HEADER APOPTOSIS 25-JUN-24 9CDT TITLE CRYSTAL STRUCTURE OF MCL-1-PEPTIDE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: INDUCED MYELOID LEUKEMIA CELL DIFFERENTIATION PROTEIN MCL- COMPND 3 1; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: BCL-2-LIKE PROTEIN 3,BCL2-L-3,BCL-2-RELATED PROTEIN COMPND 6 EAT/MCL1,MCL1/EAT; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: MCB_D2 PEPTIDE; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MCL1, BCL2L3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS DE NOVO DESIGN, DEEP LEARNING, MACRO CYCLE, MCL-1, APOTOSIS KEYWDS 2 REGULATOR, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,S.RETTIE,A.KANG,G.BHARDWAJ REVDAT 2 10-DEC-25 9CDT 1 JRNL REVDAT 1 02-JUL-25 9CDT 0 JRNL AUTH S.A.RETTIE,D.JUERGENS,V.ADEBOMI,Y.F.BUESO,Q.ZHAO, JRNL AUTH 2 A.N.LEVEILLE,A.LIU,A.K.BERA,J.A.WILMS,A.UFFING,A.KANG, JRNL AUTH 3 E.BRACKENBROUGH,M.LAMB,S.R.GERBEN,A.MURRAY,P.M.LEVINE, JRNL AUTH 4 M.SCHNEIDER,V.VASIREDDY,S.OVCHINNIKOV,O.H.WEIERGRABER, JRNL AUTH 5 D.WILLBOLD,J.A.KRITZER,J.D.MOUGOUS,D.BAKER,F.DIMAIO, JRNL AUTH 6 G.BHARDWAJ JRNL TITL ACCURATE DE NOVO DESIGN OF HIGH-AFFINITY PROTEIN-BINDING JRNL TITL 2 MACROCYCLES USING DEEP LEARNING. JRNL REF NAT.CHEM.BIOL. V. 21 1948 2025 JRNL REFN ESSN 1552-4469 JRNL PMID 40542165 JRNL DOI 10.1038/S41589-025-01929-W REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 10245 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1025 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 33.4300 - 4.0200 0.99 1435 160 0.1845 0.2179 REMARK 3 2 4.0100 - 3.1900 1.00 1373 152 0.1982 0.2946 REMARK 3 3 3.1900 - 2.7800 1.00 1347 150 0.2453 0.2849 REMARK 3 4 2.7800 - 2.5300 1.00 1327 147 0.2459 0.2908 REMARK 3 5 2.5300 - 2.3500 1.00 1339 149 0.2569 0.2953 REMARK 3 6 2.3500 - 2.2100 0.81 1074 120 0.2843 0.3438 REMARK 3 7 2.2100 - 2.1000 1.00 1325 147 0.3235 0.4221 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) : 0.308 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.646 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.00 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 1342 REMARK 3 ANGLE : 0.477 1807 REMARK 3 CHIRALITY : 0.035 202 REMARK 3 PLANARITY : 0.003 230 REMARK 3 DIHEDRAL : 3.809 179 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESSEQ 0:149) REMARK 3 ORIGIN FOR THE GROUP (A): -9.2067 12.9201 -11.8864 REMARK 3 T TENSOR REMARK 3 T11: 0.3722 T22: 0.3707 REMARK 3 T33: 0.3392 T12: -0.0496 REMARK 3 T13: 0.0845 T23: -0.0323 REMARK 3 L TENSOR REMARK 3 L11: 5.0276 L22: 3.5547 REMARK 3 L33: 3.1037 L12: -0.1886 REMARK 3 L13: 0.9029 L23: -0.1195 REMARK 3 S TENSOR REMARK 3 S11: 0.1316 S12: -0.6630 S13: 0.1779 REMARK 3 S21: 0.5812 S22: -0.1685 S23: 0.2814 REMARK 3 S31: 0.1642 S32: -0.1889 S33: 0.0434 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN B AND RESSEQ 152:167) REMARK 3 ORIGIN FOR THE GROUP (A): -9.3646 9.1296 -29.2342 REMARK 3 T TENSOR REMARK 3 T11: 0.7176 T22: 0.7992 REMARK 3 T33: 0.6240 T12: -0.0120 REMARK 3 T13: -0.0971 T23: 0.0310 REMARK 3 L TENSOR REMARK 3 L11: 0.5047 L22: 0.1147 REMARK 3 L33: 0.4496 L12: 0.0086 REMARK 3 L13: -0.4740 L23: -0.0292 REMARK 3 S TENSOR REMARK 3 S11: -0.2705 S12: 2.0383 S13: -0.0272 REMARK 3 S21: -1.9882 S22: -0.4543 S23: 0.2984 REMARK 3 S31: 0.1426 S32: -0.6516 S33: -0.0310 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 9CDT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1000285313. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-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 : 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) : 0.92010 REMARK 200 MONOCHROMATOR : SI(111) DCM REMARK 200 OPTICS : KB BIMORPH MIRRORS 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10245 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 33.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 0.86000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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 (%): 45.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CHLORIDE, 0.1 M BIS-TRIS REMARK 280 PH 6.5, AND 25% W/V POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 26.24200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.68300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.24200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.68300 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: 1180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 VAL A 150 REMARK 465 GLU A 151 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 ARG A 129 CD NE CZ NH1 NH2 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 ASP A 65 71.48 50.86 REMARK 500 ASP B 166 65.30 -103.97 REMARK 500 REMARK 500 REMARK: NULL DBREF 9CDT A 1 151 UNP Q07820 MCL1_HUMAN 172 322 DBREF 9CDT B 152 167 PDB 9CDT 9CDT 152 167 SEQADV 9CDT SER A 0 UNP Q07820 EXPRESSION TAG SEQRES 1 A 152 SER ASP GLU LEU TYR ARG GLN SER LEU GLU ILE ILE SER SEQRES 2 A 152 ARG TYR LEU ARG GLU GLN ALA THR GLY ALA LYS ASP THR SEQRES 3 A 152 LYS PRO MET GLY ARG SER GLY ALA THR SER ARG LYS ALA SEQRES 4 A 152 LEU GLU THR LEU ARG ARG VAL GLY ASP GLY VAL GLN ARG SEQRES 5 A 152 ASN HIS GLU THR ALA PHE GLN GLY MET LEU ARG LYS LEU SEQRES 6 A 152 ASP ILE LYS ASN GLU ASP ASP VAL LYS SER LEU SER ARG SEQRES 7 A 152 VAL MET ILE HIS VAL PHE SER ASP GLY VAL THR ASN TRP SEQRES 8 A 152 GLY ARG ILE VAL THR LEU ILE SER PHE GLY ALA PHE VAL SEQRES 9 A 152 ALA LYS HIS LEU LYS THR ILE ASN GLN GLU SER CYS ILE SEQRES 10 A 152 GLU PRO LEU ALA GLU SER ILE THR ASP VAL LEU VAL ARG SEQRES 11 A 152 THR LYS ARG ASP TRP LEU VAL LYS GLN ARG GLY TRP ASP SEQRES 12 A 152 GLY PHE VAL GLU PHE PHE HIS VAL GLU SEQRES 1 B 16 PRO PRO GLU ILE ALA TRP LEU ALA ASP ALA VAL GLY LEU SEQRES 2 B 16 LYS ASP ALA FORMUL 3 HOH *31(H2 O) HELIX 1 AA1 ASP A 1 GLY A 21 1 21 HELIX 2 AA2 SER A 31 HIS A 53 1 23 HELIX 3 AA3 HIS A 53 ASP A 65 1 13 HELIX 4 AA4 ASN A 68 PHE A 83 1 16 HELIX 5 AA5 ASN A 89 ILE A 110 1 22 HELIX 6 AA6 GLN A 112 SER A 114 5 3 HELIX 7 AA7 CYS A 115 GLN A 138 1 24 HELIX 8 AA8 ARG A 139 HIS A 149 1 11 HELIX 9 AA9 PRO B 152 GLU B 154 5 3 HELIX 10 AB1 ILE B 155 GLY B 163 1 9 LINK N PRO B 152 C ALA B 167 1555 1555 1.39 CRYST1 52.484 75.366 43.371 90.00 90.00 90.00 P 21 21 2 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 0.019053 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013269 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023057 0.00000 CONECT 1204 1318 CONECT 1318 1204 MASTER 264 0 0 10 0 0 0 6 1350 2 2 14 END