data_5CJT # _model_server_result.job_id 9ofkPQVFT1FSsT52R3zkpQ _model_server_result.datetime_utc '2025-06-24 19:49:40' _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 5cjt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":1103}' # _entry.id 5CJT # _exptl.entry_id 5CJT _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 5CJT _cell.length_a 316.84 _cell.length_b 316.84 _cell.length_c 342.65 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CJT _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? metalc ? metalc2 A OG SER 243 A SER 223 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc3 A OD1 ASP 269 A ASP 249 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? metalc ? metalc4 A OD1 ASP 282 A ASP 262 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc5 A OD1 ASP 282 A ASP 262 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? metalc ? metalc6 A OE2 GLU 330 A GLU 310 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc7 A OE2 GLU 330 A GLU 310 1_555 H MG MG . A MG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc8 C CO B12 . A B12 1101 1_555 D C5' 5AD . A 5AD 1102 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.164 ? metalc ? metalc9 F O1B GDP . A GDP 1104 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc10 F O3B GDP . A GDP 1104 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc11 B NE2 HIS 59 B HIS 39 1_555 I CO B12 . B B12 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc12 B OG SER 243 B SER 223 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc13 B O ILE 268 B ILE 248 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? metalc ? metalc14 B OD1 ASP 269 B ASP 249 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? metalc ? metalc15 B OD1 ASP 282 B ASP 262 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc16 B OD1 ASP 282 B ASP 262 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.859 ? metalc ? metalc17 B OD2 ASP 282 B ASP 262 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? metalc ? metalc18 B OE2 GLU 330 B GLU 310 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.687 ? metalc ? metalc19 B OE2 GLU 330 B GLU 310 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? metalc ? metalc20 B O THR 331 B THR 311 1_555 M MG MG . B MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.996 ? metalc ? metalc21 K O1B GDP . B GDP 1103 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? metalc ? metalc22 K O3B GDP . B GDP 1103 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? # _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 403 n n PB O2B GDP sing 404 n n PB O3B GDP sing 405 n n PB O3A GDP sing 406 n n O2B HOB2 GDP sing 407 n n O3B HOB3 GDP sing 408 n n O3A PA GDP sing 409 n n PA O1A GDP doub 410 n n PA O2A GDP sing 411 n n PA O5' GDP sing 412 n n O2A HOA2 GDP sing 413 n n O5' C5' GDP sing 414 n n C5' C4' GDP sing 415 n n C5' H5' GDP sing 416 n n C5' "H5''" GDP sing 417 n n C4' O4' GDP sing 418 n n C4' C3' GDP sing 419 n n C4' H4' GDP sing 420 n n O4' C1' GDP sing 421 n n C3' O3' GDP sing 422 n n C3' C2' GDP sing 423 n n C3' H3' GDP sing 424 n n O3' HO3' GDP sing 425 n n C2' O2' GDP sing 426 n n C2' C1' GDP sing 427 n n C2' H2' GDP sing 428 n n O2' HO2' GDP sing 429 n n C1' N9 GDP sing 430 n n C1' H1' GDP sing 431 n n N9 C8 GDP sing 432 n y N9 C4 GDP sing 433 n y C8 N7 GDP doub 434 n y C8 H8 GDP sing 435 n n N7 C5 GDP sing 436 n y C5 C6 GDP sing 437 n n C5 C4 GDP doub 438 n y C6 O6 GDP doub 439 n n C6 N1 GDP sing 440 n n N1 C2 GDP sing 441 n n N1 HN1 GDP sing 442 n n C2 N2 GDP sing 443 n n C2 N3 GDP doub 444 n n N2 HN21 GDP sing 445 n n N2 HN22 GDP sing 446 n n N3 C4 GDP sing 447 n n # _atom_sites.entry_id 5CJT _atom_sites.fract_transf_matrix[1][1] 0.003156 _atom_sites.fract_transf_matrix[1][2] 0.001822 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003644 _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] 0.002918 _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 CO6 A 1 1103 1211 CO6 CO6 . 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 CO6 B 1 1102 1212 CO6 CO6 . 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 . . . K 5 -276.331 -106.401 -46.802 1 73.15 ? PB GDP 1103 B 1 HETATM 2 O O1B GDP . . . K 5 -275.316 -107.511 -46.438 1 75.5 ? O1B GDP 1103 B 1 HETATM 3 O O2B GDP . . . K 5 -276.805 -106.609 -48.241 1 69.72 ? O2B GDP 1103 B 1 HETATM 4 O O3B GDP . . . K 5 -277.481 -106.482 -45.904 1 73.26 ? O3B GDP 1103 B 1 HETATM 5 O O3A GDP . . . K 5 -275.664 -104.995 -46.671 1 110.27 ? O3A GDP 1103 B 1 HETATM 6 P PA GDP . . . K 5 -275.189 -104.425 -45.264 1 78.84 ? PA GDP 1103 B 1 HETATM 7 O O1A GDP . . . K 5 -276.341 -103.739 -44.58 1 82.63 ? O1A GDP 1103 B 1 HETATM 8 O O2A GDP . . . K 5 -274.73 -105.474 -44.417 1 75.83 ? O2A GDP 1103 B 1 HETATM 9 O O5' GDP . . . K 5 -274.055 -103.369 -45.487 1 62.68 ? O5' GDP 1103 B 1 HETATM 10 C C5' GDP . . . K 5 -272.911 -103.738 -45.967 1 63.81 ? C5' GDP 1103 B 1 HETATM 11 C C4' GDP . . . K 5 -271.924 -102.546 -45.996 1 62.62 ? C4' GDP 1103 B 1 HETATM 12 O O4' GDP . . . K 5 -272.405 -101.442 -46.864 1 62.74 ? O4' GDP 1103 B 1 HETATM 13 C C3' GDP . . . K 5 -271.591 -101.917 -44.702 1 61.34 ? C3' GDP 1103 B 1 HETATM 14 O O3' GDP . . . K 5 -270.233 -101.536 -44.61 1 62.86 ? O3' GDP 1103 B 1 HETATM 15 C C2' GDP . . . K 5 -272.399 -100.709 -44.687 1 59.47 ? C2' GDP 1103 B 1 HETATM 16 O O2' GDP . . . K 5 -271.873 -99.682 -43.824 1 58.65 ? O2' GDP 1103 B 1 HETATM 17 C C1' GDP . . . K 5 -272.333 -100.277 -46.104 1 63.45 ? C1' GDP 1103 B 1 HETATM 18 N N9 GDP . . . K 5 -273.36 -99.284 -46.537 1 69.61 ? N9 GDP 1103 B 1 HETATM 19 C C8 GDP . . . K 5 -274.616 -99.302 -46.273 1 73.33 ? C8 GDP 1103 B 1 HETATM 20 N N7 GDP . . . K 5 -275.195 -98.251 -46.835 1 74.63 ? N7 GDP 1103 B 1 HETATM 21 C C5 GDP . . . K 5 -274.25 -97.551 -47.477 1 73.65 ? C5 GDP 1103 B 1 HETATM 22 C C6 GDP . . . K 5 -274.255 -96.337 -48.259 1 75.22 ? C6 GDP 1103 B 1 HETATM 23 O O6 GDP . . . K 5 -275.424 -95.661 -48.465 1 78.01 ? O6 GDP 1103 B 1 HETATM 24 N N1 GDP . . . K 5 -273.106 -95.881 -48.785 1 71.91 ? N1 GDP 1103 B 1 HETATM 25 C C2 GDP . . . K 5 -272.015 -96.519 -48.592 1 70.86 ? C2 GDP 1103 B 1 HETATM 26 N N2 GDP . . . K 5 -270.765 -95.993 -49.182 1 72.73 ? N2 GDP 1103 B 1 HETATM 27 N N3 GDP . . . K 5 -271.972 -97.688 -47.846 1 69.46 ? N3 GDP 1103 B 1 HETATM 28 C C4 GDP . . . K 5 -273.096 -98.183 -47.3 1 70.62 ? C4 GDP 1103 B 1 # _model_server_stats.io_time_ms 35 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 374 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #