data_4PHF # _model_server_result.job_id BRtkuaWup8nZQmpC0ruj-Q _model_server_result.datetime_utc '2024-12-01 12:13:10' _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 4phf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4PHF # _exptl.entry_id 4PHF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 556.358 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "N-[3-(propanoylamino)propyl]guanosine 5'-(trihydrogen 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 4PHF _cell.length_a 49.31 _cell.length_b 54.9 _cell.length_c 60.47 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PHF _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 PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _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 covale ? covale1 A SG CYS 37 A CYS 35 1_555 B CAA 2UH . A 2UH 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.635 ? metalc ? metalc1 A OG1 THR 24 A THR 22 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc2 B O3B 2UH . A 2UH 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc3 C MG MG . A MG 202 1_555 E O HOH . A HOH 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc4 C MG MG . A MG 202 1_555 E O HOH . A HOH 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc5 C MG MG . A MG 202 1_555 E O HOH . A HOH 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc6 C MG MG . A MG 202 1_555 E O HOH . A HOH 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? # _chem_comp.formula 'C16 H26 N6 O12 P2' _chem_comp.formula_weight 556.358 _chem_comp.id 2UH _chem_comp.mon_nstd_flag . _chem_comp.name "N-[3-(propanoylamino)propyl]guanosine 5'-(trihydrogen diphosphate)" _chem_comp.type non-polymer _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 CAA CAL 2UH sing 1 n n CAL CAY 2UH sing 2 n n NAS CAY 2UH sing 3 n n NAS CAN 2UH sing 4 n n CAM CAN 2UH sing 5 n n CAM CAO 2UH sing 6 n n CAY OAB 2UH doub 7 n n N4 CAO 2UH sing 8 n n N4 C2 2UH sing 9 n n N1 C2 2UH sing 10 n n N1 C6 2UH sing 11 n n O6 C6 2UH doub 12 n n C2 N3 2UH doub 13 n n C6 C5 2UH sing 14 n n N3 C4 2UH sing 15 n n C5 C4 2UH doub 16 n y C5 N7 2UH sing 17 n y C4 N9 2UH sing 18 n y O2' C2' 2UH sing 19 n n N7 C8 2UH doub 20 n y N9 C8 2UH sing 21 n y N9 C1' 2UH sing 22 n n C2' C1' 2UH sing 23 n n C2' C3' 2UH sing 24 n n C1' O4' 2UH sing 25 n n O3' C3' 2UH sing 26 n n C3' C4' 2UH sing 27 n n O4' C4' 2UH sing 28 n n C4' C5' 2UH sing 29 n n O2A PA 2UH doub 30 n n O5' C5' 2UH sing 31 n n O5' PA 2UH sing 32 n n PA O1A 2UH sing 33 n n PA O3A 2UH sing 34 n n O3A PB 2UH sing 35 n n O1B PB 2UH doub 36 n n PB O2B 2UH sing 37 n n PB O3B 2UH sing 38 n n O3B H1 2UH sing 39 n n O2B H2 2UH sing 40 n n O1A H3 2UH sing 41 n n C5' H4 2UH sing 42 n n C5' H5 2UH sing 43 n n C4' H6 2UH sing 44 n n C3' H7 2UH sing 45 n n O3' H8 2UH sing 46 n n C2' H9 2UH sing 47 n n O2' H10 2UH sing 48 n n C1' H11 2UH sing 49 n n C8 H12 2UH sing 50 n n N1 H13 2UH sing 51 n n N4 H14 2UH sing 52 n n CAO H15 2UH sing 53 n n CAO H16 2UH sing 54 n n CAM H17 2UH sing 55 n n CAM H18 2UH sing 56 n n CAN H19 2UH sing 57 n n CAN H20 2UH sing 58 n n NAS H21 2UH sing 59 n n CAL H22 2UH sing 60 n n CAL H23 2UH sing 61 n n CAA H24 2UH sing 62 n n CAA H25 2UH sing 63 n n CAA H26 2UH sing 64 n n # _atom_sites.entry_id 4PHF _atom_sites.fract_transf_matrix[1][1] 0.02028 _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] 0.018215 _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] 0.016537 _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 B 2 2UH A 1 201 400 2UH aGD . C 3 MG A 1 202 500 MG MG . D 4 NO3 A 1 203 1 NO3 NO3 . E 5 HOH A 1 301 53 HOH HOH . E 5 HOH A 2 302 11 HOH HOH . E 5 HOH A 3 303 6 HOH HOH . E 5 HOH A 4 304 35 HOH HOH . E 5 HOH A 5 305 13 HOH HOH . E 5 HOH A 6 306 26 HOH HOH . E 5 HOH A 7 307 22 HOH HOH . E 5 HOH A 8 308 25 HOH HOH . E 5 HOH A 9 309 58 HOH HOH . E 5 HOH A 10 310 7 HOH HOH . E 5 HOH A 11 311 56 HOH HOH . E 5 HOH A 12 312 12 HOH HOH . E 5 HOH A 13 313 29 HOH HOH . E 5 HOH A 14 314 44 HOH HOH . E 5 HOH A 15 315 55 HOH HOH . E 5 HOH A 16 316 38 HOH HOH . E 5 HOH A 17 317 40 HOH HOH . E 5 HOH A 18 318 9 HOH HOH . E 5 HOH A 19 319 16 HOH HOH . E 5 HOH A 20 320 61 HOH HOH . E 5 HOH A 21 321 10 HOH HOH . E 5 HOH A 22 322 48 HOH HOH . E 5 HOH A 23 323 54 HOH HOH . E 5 HOH A 24 324 47 HOH HOH . E 5 HOH A 25 325 1 HOH HOH . E 5 HOH A 26 326 2 HOH HOH . E 5 HOH A 27 327 3 HOH HOH . E 5 HOH A 28 328 4 HOH HOH . E 5 HOH A 29 329 5 HOH HOH . E 5 HOH A 30 330 8 HOH HOH . E 5 HOH A 31 331 14 HOH HOH . E 5 HOH A 32 332 15 HOH HOH . E 5 HOH A 33 333 17 HOH HOH . E 5 HOH A 34 334 18 HOH HOH . E 5 HOH A 35 335 19 HOH HOH . E 5 HOH A 36 336 20 HOH HOH . E 5 HOH A 37 337 21 HOH HOH . E 5 HOH A 38 338 23 HOH HOH . E 5 HOH A 39 339 24 HOH HOH . E 5 HOH A 40 340 27 HOH HOH . E 5 HOH A 41 341 28 HOH HOH . E 5 HOH A 42 342 30 HOH HOH . E 5 HOH A 43 343 31 HOH HOH . E 5 HOH A 44 344 32 HOH HOH . E 5 HOH A 45 345 33 HOH HOH . E 5 HOH A 46 346 34 HOH HOH . E 5 HOH A 47 347 36 HOH HOH . E 5 HOH A 48 348 37 HOH HOH . E 5 HOH A 49 349 39 HOH HOH . E 5 HOH A 50 350 41 HOH HOH . E 5 HOH A 51 351 42 HOH HOH . E 5 HOH A 52 352 43 HOH HOH . E 5 HOH A 53 353 45 HOH HOH . E 5 HOH A 54 354 46 HOH HOH . E 5 HOH A 55 355 49 HOH HOH . E 5 HOH A 56 356 50 HOH HOH . E 5 HOH A 57 357 51 HOH HOH . E 5 HOH A 58 358 52 HOH HOH . E 5 HOH A 59 359 57 HOH HOH . E 5 HOH A 60 360 59 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 O O3B 2UH . . . B 2 -26.749 3.253 2.305 1 22.22 ? O3B 2UH 201 A 1 HETATM 2 P PB 2UH . . . B 2 -26.025 4.481 2.585 1 23.21 ? PB 2UH 201 A 1 HETATM 3 O O1B 2UH . . . B 2 -24.578 4.322 2.866 1 21.67 ? O1B 2UH 201 A 1 HETATM 4 O O2B 2UH . . . B 2 -26.704 5.526 3.374 1 22.49 ? O2B 2UH 201 A 1 HETATM 5 O O3A 2UH . . . B 2 -25.912 5.237 1.136 1 23.62 ? O3A 2UH 201 A 1 HETATM 6 P PA 2UH . . . B 2 -26.851 5.101 -0.201 1 24.59 ? PA 2UH 201 A 1 HETATM 7 O O1A 2UH . . . B 2 -28.302 5.309 0.134 1 22.42 ? O1A 2UH 201 A 1 HETATM 8 O O2A 2UH . . . B 2 -26.515 3.908 -1.009 1 23.87 ? O2A 2UH 201 A 1 HETATM 9 O O5' 2UH . . . B 2 -26.517 6.424 -0.971 1 25.37 ? O5' 2UH 201 A 1 HETATM 10 C C5' 2UH . . . B 2 -26.678 7.708 -0.415 1 25.39 ? C5' 2UH 201 A 1 HETATM 11 C C4' 2UH . . . B 2 -26.586 8.698 -1.574 1 28.31 ? C4' 2UH 201 A 1 HETATM 12 O O4' 2UH . . . B 2 -25.318 8.445 -2.292 1 28.77 ? O4' 2UH 201 A 1 HETATM 13 C C3' 2UH . . . B 2 -27.666 8.539 -2.65 1 30.65 ? C3' 2UH 201 A 1 HETATM 14 O O3' 2UH . . . B 2 -27.898 9.829 -3.252 1 33.35 ? O3' 2UH 201 A 1 HETATM 15 C C2' 2UH . . . B 2 -27.004 7.668 -3.732 1 28.73 ? C2' 2UH 201 A 1 HETATM 16 O O2' 2UH . . . B 2 -27.59 7.855 -5.042 1 30.18 ? O2' 2UH 201 A 1 HETATM 17 C C1' 2UH . . . B 2 -25.579 8.305 -3.674 1 28.74 ? C1' 2UH 201 A 1 HETATM 18 N N9 2UH . . . B 2 -24.546 7.427 -4.284 1 27.09 ? N9 2UH 201 A 1 HETATM 19 C C4 2UH . . . B 2 -23.628 7.727 -5.213 1 25.38 ? C4 2UH 201 A 1 HETATM 20 N N3 2UH . . . B 2 -23.405 8.897 -5.82 1 27.77 ? N3 2UH 201 A 1 HETATM 21 C C8 2UH . . . B 2 -24.394 6.164 -3.92 1 23.39 ? C8 2UH 201 A 1 HETATM 22 N N7 2UH . . . B 2 -23.405 5.668 -4.668 1 23.4 ? N7 2UH 201 A 1 HETATM 23 C C5 2UH . . . B 2 -22.878 6.606 -5.475 1 24.17 ? C5 2UH 201 A 1 HETATM 24 C C6 2UH . . . B 2 -21.859 6.614 -6.4 1 23.16 ? C6 2UH 201 A 1 HETATM 25 O O6 2UH . . . B 2 -21.099 5.641 -6.764 1 21.53 ? O6 2UH 201 A 1 HETATM 26 N N1 2UH . . . B 2 -21.674 7.839 -7.032 1 22.98 ? N1 2UH 201 A 1 HETATM 27 C C2 2UH . . . B 2 -22.463 8.987 -6.766 1 25.43 ? C2 2UH 201 A 1 HETATM 28 N N4 2UH . . . B 2 -22.172 10.125 -7.378 1 27.41 ? N4 2UH 201 A 1 HETATM 29 C CAO 2UH . . . B 2 -22.858 11.421 -7.202 0.99 33.34 ? CAO 2UH 201 A 1 HETATM 30 C CAM 2UH . . . B 2 -24.07 11.354 -8.109 0.99 36.98 ? CAM 2UH 201 A 1 HETATM 31 C CAN 2UH . . . B 2 -25.129 12.349 -7.534 0.99 40.66 ? CAN 2UH 201 A 1 HETATM 32 N NAS 2UH . . . B 2 -26.377 12.246 -8.332 0.99 44.28 ? NAS 2UH 201 A 1 HETATM 33 C CAY 2UH . . . B 2 -27.499 11.573 -7.945 0.99 46.83 ? CAY 2UH 201 A 1 HETATM 34 O OAB 2UH . . . B 2 -27.654 11.062 -6.835 0.99 50.75 ? OAB 2UH 201 A 1 HETATM 35 C CAL 2UH . . . B 2 -28.687 11.627 -8.917 0.99 47.41 ? CAL 2UH 201 A 1 HETATM 36 C CAA 2UH . . . B 2 -28.751 10.308 -9.747 0.99 46.64 ? CAA 2UH 201 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 36 #