data_5KNR # _model_server_result.job_id Kv4K7wE8D1vQpkwE9-BXtA _model_server_result.datetime_utc '2024-11-07 19:26:56' _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 5knr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 5KNR # _exptl.entry_id 5KNR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 454.313 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2-{[2-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)ethyl][2-(2-phosphonoethoxy)ethyl]amino}ethyl)phosphonic 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 5KNR _cell.length_a 84.617 _cell.length_b 84.617 _cell.length_c 167.116 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KNR _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 ? tetrameric 4 author_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 1 1,2 A,B,C,D,E,F,G 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 -111.410667 # 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc2 A OD1 ASP 104 A ASP 104 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc3 C OAC 3L5 . A 3L5 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc4 D MG MG . A MG 202 1_555 F O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? # _chem_comp.formula 'C13 H24 N6 O8 P2' _chem_comp.formula_weight 454.313 _chem_comp.id 3L5 _chem_comp.mon_nstd_flag . _chem_comp.name '(2-{[2-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)ethyl][2-(2-phosphonoethoxy)ethyl]amino}ethyl)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 OAE PBB 3L5 doub 1 n n OAF PBB 3L5 sing 2 n n OAC PBB 3L5 sing 3 n n PBB CAP 3L5 sing 4 n n N2 C2 3L5 sing 5 n n C2 N1 3L5 doub 6 n n C2 N3 3L5 sing 7 n n N1 C6 3L5 sing 8 n n N3 C4 3L5 sing 9 n n C6 O6 3L5 doub 10 n n C6 C5 3L5 sing 11 n n C4 C5 3L5 doub 12 n y C4 N9 3L5 sing 13 n y C5 N7 3L5 sing 14 n y CAP CAK 3L5 sing 15 n n CAK OAU 3L5 sing 16 n n N9 CAO 3L5 sing 17 n n N9 C8 3L5 sing 18 n y N7 C8 3L5 doub 19 n y CAO CAM 3L5 sing 20 n n OAU CAJ 3L5 sing 21 n n CAM NAZ 3L5 sing 22 n n NAZ CAN 3L5 sing 23 n n NAZ CAL 3L5 sing 24 n n CAJ CAL 3L5 sing 25 n n CAN CAQ 3L5 sing 26 n n OAD PBC 3L5 doub 27 n n CAQ PBC 3L5 sing 28 n n PBC OAG 3L5 sing 29 n n PBC OAH 3L5 sing 30 n n OAF H1 3L5 sing 31 n n OAC H2 3L5 sing 32 n n CAP H3 3L5 sing 33 n n CAP H4 3L5 sing 34 n n CAK H5 3L5 sing 35 n n CAK H6 3L5 sing 36 n n CAJ H7 3L5 sing 37 n n CAJ H8 3L5 sing 38 n n CAL H9 3L5 sing 39 n n CAL H10 3L5 sing 40 n n CAN H12 3L5 sing 41 n n CAN H13 3L5 sing 42 n n CAQ H14 3L5 sing 43 n n CAQ H15 3L5 sing 44 n n OAG H16 3L5 sing 45 n n OAH H17 3L5 sing 46 n n CAM H18 3L5 sing 47 n n CAM H19 3L5 sing 48 n n CAO H20 3L5 sing 49 n n CAO H21 3L5 sing 50 n n N3 H22 3L5 sing 51 n n N2 H23 3L5 sing 52 n n N2 H24 3L5 sing 53 n n C8 H25 3L5 sing 54 n n # _atom_sites.entry_id 5KNR _atom_sites.fract_transf_matrix[1][1] 0.011818 _atom_sites.fract_transf_matrix[1][2] 0.006823 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013646 _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] 0.005984 _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 3L5 A 1 201 1 3L5 DRG . D 3 MG A 1 202 1 MG MG . E 2 3L5 B 1 201 2 3L5 DRG . F 4 HOH A 1 301 16 HOH HOH . F 4 HOH A 2 302 23 HOH HOH . F 4 HOH A 3 303 9 HOH HOH . F 4 HOH A 4 304 6 HOH HOH . F 4 HOH A 5 305 11 HOH HOH . F 4 HOH A 6 306 5 HOH HOH . F 4 HOH A 7 307 8 HOH HOH . F 4 HOH A 8 308 10 HOH HOH . F 4 HOH A 9 309 22 HOH HOH . F 4 HOH A 10 310 20 HOH HOH . F 4 HOH A 11 311 15 HOH HOH . G 4 HOH B 1 301 3 HOH HOH . G 4 HOH B 2 302 24 HOH HOH . G 4 HOH B 3 303 7 HOH HOH . G 4 HOH B 4 304 19 HOH HOH . G 4 HOH B 5 305 13 HOH HOH . G 4 HOH B 6 306 2 HOH HOH . G 4 HOH B 7 307 21 HOH HOH . G 4 HOH B 8 308 4 HOH HOH . G 4 HOH B 9 309 1 HOH HOH . G 4 HOH B 10 310 17 HOH HOH . G 4 HOH B 11 311 14 HOH HOH . G 4 HOH B 12 312 18 HOH HOH . G 4 HOH B 13 313 12 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 3L5 . . . E 2 -32.245 42.799 -41.237 1 153.85 ? OAE 3L5 201 B 1 HETATM 2 P PBB 3L5 . . . E 2 -31.096 42.771 -42.205 1 158.84 ? PBB 3L5 201 B 1 HETATM 3 O OAF 3L5 . . . E 2 -29.84 42.355 -41.482 1 156.35 ? OAF 3L5 201 B 1 HETATM 4 O OAC 3L5 . . . E 2 -30.894 44.155 -42.796 1 155.05 ? OAC 3L5 201 B 1 HETATM 5 C CAP 3L5 . . . E 2 -31.453 41.586 -43.538 1 123.17 ? CAP 3L5 201 B 1 HETATM 6 C CAK 3L5 . . . E 2 -31.808 40.183 -42.986 1 99.42 ? CAK 3L5 201 B 1 HETATM 7 O OAU 3L5 . . . E 2 -33.059 39.769 -43.553 1 101.08 ? OAU 3L5 201 B 1 HETATM 8 C CAJ 3L5 . . . E 2 -34.209 40.309 -42.908 1 80.38 ? CAJ 3L5 201 B 1 HETATM 9 C CAL 3L5 . . . E 2 -34.957 41.227 -43.91 1 73.2 ? CAL 3L5 201 B 1 HETATM 10 N NAZ 3L5 . . . E 2 -36.26 41.615 -43.377 1 71.37 ? NAZ 3L5 201 B 1 HETATM 11 C CAN 3L5 . . . E 2 -37.311 41.17 -44.292 1 60.63 ? CAN 3L5 201 B 1 HETATM 12 C CAQ 3L5 . . . E 2 -38.127 40.041 -43.664 1 69.23 ? CAQ 3L5 201 B 1 HETATM 13 P PBC 3L5 . . . E 2 -39.482 39.524 -44.728 1 74.07 ? PBC 3L5 201 B 1 HETATM 14 O OAG 3L5 . . . E 2 -38.943 38.745 -45.89 1 68.48 ? OAG 3L5 201 B 1 HETATM 15 O OAH 3L5 . . . E 2 -40.442 38.652 -43.953 1 61.05 ? OAH 3L5 201 B 1 HETATM 16 O OAD 3L5 . . . E 2 -40.213 40.756 -45.233 1 58.61 ? OAD 3L5 201 B 1 HETATM 17 C CAM 3L5 . . . E 2 -36.312 43.12 -43.233 1 75.38 ? CAM 3L5 201 B 1 HETATM 18 C CAO 3L5 . . . E 2 -37.781 43.61 -42.968 1 78.12 ? CAO 3L5 201 B 1 HETATM 19 N N9 3L5 . . . E 2 -37.938 44.223 -41.65 1 78.71 ? N9 3L5 201 B 1 HETATM 20 C C4 3L5 . . . E 2 -36.989 44.932 -40.954 1 77.72 ? C4 3L5 201 B 1 HETATM 21 N N3 3L5 . . . E 2 -35.7 45.286 -41.197 1 80.38 ? N3 3L5 201 B 1 HETATM 22 C C2 3L5 . . . E 2 -35 45.992 -40.324 1 85.11 ? C2 3L5 201 B 1 HETATM 23 N N2 3L5 . . . E 2 -33.691 46.323 -40.625 1 84.49 ? N2 3L5 201 B 1 HETATM 24 N N1 3L5 . . . E 2 -35.529 46.39 -39.162 1 79.34 ? N1 3L5 201 B 1 HETATM 25 C C6 3L5 . . . E 2 -36.798 46.086 -38.837 1 69.24 ? C6 3L5 201 B 1 HETATM 26 O O6 3L5 . . . E 2 -37.334 46.508 -37.624 1 62.56 ? O6 3L5 201 B 1 HETATM 27 C C5 3L5 . . . E 2 -37.597 45.327 -39.744 1 70.41 ? C5 3L5 201 B 1 HETATM 28 N N7 3L5 . . . E 2 -38.871 44.846 -39.762 1 65.4 ? N7 3L5 201 B 1 HETATM 29 C C8 3L5 . . . E 2 -39.051 44.187 -40.92 1 76.26 ? C8 3L5 201 B 1 # _model_server_stats.io_time_ms 77 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 29 #