data_2ZJZ # _model_server_result.job_id YF9ohQce3QR89wfOGpK79Q _model_server_result.datetime_utc '2024-10-18 20:31:33' _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 2zjz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":355}' # _entry.id 2ZJZ # _exptl.entry_id 2ZJZ _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 90 _cell.entry_id 2ZJZ _cell.length_a 101.38 _cell.length_b 164.07 _cell.length_c 53.41 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZJZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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 _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 ? 2 C N N ? 2 D N N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 216 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 214 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 216 _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 214 _struct_conn.ptnr2_symmetry 1_555 _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 2.026 _struct_conn.pdbx_value_order ? # _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 2ZJZ _atom_sites.fract_transf_matrix[1][1] 0.009864 _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] 0.006095 _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] 0.018723 _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 1 355 355 GDP GDP . D 2 GDP B 1 355 1355 GDP GDP . E 3 HOH A 1 356 1 HOH HOH . E 3 HOH A 2 357 2 HOH HOH . E 3 HOH A 3 358 3 HOH HOH . E 3 HOH A 4 359 4 HOH HOH . E 3 HOH A 5 360 5 HOH HOH . E 3 HOH A 6 361 6 HOH HOH . E 3 HOH A 7 362 7 HOH HOH . E 3 HOH A 8 363 8 HOH HOH . E 3 HOH A 9 364 9 HOH HOH . E 3 HOH A 10 365 10 HOH HOH . E 3 HOH A 11 366 11 HOH HOH . E 3 HOH A 12 367 13 HOH HOH . E 3 HOH A 13 368 14 HOH HOH . E 3 HOH A 14 369 15 HOH HOH . E 3 HOH A 15 370 16 HOH HOH . E 3 HOH A 16 371 17 HOH HOH . E 3 HOH A 17 372 18 HOH HOH . E 3 HOH A 18 373 21 HOH HOH . E 3 HOH A 19 374 22 HOH HOH . E 3 HOH A 20 375 23 HOH HOH . E 3 HOH A 21 376 24 HOH HOH . E 3 HOH A 22 377 25 HOH HOH . E 3 HOH A 23 378 27 HOH HOH . E 3 HOH A 24 379 28 HOH HOH . E 3 HOH A 25 380 29 HOH HOH . E 3 HOH A 26 381 30 HOH HOH . E 3 HOH A 27 382 31 HOH HOH . E 3 HOH A 28 383 32 HOH HOH . E 3 HOH A 29 384 33 HOH HOH . E 3 HOH A 30 385 34 HOH HOH . E 3 HOH A 31 386 35 HOH HOH . E 3 HOH A 32 387 36 HOH HOH . E 3 HOH A 33 388 39 HOH HOH . E 3 HOH A 34 389 40 HOH HOH . E 3 HOH A 35 390 41 HOH HOH . E 3 HOH A 36 391 42 HOH HOH . E 3 HOH A 37 392 43 HOH HOH . E 3 HOH A 38 393 44 HOH HOH . E 3 HOH A 39 394 45 HOH HOH . E 3 HOH A 40 395 49 HOH HOH . E 3 HOH A 41 396 50 HOH HOH . E 3 HOH A 42 397 51 HOH HOH . E 3 HOH A 43 398 52 HOH HOH . E 3 HOH A 44 399 53 HOH HOH . E 3 HOH A 45 400 55 HOH HOH . E 3 HOH A 46 401 56 HOH HOH . F 3 HOH B 1 356 12 HOH HOH . F 3 HOH B 2 357 19 HOH HOH . F 3 HOH B 3 358 20 HOH HOH . F 3 HOH B 4 359 26 HOH HOH . F 3 HOH B 5 360 37 HOH HOH . F 3 HOH B 6 361 38 HOH HOH . F 3 HOH B 7 362 46 HOH HOH . F 3 HOH B 8 363 47 HOH HOH . F 3 HOH B 9 364 48 HOH HOH . F 3 HOH B 10 365 54 HOH HOH . F 3 HOH B 11 366 57 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 29.293 122.413 -5.263 1 48.09 ? PB GDP 355 B 1 HETATM 2 O O1B GDP . . . D 2 30.768 122.47 -5.154 1 52.23 ? O1B GDP 355 B 1 HETATM 3 O O2B GDP . . . D 2 28.608 121.512 -4.119 1 58.35 ? O2B GDP 355 B 1 HETATM 4 O O3B GDP . . . D 2 28.588 123.854 -5.144 1 30.13 ? O3B GDP 355 B 1 HETATM 5 O O3A GDP . . . D 2 28.802 121.783 -6.661 1 47.6 ? O3A GDP 355 B 1 HETATM 6 P PA GDP . . . D 2 28.445 122.724 -7.917 1 51.6 ? PA GDP 355 B 1 HETATM 7 O O1A GDP . . . D 2 29.602 123.608 -8.184 1 57.59 ? O1A GDP 355 B 1 HETATM 8 O O2A GDP . . . D 2 27.127 123.351 -7.665 1 33.92 ? O2A GDP 355 B 1 HETATM 9 O O5' GDP . . . D 2 28.332 121.64 -9.102 1 39.76 ? O5' GDP 355 B 1 HETATM 10 C C5' GDP . . . D 2 29.509 120.912 -9.462 1 43.6 ? C5' GDP 355 B 1 HETATM 11 C C4' GDP . . . D 2 29.486 120.467 -10.926 1 46.44 ? C4' GDP 355 B 1 HETATM 12 O O4' GDP . . . D 2 28.445 119.491 -11.115 1 45.83 ? O4' GDP 355 B 1 HETATM 13 C C3' GDP . . . D 2 29.139 121.654 -11.828 1 33.31 ? C3' GDP 355 B 1 HETATM 14 O O3' GDP . . . D 2 29.63 121.414 -13.149 1 45.82 ? O3' GDP 355 B 1 HETATM 15 C C2' GDP . . . D 2 27.612 121.59 -11.797 1 54.8 ? C2' GDP 355 B 1 HETATM 16 O O2' GDP . . . D 2 27.069 122.24 -12.951 1 37.76 ? O2' GDP 355 B 1 HETATM 17 C C1' GDP . . . D 2 27.417 120.079 -11.933 1 50.04 ? C1' GDP 355 B 1 HETATM 18 N N9 GDP . . . D 2 26.084 119.627 -11.467 1 49.97 ? N9 GDP 355 B 1 HETATM 19 C C8 GDP . . . D 2 25.46 120.029 -10.362 1 55.72 ? C8 GDP 355 B 1 HETATM 20 N N7 GDP . . . D 2 24.321 119.356 -10.219 1 50.47 ? N7 GDP 355 B 1 HETATM 21 C C5 GDP . . . D 2 24.211 118.521 -11.247 1 56.23 ? C5 GDP 355 B 1 HETATM 22 C C6 GDP . . . D 2 23.254 117.58 -11.614 1 59.03 ? C6 GDP 355 B 1 HETATM 23 O O6 GDP . . . D 2 22.268 117.378 -10.908 1 58.6 ? O6 GDP 355 B 1 HETATM 24 N N1 GDP . . . D 2 23.447 116.844 -12.79 1 50.86 ? N1 GDP 355 B 1 HETATM 25 C C2 GDP . . . D 2 24.595 117.07 -13.563 1 57.2 ? C2 GDP 355 B 1 HETATM 26 N N2 GDP . . . D 2 24.793 116.384 -14.685 1 63.68 ? N2 GDP 355 B 1 HETATM 27 N N3 GDP . . . D 2 25.499 117.978 -13.168 1 59.55 ? N3 GDP 355 B 1 HETATM 28 C C4 GDP . . . D 2 25.333 118.696 -12.046 1 43.18 ? C4 GDP 355 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #