 HOH A 20 242 242 HOH HOH . G 7 HOH A 21 243 243 HOH HOH . G 7 HOH A 22 244 244 HOH HOH . G 7 HOH A 23 245 245 HOH HOH . G 7 HOH A 24 246 246 HOH HOH . G 7 HOH A 25 247 247 HOH HOH . G 7 HOH A 26 248 248 HOH HOH . G 7 HOH A 27 249 249 HOH HOH . G 7 HOH A 28 250 250 HOH HOH . G 7 HOH A 29 251 251 HOH HOH . G 7 HOH A 30 252 252 HOH HOH . G 7 HOH A 31 253 253 HOH HOH . G 7 HOH A 32 254 254 HOH HOH . G 7 HOH A 33 255 255 HOH HOH . G 7 HOH A 34 256 256 HOH HOH . G 7 HOH A 35 257 257 HOH HOH . G 7 HOH A 36 258 258 HOH HOH . G 7 HOH A 37 259 259 HOH HOH . G 7 HOH A 38 260 260 HOH HOH . G 7 HOH A 39 261 261 HOH HOH . G 7 HOH A 40 262 262 HOH HOH . G 7 HOH A 41 263 263 HOH HOH . G 7 HOH A 42 264 264 HOH HOH . G 7 HOH A 43 265 265 HOH HOH . G 7 HOH A 44 266 266 HOH HOH . G 7 HOH A 45 267 267 HOH HOH . G 7 HOH A 46 268 268 HOH HOH . G 7 HOH A 47 269 269 HOH HOH . G 7 HOH A 48 270 270 HOH HOH . G 7 HOH A 49 271 271 HOH HOH . G 7 HOH A 50 272 272 HOH HOH . G 7 HOH A 51 273 273 HOH HOH . G 7 HOH A 52 274 274 HOH HOH . G 7 HOH A 53 275 275 HOH HOH . G 7 HOH A 54 276 276 HOH HOH . G 7 HOH A 55 277 277 HOH HOH . G 7 HOH A 56 278 278 HOH HOH . G 7 HOH A 57 279 279 HOH HOH . G 7 HOH A 58 280 280 HOH HOH . G 7 HOH A 59 281 281 HOH HOH . G 7 HOH A 60 282 282 HOH HOH . G 7 HOH A 61 283 283 HOH HOH . G 7 HOH A 62 284 284 HOH HOH . G 7 HOH A 63 285 285 HOH HOH . G 7 HOH A 64 286 286 HOH HOH . G 7 HOH A 65 287 287 HOH HOH . G 7 HOH A 66 288 288 HOH HOH . G 7 HOH A 67 289 289 HOH HOH . H 7 HOH B 1 801 801 HOH HOH . H 7 HOH B 2 802 802 HOH HOH . H 7 HOH B 3 803 803 HOH HOH . H 7 HOH B 4 804 804 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 5 21.235 -9.308 -43.655 1 28.74 ? PB GDP 220 A 1 HETATM 2 O O1B GDP . . . E 5 20.237 -8.548 -42.781 1 27.47 ? O1B GDP 220 A 1 HETATM 3 O O2B GDP . . . E 5 22.566 -9.366 -42.934 1 29.41 ? O2B GDP 220 A 1 HETATM 4 O O3B GDP . . . E 5 20.812 -10.719 -43.946 1 24.62 ? O3B GDP 220 A 1 HETATM 5 O O3A GDP . . . E 5 21.443 -8.557 -45.063 1 29.2 ? O3A GDP 220 A 1 HETATM 6 P PA GDP . . . E 5 21.34 -6.951 -45.236 1 27.52 ? PA GDP 220 A 1 HETATM 7 O O1A GDP . . . E 5 19.89 -6.627 -45.428 1 29.66 ? O1A GDP 220 A 1 HETATM 8 O O2A GDP . . . E 5 21.96 -6.141 -44.164 1 27.7 ? O2A GDP 220 A 1 HETATM 9 O O5' GDP . . . E 5 22.064 -6.749 -46.657 1 31 ? O5' GDP 220 A 1 HETATM 10 C C5' GDP . . . E 5 23.345 -7.303 -46.974 1 32.6 ? C5' GDP 220 A 1 HETATM 11 C C4' GDP . . . E 5 23.86 -6.638 -48.256 1 33.23 ? C4' GDP 220 A 1 HETATM 12 O O4' GDP . . . E 5 23.144 -7.143 -49.392 1 33.3 ? O4' GDP 220 A 1 HETATM 13 C C3' GDP . . . E 5 23.613 -5.148 -48.254 1 35.59 ? C3' GDP 220 A 1 HETATM 14 O O3' GDP . . . E 5 24.751 -4.531 -48.84 1 40.52 ? O3' GDP 220 A 1 HETATM 15 C C2' GDP . . . E 5 22.437 -4.931 -49.177 1 35.14 ? C2' GDP 220 A 1 HETATM 16 O O2' GDP . . . E 5 22.55 -3.69 -49.862 1 35.67 ? O2' GDP 220 A 1 HETATM 17 C C1' GDP . . . E 5 22.568 -6.07 -50.138 1 32.53 ? C1' GDP 220 A 1 HETATM 18 N N9 GDP . . . E 5 21.281 -6.556 -50.675 1 33.25 ? N9 GDP 220 A 1 HETATM 19 C C8 GDP . . . E 5 20.217 -6.942 -49.96 1 30.94 ? C8 GDP 220 A 1 HETATM 20 N N7 GDP . . . E 5 19.246 -7.376 -50.761 1 30.57 ? N7 GDP 220 A 1 HETATM 21 C C5 GDP . . . E 5 19.677 -7.261 -52.018 1 30.82 ? C5 GDP 220 A 1 HETATM 22 C C6 GDP . . . E 5 19.105 -7.527 -53.346 1 31.45 ? C6 GDP 220 A 1 HETATM 23 O O6 GDP . . . E 5 17.949 -7.974 -53.448 1 31.75 ? O6 GDP 220 A 1 HETATM 24 N N1 GDP . . . E 5 19.881 -7.291 -54.42 1 32.53 ? N1 GDP 220 A 1 HETATM 25 C C2 GDP . . . E 5 21.135 -6.795 -54.325 1 31.92 ? C2 GDP 220 A 1 HETATM 26 N N2 GDP . . . E 5 21.82 -6.588 -55.47 1 31.94 ? N2 GDP 220 A 1 HETATM 27 N N3 GDP . . . E 5 21.726 -6.504 -53.129 1 32.58 ? N3 GDP 220 A 1 HETATM 28 C C4 GDP . . . E 5 21.035 -6.728 -51.97 1 31.52 ? C4 GDP 220 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 28 #