data_8WMO # _model_server_result.job_id 5lGZXCvxwTqkF2V5bJDCvw _model_server_result.datetime_utc '2024-11-24 15:00:02' _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 8wmo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":501}' # _entry.id 8WMO # _exptl.entry_id 8WMO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 9 _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 8WMO _cell.length_a 103.82 _cell.length_b 156.446 _cell.length_c 179.393 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8WMO _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _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,X,Y,Z,AA,BA,CA,DA,EA,FA _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 9 _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 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc2 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc3 K O1A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc4 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? metalc ? metalc5 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc6 C O THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc7 C OG1 THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc8 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc9 C OE1 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? metalc ? metalc10 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc11 P O1G GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc12 P O1B GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc13 W O1A GTP . D GTP 501 1_555 X MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? # _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 143 n n PB O2B GDP sing 144 n n PB O3B GDP sing 145 n n PB O3A GDP sing 146 n n O2B HOB2 GDP sing 147 n n O3B HOB3 GDP sing 148 n n O3A PA GDP sing 149 n n PA O1A GDP doub 150 n n PA O2A GDP sing 151 n n PA O5' GDP sing 152 n n O2A HOA2 GDP sing 153 n n O5' C5' GDP sing 154 n n C5' C4' GDP sing 155 n n C5' H5' GDP sing 156 n n C5' "H5''" GDP sing 157 n n C4' O4' GDP sing 158 n n C4' C3' GDP sing 159 n n C4' H4' GDP sing 160 n n O4' C1' GDP sing 161 n n C3' O3' GDP sing 162 n n C3' C2' GDP sing 163 n n C3' H3' GDP sing 164 n n O3' HO3' GDP sing 165 n n C2' O2' GDP sing 166 n n C2' C1' GDP sing 167 n n C2' H2' GDP sing 168 n n O2' HO2' GDP sing 169 n n C1' N9 GDP sing 170 n n C1' H1' GDP sing 171 n n N9 C8 GDP sing 172 n y N9 C4 GDP sing 173 n y C8 N7 GDP doub 174 n y C8 H8 GDP sing 175 n n N7 C5 GDP sing 176 n y C5 C6 GDP sing 177 n n C5 C4 GDP doub 178 n y C6 O6 GDP doub 179 n n C6 N1 GDP sing 180 n n N1 C2 GDP sing 181 n n N1 HN1 GDP sing 182 n n C2 N2 GDP sing 183 n n C2 N3 GDP doub 184 n n N2 HN21 GDP sing 185 n n N2 HN22 GDP sing 186 n n N3 C4 GDP sing 187 n n # _atom_sites.entry_id 8WMO _atom_sites.fract_transf_matrix[1][1] 0.009632 _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] 0.006392 _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] 0.005574 _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 EDO A 1 503 505 EDO EDO . J 8 PEG A 1 504 506 PEG PEG . K 9 GDP B 1 501 501 GDP GDP . L 6 MG B 1 502 502 MG MG . M 10 MES B 1 503 503 MES MES . N 11 WIW B 1 504 504 WIW B1N . O 7 EDO B 1 505 505 EDO EDO . P 5 GTP C 1 501 501 GTP GTP . Q 6 MG C 1 502 502 MG MG . R 12 CA C 1 503 503 CA CA . S 7 EDO C 1 504 504 EDO EDO . T 7 EDO C 1 505 505 EDO EDO . U 7 EDO C 1 506 506 EDO EDO . V 7 EDO C 1 507 507 EDO EDO . W 5 GTP D 1 501 501 GTP GTP . X 6 MG D 1 502 502 MG MG . Y 7 EDO D 1 503 503 EDO EDO . Z 7 EDO D 1 504 504 EDO EDO . AA 13 ACP F 1 401 401 ACP ACP . BA 14 HOH A 1 601 31 HOH HOH . BA 14 HOH A 2 602 30 HOH HOH . BA 14 HOH A 3 603 17 HOH HOH . BA 14 HOH A 4 604 11 HOH HOH . BA 14 HOH A 5 605 26 HOH HOH . BA 14 HOH A 6 606 27 HOH HOH . BA 14 HOH A 7 607 29 HOH HOH . CA 14 HOH B 1 601 18 HOH HOH . CA 14 HOH B 2 602 5 HOH HOH . CA 14 HOH B 3 603 1 HOH HOH . CA 14 HOH B 4 604 28 HOH HOH . CA 14 HOH B 5 605 25 HOH HOH . CA 14 HOH B 6 606 2 HOH HOH . DA 14 HOH C 1 601 12 HOH HOH . DA 14 HOH C 2 602 3 HOH HOH . DA 14 HOH C 3 603 4 HOH HOH . DA 14 HOH C 4 604 6 HOH HOH . DA 14 HOH C 5 605 24 HOH HOH . DA 14 HOH C 6 606 7 HOH HOH . EA 14 HOH D 1 601 9 HOH HOH . EA 14 HOH D 2 602 13 HOH HOH . EA 14 HOH D 3 603 22 HOH HOH . EA 14 HOH D 4 604 23 HOH HOH . EA 14 HOH D 5 605 10 HOH HOH . EA 14 HOH D 6 606 21 HOH HOH . EA 14 HOH D 7 607 16 HOH HOH . EA 14 HOH D 8 608 14 HOH HOH . EA 14 HOH D 9 609 8 HOH HOH . FA 14 HOH F 1 501 19 HOH HOH . FA 14 HOH F 2 502 15 HOH HOH . FA 14 HOH F 3 503 20 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 9 -19.223 48.97 -15.938 1 46.54 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . K 9 -18.914 49.921 -14.796 1 49.59 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . K 9 -19.868 49.546 -17.171 1 50.88 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . K 9 -20.28 47.944 -15.543 1 49.21 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . K 9 -17.926 48.122 -16.399 1 58.84 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . K 9 -16.514 48.468 -17.033 1 51.84 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . K 9 -15.512 48.295 -15.941 1 55.94 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . K 9 -16.429 49.762 -17.699 1 48.81 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . K 9 -16.45 47.361 -18.176 1 41.55 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . K 9 -15.365 46.455 -18.338 1 55.47 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . K 9 -14.893 46.48 -19.795 1 57.6 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . K 9 -14.327 47.74 -20.162 1 59.27 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . K 9 -13.76 45.54 -20.045 1 57.91 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . K 9 -13.866 45.216 -21.434 1 55.36 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . K 9 -12.536 46.38 -19.784 1 53.26 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . K 9 -11.437 45.897 -20.53 1 65.77 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . K 9 -12.938 47.677 -20.375 1 86.62 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . K 9 -12.48 48.796 -19.582 1 55.18 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . K 9 -12.769 49.037 -18.303 1 54.27 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . K 9 -12.219 50.2 -17.88 1 53.9 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . K 9 -11.55 50.729 -18.93 1 55.82 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . K 9 -10.76 51.937 -19.213 1 49.58 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . K 9 -10.552 52.781 -18.343 1 54.86 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . K 9 -10.268 52.101 -20.426 1 50.7 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . K 9 -10.467 51.217 -21.414 1 50.84 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . K 9 -9.927 51.429 -22.631 1 43.44 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . K 9 -11.191 50.1 -21.245 1 49.53 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . K 9 -11.747 49.802 -20.049 1 54.7 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #