HEADER DE NOVO PROTEIN 13-JUN-23 8T5E TITLE DE NOVO DESIGN OF HIGH-AFFINITY PROTEIN BINDERS TO BIOACTIVE HELICAL TITLE 2 PEPTIDES COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIM_FULLDIFF; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: BCL-2-LIKE PROTEIN 11; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: BCL2-L-11,BCL2-INTERACTING MEDIATOR OF CELL DEATH; COMPND 9 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 ALPHA-HELICAL PEPTIDES, PROTEIN DESIGN, DIFFUSION, DEEP LEARNING, DE KEYWDS 2 NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.V.TORRES,P.J.Y.LEUNG,A.K.BERA,D.BAKER,A.KANG REVDAT 3 06-NOV-24 8T5E 1 REMARK REVDAT 2 14-FEB-24 8T5E 1 JRNL REVDAT 1 10-JAN-24 8T5E 0 JRNL AUTH S.VAZQUEZ TORRES,P.J.Y.LEUNG,P.VENKATESH,I.D.LUTZ,F.HINK, JRNL AUTH 2 H.H.HUYNH,J.BECKER,A.H.YEH,D.JUERGENS,N.R.BENNETT, JRNL AUTH 3 A.N.HOOFNAGLE,E.HUANG,M.J.MACCOSS,M.EXPOSIT,G.R.LEE, JRNL AUTH 4 A.K.BERA,A.KANG,J.DE LA CRUZ,P.M.LEVINE,X.LI,M.LAMB, JRNL AUTH 5 S.R.GERBEN,A.MURRAY,P.HEINE,E.N.KORKMAZ,J.NIVALA,L.STEWART, JRNL AUTH 6 J.L.WATSON,J.M.ROGERS,D.BAKER JRNL TITL DE NOVO DESIGN OF HIGH-AFFINITY BINDERS OF BIOACTIVE HELICAL JRNL TITL 2 PEPTIDES. JRNL REF NATURE V. 626 435 2024 JRNL REFN ESSN 1476-4687 JRNL PMID 38109936 JRNL DOI 10.1038/S41586-023-06953-1 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_4761 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 2820 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.640 REMARK 3 FREE R VALUE TEST SET COUNT : 159 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 49.6200 - 3.0000 0.99 2661 159 0.2392 0.2644 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) : 0.321 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.177 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 75.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 77.56 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 : 0.003 1253 REMARK 3 ANGLE : 0.496 1675 REMARK 3 CHIRALITY : 0.032 189 REMARK 3 PLANARITY : 0.004 219 REMARK 3 DIHEDRAL : 4.029 176 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 8T5E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1000275258. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97911 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2861 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 74.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 0.17300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.800 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 (%): 28.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRIC ACID PH 2.5, 20% (W/V) REMARK 280 PEG 6000, PH 4, 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 12.89500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.15000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.33350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.15000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.89500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.33350 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: 2170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8080 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 MET A -2 REMARK 465 SER A -1 REMARK 465 GLY A 0 REMARK 465 GLU A 1 REMARK 465 GLN A 116 REMARK 465 THR A 117 REMARK 465 PRO A 118 REMARK 465 GLU A 119 REMARK 465 GLY A 136 REMARK 465 SER A 137 REMARK 465 GLY A 138 REMARK 465 ASP B 139 REMARK 465 MET B 140 REMARK 465 ARG B 141 REMARK 465 ARG B 164 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 GLU A 115 CG CD OE1 OE2 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 GLU A 3 -9.53 -56.50 REMARK 500 SER A 38 -135.02 62.74 REMARK 500 ILE A 101 -60.46 -94.28 REMARK 500 TYR B 160 66.84 -101.84 REMARK 500 TYR B 161 -112.53 -96.87 REMARK 500 REMARK 500 REMARK: NULL DBREF 8T5E A -2 138 PDB 8T5E 8T5E -2 138 DBREF 8T5E B 139 164 UNP O43521 B2L11_HUMAN 141 166 SEQRES 1 A 141 MET SER GLY GLU GLU GLU ARG LYS GLU LYS ARG GLU LYS SEQRES 2 A 141 VAL ARG ALA GLY LEU LYS ARG ALA ILE ALA GLU LEU PRO SEQRES 3 A 141 ALA GLU VAL ALA ALA ARG CYS LEU ALA LEU LEU ASP ASP SEQRES 4 A 141 ALA SER ASP GLU GLU PHE ILE GLU ALA VAL LEU GLU VAL SEQRES 5 A 141 LEU GLU ALA MET ARG GLU ALA LEU VAL ALA MET ALA ARG SEQRES 6 A 141 GLU GLY ARG LEU ASP ALA VAL ARG ARG ALA THR SER HIS SEQRES 7 A 141 ILE ASN GLU VAL LEU VAL ASP ALA ALA GLU LEU ALA LEU SEQRES 8 A 141 GLU LYS GLY ARG GLU TYR PHE ARG ARG LEU CYS LEU ILE SEQRES 9 A 141 VAL CYS ASP MET MET ILE GLU LEU ILE ARG LEU GLU PRO SEQRES 10 A 141 GLU GLN THR PRO GLU LEU ARG ARG ILE ARG GLU ARG LEU SEQRES 11 A 141 GLU GLU ILE ARG ARG ARG LEU GLU GLY SER GLY SEQRES 1 B 26 ASP MET ARG PRO GLU ILE TRP ILE ALA GLN GLU LEU ARG SEQRES 2 B 26 ARG ILE GLY ASP GLU PHE ASN ALA TYR TYR ALA ARG ARG HELIX 1 AA1 GLU A 2 ALA A 20 1 19 HELIX 2 AA2 PRO A 23 ASP A 36 1 14 HELIX 3 AA3 GLU A 41 GLY A 64 1 24 HELIX 4 AA4 ARG A 65 GLU A 78 1 14 HELIX 5 AA5 VAL A 79 GLY A 91 1 13 HELIX 6 AA6 GLY A 91 ARG A 111 1 21 HELIX 7 AA7 ARG A 121 GLU A 135 1 15 HELIX 8 AA8 GLU B 143 TYR B 160 1 18 SSBOND 1 CYS A 99 CYS A 103 1555 1555 2.04 CRYST1 25.790 66.667 74.300 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 0.038775 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015000 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013459 0.00000