data_5KNV # _model_server_result.job_id wQWx7JwI5C032KY1pKJllw _model_server_result.datetime_utc '2024-10-18 16:25:39' _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 5knv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 5KNV # _exptl.entry_id 5KNV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 423.299 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-[2-(6-oxidanylidene-1~{H}-purin-9-yl)ethyl-(4-phosphonobutyl)amino]ethylphosphonic 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 5KNV _cell.length_a 84.725 _cell.length_b 84.725 _cell.length_c 167.204 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KNV _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 1 1,2 A,B,C,D,E,F,G,H 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 -111.469333 # 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 OE2 GLU 103 A GLU 103 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.925 ? metalc ? metalc2 A OD1 ASP 104 A ASP 104 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc3 D MG MG . A MG 202 1_555 G O HOH . A HOH 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc4 B OE2 GLU 103 B GLU 103 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc5 B OD1 ASP 104 B ASP 104 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc6 F MG MG . B MG 202 1_555 H O HOH . B HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc7 F MG MG . B MG 202 1_555 H O HOH . B HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc8 F MG MG . B MG 202 1_555 H O HOH . B HOH 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc9 F MG MG . B MG 202 1_555 H O HOH . B HOH 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? # _chem_comp.formula 'C13 H23 N5 O7 P2' _chem_comp.formula_weight 423.299 _chem_comp.id 6W9 _chem_comp.mon_nstd_flag . _chem_comp.name '2-[2-(6-oxidanylidene-1~{H}-purin-9-yl)ethyl-(4-phosphonobutyl)amino]ethylphosphonic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 9-[N-(Phosphonoethyl)-N-(phosphonobutyl)-2-aminoethyl]-hypoxanthine # 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 OAC PBA 6W9 doub 1 n n OAD PAZ 6W9 doub 2 n n OAE PAZ 6W9 sing 3 n n PAZ CAP 6W9 sing 4 n n PAZ OAB 6W9 sing 5 n n PBA OAF 6W9 sing 6 n n PBA CAQ 6W9 sing 7 n n PBA OAG 6W9 sing 8 n n CAQ CAN 6W9 sing 9 n n CAJ CAK 6W9 sing 10 n n CAJ CAL 6W9 sing 11 n n CAP CAK 6W9 sing 12 n n CAL NAX 6W9 sing 13 n n CAN NAX 6W9 sing 14 n n NAX CAM 6W9 sing 15 n n CAO CAM 6W9 sing 16 n n CAO N9 6W9 sing 17 n n N9 C8 6W9 sing 18 n y N9 C4 6W9 sing 19 n y C8 N7 6W9 doub 20 n y C4 N3 6W9 sing 21 n n C4 C5 6W9 doub 22 n y N3 C2 6W9 doub 23 n n N7 C5 6W9 sing 24 n y C5 C6 6W9 sing 25 n n C2 N1 6W9 sing 26 n n C6 N1 6W9 sing 27 n n C6 O6 6W9 doub 28 n n C8 H1 6W9 sing 29 n n N1 H2 6W9 sing 30 n n OAE H3 6W9 sing 31 n n OAB H4 6W9 sing 32 n n CAP H5 6W9 sing 33 n n CAP H6 6W9 sing 34 n n CAK H7 6W9 sing 35 n n CAK H8 6W9 