HEADER DE NOVO PROTEIN 20-JUN-24 9CC5 TITLE DE NOVO DESIGN OF HIGH-AFFINITY PROTEIN BINDERS TO BIO ACTIVE PEPTIDE TITLE 2 AMYLIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLIN-NHO-22 BINDER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ISLET AMYLOID POLYPEPTIDE; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: AMYLIN,DIABETES-ASSOCIATED PEPTIDE,DAP,INSULINOMA AMYLOID COMPND 9 PEPTIDE; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606 KEYWDS PROTEIN DESIGN, DIFFUSION, DEEP LEARNING, DE NOVO PROTEIN, BINDERS, KEYWDS 2 IDP, IDR, AMYLOID, PHASE SEPARATION EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,C.LIU,A.KANG,D.BAKER REVDAT 4 10-SEP-25 9CC5 1 COMPND REMARK HELIX SHEET REVDAT 4 2 1 SSBOND ATOM REVDAT 3 27-AUG-25 9CC5 1 REVDAT 2 13-AUG-25 9CC5 1 REVDAT 1 14-MAY-25 9CC5 0 JRNL AUTH C.LIU,K.WU,H.CHOI,H.L.HAN,X.ZHANG,J.L.WATSON,G.AHN, JRNL AUTH 2 J.Z.ZHANG,S.SHIJO,L.L.GOOD,C.M.FISCHER,A.K.BERA,A.KANG, JRNL AUTH 3 E.BRACKENBROUGH,B.COVENTRY,D.R.HICK,S.QAMAR,X.LI, JRNL AUTH 4 J.DECARREAU,S.R.GERBEN,W.YANG,I.GORESHNIK,D.VAFEADOS,X.WANG, JRNL AUTH 5 M.LAMB,A.MURRAY,S.KENNY,M.S.BAUER,A.N.HOOFNAGLE,P.ZHU, JRNL AUTH 6 T.P.J.KNOWLES,D.BAKER JRNL TITL DIFFUSING PROTEIN BINDERS TO INTRINSICALLY DISORDERED JRNL TITL 2 PROTEINS. JRNL REF NATURE V. 644 809 2025 JRNL REFN ESSN 1476-4687 JRNL PMID 40739343 JRNL DOI 10.1038/S41586-025-09248-9 REMARK 2 REMARK 2 RESOLUTION. 1.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 12854 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1295 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 33.3200 - 3.8800 0.97 1364 156 0.2243 0.2306 REMARK 3 2 3.8800 - 3.0800 0.99 1304 146 0.1938 0.2629 REMARK 3 3 3.0800 - 2.6900 1.00 1290 148 0.2045 0.2632 REMARK 3 4 2.6900 - 2.4400 1.00 1293 138 0.1877 0.2652 REMARK 3 5 2.4400 - 2.2700 1.00 1267 143 0.1989 0.2284 REMARK 3 6 2.2700 - 2.1400 1.00 1267 146 0.2174 0.2682 REMARK 3 7 2.1400 - 2.0300 1.00 1243 140 0.2220 0.2935 REMARK 3 8 2.0300 - 1.9400 1.00 1276 137 0.2471 0.3196 REMARK 3 9 1.9400 - 1.8700 0.99 1255 141 0.2782 0.3134 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) : 0.245 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.903 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.51 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 : 0.004 1301 REMARK 3 ANGLE : 0.591 1760 REMARK 3 CHIRALITY : 0.047 206 REMARK 3 PLANARITY : 0.005 235 REMARK 3 DIHEDRAL : 18.681 498 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 7.8245 6.9122 15.9733 REMARK 3 T TENSOR REMARK 3 T11: 0.1567 T22: 0.1759 REMARK 3 T33: 0.1733 T12: 0.0013 REMARK 3 T13: 0.0041 T23: 0.0182 REMARK 3 L TENSOR REMARK 3 L11: 0.5080 L22: 1.2514 REMARK 3 L33: 0.8267 L12: 0.1199 REMARK 3 L13: 0.1749 L23: -0.0538 REMARK 3 S TENSOR REMARK 3 S11: -0.0270 S12: -0.0321 S13: 0.0136 REMARK 3 S21: -0.0285 S22: 0.0211 S23: -0.0002 REMARK 3 S31: 0.0207 S32: -0.0219 S33: 0.0000 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 9CC5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1000285013. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9201 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12855 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 33.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.15900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.9400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 1.79000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.220 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 (%): 36.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SUCCINIC ACID, SODIUM PHOSPHATE REMARK 280 MONOBASIC MONOHYDRATE, GLYCINE MIXTURE AT PH 6 AND 30% W/V PEG REMARK 280 1000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 16.66800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.84200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.25950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.84200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.66800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 17.25950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 A 1 REMARK 465 ASN B 164 REMARK 465 VAL B 165 REMARK 465 GLY B 166 REMARK 465 SER B 167 REMARK 465 ASN B 168 REMARK 465 THR B 169 REMARK 465 TYR B 170 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 243 O HOH A 244 2.17 REMARK 500 O HOH A 241 O HOH A 243 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 13 31.14 72.61 REMARK 500 REMARK 500 REMARK: NULL DBREF 9CC5 A 1 133 PDB 9CC5 9CC5 1 133 DBREF 9CC5 B 134 170 UNP P10997 IAPP_HUMAN 34 70 SEQRES 1 A 133 SER LEU ILE VAL ALA VAL ALA SER PRO VAL VAL VAL ALA SEQRES 2 A 133 ALA HIS SER PRO GLU ASP GLU GLU ARG ALA GLU LYS GLU SEQRES 3 A 133 ALA GLU ARG LEU ARG ARG ARG PHE ALA GLU GLU LEU ARG SEQRES 4 A 133 LYS LYS GLY PHE GLU VAL VAL GLU LEU ASP GLU GLU THR SEQRES 5 A 133 ASP GLU GLU LEU ARG ARG TRP LEU THR LYS ALA ILE ARG SEQRES 6 A 133 GLU ALA THR GLN ALA PRO THR GLN GLU GLU PHE ASN GLN SEQRES 7 A 133 ALA VAL ALA GLU ALA ILE GLU LYS ALA LEU GLU ARG ILE SEQRES 8 A 133 GLU GLU ILE ALA ARG ARG ARG HIS PRO ASP ARG GLU VAL SEQRES 9 A 133 ALA ALA VAL LEU THR VAL ALA VAL VAL HIS ASP GLY GLU SEQRES 10 A 133 VAL ILE ALA THR ILE PHE ALA SER PRO ARG LEU ARG GLU SEQRES 11 A 133 ALA LEU LYS SEQRES 1 B 37 LYS CYS ASN THR ALA THR CYS ALA THR GLN ARG LEU ALA SEQRES 2 B 37 ASN PHE LEU VAL HIS SER SER ASN ASN PHE GLY ALA ILE SEQRES 3 B 37 LEU SER SER THR ASN VAL GLY SER ASN THR TYR FORMUL 3 HOH *48(H2 O) HELIX 1 AA1 SER A 16 LYS A 41 1 26 HELIX 2 AA2 ASP A 49 THR A 68 1 20 HELIX 3 AA3 THR A 72 HIS A 99 1 28 HELIX 4 AA4 SER A 125 LYS A 133 1 9 HELIX 5 AA5 THR B 139 GLY B 157 1 19 SHEET 1 AA1 4 VAL A 10 VAL A 12 0 SHEET 2 AA1 4 VAL A 104 HIS A 114 1 O THR A 109 N VAL A 10 SHEET 3 AA1 4 ILE A 3 VAL A 6 1 N ALA A 5 O ALA A 105 SHEET 4 AA1 4 GLU A 44 GLU A 47 1 O GLU A 44 N VAL A 4 SHEET 1 AA2 4 VAL A 10 VAL A 12 0 SHEET 2 AA2 4 VAL A 104 HIS A 114 1 O THR A 109 N VAL A 10 SHEET 3 AA2 4 GLU A 117 ALA A 124 -1 O PHE A 123 N LEU A 108 SHEET 4 AA2 4 ILE B 159 SER B 162 -1 O SER B 161 N ALA A 120 SSBOND 1 CYS B 135 CYS B 140 1555 1555 2.04 CRYST1 33.336 34.519 127.684 90.00 90.00 90.00 P 21 21 21 4 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 0.029998 0.000000 0.000000 0.00000 SCALE2 0.000000 0.028970 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007832 0.00000 CONECT 1077 1110 CONECT 1110 1077 MASTER 260 0 0 5 8 0 0 6 1329 2 2 14 END