data_5KNU # _model_server_result.job_id 45yo2LO2hx6HCluvoJcj0g _model_server_result.datetime_utc '2025-01-05 23:12:42' _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 5knu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 5KNU # _exptl.entry_id 5KNU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 408.284 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-[(4-oxidanylidene-3,5-dihydropyrrolo[3,2-d]pyrimidin-7-yl)methyl-(3-phosphonopropyl)amino]propylphosphonic acid' _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 5KNU _cell.length_a 84.975 _cell.length_b 84.975 _cell.length_c 167.723 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KNU _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # 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 tetrameric 4 author_and_software_defined_assembly 1 PISA dimeric 2 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,E,F,G,H,I 1 1,2 A,B,C,D,E,F,G,H,I 2 1 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_554 -x,-x+y,-z-2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -111.815333 # 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 F 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 103 A GLU 103 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc2 A OE2 GLU 103 A GLU 103 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc3 A OD1 ASP 104 A ASP 104 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc4 D MG MG . A MG 202 1_555 H O HOH . A HOH 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc5 D MG MG . A MG 202 1_555 H O HOH . A HOH 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc6 D MG MG . A MG 202 1_555 H O HOH . A HOH 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc7 D MG MG . A MG 202 1_555 H O HOH . A HOH 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc8 B OE1 GLU 103 B GLU 103 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc9 B OE2 GLU 103 B GLU 103 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc10 B OD1 ASP 104 B ASP 104 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc11 G MG MG . B MG 202 1_555 I O HOH . B HOH 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc12 G MG MG . B MG 202 1_555 I O HOH . B HOH 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc13 G MG MG . B MG 202 1_555 I O HOH . B HOH 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? # _chem_comp.formula 'C13 H22 N4 O7 P2' _chem_comp.formula_weight 408.284 _chem_comp.id 6WA _chem_comp.mon_nstd_flag . _chem_comp.name '3-[(4-oxidanylidene-3,5-dihydropyrrolo[3,2-d]pyrimidin-7-yl)methyl-(3-phosphonopropyl)amino]propylphosphonic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 9-[N,N-(Bis-3-phosphonopropyl)aminomethyl]-9-deazahypoxanthine # 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 OAF PAZ 6WA doub 1 n n OAC PAZ 6WA sing 2 n n PAZ CAO 6WA sing 3 n n PAZ OAG 6WA sing 4 n n CAO CAK 6WA sing 5 n n OAE PAY 6WA doub 6 n n CAK CAM 6WA sing 7 n n CAM NAX 6WA sing 8 n n PAY OAD 6WA sing 9 n n PAY OAB 6WA sing 10 n n PAY CAN 6WA sing 11 n n CAJ CAN 6WA sing 12 n n CAJ CAL 6WA sing 13 n n CAP NAX 6WA sing 14 n n CAP CAT 6WA sing 15 n n NAX CAL 6WA sing 16 n n CAT CAI 6WA doub 17 n y CAT CAV 6WA sing 18 n y CAI NAS 6WA sing 19 n y CAV NAQ 6WA sing 20 n n CAV CAW 6WA doub 21 n y NAQ CAH 6WA doub 22 n n NAS CAW 6WA sing 23 n y CAW CAU 6WA sing 24 n n CAH NAR 6WA sing 25 n n CAU NAR 6WA sing 26 n n CAU OAA 6WA doub 27 n n OAD H1 6WA sing 28 n n OAB H2 6WA sing 29 n n CAN H3 6WA sing 30 n n CAN H4 6WA sing 31 n n CAJ H5 6WA sing 32 n n CAJ H6 6WA sing 33 n n CAL H7 6WA sing 34 n n CAL H8 6WA sing 35 n n CAM H10 6WA sing 36 n n CAM H11 6WA sing 37 n n CAK H12 6WA sing 38 n n CAK H13 6WA sing 39 n n CAO H14 6WA sing 40 n n CAO H15 6WA sing 41 n n OAG H16 6WA sing 42 n n OAC H17 6WA sing 43 n n CAP H18 6WA sing 44 n n CAP H19 6WA sing 45 n n CAH H20 6WA sing 46 n n NAR H21 6WA sing 47 n n NAS H22 6WA sing 48 n n CAI H23 6WA sing 49 n n # _atom_sites.entry_id 5KNU _atom_sites.fract_transf_matrix[1][1] 0.011768 _atom_sites.fract_transf_matrix[1][2] 0.006794 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013589 _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] 0.005962 _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 6WA A 1 201 1 6WA DRG . D 3 MG A 1 202 1 MG MG . E 4 EPE A 1 203 1 EPE EPE . F 2 6WA B 1 201 2 6WA DRG . G 3 MG B 1 202 2 MG MG . H 5 HOH A 1 301 40 HOH HOH . H 5 HOH A 2 302 11 HOH HOH . H 5 HOH A 3 303 44 HOH HOH . H 5 HOH A 4 304 31 HOH HOH . H 5 HOH A 5 305 26 HOH HOH . H 5 HOH A 6 306 66 HOH HOH . H 5 HOH A 7 307 49 HOH HOH . H 5 HOH A 8 308 29 HOH HOH . H 5 HOH A 9 309 7 HOH HOH . H 5 HOH A 10 310 32 HOH HOH . H 5 HOH A 11 311 25 HOH HOH . H 5 HOH A 12 312 48 HOH HOH . H 5 HOH A 13 313 27 HOH HOH . H 5 HOH A 14 314 5 HOH HOH . H 5 HOH A 15 315 23 HOH HOH . H 5 HOH A 16 316 3 HOH HOH . H 5 HOH A 17 317 30 HOH HOH . H 5 HOH A 18 318 60 HOH HOH . H 5 HOH A 19 319 42 HOH HOH . H 5 HOH A 20 320 22 HOH HOH . H 5 HOH A 21 321 24 HOH HOH . H 5 HOH A 22 322 8 HOH HOH . H 5 HOH A 23 323 47 HOH HOH . H 5 HOH A 24 324 62 HOH HOH . H 5 HOH A 25 325 6 HOH HOH . H 5 HOH A 26 326 10 HOH HOH . H 5 HOH A 27 327 37 HOH HOH . H 5 HOH A 28 328 17 HOH HOH . H 5 HOH A 29 329 12 HOH HOH . H 5 HOH A 30 330 41 HOH HOH . H 5 HOH A 31 331 28 HOH HOH . H 5 HOH A 32 332 9 HOH HOH . H 5 HOH A 33 333 59 HOH HOH . I 5 HOH B 1 301 33 HOH HOH . I 5 HOH B 2 302 1 HOH HOH . I 5 HOH B 3 303 54 HOH HOH . I 5 HOH B 4 304 52 HOH HOH . I 5 HOH B 5 305 34 HOH HOH . I 5 HOH B 6 306 18 HOH HOH . I 5 HOH B 7 307 2 HOH HOH . I 5 HOH B 8 308 53 HOH HOH . I 5 HOH B 9 309 14 HOH HOH . I 5 HOH B 10 310 20 HOH HOH . I 5 HOH B 11 311 61 HOH HOH . I 5 HOH B 12 312 19 HOH HOH . I 5 HOH B 13 313 57 HOH HOH . I 5 HOH B 14 314 55 HOH HOH . I 5 HOH B 15 315 56 HOH HOH . I 5 HOH B 16 316 50 HOH HOH . I 5 HOH B 17 317 63 HOH HOH . I 5 HOH B 18 318 39 HOH HOH . I 5 HOH B 19 319 64 HOH HOH . I 5 HOH B 20 320 46 HOH HOH . I 5 HOH B 21 321 65 HOH HOH . I 5 HOH B 22 322 16 HOH HOH . I 5 HOH B 23 323 43 HOH HOH . I 5 HOH B 24 324 4 HOH HOH . I 5 HOH B 25 325 13 HOH HOH . I 5 HOH B 26 326 15 HOH HOH . I 5 HOH B 27 327 36 HOH HOH . I 5 HOH B 28 328 21 HOH HOH . I 5 HOH B 29 329 58 HOH HOH . I 5 HOH B 30 330 51 HOH HOH . I 5 HOH B 31 331 38 HOH HOH . I 5 HOH B 32 332 35 HOH HOH . I 5 HOH B 33 333 45 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 OAD 6WA . . . C 2 -3.08 29.4 -42.933 1 37.7 ? OAD 6WA 201 A 1 HETATM 2 P PAY 6WA . . . C 2 -3.969 30.621 -43.024 1 49.37 ? PAY 6WA 201 A 1 HETATM 3 O OAE 6WA . . . C 2 -4.191 30.99 -44.475 1 54.49 ? OAE 6WA 201 A 1 HETATM 4 O OAB 6WA . . . C 2 -3.29 31.774 -42.317 1 46.67 ? OAB 6WA 201 A 1 HETATM 5 C CAN 6WA . . . C 2 -5.579 30.268 -42.227 1 41.8 ? CAN 6WA 201 A 1 HETATM 6 C CAJ 6WA . . . C 2 -6.233 28.983 -42.766 1 31.95 ? CAJ 6WA 201 A 1 HETATM 7 C CAL 6WA . . . C 2 -7.409 28.52 -41.873 1 47.24 ? CAL 6WA 201 A 1 HETATM 8 N NAX 6WA . . . C 2 -8.032 27.293 -42.375 1 48.81 ? NAX 6WA 201 A 1 HETATM 9 C CAM 6WA . . . C 2 -8.484 27.558 -43.748 1 65.89 ? CAM 6WA 201 A 1 HETATM 10 C CAK 6WA . . . C 2 -9.925 27.031 -43.936 1 74.48 ? CAK 6WA 201 A 1 HETATM 11 C CAO 6WA . . . C 2 -10.773 27.979 -44.8 1 96.55 ? CAO 6WA 201 A 1 HETATM 12 P PAZ 6WA . . . C 2 -12.285 27.147 -45.407 1 133.23 ? PAZ 6WA 201 A 1 HETATM 13 O OAF 6WA . . . C 2 -11.93 26.28 -46.596 1 102.93 ? OAF 6WA 201 A 1 HETATM 14 O OAG 6WA . . . C 2 -12.865 26.283 -44.306 1 88.36 ? OAG 6WA 201 A 1 HETATM 15 O OAC 6WA . . . C 2 -13.297 28.195 -45.815 1 93.1 ? OAC 6WA 201 A 1 HETATM 16 C CAP 6WA . . . C 2 -7.093 26.175 -42.436 1 48.8 ? CAP 6WA 201 A 1 HETATM 17 C CAT 6WA . . . C 2 -6.521 25.89 -41.031 1 46.45 ? CAT 6WA 201 A 1 HETATM 18 C CAV 6WA . . . C 2 -7.207 25.274 -39.932 1 50.19 ? CAV 6WA 201 A 1 HETATM 19 N NAQ 6WA . . . C 2 -8.462 24.775 -39.742 1 45.16 ? NAQ 6WA 201 A 1 HETATM 20 C CAH 6WA . . . C 2 -8.81 24.253 -38.572 1 40.93 ? CAH 6WA 201 A 1 HETATM 21 N NAR 6WA . . . C 2 -7.97 24.192 -37.542 1 42.62 ? NAR 6WA 201 A 1 HETATM 22 C CAU 6WA . . . C 2 -6.712 24.666 -37.65 1 42.81 ? CAU 6WA 201 A 1 HETATM 23 O OAA 6WA . . . C 2 -5.821 24.598 -36.555 1 42.59 ? OAA 6WA 201 A 1 HETATM 24 C CAW 6WA . . . C 2 -6.276 25.239 -38.883 1 51.4 ? CAW 6WA 201 A 1 HETATM 25 N NAS 6WA . . . C 2 -5.12 25.78 -39.295 1 46.68 ? NAS 6WA 201 A 1 HETATM 26 C CAI 6WA . . . C 2 -5.225 26.178 -40.563 1 48.24 ? CAI 6WA 201 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 26 #