sing 36 n n CAJ H9 6W9 sing 37 n n CAJ H10 6W9 sing 38 n n CAL H11 6W9 sing 39 n n CAL H12 6W9 sing 40 n n CAN H14 6W9 sing 41 n n CAN H15 6W9 sing 42 n n CAQ H16 6W9 sing 43 n n CAQ H17 6W9 sing 44 n n OAF H18 6W9 sing 45 n n OAG H19 6W9 sing 46 n n CAM H20 6W9 sing 47 n n CAM H21 6W9 sing 48 n n CAO H22 6W9 sing 49 n n CAO H23 6W9 sing 50 n n C2 H24 6W9 sing 51 n n # _atom_sites.entry_id 5KNV _atom_sites.fract_transf_matrix[1][1] 0.011803 _atom_sites.fract_transf_matrix[1][2] 0.006814 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013629 _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] 0.005981 _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 6W9 A 1 201 1 6W9 DRG . D 3 MG A 1 202 1 MG MG . E 2 6W9 B 1 201 2 6W9 DRG . F 3 MG B 1 202 2 MG MG . G 4 HOH A 1 301 83 HOH HOH . G 4 HOH A 2 302 76 HOH HOH . G 4 HOH A 3 303 65 HOH HOH . G 4 HOH A 4 304 25 HOH HOH . G 4 HOH A 5 305 84 HOH HOH . G 4 HOH A 6 306 12 HOH HOH . G 4 HOH A 7 307 2 HOH HOH . G 4 HOH A 8 308 30 HOH HOH . G 4 HOH A 9 309 72 HOH HOH . G 4 HOH A 10 310 3 HOH HOH . G 4 HOH A 11 311 4 HOH HOH . G 4 HOH A 12 312 63 HOH HOH . G 4 HOH A 13 313 28 HOH HOH . G 4 HOH A 14 314 39 HOH HOH . G 4 HOH A 15 315 16 HOH HOH . G 4 HOH A 16 316 5 HOH HOH . G 4 HOH A 17 317 24 HOH HOH . G 4 HOH A 18 318 60 HOH HOH . G 4 HOH A 19 319 29 HOH HOH . G 4 HOH A 20 320 64 HOH HOH . G 4 HOH A 21 321 77 HOH HOH . G 4 HOH A 22 322 51 HOH HOH . G 4 HOH A 23 323 15 HOH HOH . G 4 HOH A 24 324 23 HOH HOH . G 4 HOH A 25 325 68 HOH HOH . G 4 HOH A 26 326 35 HOH HOH . G 4 HOH A 27 327 61 HOH HOH . G 4 HOH A 28 328 27 HOH HOH . G 4 HOH A 29 329 6 HOH HOH . G 4 HOH A 30 330 70 HOH HOH . G 4 HOH A 31 331 71 HOH HOH . G 4 HOH A 32 332 22 HOH HOH . G 4 HOH A 33 333 66 HOH HOH . G 4 HOH A 34 334 7 HOH HOH . G 4 HOH A 35 335 31 HOH HOH . G 4 HOH A 36 336 10 HOH HOH . G 4 HOH A 37 337 21 HOH HOH . G 4 HOH A 38 338 57 HOH HOH . G 4 HOH A 39 339 88 HOH HOH . G 4 HOH A 40 340 62 HOH HOH . G 4 HOH A 41 341 9 HOH HOH . G 4 HOH A 42 342 53 HOH HOH . G 4 HOH A 43 343 80 HOH HOH . G 4 HOH A 44 344 78 HOH HOH . H 4 HOH B 1 301 74 HOH HOH . H 4 HOH B 2 302 89 HOH HOH . H 4 HOH B 3 303 81 HOH HOH . H 4 HOH B 4 304 86 HOH HOH . H 4 HOH B 5 305 91 HOH HOH . H 4 HOH B 6 306 90 HOH HOH . H 4 HOH B 7 307 45 HOH HOH . H 4 HOH B 8 308 69 HOH HOH . H 4 HOH B 9 309 55 HOH HOH . H 4 HOH B 10 310 26 HOH HOH . H 4 HOH B 11 311 50 HOH HOH . H 4 HOH B 12 312 73 HOH HOH . H 4 HOH B 13 313 32 HOH HOH . H 4 HOH B 14 314 75 HOH HOH . H 4 HOH B 15 315 1 HOH HOH . H 4 HOH B 16 316 46 HOH HOH . H 4 HOH B 17 317 8 HOH HOH . H 4 HOH B 18 318 44 HOH HOH . H 4 HOH B 19 319 17 HOH HOH . H 4 HOH B 20 320 19 HOH HOH . H 4 HOH B 21 321 40 HOH HOH . H 4 HOH B 22 322 13 HOH HOH . H 4 HOH B 23 323 47 HOH HOH . H 4 HOH B 24 324 92 HOH HOH . H 4 HOH B 25 325 37 HOH HOH . H 4 HOH B 26 326 14 HOH HOH . H 4 HOH B 27 327 85 