data_8EZG # _model_server_result.job_id ro2pFCu7Fthi4XTH6AFk4Q _model_server_result.datetime_utc '2024-11-22 11:42:20' _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 8ezg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 8EZG # _exptl.entry_id 8EZG _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 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 120 _cell.entry_id 8EZG _cell.length_a 156.477 _cell.length_b 156.477 _cell.length_c 64.624 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8EZG _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # _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 _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 OG SER 17 A SER 17 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc2 C O1B GDP . A GDP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc3 D MG MG . A MG 202 1_555 F O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc4 D MG MG . A MG 202 1_555 F O HOH . A HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc5 D MG MG . A MG 202 1_555 F O HOH . A HOH 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc6 D MG MG . A MG 202 1_555 F O HOH . A HOH 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc7 B OG SER 20 B SER 21 1_555 E NA NA . B NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? metalc ? metalc8 B O TRP 21 B TRP 22 1_555 E NA NA . B NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? metalc ? metalc9 B O SER 54 B SER 55 1_555 E NA NA . B NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? metalc ? metalc10 B OG SER 54 B SER 55 1_555 E NA NA . B NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.603 ? metalc ? metalc11 E NA NA . B NA 201 1_555 G O HOH . B HOH 320 12_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.505 ? metalc ? metalc12 E NA NA . B NA 201 1_555 G O HOH . B HOH 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? metalc ? metalc13 E NA NA . B NA 201 1_555 G O HOH . B HOH 324 12_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? # _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 8EZG _atom_sites.fract_transf_matrix[1][1] 0.006391 _atom_sites.fract_transf_matrix[1][2] 0.00369 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007379 _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] 0.015474 _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 GDP A 1 201 201 GDP GDP . D 4 MG A 1 202 202 MG MG . E 5 NA B 1 201 201 NA NA . F 6 HOH A 1 301 50 HOH HOH . F 6 HOH A 2 302 102 HOH HOH . F 6 HOH A 3 303 96 HOH HOH . F 6 HOH A 4 304 31 HOH HOH . F 6 HOH A 5 305 108 HOH HOH . F 6 HOH A 6 306 85 HOH HOH . F 6 HOH A 7 307 22 HOH HOH . F 6 HOH A 8 308 87 HOH HOH . F 6 HOH A 9 309 104 HOH HOH . F 6 HOH A 10 310 36 HOH HOH . F 6 HOH A 11 311 75 HOH HOH . F 6 HOH A 12 312 116 HOH HOH . F 6 HOH A 13 313 28 HOH HOH . F 6 HOH A 14 314 109 HOH HOH . F 6 HOH A 15 315 103 HOH HOH . F 6 HOH A 16 316 79 HOH HOH . F 6 HOH A 17 317 27 HOH HOH . F 6 HOH A 18 318 35 HOH HOH . F 6 HOH A 19 319 95 HOH HOH . F 6 HOH A 20 320 7 HOH HOH . F 6 HOH A 21 321 60 HOH HOH . F 6 HOH A 22 322 56 HOH HOH . F 6 HOH A 23 323 91 HOH HOH . F 6 HOH A 24 324 23 HOH HOH . F 6 HOH A 25 325 119 HOH HOH . F 6 HOH A 26 326 6 HOH HOH . F 6 HOH A 27 327 11 HOH HOH . F 6 HOH A 28 328 67 HOH HOH . F 6 HOH A 29 329 58 HOH HOH . F 6 HOH A 30 330 121 HOH HOH . F 6 HOH A 31 331 54 HOH HOH . F 6 HOH A 32 332 43 HOH HOH . F 6 HOH A 33 333 124 HOH HOH . F 6 HOH A 34 334 10 HOH HOH . F 6 HOH A 35 335 97 HOH HOH . F 6 HOH A 36 336 57 HOH HOH . F 6 HOH A 37 337 78 HOH HOH . F 6 HOH A 38 338 118 HOH HOH . F 6 HOH A 39 339 107 HOH HOH . F 6 HOH A 40 340 61 HOH HOH . F 6 HOH A 41 341 80 HOH HOH . F 6 HOH A 42 342 64 HOH HOH . F 6 HOH A 43 343 30 HOH HOH . F 6 HOH A 44 344 24 HOH HOH . F 6 HOH A 45 345 71 HOH HOH . F 6 HOH A 46 346 63 HOH HOH . F 6 HOH A 47 347 65 HOH HOH . F 6 HOH A 48 348 105 HOH HOH . F 6 HOH A 49 349 48 HOH HOH . F 6 HOH A 50 350 47 HOH HOH . F 6 HOH A 51 351 117 HOH HOH . F 6 HOH A 52 352 120 HOH HOH . F 6 HOH A 53 353 94 HOH HOH . F 6 HOH A 54 354 100 HOH HOH . F 6 HOH A 55 355 106 HOH HOH . F 6 HOH A 56 356 33 HOH HOH . F 6 HOH A 57 357 39 HOH HOH . F 6 HOH A 58 358 125 HOH HOH . F 6 HOH A 59 359 101 HOH HOH . F 6 HOH A 60 360 98 HOH HOH . F 6 HOH A 61 361 88 HOH HOH . F 6 HOH A 62 362 110 HOH HOH . F 6 HOH A 63 363 122 HOH HOH . G 6 HOH B 1 301 1 HOH HOH . G 6 HOH B 2 302 19 HOH HOH . G 6 HOH B 3 303 86 HOH HOH . G 6 HOH B 4 304 73 HOH HOH . G 6 HOH B 5 305 76 HOH HOH . G 6 HOH B 6 306 13 HOH HOH . G 6 HOH B 7 307 53 HOH HOH . G 6 HOH B 8 308 112 HOH HOH . G 6 HOH B 9 309 55 HOH HOH . G 6 HOH B 10 310 68 HOH HOH . G 6 HOH B 11 311 21 HOH HOH . G 6 HOH B 12 312 16 HOH HOH . G 6 HOH B 13 313 52 HOH HOH . G 6 HOH B 14 314 74 HOH HOH . G 6 HOH B 15 315 81 HOH HOH . G 6 HOH B 16 316 59 HOH HOH . G 6 HOH B 17 317 62 HOH HOH . G 6 HOH B 18 318 2 HOH HOH . G 6 HOH B 19 319 25 HOH HOH . G 6 HOH B 20 320 4 HOH HOH . G 6 HOH B 21 321 8 HOH HOH . G 6 HOH B 22 322 14 HOH HOH . G 6 HOH B 23 323 18 HOH HOH . G 6 HOH B 24 324 51 HOH HOH . G 6 HOH B 25 325 34 HOH HOH . G 6 HOH B 26 326 66 HOH HOH . G 6 HOH B 27 327 17 HOH HOH . G 6 HOH B 28 328 32 HOH HOH . G 6 HOH B 29 329 38 HOH HOH . G 6 HOH B 30 330 115 HOH HOH . G 6 HOH B 31 331 15 HOH HOH . G 6 HOH B 32 332 29 HOH HOH . G 6 HOH B 33 333 113 HOH HOH . G 6 HOH B 34 334 12 HOH HOH . G 6 HOH B 35 335 3 HOH HOH . G 6 HOH B 36 336 20 HOH HOH . G 6 HOH B 37 337 42 HOH HOH . G 6 HOH B 38 338 89 HOH HOH . G 6 HOH B 39 339 5 HOH HOH . G 6 HOH B 40 340 70 HOH HOH . G 6 HOH B 41 341 9 HOH HOH . G 6 HOH B 42 342 82 HOH HOH . G 6 HOH B 43 343 37 HOH HOH . G 6 HOH B 44 344 84 HOH HOH . G 6 HOH B 45 345 26 HOH HOH . G 6 HOH B 46 346 45 HOH HOH . G 6 HOH B 47 347 92 HOH HOH . G 6 HOH B 48 348 49 HOH HOH . G 6 HOH B 49 349 69 HOH HOH . G 6 HOH B 50 350 72 HOH HOH . G 6 HOH B 51 351 40 HOH HOH . G 6 HOH B 52 352 77 HOH HOH . G 6 HOH B 53 353 41 HOH HOH . G 6 HOH B 54 354 111 HOH HOH . G 6 HOH B 55 355 83 HOH HOH . G 6 HOH B 56 356 126 HOH HOH . G 6 HOH B 57 357 44 HOH HOH . G 6 HOH B 58 358 114 HOH HOH . G 6 HOH B 59 359 99 HOH HOH . G 6 HOH B 60 360 93 HOH HOH . G 6 HOH B 61 361 46 HOH HOH . G 6 HOH B 62 362 123 HOH HOH . G 6 HOH B 63 363 90 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 . . . C 3 -60.715 49.501 -7.088 1 36.1 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . C 3 -61.544 48.254 -6.799 1 33.09 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . C 3 -59.275 49.229 -6.716 1 33.29 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . C 3 -61.265 50.691 -6.332 1 33.5 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . C 3 -60.686 49.863 -8.654 1 48.28 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . C 3 -61.82 49.408 -9.705 1 37.15 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . C 3 -61.709 47.903 -9.911 1 29 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . C 3 -63.172 49.86 -9.181 1 28.11 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . C 3 -61.336 50.207 -11.033 1 39.18 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . C 3 -61.525 51.63 -11.134 1 40.3 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . C 3 -61.484 52.07 -12.591 1 45.06 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . C 3 -60.305 51.569 -13.254 1 41.74 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . C 3 -62.672 51.491 -13.346 1 46.37 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . C 3 -63.09 52.45 -14.325 1 50.56 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . C 3 -62.093 50.274 -14.04 1 41.55 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . C 3 -62.869 49.921 -15.178 1 46.69 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . C 3 -60.704 50.782 -14.392 1 37.45 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . C 3 -59.698 49.722 -14.524 1 29.94 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . C 3 -59.446 48.776 -13.612 1 33.29 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . C 3 -58.429 47.973 -14.031 1 32.78 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . C 3 -58.01 48.431 -15.219 1 30.43 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . C 3 -56.979 48.042 -16.189 1 32.07 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . C 3 -56.226 47.059 -15.969 1 31.98 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . C 3 -56.881 48.774 -17.303 1 33.75 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . C 3 -57.659 49.837 -17.581 1 39.24 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . C 3 -57.468 50.51 -18.761 1 36.82 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . C 3 -58.628 50.248 -16.72 1 29.94 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . C 3 -58.842 49.592 -15.546 1 36.44 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #