data_7DBB # _model_server_result.job_id GMGYEjBzB-NWRniYcJBU1Q _model_server_result.datetime_utc '2024-11-23 00:03:15' _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 7dbb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":501}' # _entry.id 7DBB # _exptl.entry_id 7DBB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 8 _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 90 _cell.entry_id 7DBB _cell.length_a 105 _cell.length_b 157.573 _cell.length_c 181.629 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7DBB _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W _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 8 _struct_asym.id K _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 OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.851 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? metalc ? metalc8 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc10 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc11 B OE1 GLU 111 B GLU 113 1_555 M CA CA . B CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? metalc ? metalc12 K O1A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc13 C OD1 ASP 39 C ASP 39 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc14 C OD2 ASP 39 C ASP 39 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.908 ? metalc ? metalc15 C O THR 41 C THR 41 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc16 C OG1 THR 41 C THR 41 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? metalc ? metalc17 C O GLY 44 C GLY 44 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc18 C OE1 GLU 55 C GLU 55 1_555 T CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc19 R O1G GTP . C GTP 501 1_555 S MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc20 R O1B GTP . C GTP 501 1_555 S MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.899 ? metalc ? metalc21 U MG MG . D MG 601 1_555 V O3G GTP . D GTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc22 U MG MG . D MG 601 1_555 V O2B GTP . D GTP 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? # _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 134 n n PB O2B GDP sing 135 n n PB O3B GDP sing 136 n n PB O3A GDP sing 137 n n O2B HOB2 GDP sing 138 n n O3B HOB3 GDP sing 139 n n O3A PA GDP sing 140 n n PA O1A GDP doub 141 n n PA O2A GDP sing 142 n n PA O5' GDP sing 143 n n O2A HOA2 GDP sing 144 n n O5' C5' GDP sing 145 n n C5' C4' GDP sing 146 n n C5' H5' GDP sing 147 n n C5' "H5''" GDP sing 148 n n C4' O4' GDP sing 149 n n C4' C3' GDP sing 150 n n C4' H4' GDP sing 151 n n O4' C1' GDP sing 152 n n C3' O3' GDP sing 153 n n C3' C2' GDP sing 154 n n C3' H3' GDP sing 155 n n O3' HO3' GDP sing 156 n n C2' O2' GDP sing 157 n n C2' C1' GDP sing 158 n n C2' H2' GDP sing 159 n n O2' HO2' GDP sing 160 n n C1' N9 GDP sing 161 n n C1' H1' GDP sing 162 n n N9 C8 GDP sing 163 n y N9 C4 GDP sing 164 n y C8 N7 GDP doub 165 n y C8 H8 GDP sing 166 n n N7 C5 GDP sing 167 n y C5 C6 GDP sing 168 n n C5 C4 GDP doub 169 n y C6 O6 GDP doub 170 n n C6 N1 GDP sing 171 n n N1 C2 GDP sing 172 n n N1 HN1 GDP sing 173 n n C2 N2 GDP sing 174 n n C2 N3 GDP doub 175 n n N2 HN21 GDP sing 176 n n N2 HN22 GDP sing 177 n n N3 C4 GDP sing 178 n n # _atom_sites.entry_id 7DBB _atom_sites.fract_transf_matrix[1][1] 0.009524 _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] 0.006346 _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] 0.005506 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 7 CA A 1 504 505 CA CA . K 8 GDP B 1 501 501 GDP GDP . L 6 MG B 1 502 502 MG MG . M 7 CA B 1 503 503 CA CA . N 9 MES B 1 504 504 MES MES . O 9 MES B 1 505 505 MES MES . P 6 MG B 1 506 506 MG MG . Q 10 H1F B 1 507 601 H1F SSE . R 5 GTP C 1 501 501 GTP GTP . S 6 MG C 1 502 502 MG MG . T 7 CA C 1 503 503 CA CA . U 6 MG D 1 601 601 MG MG . V 5 GTP D 1 602 701 GTP GTP . W 11 ACP F 1 401 703 ACP ACP . # 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 8 18.794 49.617 15.766 1 31.22 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . K 8 18.17 50.65 14.885 1 44.25 -1 O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . K 8 19.555 50.26 16.865 1 35.85 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . K 8 19.627 48.623 14.936 1 43.66 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . K 8 17.617 48.733 16.482 1 30.04 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . K 8 16.119 49.244 16.996 1 21.45 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . K 8 15.085 49.087 15.812 1 41.68 -1 O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . K 8 16.199 50.67 17.492 1 28.6 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . K 8 15.954 48.101 18.211 1 21.2 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . K 8 15.009 47.102 18.231 1 22.85 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . K 8 14.4 47.201 19.613 1 34.14 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . K 8 14.017 48.762 19.868 1 26.1 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . K 8 13.343 46.461 19.776 1 27.7 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . K 8 13.218 46.022 21.187 1 29.42 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . K 8 12.173 47.451 19.469 1 35.26 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . K 8 11.1 47.114 20.207 1 37.76 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . K 8 12.707 48.726 20.044 1 26.09 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . K 8 12.124 49.917 19.392 1 38.9 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . K 8 12.42 50.079 18.098 1 33.04 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . K 8 11.806 51.242 17.738 1 36.67 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . K 8 11.166 51.747 18.818 1 36.56 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . K 8 10.31 52.969 19.1 1 34.44 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . K 8 10.081 53.769 18.264 1 39.02 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . K 8 9.785 53.17 20.433 1 39.94 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . K 8 10.063 52.251 21.496 1 35.66 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . K 8 9.533 52.41 22.891 1 32.93 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . K 8 10.847 51.103 21.221 1 32.22 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . K 8 11.378 50.902 19.835 1 41.14 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #