data_2XKB # _model_server_result.job_id Se-zXJChMa5O8sL0rG2gmQ _model_server_result.datetime_utc '2025-09-04 05:48:06' _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 2xkb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":900}' # _entry.id 2XKB # _exptl.entry_id 2XKB _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 11 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 92.51 _cell.angle_gamma 90 _cell.entry_id 2XKB _cell.length_a 52.947 _cell.length_b 541.099 _cell.length_c 86.128 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2XKB _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 PISA monomeric 1 author_and_software_defined_assembly 5 PISA monomeric 1 author_and_software_defined_assembly 6 PISA monomeric 1 author_and_software_defined_assembly 7 PISA monomeric 1 author_and_software_defined_assembly 8 PISA monomeric 1 author_and_software_defined_assembly 9 PISA monomeric 1 author_and_software_defined_assembly 10 PISA monomeric 1 author_and_software_defined_assembly 11 PISA monomeric 1 author_and_software_defined_assembly 12 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,M,N 1 1 B,O,P 2 1 G,U,V 3 1 I,W,X 4 1 C,Q 5 1 D,R 6 1 E,S 7 1 F,T 8 1 J,Y 9 1 K,Z 10 1 L,AA 11 1 H 12 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 M N N ? 2 O N N ? 2 Q N N ? 2 R N N ? 2 S N N ? 2 T N N ? 2 U N N ? 2 W N N ? 2 Y N N ? 2 Z N N ? 2 AA 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 metalc ? metalc1 A OD2 ASP 64 A ASP 64 1_555 N MG MG . A MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc2 M O1B GDP . A GDP 900 1_555 N MG MG . A MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? metalc ? metalc3 B OD2 ASP 64 B ASP 64 1_555 P MG MG . B MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc4 O O1B GDP . B GDP 900 1_555 P MG MG . B MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc5 G OD2 ASP 64 G ASP 64 1_555 V MG MG . G MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.687 ? metalc ? metalc6 U O1B GDP . G GDP 900 1_555 V MG MG . G MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc7 I OD2 ASP 64 I ASP 64 1_555 X MG MG . I MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? metalc ? metalc8 W O1B GDP . I GDP 900 1_555 X MG MG . I MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? # _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 2XKB _atom_sites.fract_transf_matrix[1][1] 0.018887 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000828 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.001848 _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] 0.011622 _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 M 2 GDP A 1 900 900 GDP GDP . N 3 MG A 1 999 999 MG MG . O 2 GDP B 1 900 900 GDP GDP . P 3 MG B 1 999 999 MG MG . Q 2 GDP C 1 900 900 GDP GDP . R 2 GDP D 1 900 900 GDP GDP . S 2 GDP E 1 900 900 GDP GDP . T 2 GDP F 1 900 900 GDP GDP . U 2 GDP G 1 900 900 GDP GDP . V 3 MG G 1 999 999 MG MG . W 2 GDP I 1 900 900 GDP GDP . X 3 MG I 1 999 999 MG MG . Y 2 GDP J 1 900 900 GDP GDP . Z 2 GDP K 1 900 900 GDP GDP . AA 2 GDP L 1 900 900 GDP GDP . # 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 . . . U 2 -5.785 -167.89 75.599 1 38.04 ? PB GDP 900 G 1 HETATM 2 O O1B GDP . . . U 2 -4.3 -168.034 75.835 1 39.39 ? O1B GDP 900 G 1 HETATM 3 O O2B GDP . . . U 2 -6.101 -166.434 75.297 1 37.59 ? O2B GDP 900 G 1 HETATM 4 O O3B GDP . . . U 2 -6.194 -168.841 74.507 1 37.87 ? O3B GDP 900 G 1 HETATM 5 O O3A GDP . . . U 2 -6.637 -168.345 76.856 1 37.81 ? O3A GDP 900 G 1 HETATM 6 P PA GDP . . . U 2 -5.979 -168.628 78.276 1 37.95 ? PA GDP 900 G 1 HETATM 7 O O1A GDP . . . U 2 -5.068 -167.453 78.641 1 37.43 ? O1A GDP 900 G 1 HETATM 8 O O2A GDP . . . U 2 -5.32 -169.992 78.235 1 35.88 ? O2A GDP 900 G 1 HETATM 9 O O5' GDP . . . U 2 -7.323 -168.641 79.175 1 37.34 ? O5' GDP 900 G 1 HETATM 10 C C5' GDP . . . U 2 -8.587 -169.037 78.653 1 36.79 ? C5' GDP 900 G 1 HETATM 11 C C4' GDP . . . U 2 -9.277 -169.741 79.796 1 38.25 ? C4' GDP 900 G 1 HETATM 12 O O4' GDP . . . U 2 -8.413 -170.724 80.363 1 39.08 ? O4' GDP 900 G 1 HETATM 13 C C3' GDP . . . U 2 -9.594 -168.771 80.925 1 39.09 ? C3' GDP 900 G 1 HETATM 14 O O3' GDP . . . U 2 -10.925 -169.049 81.387 1 37.86 ? O3' GDP 900 G 1 HETATM 15 C C2' GDP . . . U 2 -8.554 -169.075 81.986 1 39.53 ? C2' GDP 900 G 1 HETATM 16 O O2' GDP . . . U 2 -9.04 -168.827 83.296 1 40.38 ? O2' GDP 900 G 1 HETATM 17 C C1' GDP . . . U 2 -8.305 -170.555 81.784 1 40.7 ? C1' GDP 900 G 1 HETATM 18 N N9 GDP . . . U 2 -6.965 -171.012 82.249 1 42.49 ? N9 GDP 900 G 1 HETATM 19 C C8 GDP . . . U 2 -5.789 -170.366 82.058 1 43.49 ? C8 GDP 900 G 1 HETATM 20 N N7 GDP . . . U 2 -4.752 -171.063 82.583 1 44.03 ? N7 GDP 900 G 1 HETATM 21 C C5 GDP . . . U 2 -5.266 -172.19 83.117 1 43.75 ? C5 GDP 900 G 1 HETATM 22 C C6 GDP . . . U 2 -4.724 -173.369 83.832 1 44.03 ? C6 GDP 900 G 1 HETATM 23 O O6 GDP . . . U 2 -3.499 -173.459 84.055 1 44.11 ? O6 GDP 900 G 1 HETATM 24 N N1 GDP . . . U 2 -5.581 -174.321 84.236 1 43.99 ? N1 GDP 900 G 1 HETATM 25 C C2 GDP . . . U 2 -6.907 -174.242 84.012 1 43.32 ? C2 GDP 900 G 1 HETATM 26 N N2 GDP . . . U 2 -7.697 -175.25 84.445 1 42.66 ? N2 GDP 900 G 1 HETATM 27 N N3 GDP . . . U 2 -7.468 -173.19 83.357 1 43.48 ? N3 GDP 900 G 1 HETATM 28 C C4 GDP . . . U 2 -6.719 -172.153 82.899 1 43.03 ? C4 GDP 900 G 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #