data_3DZ8 # _model_server_result.job_id BqrFghwdbFZ-Nn2fYDi2og _model_server_result.datetime_utc '2024-11-04 22:51:03' _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 3dz8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 3DZ8 # _exptl.entry_id 3DZ8 _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 110.91 _cell.angle_gamma 90 _cell.entry_id 3DZ8 _cell.length_a 56.969 _cell.length_b 50.875 _cell.length_c 73.553 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DZ8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 30.717858 0 68.708961 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 3DZ8 _atom_sites.fract_transf_matrix[1][1] 0.017553 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006708 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019656 _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] 0.014554 _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 B 2 GDP A 1 201 201 GDP GDP . C 3 UNX A 1 501 501 UNX UNX . D 3 UNX A 1 502 502 UNX UNX . E 3 UNX A 1 503 503 UNX UNX . F 3 UNX A 1 504 504 UNX UNX . G 3 UNX A 1 505 505 UNX UNX . H 3 UNX A 1 506 506 UNX UNX . I 4 HOH A 1 507 1 HOH HOH . I 4 HOH A 2 508 2 HOH HOH . I 4 HOH A 3 509 3 HOH HOH . I 4 HOH A 4 510 4 HOH HOH . I 4 HOH A 5 511 5 HOH HOH . I 4 HOH A 6 512 6 HOH HOH . I 4 HOH A 7 513 7 HOH HOH . I 4 HOH A 8 514 8 HOH HOH . I 4 HOH A 9 515 9 HOH HOH . I 4 HOH A 10 516 10 HOH HOH . I 4 HOH A 11 517 11 HOH HOH . I 4 HOH A 12 518 12 HOH HOH . I 4 HOH A 13 519 13 HOH HOH . I 4 HOH A 14 520 14 HOH HOH . I 4 HOH A 15 521 15 HOH HOH . I 4 HOH A 16 522 16 HOH HOH . I 4 HOH A 17 523 17 HOH HOH . I 4 HOH A 18 524 18 HOH HOH . I 4 HOH A 19 525 19 HOH HOH . I 4 HOH A 20 526 20 HOH HOH . I 4 HOH A 21 527 21 HOH HOH . I 4 HOH A 22 528 22 HOH HOH . I 4 HOH A 23 529 23 HOH HOH . I 4 HOH A 24 530 24 HOH HOH . I 4 HOH A 25 531 25 HOH HOH . I 4 HOH A 26 532 26 HOH HOH . I 4 HOH A 27 533 27 HOH HOH . I 4 HOH A 28 534 28 HOH HOH . I 4 HOH A 29 535 29 HOH HOH . I 4 HOH A 30 536 30 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 . . . B 2 3.858 10.21 20.135 1 21.14 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 4.537 9.475 21.302 1 20.29 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 3.115 11.399 20.624 1 21.41 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 4.831 10.588 19.038 1 21.04 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 2.811 9.24 19.382 1 20.37 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 1.998 8.019 20.025 1 19.76 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 2.773 6.708 20.106 1 18.47 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 1.248 8.482 21.273 1 19.06 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 0.907 7.72 18.859 1 19.99 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 0.007 8.75 18.472 1 20.67 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 -1.189 8.151 17.76 1 20.2 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 -0.745 7.474 16.58 1 20.19 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 -1.839 7.107 18.652 1 20.87 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 -3.251 7.063 18.456 1 20.57 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 -1.246 5.797 18.176 1 20.12 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 -2.114 4.7 18.398 1 21.1 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 -1.056 6.083 16.68 1 19.69 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 0.025 5.287 16.097 1 19.79 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 1.298 5.244 16.548 1 21.07 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 2.055 4.422 15.788 1 19.89 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 1.249 3.943 14.811 1 21.15 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 1.415 3.048 13.65 1 21.64 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 2.491 2.488 13.41 1 20.03 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 0.339 2.806 12.874 1 22.81 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 -0.857 3.366 13.132 1 22.11 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 -1.889 3.101 12.324 1 21.71 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 -1.076 4.222 14.164 1 23.39 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 -0.075 4.523 15.019 1 21.55 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #