data_4O2R # _model_server_result.job_id -lg1eXLA0qD0ayL0GkuRow _model_server_result.datetime_utc '2024-11-19 22:15:31' _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 4o2r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 4O2R # _exptl.entry_id 4O2R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _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 90 _cell.entry_id 4O2R _cell.length_a 70.334 _cell.length_b 79.167 _cell.length_c 57.301 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4O2R _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 ? 2 C N N ? 2 E 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 OG SER 22 A SER 20 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.875 ? metalc ? metalc2 A OD1 ASP 62 A ASP 60 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? metalc ? metalc3 A O THR 63 A THR 61 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.988 ? metalc ? metalc4 C O3B GDP . A GDP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.888 ? metalc ? metalc5 D MG MG . A MG 202 1_555 G O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.69 ? metalc ? metalc6 D MG MG . A MG 202 1_555 G O HOH . A HOH 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.867 ? metalc ? metalc7 B OG SER 22 B SER 20 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc8 B OG1 THR 40 B THR 38 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? metalc ? metalc9 B OD1 ASP 62 B ASP 60 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? metalc ? metalc10 B O THR 63 B THR 61 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.921 ? metalc ? metalc11 E O3B GDP . B GDP 201 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? metalc ? metalc12 F MG MG . B MG 202 1_555 H O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.942 ? # _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 70 n n PB O2B GDP sing 71 n n PB O3B GDP sing 72 n n PB O3A GDP sing 73 n n O2B HOB2 GDP sing 74 n n O3B HOB3 GDP sing 75 n n O3A PA GDP sing 76 n n PA O1A GDP doub 77 n n PA O2A GDP sing 78 n n PA O5' GDP sing 79 n n O2A HOA2 GDP sing 80 n n O5' C5' GDP sing 81 n n C5' C4' GDP sing 82 n n C5' H5' GDP sing 83 n n C5' "H5''" GDP sing 84 n n C4' O4' GDP sing 85 n n C4' C3' GDP sing 86 n n C4' H4' GDP sing 87 n n O4' C1' GDP sing 88 n n C3' O3' GDP sing 89 n n C3' C2' GDP sing 90 n n C3' H3' GDP sing 91 n n O3' HO3' GDP sing 92 n n C2' O2' GDP sing 93 n n C2' C1' GDP sing 94 n n C2' H2' GDP sing 95 n n O2' HO2' GDP sing 96 n n C1' N9 GDP sing 97 n n C1' H1' GDP sing 98 n n N9 C8 GDP sing 99 n y N9 C4 GDP sing 100 n y C8 N7 GDP doub 101 n y C8 H8 GDP sing 102 n n N7 C5 GDP sing 103 n y C5 C6 GDP sing 104 n n C5 C4 GDP doub 105 n y C6 O6 GDP doub 106 n n C6 N1 GDP sing 107 n n N1 C2 GDP sing 108 n n N1 HN1 GDP sing 109 n n C2 N2 GDP sing 110 n n C2 N3 GDP doub 111 n n N2 HN21 GDP sing 112 n n N2 HN22 GDP sing 113 n n N3 C4 GDP sing 114 n n # _atom_sites.entry_id 4O2R _atom_sites.fract_transf_matrix[1][1] 0.014218 _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] 0.012632 _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] 0.017452 _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 GDP A 1 201 201 GDP GDP . D 3 MG A 1 202 202 MG MG . E 2 GDP B 1 201 201 GDP GDP . F 3 MG B 1 202 202 MG MG . G 4 HOH A 1 301 301 HOH HOH . G 4 HOH A 2 302 302 HOH HOH . G 4 HOH A 3 303 303 HOH HOH . G 4 HOH A 4 304 304 HOH HOH . G 4 HOH A 5 305 305 HOH HOH . G 4 HOH A 6 306 306 HOH HOH . G 4 HOH A 7 307 307 HOH HOH . G 4 HOH A 8 308 308 HOH HOH . G 4 HOH A 9 309 309 HOH HOH . G 4 HOH A 10 310 310 HOH HOH . G 4 HOH A 11 311 311 HOH HOH . G 4 HOH A 12 312 312 HOH HOH . G 4 HOH A 13 313 313 HOH HOH . G 4 HOH A 14 314 314 HOH HOH . G 4 HOH A 15 315 315 HOH HOH . G 4 HOH A 16 316 316 HOH HOH . G 4 HOH A 17 317 317 HOH HOH . G 4 HOH A 18 318 318 HOH HOH . G 4 HOH A 19 319 319 HOH HOH . G 4 HOH A 20 320 320 HOH HOH . G 4 HOH A 21 321 321 HOH HOH . G 4 HOH A 22 322 322 HOH HOH . G 4 HOH A 23 323 323 HOH HOH . G 4 HOH A 24 324 324 HOH HOH . G 4 HOH A 25 325 325 HOH HOH . G 4 HOH A 26 326 326 HOH HOH . G 4 HOH A 27 327 327 HOH HOH . G 4 HOH A 28 328 328 HOH HOH . G 4 HOH A 29 329 329 HOH HOH . G 4 HOH A 30 330 330 HOH HOH . G 4 HOH A 31 331 331 HOH HOH . G 4 HOH A 32 332 332 HOH HOH . G 4 HOH A 33 333 333 HOH HOH . G 4 HOH A 34 334 334 HOH HOH . G 4 HOH A 35 335 335 HOH HOH . G 4 HOH A 36 336 336 HOH HOH . G 4 HOH A 37 337 337 HOH HOH . G 4 HOH A 38 338 338 HOH HOH . G 4 HOH A 39 339 339 HOH HOH . G 4 HOH A 40 340 340 HOH HOH . G 4 HOH A 41 341 341 HOH HOH . G 4 HOH A 42 342 342 HOH HOH . G 4 HOH A 43 343 343 HOH HOH . G 4 HOH A 44 344 344 HOH HOH . G 4 HOH A 45 345 345 HOH HOH . G 4 HOH A 46 346 346 HOH HOH . G 4 HOH A 47 347 347 HOH HOH . G 4 HOH A 48 348 348 HOH HOH . G 4 HOH A 49 349 349 HOH HOH . G 4 HOH A 50 350 350 HOH HOH . G 4 HOH A 51 351 351 HOH HOH . G 4 HOH A 52 352 352 HOH HOH . G 4 HOH A 53 353 353 HOH HOH . G 4 HOH A 54 354 354 HOH HOH . G 4 HOH A 55 355 355 HOH HOH . G 4 HOH A 56 356 356 HOH HOH . G 4 HOH A 57 357 357 HOH HOH . G 4 HOH A 58 358 358 HOH HOH . G 4 HOH A 59 359 359 HOH HOH . G 4 HOH A 60 360 360 HOH HOH . G 4 HOH A 61 361 361 HOH HOH . G 4 HOH A 62 362 362 HOH HOH . G 4 HOH A 63 363 363 HOH HOH . G 4 HOH A 64 364 364 HOH HOH . G 4 HOH A 65 365 365 HOH HOH . G 4 HOH A 66 366 366 HOH HOH . G 4 HOH A 67 367 367 HOH HOH . G 4 HOH A 68 368 368 HOH HOH . G 4 HOH A 69 369 369 HOH HOH . G 4 HOH A 70 370 370 HOH HOH . G 4 HOH A 71 371 371 HOH HOH . G 4 HOH A 72 372 372 HOH HOH . G 4 HOH A 73 373 373 HOH HOH . G 4 HOH A 74 374 374 HOH HOH . G 4 HOH A 75 375 375 HOH HOH . G 4 HOH A 76 376 376 HOH HOH . G 4 HOH A 77 377 377 HOH HOH . G 4 HOH A 78 378 378 HOH HOH . G 4 HOH A 79 379 379 HOH HOH . G 4 HOH A 80 380 380 HOH HOH . G 4 HOH A 81 381 381 HOH HOH . G 4 HOH A 82 382 382 HOH HOH . G 4 HOH A 83 383 383 HOH HOH . G 4 HOH A 84 384 384 HOH HOH . G 4 HOH A 85 385 385 HOH HOH . G 4 HOH A 86 386 386 HOH HOH . H 4 HOH B 1 301 301 HOH HOH . H 4 HOH B 2 302 302 HOH HOH . H 4 HOH B 3 303 303 HOH HOH . H 4 HOH B 4 304 304 HOH HOH . H 4 HOH B 5 305 305 HOH HOH . H 4 HOH B 6 306 306 HOH HOH . H 4 HOH B 7 307 307 HOH HOH . H 4 HOH B 8 308 308 HOH HOH . H 4 HOH B 9 309 309 HOH HOH . H 4 HOH B 10 310 310 HOH HOH . H 4 HOH B 11 311 311 HOH HOH . H 4 HOH B 12 312 312 HOH HOH . H 4 HOH B 13 313 313 HOH HOH . H 4 HOH B 14 314 314 HOH HOH . H 4 HOH B 15 315 315 HOH HOH . H 4 HOH B 16 316 316 HOH HOH . H 4 HOH B 17 317 317 HOH HOH . H 4 HOH B 18 318 318 HOH HOH . H 4 HOH B 19 319 319 HOH HOH . H 4 HOH B 20 320 320 HOH HOH . H 4 HOH B 21 321 321 HOH HOH . H 4 HOH B 22 322 322 HOH HOH . H 4 HOH B 23 323 323 HOH HOH . H 4 HOH B 24 324 324 HOH HOH . H 4 HOH B 25 325 325 HOH HOH . H 4 HOH B 26 326 326 HOH HOH . H 4 HOH B 27 327 327 HOH HOH . H 4 HOH B 28 328 328 HOH HOH . H 4 HOH B 29 329 329 HOH HOH . H 4 HOH B 30 330 330 HOH HOH . H 4 HOH B 31 331 331 HOH HOH . H 4 HOH B 32 332 332 HOH HOH . H 4 HOH B 33 333 333 HOH HOH . H 4 HOH B 34 334 334 HOH HOH . H 4 HOH B 35 335 335 HOH HOH . H 4 HOH B 36 336 336 HOH HOH . H 4 HOH B 37 337 337 HOH HOH . H 4 HOH B 38 338 338 HOH HOH . H 4 HOH B 39 339 339 HOH HOH . H 4 HOH B 40 340 340 HOH HOH . H 4 HOH B 41 341 341 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 . . . E 2 -9.135 3.353 -0.569 1 20.73 ? PB GDP 201 B 1 HETATM 2 O O1B GDP . . . E 2 -8.343 2.167 -0.041 1 21.28 ? O1B GDP 201 B 1 HETATM 3 O O2B GDP . . . E 2 -10.067 2.847 -1.659 1 21.67 ? O2B GDP 201 B 1 HETATM 4 O O3B GDP . . . E 2 -9.973 3.975 0.533 1 24.55 ? O3B GDP 201 B 1 HETATM 5 O O3A GDP . . . E 2 -8.091 4.404 -1.206 1 19.46 ? O3A GDP 201 B 1 HETATM 6 P PA GDP . . . E 2 -7.589 5.768 -0.486 1 19.68 ? PA GDP 201 B 1 HETATM 7 O O1A GDP . . . E 2 -7.134 5.499 0.931 1 23.6 ? O1A GDP 201 B 1 HETATM 8 O O2A GDP . . . E 2 -8.656 6.831 -0.568 1 15.72 ? O2A GDP 201 B 1 HETATM 9 O O5' GDP . . . E 2 -6.356 6.182 -1.43 1 19.3 ? O5' GDP 201 B 1 HETATM 10 C C5' GDP . . . E 2 -5.11 5.499 -1.31 1 17.95 ? C5' GDP 201 B 1 HETATM 11 C C4' GDP . . . E 2 -4.019 6.429 -1.817 1 18.85 ? C4' GDP 201 B 1 HETATM 12 O O4' GDP . . . E 2 -4.335 6.866 -3.148 1 17.83 ? O4' GDP 201 B 1 HETATM 13 C C3' GDP . . . E 2 -3.926 7.666 -0.94 1 20.4 ? C3' GDP 201 B 1 HETATM 14 O O3' GDP . . . E 2 -2.554 8.002 -0.728 1 18.08 ? O3' GDP 201 B 1 HETATM 15 C C2' GDP . . . E 2 -4.569 8.771 -1.747 1 20.52 ? C2' GDP 201 B 1 HETATM 16 O O2' GDP . . . E 2 -3.937 10.032 -1.489 1 29.07 ? O2' GDP 201 B 1 HETATM 17 C C1' GDP . . . E 2 -4.373 8.305 -3.184 1 23.48 ? C1' GDP 201 B 1 HETATM 18 N N9 GDP . . . E 2 -5.495 8.759 -4.04 1 22.19 ? N9 GDP 201 B 1 HETATM 19 C C8 GDP . . . E 2 -6.789 8.44 -3.874 1 16.79 ? C8 GDP 201 B 1 HETATM 20 N N7 GDP . . . E 2 -7.553 9.015 -4.84 1 16.92 ? N7 GDP 201 B 1 HETATM 21 C C5 GDP . . . E 2 -6.739 9.707 -5.655 1 15.71 ? C5 GDP 201 B 1 HETATM 22 C C6 GDP . . . E 2 -6.897 10.528 -6.885 1 14.31 ? C6 GDP 201 B 1 HETATM 23 O O6 GDP . . . E 2 -8.037 10.72 -7.387 1 12.27 ? O6 GDP 201 B 1 HETATM 24 N N1 GDP . . . E 2 -5.782 11.069 -7.418 1 14.24 ? N1 GDP 201 B 1 HETATM 25 C C2 GDP . . . E 2 -4.545 10.874 -6.888 1 15.78 ? C2 GDP 201 B 1 HETATM 26 N N2 GDP . . . E 2 -3.465 11.448 -7.476 1 8.77 ? N2 GDP 201 B 1 HETATM 27 N N3 GDP . . . E 2 -4.339 10.127 -5.771 1 19.41 ? N3 GDP 201 B 1 HETATM 28 C C4 GDP . . . E 2 -5.376 9.527 -5.128 1 21.08 ? C4 GDP 201 B 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 363 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #