data_4XC6 # _model_server_result.job_id wp-ri8B3f4Rz_aDV91rzsQ _model_server_result.datetime_utc '2024-11-24 11:25:45' _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 4xc6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1102}' # _entry.id 4XC6 # _exptl.entry_id 4XC6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 4XC6 _cell.length_a 318.76 _cell.length_b 318.76 _cell.length_c 343.52 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XC6 _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 _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 ? 4 E N N ? 4 J 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc2 A OG SER 243 A SER 223 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc3 A OD1 ASP 269 A ASP 249 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc4 A OD1 ASP 282 A ASP 262 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc5 A OD2 ASP 282 A ASP 262 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? metalc ? metalc6 A OE2 GLU 330 A GLU 310 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc7 A OE2 GLU 330 A GLU 310 1_555 G MG MG . A MG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? metalc ? metalc8 E O2B GDP . A GDP 1103 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc9 E O3B GDP . A GDP 1103 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc10 B NE2 HIS 59 B HIS 39 1_555 I CO B12 . B B12 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc11 B OG SER 243 B SER 223 1_555 K MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc12 B O ILE 268 B ILE 248 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? metalc ? metalc13 B OD1 ASP 269 B ASP 249 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? metalc ? metalc14 B OD1 ASP 282 B ASP 262 1_555 K MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc15 B OD2 ASP 282 B ASP 262 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? metalc ? metalc16 B OE2 GLU 330 B GLU 310 1_555 K MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? metalc ? metalc17 B OE2 GLU 330 B GLU 310 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.618 ? metalc ? metalc18 B O THR 331 B THR 311 1_555 L MG MG . B MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? metalc ? metalc19 J O2B GDP . B GDP 1102 1_555 K MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? metalc ? metalc20 J O3B GDP . B GDP 1102 1_555 K MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? # _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 312 n n PB O2B GDP sing 313 n n PB O3B GDP sing 314 n n PB O3A GDP sing 315 n n O2B HOB2 GDP sing 316 n n O3B HOB3 GDP sing 317 n n O3A PA GDP sing 318 n n PA O1A GDP doub 319 n n PA O2A GDP sing 320 n n PA O5' GDP sing 321 n n O2A HOA2 GDP sing 322 n n O5' C5' GDP sing 323 n n C5' C4' GDP sing 324 n n C5' H5' GDP sing 325 n n C5' "H5''" GDP sing 326 n n C4' O4' GDP sing 327 n n C4' C3' GDP sing 328 n n C4' H4' GDP sing 329 n n O4' C1' GDP sing 330 n n C3' O3' GDP sing 331 n n C3' C2' GDP sing 332 n n C3' H3' GDP sing 333 n n O3' HO3' GDP sing 334 n n C2' O2' GDP sing 335 n n C2' C1' GDP sing 336 n n C2' H2' GDP sing 337 n n O2' HO2' GDP sing 338 n n C1' N9 GDP sing 339 n n C1' H1' GDP sing 340 n n N9 C8 GDP sing 341 n y N9 C4 GDP sing 342 n y C8 N7 GDP doub 343 n y C8 H8 GDP sing 344 n n N7 C5 GDP sing 345 n y C5 C6 GDP sing 346 n n C5 C4 GDP doub 347 n y C6 O6 GDP doub 348 n n C6 N1 GDP sing 349 n n N1 C2 GDP sing 350 n n N1 HN1 GDP sing 351 n n C2 N2 GDP sing 352 n n C2 N3 GDP doub 353 n n N2 HN21 GDP sing 354 n n N2 HN22 GDP sing 355 n n N3 C4 GDP sing 356 n n # _atom_sites.entry_id 4XC6 _atom_sites.fract_transf_matrix[1][1] 0.003137 _atom_sites.fract_transf_matrix[1][2] 0.001811 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003622 _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 GDP A 1 1103 1200 GDP GDP . F 5 MG A 1 1104 1 MG MG . G 5 MG A 1 1105 3 MG MG . H 6 ACT A 1 1106 1 ACT ACT . I 2 B12 B 1 1101 1198 B12 B12 . J 4 GDP B 1 1102 1201 GDP GDP . K 5 MG B 1 1103 2 MG MG . L 5 MG B 1 1104 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 . . . J 4 -278.001 -107.034 -46.888 1 68.95 ? PB GDP 1102 B 1 HETATM 2 O O1B GDP . . . J 4 -278.476 -107.211 -48.331 1 65.15 ? O1B GDP 1102 B 1 HETATM 3 O O2B GDP . . . J 4 -276.999 -108.168 -46.557 1 71.26 ? O2B GDP 1102 B 1 HETATM 4 O O3B GDP . . . J 4 -279.152 -107.123 -45.993 1 67.66 ? O3B GDP 1102 B 1 HETATM 5 O O3A GDP . . . J 4 -277.323 -105.632 -46.729 1 76.64 ? O3A GDP 1102 B 1 HETATM 6 P PA GDP . . . J 4 -276.861 -105.06 -45.316 1 76.12 ? PA GDP 1102 B 1 HETATM 7 O O1A GDP . . . J 4 -278.011 -104.362 -44.64 1 79.97 ? O1A GDP 1102 B 1 HETATM 8 O O2A GDP . . . J 4 -276.411 -106.1 -44.453 1 72.26 ? O2A GDP 1102 B 1 HETATM 9 O O5' GDP . . . J 4 -275.722 -104.01 -45.542 1 53.46 ? O5' GDP 1102 B 1 HETATM 10 C C5' GDP . . . J 4 -274.585 -104.383 -46.035 1 55.93 ? C5' GDP 1102 B 1 HETATM 11 C C4' GDP . . . J 4 -273.573 -103.211 -46.027 1 54.41 ? C4' GDP 1102 B 1 HETATM 12 O O4' GDP . . . J 4 -274.008 -102.087 -46.894 1 54.2 ? O4' GDP 1102 B 1 HETATM 13 C C3' GDP . . . J 4 -273.264 -102.597 -44.721 1 55.26 ? C3' GDP 1102 B 1 HETATM 14 O O3' GDP . . . J 4 -271.91 -102.211 -44.606 1 60.95 ? O3' GDP 1102 B 1 HETATM 15 C C2' GDP . . . J 4 -274.084 -101.396 -44.701 1 51.57 ? C2' GDP 1102 B 1 HETATM 16 O O2' GDP . . . J 4 -273.583 -100.374 -43.819 1 55.17 ? O2' GDP 1102 B 1 HETATM 17 C C1' GDP . . . J 4 -274.003 -100.937 -46.107 1 52.55 ? C1' GDP 1102 B 1 HETATM 18 N N9 GDP . . . J 4 -275.059 -99.974 -46.539 1 57.64 ? N9 GDP 1102 B 1 HETATM 19 C C8 GDP . . . J 4 -276.31 -100.015 -46.255 1 62.17 ? C8 GDP 1102 B 1 HETATM 20 N N7 GDP . . . J 4 -276.921 -98.986 -46.827 1 64.5 ? N7 GDP 1102 B 1 HETATM 21 C C5 GDP . . . J 4 -276.003 -98.277 -47.495 1 63.5 ? C5 GDP 1102 B 1 HETATM 22 C C6 GDP . . . J 4 -276.045 -97.077 -48.296 1 67.01 ? C6 GDP 1102 B 1 HETATM 23 O O6 GDP . . . J 4 -277.232 -96.43 -48.493 1 72.68 ? O6 GDP 1102 B 1 HETATM 24 N N1 GDP . . . J 4 -274.913 -96.605 -48.845 1 61.75 ? N1 GDP 1102 B 1 HETATM 25 C C2 GDP . . . J 4 -273.805 -97.216 -48.659 1 55.88 ? C2 GDP 1102 B 1 HETATM 26 N N2 GDP . . . J 4 -272.573 -96.679 -49.274 1 54.41 ? N2 GDP 1102 B 1 HETATM 27 N N3 GDP . . . J 4 -273.729 -98.371 -47.896 1 57.01 ? N3 GDP 1102 B 1 HETATM 28 C C4 GDP . . . J 4 -274.833 -98.881 -47.324 1 59.78 ? C4 GDP 1102 B 1 # _model_server_stats.io_time_ms 119 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #