data_5ZXH # _model_server_result.job_id GEnkEDTOcrVZA6ff3Prvvg _model_server_result.datetime_utc '2025-07-07 22:32:35' _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 5zxh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":501}' # _entry.id 5ZXH # _exptl.entry_id 5ZXH _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 5ZXH _cell.length_a 104.91 _cell.length_b 157.06 _cell.length_c 182.838 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZXH _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,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 8 _struct_asym.id J _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.755 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc8 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc10 H MG MG . A MG 502 1_555 W O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc11 H MG MG . A MG 502 1_555 W O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.833 ? metalc ? metalc12 H MG MG . A MG 502 1_555 W O HOH . A HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc13 H MG MG . A MG 502 1_555 X O HOH . B HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc14 B OE1 GLN 11 B GLN 11 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc15 B OE1 GLU 111 B GLU 111 1_555 M CA CA . B CA 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc16 B OD2 ASP 177 B ASP 177 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc17 J O1A GDP . B GDP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? metalc ? metalc18 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? metalc ? metalc19 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.662 ? metalc ? metalc20 C O THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc21 C OG1 THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc22 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.659 ? metalc ? metalc23 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc24 P O1G GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc25 P O1B GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc26 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc27 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc28 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc29 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc30 S O1G GTP . D GTP 501 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc31 S O2G GTP . D GTP 501 1_555 T MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.991 ? # _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 182 n n PB O2B GDP sing 183 n n PB O3B GDP sing 184 n n PB O3A GDP sing 185 n n O2B HOB2 GDP sing 186 n n O3B HOB3 GDP sing 187 n n O3A PA GDP sing 188 n n PA O1A GDP doub 189 n n PA O2A GDP sing 190 n n PA O5' GDP sing 191 n n O2A HOA2 GDP sing 192 n n O5' C5' GDP sing 193 n n C5' C4' GDP sing 194 n n C5' H5' GDP sing 195 n n C5' "H5''" GDP sing 196 n n C4' O4' GDP sing 197 n n C4' C3' GDP sing 198 n n C4' H4' GDP sing 199 n n O4' C1' GDP sing 200 n n C3' O3' GDP sing 201 n n C3' C2' GDP sing 202 n n C3' H3' GDP sing 203 n n O3' HO3' GDP sing 204 n n C2' O2' GDP sing 205 n n C2' C1' GDP sing 206 n n C2' H2' GDP sing 207 n n O2' HO2' GDP sing 208 n n C1' N9 GDP sing 209 n n C1' H1' GDP sing 210 n n N9 C8 GDP sing 211 n y N9 C4 GDP sing 212 n y C8 N7 GDP doub 213 n y C8 H8 GDP sing 214 n n N7 C5 GDP sing 215 n y C5 C6 GDP sing 216 n n C5 C4 GDP doub 217 n y C6 O6 GDP doub 218 n n C6 N1 GDP sing 219 n n N1 C2 GDP sing 220 n n N1 HN1 GDP sing 221 n n C2 N2 GDP sing 222 n n C2 N3 GDP doub 223 n n N2 HN21 GDP sing 224 n n N2 HN22 GDP sing 225 n n N3 C4 GDP sing 226 n n # _atom_sites.entry_id 5ZXH _atom_sites.fract_transf_matrix[1][1] 0.009532 _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] 0.006367 _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] 0.005469 _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 GDP B 1 501 501 GDP GDP . K 6 MG B 1 502 502 MG MG . L 9 MES B 1 503 505 MES MES . M 7 CA B 1 504 2 CA CA . N 9 MES B 1 505 505 MES MES . O 10 9LX B 1 506 1 9LX LZP . P 5 GTP C 1 501 501 GTP GTP . Q 6 MG C 1 502 502 MG MG . R 7 CA C 1 503 1 CA CA . S 5 GTP D 1 501 501 GTP GTP . T 6 MG D 1 502 502 MG MG . U 10 9LX D 1 503 2 9LX LZP . V 11 ACP F 1 401 401 ACP ACP . W 12 HOH A 1 601 7 HOH HOH . W 12 HOH A 2 602 4 HOH HOH . W 12 HOH A 3 603 8 HOH HOH . W 12 HOH A 4 604 2 HOH HOH . W 12 HOH A 5 605 5 HOH HOH . W 12 HOH A 6 606 1 HOH HOH . W 12 HOH A 7 607 10 HOH HOH . X 12 HOH B 1 601 3 HOH HOH . X 12 HOH B 2 602 9 HOH HOH . X 12 HOH B 3 603 11 HOH HOH . X 12 HOH B 4 604 6 HOH HOH . Y 12 HOH C 1 601 15 HOH HOH . Y 12 HOH C 2 602 13 HOH HOH . Y 12 HOH C 3 603 14 HOH HOH . Y 12 HOH C 4 604 12 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 . . . J 8 -18.763 -49.545 15.863 1 17.68 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . J 8 -18.318 -50.582 14.886 1 19.85 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . J 8 -19.358 -50.169 17.064 1 18.86 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . J 8 -19.573 -48.433 15.179 1 19.78 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . J 8 -17.478 -48.712 16.35 1 17.88 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . J 8 -16.061 -49.217 16.925 1 17.51 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . J 8 -15.018 -49.06 15.831 1 18.39 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . J 8 -16.285 -50.6 17.436 1 18.35 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . J 8 -15.91 -48.19 18.172 1 17.68 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . J 8 -14.917 -47.202 18.309 1 20.57 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . J 8 -14.265 -47.337 19.676 1 23.28 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . J 8 -13.754 -48.662 19.855 1 24.19 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . J 8 -13.055 -46.449 19.851 1 24.52 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . J 8 -12.926 -46.133 21.246 1 25.94 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . J 8 -11.905 -47.321 19.377 1 25.16 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . J 8 -10.648 -46.935 19.957 1 28.6 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . J 8 -12.333 -48.652 19.907 1 24.02 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . J 8 -11.902 -49.845 19.169 1 23.31 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . J 8 -12.206 -50.173 17.911 1 23.58 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . J 8 -11.697 -51.394 17.597 1 23.08 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . J 8 -11.067 -51.846 18.684 1 22.35 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . J 8 -10.309 -53.051 19.037 1 23.43 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . J 8 -10.142 -53.965 18.186 1 22.64 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . J 8 -9.816 -53.13 20.3 1 23.84 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . J 8 -9.977 -52.178 21.238 1 22.4 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . J 8 -9.425 -52.381 22.46 1 22.31 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . J 8 -10.653 -51.042 20.969 1 21.84 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . J 8 -11.204 -50.837 19.732 1 22.8 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 226 _model_server_stats.query_time_ms 452 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 28 #