data_2IK8 # _model_server_result.job_id mRheOtmQx28U0muBrTgBUQ _model_server_result.datetime_utc '2024-10-11 00:29:20' _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 2ik8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":401}' # _entry.id 2IK8 # _exptl.entry_id 2IK8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _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 2IK8 _cell.length_a 82.656 _cell.length_b 104.312 _cell.length_c 124.048 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2IK8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_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,E,F,G,H,I,J,K,L,S,T 1 1 C,D,M,N,O,P,Q,R,U,V 2 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 ? 6 K N N ? 6 Q 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 OG SER 17 A SER 47 1_555 F MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc2 A OG1 THR 151 A THR 181 1_555 F MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.657 ? metalc ? metalc3 E F1 ALF . A ALF 355 1_555 F MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc4 E AL ALF . A ALF 355 1_555 F MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.337 ? metalc ? metalc5 E F3 ALF . A ALF 355 1_555 F MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.058 ? metalc ? metalc6 E AL ALF . A ALF 355 1_555 K O2B GDP . A GDP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? metalc ? metalc7 E AL ALF . A ALF 355 1_555 K O1B GDP . A GDP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.596 ? metalc ? metalc8 E AL ALF . A ALF 355 1_555 S O HOH . A HOH 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.717 ? metalc ? metalc9 E AL ALF . A ALF 355 1_555 S O HOH . A HOH 416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc10 F MG MG . A MG 356 1_555 K O1B GDP . A GDP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc11 F MG MG . A MG 356 1_555 S O HOH . A HOH 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.659 ? metalc ? metalc12 F MG MG . A MG 356 1_555 S O HOH . A HOH 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? metalc ? metalc13 C OG SER 17 C SER 47 1_555 N MG MG . C MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.907 ? metalc ? metalc14 C OG1 THR 151 C THR 181 1_555 N MG MG . C MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc15 M AL ALF . C ALF 355 1_555 N MG MG . C MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.235 ? metalc ? metalc16 M F3 ALF . C ALF 355 1_555 N MG MG . C MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.716 ? metalc ? metalc17 M AL ALF . C ALF 355 1_555 Q O2B GDP . C GDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.727 ? metalc ? metalc18 M AL ALF . C ALF 355 1_555 Q O1B GDP . C GDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.569 ? metalc ? metalc19 M AL ALF . C ALF 355 1_555 U O HOH . C HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc20 M AL ALF . C ALF 355 1_555 U O HOH . C HOH 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.522 ? metalc ? metalc21 N MG MG . C MG 356 1_555 Q O1B GDP . C GDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? metalc ? metalc22 N MG MG . C MG 356 1_555 Q O2B GDP . C GDP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.074 ? metalc ? metalc23 N MG MG . C MG 356 1_555 U O HOH . C HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc24 N MG MG . C MG 356 1_555 U O HOH . C HOH 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.815 ? # _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 87 n n PB O2B GDP sing 88 n n PB O3B GDP sing 89 n n PB O3A GDP sing 90 n n O2B HOB2 GDP sing 91 n n O3B HOB3 GDP sing 92 n n O3A PA GDP sing 93 n n PA O1A GDP doub 94 n n PA O2A GDP sing 95 n n PA O5' GDP sing 96 n n O2A HOA2 GDP sing 97 n n O5' C5' GDP sing 98 n n C5' C4' GDP sing 99 n n C5' H5' GDP sing 100 n n C5' "H5''" GDP sing 101 n n C4' O4' GDP sing 102 n n C4' C3' GDP sing 103 n n C4' H4' GDP sing 104 n n O4' C1' GDP sing 105 n n C3' O3' GDP sing 106 n n C3' C2' GDP sing 107 n n C3' H3' GDP sing 108 n n O3' HO3' GDP sing 109 n n C2' O2' GDP sing 110 n n C2' C1' GDP sing 111 n n C2' H2' GDP sing 112 n n O2' HO2' GDP sing 113 n n C1' N9 GDP sing 114 n n C1' H1' GDP sing 115 n n N9 C8 GDP sing 116 n y N9 C4 GDP sing 117 n y C8 N7 GDP doub 118 n y C8 H8 GDP sing 119 n n N7 C5 GDP sing 120 n y C5 C6 GDP sing 121 n n C5 C4 GDP doub 122 n y C6 O6 GDP doub 123 n n C6 N1 GDP sing 124 n n N1 C2 GDP sing 125 n n N1 HN1 GDP sing 126 n n C2 N2 GDP sing 127 n n C2 N3 GDP doub 128 n n N2 HN21 GDP sing 129 n n N2 HN22 GDP sing 130 n n N3 C4 GDP sing 131 n n # _atom_sites.entry_id 2IK8 _atom_sites.fract_transf_matrix[1][1] 0.012098 _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] 0.009587 _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] 0.008061 _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 E 3 ALF A 1 355 101 ALF ALF . F 4 MG A 1 356 201 MG MG . G 5 SO4 A 1 357 304 SO4 SO4 . H 5 SO4 A 1 358 305 SO4 SO4 . I 5 SO4 A 1 359 306 SO4 SO4 . J 5 SO4 A 1 360 308 SO4 SO4 . K 6 GDP A 1 401 401 GDP GDP . L 5 SO4 B 1 302 302 SO4 SO4 . M 3 ALF C 1 355 102 ALF ALF . N 4 MG C 1 356 202 MG MG . O 5 SO4 C 1 357 301 SO4 SO4 . P 5 SO4 C 1 358 307 SO4 SO4 . Q 6 GDP C 1 402 402 GDP GDP . R 5 SO4 D 1 303 303 SO4 SO4 . S 7 HOH A 1 402 3 HOH HOH . S 7 HOH A 2 403 5 HOH HOH . S 7 HOH A 3 404 7 HOH HOH . S 7 HOH A 4 405 16 HOH HOH . S 7 HOH A 5 406 18 HOH HOH . S 7 HOH A 6 407 21 HOH HOH . S 7 HOH A 7 408 27 HOH HOH . S 7 HOH A 8 409 30 HOH HOH . S 7 HOH A 9 410 32 HOH HOH . S 7 HOH A 10 411 34 HOH HOH . S 7 HOH A 11 412 39 HOH HOH . S 7 HOH A 12 413 41 HOH HOH . S 7 HOH A 13 414 42 HOH HOH . S 7 HOH A 14 415 43 HOH HOH . S 7 HOH A 15 416 45 HOH HOH . S 7 HOH A 16 417 46 HOH HOH . T 7 HOH B 1 13 13 HOH HOH . T 7 HOH B 2 20 20 HOH HOH . U 7 HOH C 1 403 4 HOH HOH . U 7 HOH C 2 404 8 HOH HOH . U 7 HOH C 3 405 15 HOH HOH . U 7 HOH C 4 406 17 HOH HOH . U 7 HOH C 5 407 25 HOH HOH . U 7 HOH C 6 408 26 HOH HOH . U 7 HOH C 7 409 33 HOH HOH . U 7 HOH C 8 410 36 HOH HOH . U 7 HOH C 9 411 37 HOH HOH . U 7 HOH C 10 412 44 HOH HOH . U 7 HOH C 11 413 47 HOH HOH . U 7 HOH C 12 414 48 HOH HOH . U 7 HOH C 13 415 49 HOH HOH . U 7 HOH C 14 416 50 HOH HOH . V 7 HOH D 1 6 6 HOH HOH . V 7 HOH D 2 9 9 HOH HOH . V 7 HOH D 3 24 24 HOH HOH . V 7 HOH D 4 38 38 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 . . . K 6 -10.444 30.314 -23.434 1 40.18 ? PB GDP 401 A 1 HETATM 2 O O1B GDP . . . K 6 -9.464 31.429 -23.594 1 37.11 ? O1B GDP 401 A 1 HETATM 3 O O2B GDP . . . K 6 -10.635 30 -21.972 1 40.04 ? O2B GDP 401 A 1 HETATM 4 O O3B GDP . . . K 6 -11.801 30.674 -23.991 1 41.18 ? O3B GDP 401 A 1 HETATM 5 O O3A GDP . . . K 6 -10.04 28.99 -24.244 1 40.84 ? O3A GDP 401 A 1 HETATM 6 P PA GDP . . . K 6 -8.69 28.79 -25.078 1 41.6 ? PA GDP 401 A 1 HETATM 7 O O1A GDP . . . K 6 -7.54 28.456 -24.144 1 41.5 ? O1A GDP 401 A 1 HETATM 8 O O2A GDP . . . K 6 -8.439 29.977 -25.964 1 41.16 ? O2A GDP 401 A 1 HETATM 9 O O5' GDP . . . K 6 -9.042 27.517 -25.983 1 42.13 ? O5' GDP 401 A 1 HETATM 10 C C5' GDP . . . K 6 -9.418 26.288 -25.363 1 43.19 ? C5' GDP 401 A 1 HETATM 11 C C4' GDP . . . K 6 -8.631 25.121 -25.954 1 44.13 ? C4' GDP 401 A 1 HETATM 12 O O4' GDP . . . K 6 -9.318 24.679 -27.129 1 44.36 ? O4' GDP 401 A 1 HETATM 13 C C3' GDP . . . K 6 -7.186 25.452 -26.363 1 43.97 ? C3' GDP 401 A 1 HETATM 14 O O3' GDP . . . K 6 -6.317 24.339 -26.099 1 42.09 ? O3' GDP 401 A 1 HETATM 15 C C2' GDP . . . K 6 -7.284 25.715 -27.85 1 44.65 ? C2' GDP 401 A 1 HETATM 16 O O2' GDP . . . K 6 -6.135 25.301 -28.58 1 45.64 ? O2' GDP 401 A 1 HETATM 17 C C1' GDP . . . K 6 -8.49 24.897 -28.282 1 45.82 ? C1' GDP 401 A 1 HETATM 18 N N9 GDP . . . K 6 -9.317 25.594 -29.28 1 46.21 ? N9 GDP 401 A 1 HETATM 19 C C8 GDP . . . K 6 -9.878 26.806 -29.151 1 46.28 ? C8 GDP 401 A 1 HETATM 20 N N7 GDP . . . K 6 -10.588 27.111 -30.258 1 46.37 ? N7 GDP 401 A 1 HETATM 21 C C5 GDP . . . K 6 -10.506 26.078 -31.099 1 45.97 ? C5 GDP 401 A 1 HETATM 22 C C6 GDP . . . K 6 -11.036 25.752 -32.43 1 46.26 ? C6 GDP 401 A 1 HETATM 23 O O6 GDP . . . K 6 -11.761 26.546 -33.066 1 46.2 ? O6 GDP 401 A 1 HETATM 24 N N1 GDP . . . K 6 -10.705 24.566 -32.94 1 47.06 ? N1 GDP 401 A 1 HETATM 25 C C2 GDP . . . K 6 -9.925 23.677 -32.285 1 46.72 ? C2 GDP 401 A 1 HETATM 26 N N2 GDP . . . K 6 -9.628 22.491 -32.867 1 46.56 ? N2 GDP 401 A 1 HETATM 27 N N3 GDP . . . K 6 -9.419 23.912 -31.057 1 46.4 ? N3 GDP 401 A 1 HETATM 28 C C4 GDP . . . K 6 -9.673 25.076 -30.441 1 46.23 ? C4 GDP 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #