data_4RHU # _model_server_result.job_id HsqBpY1-_TpEsqM7gBKCcg _model_server_result.datetime_utc '2024-11-08 05:52:27' _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 4rhu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":301}' # _entry.id 4RHU # _exptl.entry_id 4RHU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 441.271 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '{[(2S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)propane-1,2-diyl]bis(oxyethane-2,1-diyl)}bis(phosphonic acid)' _entity.pdbx_number_of_molecules 4 _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 4RHU _cell.length_a 94.691 _cell.length_b 94.691 _cell.length_c 335.519 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RHU _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? tetrameric 4 author_defined_assembly 1 PISA dimeric 2 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,B,C,D,G,H,I,J,K,L,M,N,O,U,V,W,X 1 1 E,F,P,Q,R,S,T,Y,Z 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 ? 4 L N N ? 4 N N N ? 4 P N N ? 4 R 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 OE1 GLU 121 A GLU 122 1_555 H MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc2 A OE2 GLU 121 A GLU 122 1_555 H MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc3 A OD1 ASP 122 A ASP 123 1_555 H MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc4 H MG MG . A MG 302 1_555 U O HOH . A HOH 415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc5 B OE1 GLU 121 B GLU 122 1_555 J MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc6 B OD1 ASP 122 B ASP 123 1_555 J MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc7 B OD2 ASP 181 B ASP 182 1_555 K MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc8 I OAF 3QE . B 3QE 301 1_555 K MG MG . B MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc9 J MG MG . B MG 302 1_555 V O HOH . B HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc10 J MG MG . B MG 302 1_555 V O HOH . B HOH 415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc11 J MG MG . B MG 302 1_555 V O HOH . B HOH 416 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc12 K MG MG . B MG 303 1_555 V O HOH . B HOH 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc13 C OE1 GLU 121 C GLU 122 1_555 M MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc14 C OD1 ASP 122 C ASP 123 1_555 M MG MG . C MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc15 M MG MG . C MG 302 1_555 W O HOH . C HOH 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc16 M MG MG . C MG 302 1_555 W O HOH . C HOH 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc17 M MG MG . C MG 302 1_555 W O HOH . C HOH 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc18 D OD1 ASP 122 D ASP 123 1_555 O MG MG . D MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? metalc ? metalc19 E OE1 GLU 121 E GLU 122 1_555 Q MG MG . E MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc20 E OD1 ASP 122 E ASP 123 1_555 Q MG MG . E MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc21 F OE2 GLU 121 F GLU 122 1_555 T MG MG . F MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc22 F OE1 GLU 121 F GLU 122 1_555 T MG MG . F MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc23 F OD1 ASP 122 F ASP 123 1_555 T MG MG . F MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc24 F OD2 ASP 181 F ASP 182 1_555 S MG MG . F MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc25 R OAF 45T . F 45T 301 1_555 S MG MG . F MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc26 S MG MG . F MG 302 1_555 Z O HOH . F HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc27 S MG MG . F MG 302 1_555 Z O HOH . F HOH 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc28 T MG MG . F MG 303 1_555 Z O HOH . F HOH 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? # _chem_comp.formula 'C12 H21 N5 O9 P2' _chem_comp.formula_weight 441.271 _chem_comp.id 45T _chem_comp.mon_nstd_flag . _chem_comp.name '{[(2S)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)propane-1,2-diyl]bis(oxyethane-2,1-diyl)}bis(phosphonic acid)' _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 O6 C6 45T doub 51 n n N1 C6 45T sing 52 n n N1 C2 45T sing 53 n n C6 C5 45T sing 54 n n N2 C2 45T sing 55 n n C2 N3 45T doub 56 n n C5 N7 45T sing 57 n y C5 C4 45T doub 58 n y N7 C8 45T doub 59 n y N3 C4 45T sing 60 n n C4 N9 45T sing 61 n y C8 N9 45T sing 62 n y N9 CAO 45T sing 63 n n CAN OAS 45T sing 64 n n CAN CAY 45T sing 65 n n OAS CAJ 45T sing 66 n n OAT CAY 45T sing 67 n n OAT CAK 45T sing 68 n n CAY CAO 45T sing 69 n n CAJ CAL 45T sing 70 n n CAL PBA 45T sing 71 n n CAM CAK 45T sing 72 n n CAM PBB 45T sing 73 n n OAE PBA 45T doub 74 n n OAD PBB 45T doub 75 n n OAC PBA 45T sing 76 n n PBA OAF 45T sing 77 n n OAG PBB 45T sing 78 n n PBB OAH 45T sing 79 n n OAF H1 45T sing 80 n n OAC H2 45T sing 81 n n CAL H3 45T sing 82 n n CAL H4 45T sing 83 n n CAJ H5 45T sing 84 n n CAJ H6 45T sing 85 n n CAN H7 45T sing 86 n n CAN H8 45T sing 87 n n CAY H9 45T sing 88 n n CAK H10 45T sing 89 n n CAK H11 45T sing 90 n n CAM H12 45T sing 91 n n CAM H13 45T sing 92 n n OAG H14 45T sing 93 n n OAH H15 45T sing 94 n n CAO H16 45T sing 95 n n CAO H17 45T sing 96 n n N2 H18 45T sing 97 n n N2 H19 45T sing 98 n n N1 H20 45T sing 99 n n C8 H21 45T sing 100 n n # _atom_sites.entry_id 4RHU _atom_sites.fract_transf_matrix[1][1] 0.010561 _atom_sites.fract_transf_matrix[1][2] 0.006097 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012194 _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] 0.00298 _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 G 2 3QE A 1 301 301 3QE 3QE . H 3 MG A 1 302 302 MG MG . I 2 3QE B 1 301 301 3QE 3QE . J 3 MG B 1 302 302 MG MG . K 3 MG B 1 303 303 MG MG . L 4 45T C 1 301 301 45T 45T . M 3 MG C 1 302 302 MG MG . N 4 45T D 1 301 301 45T 45T . O 3 MG D 1 302 302 MG MG . P 4 45T E 1 301 301 45T 45T . Q 3 MG E 1 302 302 MG MG . R 4 45T F 1 301 301 45T 45T . S 3 MG F 1 302 302 MG MG . T 3 MG F 1 303 303 MG MG . U 5 HOH A 1 401 401 HOH HOH . U 5 HOH A 2 402 402 HOH HOH . U 5 HOH A 3 403 403 HOH HOH . U 5 HOH A 4 404 404 HOH HOH . U 5 HOH A 5 405 405 HOH HOH . U 5 HOH A 6 406 406 HOH HOH . U 5 HOH A 7 407 407 HOH HOH . U 5 HOH A 8 408 408 HOH HOH . U 5 HOH A 9 409 409 HOH HOH . U 5 HOH A 10 410 410 HOH HOH . U 5 HOH A 11 411 411 HOH HOH . U 5 HOH A 12 412 412 HOH HOH . U 5 HOH A 13 413 413 HOH HOH . U 5 HOH A 14 414 414 HOH HOH . U 5 HOH A 15 415 415 HOH HOH . U 5 HOH A 16 416 416 HOH HOH . V 5 HOH B 1 401 401 HOH HOH . V 5 HOH B 2 402 402 HOH HOH . V 5 HOH B 3 403 403 HOH HOH . V 5 HOH B 4 404 404 HOH HOH . V 5 HOH B 5 405 405 HOH HOH . V 5 HOH B 6 406 406 HOH HOH . V 5 HOH B 7 407 407 HOH HOH . V 5 HOH B 8 408 408 HOH HOH . V 5 HOH B 9 409 409 HOH HOH . V 5 HOH B 10 410 410 HOH HOH . V 5 HOH B 11 411 411 HOH HOH . V 5 HOH B 12 412 412 HOH HOH . V 5 HOH B 13 413 413 HOH HOH . V 5 HOH B 14 414 414 HOH HOH . V 5 HOH B 15 415 415 HOH HOH . V 5 HOH B 16 416 416 HOH HOH . W 5 HOH C 1 401 401 HOH HOH . W 5 HOH C 2 402 402 HOH HOH . W 5 HOH C 3 403 403 HOH HOH . W 5 HOH C 4 404 404 HOH HOH . W 5 HOH C 5 405 405 HOH HOH . W 5 HOH C 6 406 406 HOH HOH . W 5 HOH C 7 407 407 HOH HOH . W 5 HOH C 8 408 408 HOH HOH . W 5 HOH C 9 409 409 HOH HOH . W 5 HOH C 10 410 410 HOH HOH . W 5 HOH C 11 411 411 HOH HOH . W 5 HOH C 12 412 412 HOH HOH . W 5 HOH C 13 413 413 HOH HOH . W 5 HOH C 14 414 414 HOH HOH . W 5 HOH C 15 415 415 HOH HOH . W 5 HOH C 16 416 416 HOH HOH . W 5 HOH C 17 417 417 HOH HOH . W 5 HOH C 18 418 418 HOH HOH . W 5 HOH C 19 419 419 HOH HOH . W 5 HOH C 20 420 420 HOH HOH . W 5 HOH C 21 421 401 HOH HOH . W 5 HOH C 22 422 402 HOH HOH . X 5 HOH D 1 401 402 HOH HOH . X 5 HOH D 2 402 403 HOH HOH . X 5 HOH D 3 403 404 HOH HOH . X 5 HOH D 4 404 405 HOH HOH . X 5 HOH D 5 405 406 HOH HOH . X 5 HOH D 6 406 407 HOH HOH . X 5 HOH D 7 407 408 HOH HOH . Y 5 HOH E 1 401 401 HOH HOH . Y 5 HOH E 2 402 403 HOH HOH . Y 5 HOH E 3 403 404 HOH HOH . Y 5 HOH E 4 404 405 HOH HOH . Y 5 HOH E 5 405 406 HOH HOH . Y 5 HOH E 6 406 407 HOH HOH . Y 5 HOH E 7 407 408 HOH HOH . Y 5 HOH E 8 408 409 HOH HOH . Y 5 HOH E 9 409 410 HOH HOH . Y 5 HOH E 10 410 411 HOH HOH . Z 5 HOH F 1 401 401 HOH HOH . Z 5 HOH F 2 402 402 HOH HOH . Z 5 HOH F 3 403 403 HOH HOH . Z 5 HOH F 4 404 404 HOH HOH . Z 5 HOH F 5 405 405 HOH HOH . Z 5 HOH F 6 406 406 HOH HOH . Z 5 HOH F 7 407 407 HOH HOH . Z 5 HOH F 8 408 408 HOH HOH . Z 5 HOH F 9 409 409 HOH HOH . Z 5 HOH F 10 410 410 HOH HOH . Z 5 HOH F 11 411 411 HOH HOH . Z 5 HOH F 12 412 412 HOH HOH . Z 5 HOH F 13 413 413 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 OAE 45T . . . N 4 55.982 14.295 -34.971 1 132.39 ? OAE 45T 301 D 1 HETATM 2 P PBA 45T . . . N 4 54.949 13.45 -34.233 1 136.17 ? PBA 45T 301 D 1 HETATM 3 O OAF 45T . . . N 4 54.889 13.792 -32.751 1 133.44 ? OAF 45T 301 D 1 HETATM 4 O OAC 45T . . . N 4 53.591 13.41 -34.913 1 133.19 ? OAC 45T 301 D 1 HETATM 5 C CAL 45T . . . N 4 55.62 11.626 -34.309 1 153.03 ? CAL 45T 301 D 1 HETATM 6 C CAJ 45T . . . N 4 55.81 11.126 -35.73 1 155.04 ? CAJ 45T 301 D 1 HETATM 7 O OAS 45T . . . N 4 56.992 10.255 -35.726 1 155.94 ? OAS 45T 301 D 1 HETATM 8 C CAN 45T . . . N 4 56.804 9.038 -36.428 1 155.41 ? CAN 45T 301 D 1 HETATM 9 C CAY 45T . . . N 4 58.078 8.112 -36.164 1 83.52 ? CAY 45T 301 D 1 HETATM 10 O OAT 45T . . . N 4 58.05 7.084 -37.116 1 77.05 ? OAT 45T 301 D 1 HETATM 11 C CAK 45T . . . N 4 58.944 5.964 -36.751 1 71.36 ? CAK 45T 301 D 1 HETATM 12 C CAM 45T . . . N 4 58.228 4.666 -37.038 1 70.62 ? CAM 45T 301 D 1 HETATM 13 P PBB 45T . . . N 4 58.943 3.179 -36.006 1 79.43 ? PBB 45T 301 D 1 HETATM 14 O OAG 45T . . . N 4 60.436 3.188 -36.259 1 69.62 ? OAG 45T 301 D 1 HETATM 15 O OAH 45T . . . N 4 58.562 3.471 -34.557 1 85.78 ? OAH 45T 301 D 1 HETATM 16 O OAD 45T . . . N 4 58.229 1.95 -36.552 1 65.74 ? OAD 45T 301 D 1 HETATM 17 C CAO 45T . . . N 4 59.421 9.019 -36.441 1 98.49 ? CAO 45T 301 D 1 HETATM 18 N N9 45T . . . N 4 59.948 9.052 -37.904 1 80.38 ? N9 45T 301 D 1 HETATM 19 C C4 45T . . . N 4 59.803 10.024 -38.9 1 74.96 ? C4 45T 301 D 1 HETATM 20 N N3 45T . . . N 4 59.156 11.241 -38.921 1 73.81 ? N3 45T 301 D 1 HETATM 21 C C2 45T . . . N 4 59.261 11.893 -40.127 1 66.58 ? C2 45T 301 D 1 HETATM 22 N N2 45T . . . N 4 58.608 13.144 -40.184 1 59.57 ? N2 45T 301 D 1 HETATM 23 N N1 45T . . . N 4 59.912 11.502 -41.29 1 60.6 ? N1 45T 301 D 1 HETATM 24 C C6 45T . . . N 4 60.534 10.297 -41.217 1 68.42 ? C6 45T 301 D 1 HETATM 25 O O6 45T . . . N 4 61.197 9.843 -42.327 1 58.01 ? O6 45T 301 D 1 HETATM 26 C C5 45T . . . N 4 60.524 9.496 -40.051 1 75.15 ? C5 45T 301 D 1 HETATM 27 N N7 45T . . . N 4 61.079 8.246 -39.74 1 79.34 ? N7 45T 301 D 1 HETATM 28 C C8 45T . . . N 4 60.719 8.002 -38.429 1 82.94 ? C8 45T 301 D 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 28 #