data_8YRK # _model_server_result.job_id ex3WHLdFyS7tdIM9fDI0Fw _model_server_result.datetime_utc '2025-04-13 20:25:17' _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 8yrk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":502}' # _entry.id 8YRK # _exptl.entry_id 8YRK _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 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 8YRK _cell.length_a 104.097 _cell.length_b 158.982 _cell.length_c 179.057 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YRK _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 9 K N N ? 9 U 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 OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.672 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc4 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc5 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.657 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc7 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc8 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc9 H MG MG . A MG 502 1_555 Y O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc10 H MG MG . A MG 502 1_555 Y O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc11 H MG MG . A MG 502 1_555 Y O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc12 H MG MG . A MG 502 1_555 Y O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc13 I CA CA . A CA 503 1_555 Y O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc14 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc15 K O1A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc16 L MG MG . B MG 502 1_555 Z O HOH . B HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.869 ? metalc ? metalc17 L MG MG . B MG 502 1_555 Z O HOH . B HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc18 L MG MG . B MG 502 1_555 Z O HOH . B HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc19 L MG MG . B MG 502 1_555 Z O HOH . B HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc20 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.853 ? metalc ? metalc21 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc22 C O THR 41 C THR 41 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc23 C OG1 THR 41 C THR 41 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc24 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.894 ? metalc ? metalc25 C OE1 GLU 55 C GLU 55 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc26 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc27 Q O1G GTP . C GTP 501 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.728 ? metalc ? metalc28 Q O3G GTP . C GTP 501 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc29 Q O1B GTP . C GTP 501 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc30 R CA CA . C CA 502 1_555 AA O HOH . C HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc31 AA O HOH . C HOH 602 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc32 AA O HOH . C HOH 603 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc33 AA O HOH . C HOH 604 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc34 AA O HOH . C HOH 607 1_555 T MG MG . D MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc35 U O1B GDP . D GDP 502 1_555 V MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? metalc ? metalc36 V MG MG . D MG 503 1_555 BA O HOH . D HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc37 V MG MG . D MG 503 1_555 BA O HOH . D HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc38 V MG MG . D MG 503 1_555 BA O HOH . D HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? # _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 192 n n PB O2B GDP sing 193 n n PB O3B GDP sing 194 n n PB O3A GDP sing 195 n n O2B HOB2 GDP sing 196 n n O3B HOB3 GDP sing 197 n n O3A PA GDP sing 198 n n PA O1A GDP doub 199 n n PA O2A GDP sing 200 n n PA O5' GDP sing 201 n n O2A HOA2 GDP sing 202 n n O5' C5' GDP sing 203 n n C5' C4' GDP sing 204 n n C5' H5' GDP sing 205 n n C5' "H5''" GDP sing 206 n n C4' O4' GDP sing 207 n n C4' C3' GDP sing 208 n n C4' H4' GDP sing 209 n n O4' C1' GDP sing 210 n n C3' O3' GDP sing 211 n n C3' C2' GDP sing 212 n n C3' H3' GDP sing 213 n n O3' HO3' GDP sing 214 n n C2' O2' GDP sing 215 n n C2' C1' GDP sing 216 n n C2' H2' GDP sing 217 n n O2' HO2' GDP sing 218 n n C1' N9 GDP sing 219 n n C1' H1' GDP sing 220 n n N9 C8 GDP sing 221 n y N9 C4 GDP sing 222 n y C8 N7 GDP doub 223 n y C8 H8 GDP sing 224 n n N7 C5 GDP sing 225 n y C5 C6 GDP sing 226 n n C5 C4 GDP doub 227 n y C6 O6 GDP doub 228 n n C6 N1 GDP sing 229 n n N1 C2 GDP sing 230 n n N1 HN1 GDP sing 231 n n C2 N2 GDP sing 232 n n C2 N3 GDP doub 233 n n N2 HN21 GDP sing 234 n n N2 HN22 GDP sing 235 n n N3 C4 GDP sing 236 n n # _atom_sites.entry_id 8YRK _atom_sites.fract_transf_matrix[1][1] 0.009606 _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] 0.00629 _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] 0.005585 _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 8 CL A 1 504 504 CL CL . 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 10 MES B 1 504 504 MES MES . O 11 GOL B 1 505 505 GOL GOL . P 12 A1D62 B 1 506 506 A1D62 LIG . Q 5 GTP C 1 501 501 GTP GTP . R 7 CA C 1 502 503 CA CA . S 13 EDO C 1 503 504 EDO EDO . T 6 MG D 1 501 502 MG MG . U 9 GDP D 1 502 501 GDP GDP . V 6 MG D 1 503 502 MG MG . W 12 A1D62 D 1 504 503 A1D62 LIG . X 14 ACP F 1 401 401 ACP ACP . Y 15 HOH A 1 601 2 HOH HOH . Y 15 HOH A 2 602 3 HOH HOH . Y 15 HOH A 3 603 4 HOH HOH . Y 15 HOH A 4 604 5 HOH HOH . Y 15 HOH A 5 605 1 HOH HOH . Z 15 HOH B 1 601 19 HOH HOH . Z 15 HOH B 2 602 8 HOH HOH . Z 15 HOH B 3 603 10 HOH HOH . Z 15 HOH B 4 604 6 HOH HOH . Z 15 HOH B 5 605 9 HOH HOH . Z 15 HOH B 6 606 7 HOH HOH . Z 15 HOH B 7 607 28 HOH HOH . Z 15 HOH B 8 608 29 HOH HOH . Z 15 HOH B 9 609 30 HOH HOH . AA 15 HOH C 1 601 26 HOH HOH . AA 15 HOH C 2 602 13 HOH HOH . AA 15 HOH C 3 603 12 HOH HOH . AA 15 HOH C 4 604 14 HOH HOH . AA 15 HOH C 5 605 15 HOH HOH . AA 15 HOH C 6 606 23 HOH HOH . AA 15 HOH C 7 607 11 HOH HOH . AA 15 HOH C 8 608 32 HOH HOH . AA 15 HOH C 9 609 27 HOH HOH . AA 15 HOH C 10 610 20 HOH HOH . AA 15 HOH C 11 611 21 HOH HOH . AA 15 HOH C 12 612 31 HOH HOH . BA 15 HOH D 1 601 16 HOH HOH . BA 15 HOH D 2 602 24 HOH HOH . BA 15 HOH D 3 603 17 HOH HOH . BA 15 HOH D 4 604 18 HOH HOH . BA 15 HOH D 5 605 33 HOH HOH . BA 15 HOH D 6 606 34 HOH HOH . CA 15 HOH E 1 201 22 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 . . . U 9 26.138 -9.643 -43.936 1 64.3 ? PB GDP 502 D 1 HETATM 2 O O1B GDP . . . U 9 25.585 -8.704 -44.976 1 51.92 ? O1B GDP 502 D 1 HETATM 3 O O2B GDP . . . U 9 26.55 -8.877 -42.701 1 68.78 ? O2B GDP 502 D 1 HETATM 4 O O3B GDP . . . U 9 27.345 -10.412 -44.432 1 64.73 ? O3B GDP 502 D 1 HETATM 5 O O3A GDP . . . U 9 25.053 -10.753 -43.548 1 76.19 ? O3A GDP 502 D 1 HETATM 6 P PA GDP . . . U 9 23.487 -10.43 -43.452 1 59.69 ? PA GDP 502 D 1 HETATM 7 O O1A GDP . . . U 9 22.688 -10.886 -44.647 1 78.81 ? O1A GDP 502 D 1 HETATM 8 O O2A GDP . . . U 9 23.271 -8.964 -43.2 1 77.19 ? O2A GDP 502 D 1 HETATM 9 O O5' GDP . . . U 9 23.186 -11.328 -42.162 1 66.39 ? O5' GDP 502 D 1 HETATM 10 C C5' GDP . . . U 9 22.443 -12.533 -42.241 1 61.69 ? C5' GDP 502 D 1 HETATM 11 C C4' GDP . . . U 9 21.598 -12.596 -40.984 1 59.81 ? C4' GDP 502 D 1 HETATM 12 O O4' GDP . . . U 9 20.824 -11.403 -40.971 1 65.12 ? O4' GDP 502 D 1 HETATM 13 C C3' GDP . . . U 9 20.625 -13.753 -41.03 1 70.85 ? C3' GDP 502 D 1 HETATM 14 O O3' GDP . . . U 9 20.526 -14.318 -39.72 1 75.21 ? O3' GDP 502 D 1 HETATM 15 C C2' GDP . . . U 9 19.302 -13.148 -41.448 1 62.93 ? C2' GDP 502 D 1 HETATM 16 O O2' GDP . . . U 9 18.23 -13.75 -40.725 1 78.06 ? O2' GDP 502 D 1 HETATM 17 C C1' GDP . . . U 9 19.428 -11.684 -41.08 1 58.99 ? C1' GDP 502 D 1 HETATM 18 N N9 GDP . . . U 9 18.864 -10.765 -42.097 1 61.11 ? N9 GDP 502 D 1 HETATM 19 C C8 GDP . . . U 9 19.358 -10.54 -43.329 1 70.09 ? C8 GDP 502 D 1 HETATM 20 N N7 GDP . . . U 9 18.613 -9.615 -43.991 1 66.68 ? N7 GDP 502 D 1 HETATM 21 C C5 GDP . . . U 9 17.628 -9.225 -43.163 1 58.38 ? C5 GDP 502 D 1 HETATM 22 C C6 GDP . . . U 9 16.494 -8.277 -43.222 1 64.59 ? C6 GDP 502 D 1 HETATM 23 O O6 GDP . . . U 9 16.271 -7.597 -44.247 1 74.11 ? O6 GDP 502 D 1 HETATM 24 N N1 GDP . . . U 9 15.71 -8.168 -42.145 1 60.23 ? N1 GDP 502 D 1 HETATM 25 C C2 GDP . . . U 9 15.918 -8.885 -41.027 1 55.74 ? C2 GDP 502 D 1 HETATM 26 N N2 GDP . . . U 9 15.071 -8.711 -39.986 1 56.84 ? N2 GDP 502 D 1 HETATM 27 N N3 GDP . . . U 9 16.931 -9.776 -40.9 1 57.53 ? N3 GDP 502 D 1 HETATM 28 C C4 GDP . . . U 9 17.802 -9.981 -41.915 1 60.58 ? C4 GDP 502 D 1 # _model_server_stats.io_time_ms 88 _model_server_stats.parse_time_ms 34 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 28 #