data_5CJV # _model_server_result.job_id DBGBMuNvIAvhy21XAGzYow _model_server_result.datetime_utc '2024-11-24 11:27:29' _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 5cjv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1104}' # _entry.id 5CJV # _exptl.entry_id 5CJV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _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 120 _cell.entry_id 5CJV _cell.length_a 317.56 _cell.length_b 317.56 _cell.length_c 343.52 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CJV _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 5 F N N ? 5 K 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 NE2 HIS 59 A HIS 39 1_555 C CO B12 . A B12 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc2 A OG SER 243 A SER 223 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc3 A OD1 ASP 269 A ASP 249 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? metalc ? metalc4 A OD1 ASP 282 A ASP 262 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc5 A OD1 ASP 282 A ASP 262 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? metalc ? metalc6 A OE2 GLU 330 A GLU 310 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? metalc ? metalc7 A OE2 GLU 330 A GLU 310 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.629 ? metalc ? metalc8 A O THR 331 A THR 311 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.957 ? metalc ? metalc9 C CO B12 . A B12 1101 1_555 D C5' 5AD . A 5AD 1102 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.181 ? metalc ? metalc10 F O2B GDP . A GDP 1104 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc11 F O3B GDP . A GDP 1104 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc12 B NE2 HIS 59 B HIS 39 1_555 I CO B12 . B B12 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc13 B OG SER 243 B SER 223 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc14 B O ILE 268 B ILE 248 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.95 ? metalc ? metalc15 B OD1 ASP 269 B ASP 249 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc16 B OD1 ASP 282 B ASP 262 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc17 B OD1 ASP 282 B ASP 262 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? metalc ? metalc18 B OD2 ASP 282 B ASP 262 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? metalc ? metalc19 B OE2 GLU 330 B GLU 310 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc20 B OE2 GLU 330 B GLU 310 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? metalc ? metalc21 B O THR 331 B THR 311 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? metalc ? metalc22 K O2B GDP . B GDP 1103 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc23 K O3B GDP . B GDP 1103 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? # _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 306 n n PB O2B GDP sing 307 n n PB O3B GDP sing 308 n n PB O3A GDP sing 309 n n O2B HOB2 GDP sing 310 n n O3B HOB3 GDP sing 311 n n O3A PA GDP sing 312 n n PA O1A GDP doub 313 n n PA O2A GDP sing 314 n n PA O5' GDP sing 315 n n O2A HOA2 GDP sing 316 n n O5' C5' GDP sing 317 n n C5' C4' GDP sing 318 n n C5' H5' GDP sing 319 n n C5' "H5''" GDP sing 320 n n C4' O4' GDP sing 321 n n C4' C3' GDP sing 322 n n C4' H4' GDP sing 323 n n O4' C1' GDP sing 324 n n C3' O3' GDP sing 325 n n C3' C2' GDP sing 326 n n C3' H3' GDP sing 327 n n O3' HO3' GDP sing 328 n n C2' O2' GDP sing 329 n n C2' C1' GDP sing 330 n n C2' H2' GDP sing 331 n n O2' HO2' GDP sing 332 n n C1' N9 GDP sing 333 n n C1' H1' GDP sing 334 n n N9 C8 GDP sing 335 n y N9 C4 GDP sing 336 n y C8 N7 GDP doub 337 n y C8 H8 GDP sing 338 n n N7 C5 GDP sing 339 n y C5 C6 GDP sing 340 n n C5 C4 GDP doub 341 n y C6 O6 GDP doub 342 n n C6 N1 GDP sing 343 n n N1 C2 GDP sing 344 n n N1 HN1 GDP sing 345 n n C2 N2 GDP sing 346 n n C2 N3 GDP doub 347 n n N2 HN21 GDP sing 348 n n N2 HN22 GDP sing 349 n n N3 C4 GDP sing 350 n n # _atom_sites.entry_id 5CJV _atom_sites.fract_transf_matrix[1][1] 0.003149 _atom_sites.fract_transf_matrix[1][2] 0.001818 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003636 _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] 0.002911 _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 C 2 B12 A 1 1101 1198 B12 B12 . D 3 5AD A 1 1102 1199 5AD 5AD . E 4 IVC A 1 1103 1211 IVC IVC . F 5 GDP A 1 1104 1200 GDP GDP . G 6 MG A 1 1105 1 MG MG . H 6 MG A 1 1106 3 MG MG . I 2 B12 B 1 1101 1198 B12 B12 . J 4 IVC B 1 1102 1211 IVC IVC . K 5 GDP B 1 1103 1201 GDP GDP . L 6 MG B 1 1104 2 MG MG . M 6 MG B 1 1105 4 MG MG . # 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 . . . F 5 -190.119 -77.896 0.887 1 91.13 ? PB GDP 1104 A 1 HETATM 2 O O1B GDP . . . F 5 -189.313 -76.618 0.66 1 88.6 ? O1B GDP 1104 A 1 HETATM 3 O O2B GDP . . . F 5 -191.612 -77.521 1.046 1 92.66 ? O2B GDP 1104 A 1 HETATM 4 O O3B GDP . . . F 5 -189.652 -78.542 2.112 1 93.21 ? O3B GDP 1104 A 1 HETATM 5 O O3A GDP . . . F 5 -189.915 -78.859 -0.331 1 70.1 ? O3A GDP 1104 A 1 HETATM 6 P PA GDP . . . F 5 -190.647 -80.269 -0.455 1 78.79 ? PA GDP 1104 A 1 HETATM 7 O O1A GDP . . . F 5 -191.949 -80.228 0.12 1 80.51 ? O1A GDP 1104 A 1 HETATM 8 O O2A GDP . . . F 5 -189.849 -81.332 0.255 1 76.87 ? O2A GDP 1104 A 1 HETATM 9 O O5' GDP . . . F 5 -190.748 -80.658 -1.965 1 89.34 ? O5' GDP 1104 A 1 HETATM 10 C C5' GDP . . . F 5 -191.514 -79.98 -2.756 1 90.27 ? C5' GDP 1104 A 1 HETATM 11 C C4' GDP . . . F 5 -191.559 -80.639 -4.152 1 89.71 ? C4' GDP 1104 A 1 HETATM 12 O O4' GDP . . . F 5 -190.203 -80.741 -4.745 1 86.09 ? O4' GDP 1104 A 1 HETATM 13 C C3' GDP . . . F 5 -192.142 -81.994 -4.243 1 92.39 ? C3' GDP 1104 A 1 HETATM 14 O O3' GDP . . . F 5 -192.901 -82.192 -5.419 1 96.35 ? O3' GDP 1104 A 1 HETATM 15 C C2' GDP . . . F 5 -190.976 -82.864 -4.3 1 87.77 ? C2' GDP 1104 A 1 HETATM 16 O O2' GDP . . . F 5 -191.24 -84.151 -4.899 1 83.39 ? O2' GDP 1104 A 1 HETATM 17 C C1' GDP . . . F 5 -190.046 -82.067 -5.141 1 87.01 ? C1' GDP 1104 A 1 HETATM 18 N N9 GDP . . . F 5 -188.609 -82.471 -5.111 1 88.5 ? N9 GDP 1104 A 1 HETATM 19 C C8 GDP . . . F 5 -187.909 -82.791 -4.084 1 87.3 ? C8 GDP 1104 A 1 HETATM 20 N N7 GDP . . . F 5 -186.677 -83.088 -4.474 1 87.81 ? N7 GDP 1104 A 1 HETATM 21 C C5 GDP . . . F 5 -186.619 -82.944 -5.806 1 91.42 ? C5 GDP 1104 A 1 HETATM 22 C C6 GDP . . . F 5 -185.581 -83.118 -6.794 1 95.29 ? C6 GDP 1104 A 1 HETATM 23 O O6 GDP . . . F 5 -184.334 -83.512 -6.401 1 98.76 ? O6 GDP 1104 A 1 HETATM 24 N N1 GDP . . . F 5 -185.848 -82.886 -8.09 1 94.92 ? N1 GDP 1104 A 1 HETATM 25 C C2 GDP . . . F 5 -187.018 -82.516 -8.448 1 95.47 ? C2 GDP 1104 A 1 HETATM 26 N N2 GDP . . . F 5 -187.293 -82.267 -9.879 1 98.31 ? N2 GDP 1104 A 1 HETATM 27 N N3 GDP . . . F 5 -188.041 -82.34 -7.528 1 94.33 ? N3 GDP 1104 A 1 HETATM 28 C C4 GDP . . . F 5 -187.819 -82.559 -6.219 1 91.81 ? C4 GDP 1104 A 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #