HEADER APOPTOSIS 19-DEC-19 6VBX TITLE CRYSTAL STRUCTURE OF MCL-1 IN COMPLEX WITH 138E12 PEPTIDE, LYS- TITLE 2 COVALENT ANTAGONIST 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: SYNTHETIC PEPTIDE; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: THIS IS A CHEMICALLY SYNTHESIZED PEPTIDE WITH COMPND 13 UNNATURAL LIGAND (SEE LIGAND SECTION) ON THE N-TERMINAL END. LIGANDS COMPND 14 IS COVALENTLY ATTACHED TO LYS234 OF CHAIN A. 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 MCL-1, APOPTOSIS, 138E12 PEPTIDE, LYS-COVALENT ANTAGONISTS EXPDTA X-RAY DIFFRACTION AUTHOR M.PELLECCHIA,J.J.PERRY,N.KENJIC,Z.ASSAR REVDAT 3 11-OCT-23 6VBX 1 REMARK REVDAT 2 09-JUN-21 6VBX 1 JRNL REVDAT 1 30-DEC-20 6VBX 0 JRNL AUTH L.GAMBINI,P.UDOMPHOLKUL,C.BAGGIO,A.MURALIDHARAN,N.KENJIC, JRNL AUTH 2 Z.ASSAR,J.J.P.PERRY,M.PELLECCHIA JRNL TITL DESIGN, SYNTHESIS, AND STRUCTURAL CHARACTERIZATION OF LYSINE JRNL TITL 2 COVALENT BH3 PEPTIDES TARGETING MCL-1. JRNL REF J.MED.CHEM. V. 64 4903 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 33797903 JRNL DOI 10.1021/ACS.JMEDCHEM.1C00005 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.OTWINOWSKI,W.MINOR REMARK 1 TITL PROCESSING OF X-RAY DIFFRACTION DATA COLLECTED IN REMARK 1 TITL 2 OSCILLATION MODE. REMARK 1 REF METH. ENZYMOL. V. 276 307 1997 REMARK 1 REFN ISSN 1557-7988 REMARK 1 PMID 27754618 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.J.MCCOY,R.W.GROSSE-KUNSTLEVE,P.D.ADAMS,M.D.WINN, REMARK 1 AUTH 2 L.C.STORONI,R.J.READ REMARK 1 TITL PHASER CRYSTALLOGRAPHIC SOFTWARE. REMARK 1 REF J APPL CRYSTALLOGR V. 40 658 2007 REMARK 1 REFN ISSN 0021-8898 REMARK 1 PMID 19461840 REMARK 1 DOI 10.1107/S0021889807021206 REMARK 1 REFERENCE 3 REMARK 1 AUTH A.A.VAGIN,R.A.STEINER,A.A.LEBEDEV,L.POTTERTON,S.MCNICHOLAS, REMARK 1 AUTH 2 F.LONG,G.N.MURSHUDOV REMARK 1 TITL REFMAC5 DICTIONARY: ORGANIZATION OF PRIOR CHEMICAL KNOWLEDGE REMARK 1 TITL 2 AND GUIDELINES FOR ITS USE. REMARK 1 REF ACTA CRYSTALLOGR. D BIOL. V. 60 2184 2004 REMARK 1 REF 2 CRYSTALLOGR. REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 15572771 REMARK 1 DOI 10.1107/S0907444904023510 REMARK 1 REFERENCE 4 REMARK 1 AUTH P.EMSLEY,K.COWTAN REMARK 1 TITL COOT: MODEL-BUILDING TOOLS FOR MOLECULAR GRAPHICS. REMARK 1 REF ACTA CRYSTALLOGR. D BIOL. V. 60 2126 2004 REMARK 1 REF 2 CRYSTALLOGR. REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 15572765 REMARK 1 DOI 10.1107/S0907444904019158 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 12721 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.252 REMARK 3 R VALUE (WORKING SET) : 0.250 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.720 REMARK 3 FREE R VALUE TEST SET COUNT : 601 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 3.1000 - 2.4600 1.00 3038 134 0.2693 0.3121 REMARK 3 2 2.4600 - 2.1500 0.99 2965 132 0.2735 0.3282 REMARK 3 3 2.1500 - 1.9500 1.00 2992 134 0.2742 0.3543 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.291 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.042 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.58 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 : 0.007 1273 REMARK 3 ANGLE : 0.807 1708 REMARK 3 CHIRALITY : 0.054 189 REMARK 3 PLANARITY : 0.004 217 REMARK 3 DIHEDRAL : 10.000 753 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 6VBX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1000246069. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.127 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12721 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 34.001 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.40 REMARK 200 R MERGE FOR SHELL (I) : 0.27600 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: 2NL9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5M POTASSIUM THIOCYANATE, 0.1M REMARK 280 SODIUM ACETATE:HCL PH4.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.22533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.61267 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.61267 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 65.22533 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 1460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 GLY A 168 REMARK 465 SER A 169 REMARK 465 HIS A 170 REMARK 465 MET A 171 REMARK 465 ASP A 172 REMARK 465 LYS A 194 REMARK 465 ASP A 195 REMARK 465 THR A 196 REMARK 465 LYS A 197 REMARK 465 PRO A 198 REMARK 465 MET A 199 REMARK 465 GLY A 200 REMARK 465 ARG A 201 REMARK 465 SER A 202 REMARK 465 GLU A 322 REMARK 465 ASP A 323 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue QX7 B 401 DBREF 6VBX A 172 323 UNP Q07820 MCL1_HUMAN 172 323 DBREF 6VBX B 401 12 PDB 6VBX 6VBX 401 12 SEQADV 6VBX GLY A 168 UNP Q07820 EXPRESSION TAG SEQADV 6VBX SER A 169 UNP Q07820 EXPRESSION TAG SEQADV 6VBX HIS A 170 UNP Q07820 EXPRESSION TAG SEQADV 6VBX MET A 171 UNP Q07820 EXPRESSION TAG SEQRES 1 A 156 GLY SER HIS MET ASP GLU LEU TYR ARG GLN SER LEU GLU SEQRES 2 A 156 ILE ILE SER ARG TYR LEU ARG GLU GLN ALA THR GLY ALA SEQRES 3 A 156 LYS ASP THR LYS PRO MET GLY ARG SER GLY ALA THR SER SEQRES 4 A 156 ARG LYS ALA LEU GLU THR LEU ARG ARG VAL GLY ASP GLY SEQRES 5 A 156 VAL GLN ARG ASN HIS GLU THR ALA PHE GLN GLY MET LEU SEQRES 6 A 156 ARG LYS LEU ASP ILE LYS ASN GLU ASP ASP VAL LYS SER SEQRES 7 A 156 LEU SER ARG VAL MET ILE HIS VAL PHE SER ASP GLY VAL SEQRES 8 A 156 THR ASN TRP GLY ARG ILE VAL THR LEU ILE SER PHE GLY SEQRES 9 A 156 ALA PHE VAL ALA LYS HIS LEU LYS THR ILE ASN GLN GLU SEQRES 10 A 156 SER CYS ILE GLU PRO LEU ALA GLU SER ILE THR ASP VAL SEQRES 11 A 156 LEU VAL ARG THR LYS ARG ASP TRP LEU VAL LYS GLN ARG SEQRES 12 A 156 GLY TRP ASP GLY PHE VAL GLU PHE PHE HIS VAL GLU ASP SEQRES 1 B 13 QX7 ILE ALA GLU GLN LEU ARG ARG ILE GLY ASP ARG PHE HET QX7 B 401 21 HETNAM QX7 N-ACETYL-3-{[5-(FLUOROSULFONYL)-2-METHYLBENZENE-1- HETNAM 2 QX7 CARBONYL]AMINO}-L-ALANINE FORMUL 2 QX7 C13 H15 F N2 O6 S FORMUL 3 HOH *44(H2 O) HELIX 1 AA1 GLU A 173 GLY A 192 1 20 HELIX 2 AA2 ALA A 204 HIS A 224 1 21 HELIX 3 AA3 HIS A 224 ASP A 236 1 13 HELIX 4 AA4 VAL A 243 SER A 255 1 13 HELIX 5 AA5 ASN A 260 ILE A 281 1 22 HELIX 6 AA6 GLN A 283 SER A 285 5 3 HELIX 7 AA7 CYS A 286 GLN A 309 1 24 HELIX 8 AA8 ARG A 310 PHE A 319 1 10 HELIX 9 AA9 ALA B 2 PHE B 12 1 11 LINK NZ LYS A 234 S15 QX7 B 401 1555 1555 1.63 LINK N ILE B 1 C QX7 B 401 1555 1555 1.43 SITE 1 AC1 6 LYS A 234 HIS A 252 ILE B 1 ALA B 2 SITE 2 AC1 6 GLU B 3 GLN B 4 CRYST1 54.607 54.607 97.838 90.00 90.00 120.00 P 32 2 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 0.018313 0.010573 0.000000 0.00000 SCALE2 0.000000 0.021146 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010221 0.00000