data_5YLJ # _model_server_result.job_id 3jRshU3JH2bZMu55w8oZfw _model_server_result.datetime_utc '2024-11-16 23:36:18' _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 5ylj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":501}' # _entry.id 5YLJ # _exptl.entry_id 5YLJ _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 5YLJ _cell.length_a 105.231 _cell.length_b 157.367 _cell.length_c 182.684 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YLJ _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 PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_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 _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 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.992 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.013 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.837 ? metalc ? metalc8 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc10 H MG MG . A MG 502 1_555 V O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc11 H MG MG . A MG 502 1_555 V O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc12 H MG MG . A MG 502 1_555 V O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc13 H MG MG . A MG 502 1_555 W O HOH . B HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc14 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc15 K O1A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc16 L MG MG . B MG 502 1_555 W O HOH . B HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? metalc ? metalc17 L MG MG . B MG 502 1_555 W O HOH . B HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc18 L MG MG . B MG 502 1_555 W O HOH . B HOH 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc19 L MG MG . B MG 502 1_555 X O HOH . C HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc20 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? metalc ? metalc21 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? metalc ? metalc22 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? metalc ? metalc23 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? metalc ? metalc24 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? metalc ? metalc25 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.891 ? metalc ? metalc26 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc27 O O1G GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc28 O O1B GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc29 P MG MG . C MG 502 1_555 X O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc30 P MG MG . C MG 502 1_555 X O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc31 P MG MG . C MG 502 1_555 X O HOH . C HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc32 P MG MG . C MG 502 1_555 X O HOH . C HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc33 R O1G GTP . D GTP 501 1_555 S MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc34 S MG MG . D MG 502 1_555 Y O HOH . D HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc35 S MG MG . D MG 502 1_555 Y O HOH . D HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc36 S MG MG . D MG 502 1_555 Y O HOH . D HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? # _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 184 n n PB O2B GDP sing 185 n n PB O3B GDP sing 186 n n PB O3A GDP sing 187 n n O2B HOB2 GDP sing 188 n n O3B HOB3 GDP sing 189 n n O3A PA GDP sing 190 n n PA O1A GDP doub 191 n n PA O2A GDP sing 192 n n PA O5' GDP sing 193 n n O2A HOA2 GDP sing 194 n n O5' C5' GDP sing 195 n n C5' C4' GDP sing 196 n n C5' H5' GDP sing 197 n n C5' "H5''" GDP sing 198 n n C4' O4' GDP sing 199 n n C4' C3' GDP sing 200 n n C4' H4' GDP sing 201 n n O4' C1' GDP sing 202 n n C3' O3' GDP sing 203 n n C3' C2' GDP sing 204 n n C3' H3' GDP sing 205 n n O3' HO3' GDP sing 206 n n C2' O2' GDP sing 207 n n C2' C1' GDP sing 208 n n C2' H2' GDP sing 209 n n O2' HO2' GDP sing 210 n n C1' N9 GDP sing 211 n n C1' H1' GDP sing 212 n n N9 C8 GDP sing 213 n y N9 C4 GDP sing 214 n y C8 N7 GDP doub 215 n y C8 H8 GDP sing 216 n n N7 C5 GDP sing 217 n y C5 C6 GDP sing 218 n n C5 C4 GDP doub 219 n y C6 O6 GDP doub 220 n n C6 N1 GDP sing 221 n n N1 C2 GDP sing 222 n n N1 HN1 GDP sing 223 n n C2 N2 GDP sing 224 n n C2 N3 GDP doub 225 n n N2 HN21 GDP sing 226 n n N2 HN22 GDP sing 227 n n N3 C4 GDP sing 228 n n # _atom_sites.entry_id 5YLJ _atom_sites.fract_transf_matrix[1][1] 0.009503 _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] 0.006355 _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] 0.005474 _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 GOL A 1 504 601 GOL GOL . K 9 GDP B 1 501 501 GDP GDP . L 6 MG B 1 502 502 MG MG . M 10 MES B 1 503 505 MES MES . N 11 8X0 B 1 504 1 8X0 MIL . O 5 GTP C 1 501 501 GTP GTP . P 6 MG C 1 502 502 MG MG . Q 7 CA C 1 503 504 CA CA . R 5 GTP D 1 501 501 GTP GTP . S 6 MG D 1 502 502 MG MG . T 11 8X0 D 1 503 2 8X0 MIL . U 12 ACP F 1 401 401 ACP ACP . V 13 HOH A 1 601 3 HOH HOH . V 13 HOH A 2 602 1 HOH HOH . V 13 HOH A 3 603 4 HOH HOH . V 13 HOH A 4 604 5 HOH HOH . W 13 HOH B 1 601 9 HOH HOH . W 13 HOH B 2 602 11 HOH HOH . W 13 HOH B 3 603 10 HOH HOH . W 13 HOH B 4 604 2 HOH HOH . W 13 HOH B 5 605 7 HOH HOH . W 13 HOH B 6 606 8 HOH HOH . W 13 HOH B 7 607 6 HOH HOH . W 13 HOH B 8 608 14 HOH HOH . W 13 HOH B 9 609 16 HOH HOH . W 13 HOH B 10 610 12 HOH HOH . W 13 HOH B 11 611 13 HOH HOH . X 13 HOH C 1 601 22 HOH HOH . X 13 HOH C 2 602 18 HOH HOH . X 13 HOH C 3 603 21 HOH HOH . X 13 HOH C 4 604 17 HOH HOH . X 13 HOH C 5 605 19 HOH HOH . X 13 HOH C 6 606 20 HOH HOH . X 13 HOH C 7 607 15 HOH HOH . Y 13 HOH D 1 601 27 HOH HOH . Y 13 HOH D 2 602 23 HOH HOH . Y 13 HOH D 3 603 25 HOH HOH . Y 13 HOH D 4 604 26 HOH HOH . Y 13 HOH D 5 605 24 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 18.743 207.084 15.808 1 37.07 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . K 9 18.129 207.935 14.728 1 38.51 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . K 9 19.198 207.872 17.009 1 37.54 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . K 9 19.774 206.093 15.321 1 38.37 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . K 9 17.537 206.14 16.316 1 36.47 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . K 9 16.13 206.68 16.902 1 36.03 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . K 9 15.072 206.463 15.846 1 36.81 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . K 9 16.3 208.068 17.467 1 36.06 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . K 9 15.936 205.682 18.163 1 36.02 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . K 9 14.987 204.623 18.235 1 37.89 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . K 9 14.342 204.658 19.623 1 40.17 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . K 9 13.886 205.974 19.92 1 40.43 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . K 9 13.12 203.767 19.77 1 41 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . K 9 13.12 203.23 21.1 1 42.01 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . K 9 11.922 204.674 19.59 1 41.21 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . K 9 10.84 204.248 20.424 1 43.23 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . K 9 12.46 206.021 20.031 1 41.59 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . K 9 11.999 207.185 19.237 1 42.08 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . K 9 12.271 207.467 17.947 1 42.29 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . K 9 11.706 208.645 17.576 1 42.64 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . K 9 11.066 209.139 18.653 1 42.84 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . K 9 10.263 210.345 18.975 1 43.19 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . K 9 10.037 211.211 18.106 1 44.5 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . K 9 9.784 210.47 20.227 1 42.98 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . K 9 10.006 209.549 21.194 1 42.23 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . K 9 9.489 209.738 22.43 1 40.81 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . K 9 10.731 208.425 20.968 1 41.95 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . K 9 11.273 208.175 19.747 1 42.39 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 60 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 28 #