HOH HOH . H 4 HOH B 28 328 36 HOH HOH . H 4 HOH B 29 329 11 HOH HOH . H 4 HOH B 30 330 52 HOH HOH . H 4 HOH B 31 331 33 HOH HOH . H 4 HOH B 32 332 49 HOH HOH . H 4 HOH B 33 333 43 HOH HOH . H 4 HOH B 34 334 20 HOH HOH . H 4 HOH B 35 335 87 HOH HOH . H 4 HOH B 36 336 42 HOH HOH . H 4 HOH B 37 337 34 HOH HOH . H 4 HOH B 38 338 18 HOH HOH . H 4 HOH B 39 339 48 HOH HOH . H 4 HOH B 40 340 54 HOH HOH . H 4 HOH B 41 341 38 HOH HOH . H 4 HOH B 42 342 58 HOH HOH . H 4 HOH B 43 343 79 HOH HOH . H 4 HOH B 44 344 82 HOH HOH . H 4 HOH B 45 345 59 HOH HOH . H 4 HOH B 46 346 56 HOH HOH . H 4 HOH B 47 347 41 HOH HOH . H 4 HOH B 48 348 67 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 C C4 6W9 . . . E 2 -7.104 25.533 -39.888 1 98.96 ? C4 6W9 201 B 1 HETATM 2 C C5 6W9 . . . E 2 -6.454 25.145 -38.721 1 91.64 ? C5 6W9 201 B 1 HETATM 3 C C6 6W9 . . . E 2 -7.099 24.355 -37.808 1 78.35 ? C6 6W9 201 B 1 HETATM 4 C C8 6W9 . . . E 2 -5.12 26.418 -39.972 1 92.95 ? C8 6W9 201 B 1 HETATM 5 N N1 6W9 . . . E 2 -8.386 23.946 -38.044 1 70.59 ? N1 6W9 201 B 1 HETATM 6 N N3 6W9 . . . E 2 -8.35 25.148 -40.139 1 97.78 ? N3 6W9 201 B 1 HETATM 7 O OAD 6W9 . . . E 2 -12.002 28.312 -45.818 1 131.41 ? OAD 6W9 201 B 1 HETATM 8 P PAZ 6W9 . . . E 2 -11.926 26.858 -45.397 1 141.5 ? PAZ 6W9 201 B 1 HETATM 9 O OAE 6W9 . . . E 2 -11.741 25.977 -46.641 1 135.08 ? OAE 6W9 201 B 1 HETATM 10 O OAB 6W9 . . . E 2 -13.223 26.464 -44.675 1 132.01 ? OAB 6W9 201 B 1 HETATM 11 C CAP 6W9 . . . E 2 -10.467 26.62 -44.238 1 128.32 ? CAP 6W9 201 B 1 HETATM 12 C CAK 6W9 . . . E 2 -10.074 27.969 -43.621 1 124.77 ? CAK 6W9 201 B 1 HETATM 13 C CAJ 6W9 . . . E 2 -8.723 28.449 -44.226 1 103.62 ? CAJ 6W9 201 B 1 HETATM 14 C CAL 6W9 . . . E 2 -8.106 29.587 -43.324 1 97.2 ? CAL 6W9 201 B 1 HETATM 15 N NAX 6W9 . . . E 2 -6.859 29.12 -42.713 1 94.67 ? NAX 6W9 201 B 1 HETATM 16 C CAN 6W9 . . . E 2 -6.102 30.225 -42.265 1 91.68 ? CAN 6W9 201 B 1 HETATM 17 C CAQ 6W9 . . . E 2 -5.78 31.189 -43.433 1 94.89 ? CAQ 6W9 201 B 1 HETATM 18 P PBA 6W9 . . . E 2 -4.165 32.042 -43.127 1 86.52 ? PBA 6W9 201 B 1 HETATM 19 O OAF 6W9 . . . E 2 -4.353 33.525 -43.191 1 54.3 ? OAF 6W9 201 B 1 HETATM 20 O OAG 6W9 . . . E 2 -3.18 31.614 -44.184 1 76.96 ? OAG 6W9 201 B 1 HETATM 21 O OAC 6W9 . . . E 2 -3.624 31.673 -41.761 1 76.1 ? OAC 6W9 201 B 1 HETATM 22 C CAM 6W9 . . . E 2 -7.153 28.267 -41.591 1 97.76 ? CAM 6W9 201 B 1 HETATM 23 C CAO 6W9 . . . E 2 -6.559 26.853 -41.809 1 103.72 ? CAO 6W9 201 B 1 HETATM 24 N N9 6W9 . . . E 2 -6.261 26.257 -40.541 1 103.05 ? N9 6W9 201 B 1 HETATM 25 C C2 6W9 . . . E 2 -9.046 24.342 -39.236 1 80.71 ? C2 6W9 201 B 1 HETATM 26 O O6 6W9 . . . E 2 -6.415 23.951 -36.585 1 66.7 ? O6 6W9 201 B 1 HETATM 27 N N7 6W9 . . . E 2 -5.167 25.724 -38.784 1 86.01 ? N7 6W9 201 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 233 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #