HEADER DE NOVO PROTEIN 11-DEC-25 9TLS TITLE DE NOVO DESIGNED SINGLE-CHAIN ANTIPARALLEL COILED-COIL HAIRPIN WITH TITLE 2 BINDING SITE FOR KLHL20, SC-APCC-2-KLHL20-3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SC-APCC-2-KLHL20-3; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS PROTEIN BINDER, COMPUTATIONAL DESIGN, COILED-COIL, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.MYLEMANS,D.N.WOOLFSON REVDAT 1 19-AUG-26 9TLS 0 JRNL AUTH B.MYLEMANS,B.KORONA,A.M.ACEVEDO-JAKE,A.MACRAE,T.A.EDWARDS, JRNL AUTH 2 D.T.HUANG,A.J.WILSON,L.S.ITZHAKI,D.N.WOOLFSON JRNL TITL DE NOVO-DESIGNED BIFUNCTIONAL JRNL REF J.AM.CHEM.SOC. 2026 JRNL REFN ESSN 1520-5126 JRNL DOI 10.1021/JACS.6C07593 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21_5207 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 42379 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 2124 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.3700 - 3.5700 1.00 2763 190 0.1673 0.1824 REMARK 3 2 3.5700 - 2.8400 1.00 2746 138 0.1714 0.2032 REMARK 3 3 2.8400 - 2.4800 1.00 2704 141 0.1798 0.2196 REMARK 3 4 2.4800 - 2.2500 1.00 2692 140 0.1674 0.1869 REMARK 3 5 2.2500 - 2.0900 1.00 2698 131 0.1679 0.1934 REMARK 3 6 2.0900 - 1.9700 1.00 2666 170 0.1885 0.2714 REMARK 3 7 1.9700 - 1.8700 1.00 2642 149 0.1960 0.2317 REMARK 3 8 1.8700 - 1.7900 1.00 2676 134 0.2001 0.2490 REMARK 3 9 1.7900 - 1.7200 1.00 2705 140 0.2039 0.2375 REMARK 3 10 1.7200 - 1.6600 1.00 2667 130 0.2096 0.2286 REMARK 3 11 1.6600 - 1.6100 1.00 2664 115 0.1938 0.2220 REMARK 3 12 1.6100 - 1.5600 1.00 2702 115 0.1992 0.2528 REMARK 3 13 1.5600 - 1.5200 1.00 2621 150 0.2126 0.2628 REMARK 3 14 1.5200 - 1.4800 1.00 2700 146 0.2239 0.2724 REMARK 3 15 1.4800 - 1.4500 0.99 2609 135 0.2525 0.2975 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.167 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.439 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1812 REMARK 3 ANGLE : 0.779 2451 REMARK 3 CHIRALITY : 0.053 287 REMARK 3 PLANARITY : 0.009 328 REMARK 3 DIHEDRAL : 13.715 709 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9TLS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1292152920. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.62 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42389 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 29.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES 10% PEG 5000 MME 12 % 1 REMARK 280 -PROPANOL, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 15.95500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER B 1 REMARK 465 HIS B 2 REMARK 465 MET B 3 REMARK 465 SER C 1 REMARK 465 HIS C 2 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 9 CG CD OE1 NE2 REMARK 470 GLN A 26 CD OE1 NE2 REMARK 470 GLN B 19 CD OE1 NE2 REMARK 470 MET C 3 CG SD CE REMARK 470 GLN C 12 CG CD OE1 NE2 DBREF 9TLS A 1 78 PDB 9TLS 9TLS 1 78 DBREF 9TLS B 1 78 PDB 9TLS 9TLS 1 78 DBREF 9TLS C 1 78 PDB 9TLS 9TLS 1 78 SEQRES 1 A 78 SER HIS MET GLY ALA ARG LEU ALA GLN LEU LYS GLN GLU SEQRES 2 A 78 ARG ALA ALA LEU LYS GLN ARG LEU ALA ALA LEU ASP GLN SEQRES 3 A 78 GLU ILE ALA ALA LEU GLN ALA ARG ILE ASP ALA GLY ALA SEQRES 4 A 78 PRO ASP LEU VAL ARG PRO VAL LEU GLU ALA ARG LEU ALA SEQRES 5 A 78 ALA LEU LYS GLN GLU ARG ALA ALA LEU GLU GLN ARG ILE SEQRES 6 A 78 ALA ALA LEU ASP TRP GLU ILE ALA ALA LEU GLU ALA GLY SEQRES 1 B 78 SER HIS MET GLY ALA ARG LEU ALA GLN LEU LYS GLN GLU SEQRES 2 B 78 ARG ALA ALA LEU LYS GLN ARG LEU ALA ALA LEU ASP GLN SEQRES 3 B 78 GLU ILE ALA ALA LEU GLN ALA ARG ILE ASP ALA GLY ALA SEQRES 4 B 78 PRO ASP LEU VAL ARG PRO VAL LEU GLU ALA ARG LEU ALA SEQRES 5 B 78 ALA LEU LYS GLN GLU ARG ALA ALA LEU GLU GLN ARG ILE SEQRES 6 B 78 ALA ALA LEU ASP TRP GLU ILE ALA ALA LEU GLU ALA GLY SEQRES 1 C 78 SER HIS MET GLY ALA ARG LEU ALA GLN LEU LYS GLN GLU SEQRES 2 C 78 ARG ALA ALA LEU LYS GLN ARG LEU ALA ALA LEU ASP GLN SEQRES 3 C 78 GLU ILE ALA ALA LEU GLN ALA ARG ILE ASP ALA GLY ALA SEQRES 4 C 78 PRO ASP LEU VAL ARG PRO VAL LEU GLU ALA ARG LEU ALA SEQRES 5 C 78 ALA LEU LYS GLN GLU ARG ALA ALA LEU GLU GLN ARG ILE SEQRES 6 C 78 ALA ALA LEU ASP TRP GLU ILE ALA ALA LEU GLU ALA GLY HET IPA A 101 4 HET IPA A 102 4 HET GOL A 103 6 HET IPA C 101 4 HET GOL C 102 6 HETNAM IPA ISOPROPYL ALCOHOL HETNAM GOL GLYCEROL HETSYN IPA 2-PROPANOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 IPA 3(C3 H8 O) FORMUL 6 GOL 2(C3 H8 O3) FORMUL 9 HOH *297(H2 O) HELIX 1 AA1 GLY A 4 GLY A 38 1 35 HELIX 2 AA2 VAL A 43 GLY A 78 1 36 HELIX 3 AA3 ALA B 5 GLY B 38 1 34 HELIX 4 AA4 VAL B 43 GLY B 78 1 36 HELIX 5 AA5 GLY C 4 ALA C 37 1 34 HELIX 6 AA6 VAL C 43 GLY C 78 1 36 CRYST1 49.903 31.910 75.183 90.00 93.52 90.00 P 1 21 1 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.020039 0.000000 0.001234 0.00000 SCALE2 0.000000 0.031338 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013326 0.00000 CONECT 1779 1780 CONECT 1780 1779 1781 1782 CONECT 1781 1780 CONECT 1782 1780 CONECT 1783 1784 CONECT 1784 1783 1785 1786 CONECT 1785 1784 CONECT 1786 1784 CONECT 1787 1788 1789 CONECT 1788 1787 CONECT 1789 1787 1790 1791 CONECT 1790 1789 CONECT 1791 1789 1792 CONECT 1792 1791 CONECT 1793 1794 CONECT 1794 1793 1795 1796 CONECT 1795 1794 CONECT 1796 1794 CONECT 1797 1798 1799 CONECT 1798 1797 CONECT 1799 1797 1800 1801 CONECT 1800 1799 CONECT 1801 1799 1802 CONECT 1802 1801 MASTER 231 0 5 6 0 0 0 6 2043 3 24 18 END