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Database: PDB
Entry: 6MBE
LinkDB: 6MBE
Original site: 6MBE 
HEADER    APOPTOSIS                               29-AUG-18   6MBE              
TITLE     HUMAN MCL-1 IN COMPLEX WITH THE DESIGNED PEPTIDE DM7                  
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: DM7;                                                       
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    ANTI-APOPTOTIC BCL-2, INHIBITOR, DESIGN, APOPTOSIS                    
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    J.M.JENSON,A.E.KEATING                                                
REVDAT   3   01-JAN-20 6MBE    1       REMARK                                   
REVDAT   2   10-APR-19 6MBE    1       JRNL                                     
REVDAT   1   06-MAR-19 6MBE    0                                                
JRNL        AUTH   V.FRAPPIER,J.M.JENSON,J.ZHOU,G.GRIGORYAN,A.E.KEATING         
JRNL        TITL   TERTIARY STRUCTURAL MOTIF SEQUENCE STATISTICS ENABLE FACILE  
JRNL        TITL 2 PREDICTION AND DESIGN OF PEPTIDES THAT BIND ANTI-APOPTOTIC   
JRNL        TITL 3 BFL-1 AND MCL-1.                                             
JRNL        REF    STRUCTURE                     V.  27   606 2019              
JRNL        REFN                   ISSN 1878-4186                               
JRNL        PMID   30773399                                                     
JRNL        DOI    10.1016/J.STR.2019.01.008                                    
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.25 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX 1.13_2998                                     
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 : NULL                                          
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 29.94                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.340                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 97.4                           
REMARK   3   NUMBER OF REFLECTIONS             : 10414                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.195                           
REMARK   3   R VALUE            (WORKING SET) : 0.192                           
REMARK   3   FREE R VALUE                     : 0.221                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.090                          
REMARK   3   FREE R VALUE TEST SET COUNT      : 1051                            
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 29.9430 -  4.4899    1.00     1266   146  0.1652 0.1879        
REMARK   3     2  4.4899 -  3.5656    1.00     1217   130  0.1663 0.2160        
REMARK   3     3  3.5656 -  3.1154    1.00     1196   137  0.2088 0.2221        
REMARK   3     4  3.1154 -  2.8308    1.00     1204   134  0.2189 0.2625        
REMARK   3     5  2.8308 -  2.6281    1.00     1177   130  0.2199 0.2590        
REMARK   3     6  2.6281 -  2.4732    1.00     1210   135  0.2198 0.2248        
REMARK   3     7  2.4732 -  2.3494    0.97     1136   128  0.2314 0.2550        
REMARK   3     8  2.3494 -  2.2471    0.82      957   111  0.2493 0.2586        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : NULL                                          
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)     : 0.230            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.250           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 39.34                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 54.34                          
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      :   NULL           NULL                                  
REMARK   3   ANGLE     :   NULL           NULL                                  
REMARK   3   CHIRALITY :   NULL           NULL                                  
REMARK   3   PLANARITY :   NULL           NULL                                  
REMARK   3   DIHEDRAL  :   NULL           NULL                                  
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 6MBE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-18.                  
REMARK 100 THE DEPOSITION ID IS D_1000236554.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 12-JAN-18                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : NULL                               
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : N                                  
REMARK 200  RADIATION SOURCE               : ROTATING ANODE                     
REMARK 200  BEAMLINE                       : NULL                               
REMARK 200  X-RAY GENERATOR MODEL          : OTHER                              
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.54                               
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU SATURN 944                  
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000                           
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000                           
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 10429                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.250                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 97.3                               
REMARK 200  DATA REDUNDANCY                : 17.60                              
REMARK 200  R MERGE                    (I) : 0.13700                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 5.0000                             
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.29                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 73.8                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 3.00                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.60400                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> 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: 3PK1                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 54.53                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M SODIUM CITRATE PH 6.5, 0.1 M       
REMARK 280  HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K       
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       38.63333            
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       19.31667            
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       19.31667            
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       38.63333            
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: 1950 ANGSTROM**2                          
REMARK 350 SURFACE AREA OF THE COMPLEX: 9090 ANGSTROM**2                        
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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     ACE B     0                                                      
REMARK 465     NH2 B    23                                                      
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 401                  
DBREF  6MBE A  172   323  UNP    Q07820   MCL1_HUMAN     172    323             
DBREF  6MBE B    0    23  PDB    6MBE     6MBE             0     23             
SEQADV 6MBE GLY A  170  UNP  Q07820              EXPRESSION TAG                 
SEQADV 6MBE SER A  171  UNP  Q07820              EXPRESSION TAG                 
SEQRES   1 A  154  GLY SER ASP GLU LEU TYR ARG GLN SER LEU GLU ILE ILE          
SEQRES   2 A  154  SER ARG TYR LEU ARG GLU GLN ALA THR GLY ALA LYS ASP          
SEQRES   3 A  154  THR LYS PRO MET GLY ARG SER GLY ALA THR SER ARG LYS          
SEQRES   4 A  154  ALA LEU GLU THR LEU ARG ARG VAL GLY ASP GLY VAL GLN          
SEQRES   5 A  154  ARG ASN HIS GLU THR ALA PHE GLN GLY MET LEU ARG LYS          
SEQRES   6 A  154  LEU ASP ILE LYS ASN GLU ASP ASP VAL LYS SER LEU SER          
SEQRES   7 A  154  ARG VAL MET ILE HIS VAL PHE SER ASP GLY VAL THR ASN          
SEQRES   8 A  154  TRP GLY ARG ILE VAL THR LEU ILE SER PHE GLY ALA PHE          
SEQRES   9 A  154  VAL ALA LYS HIS LEU LYS THR ILE ASN GLN GLU SER CYS          
SEQRES  10 A  154  ILE GLU PRO LEU ALA GLU SER ILE THR ASP VAL LEU VAL          
SEQRES  11 A  154  ARG THR LYS ARG ASP TRP LEU VAL LYS GLN ARG GLY TRP          
SEQRES  12 A  154  ASP GLY PHE VAL GLU PHE PHE HIS VAL GLU ASP                  
SEQRES   1 B   24  ACE ASP LYS THR LEU GLU GLU ILE ALA ARG GLU LEU LEU          
SEQRES   2 B   24  LYS LEU ALA LEU GLU ILE ASP LYS GLU ILE NH2                  
HET     CL  A 401       1                                                       
HETNAM      CL CHLORIDE ION                                                     
FORMUL   3   CL    CL 1-                                                        
FORMUL   4  HOH   *47(H2 O)                                                     
HELIX    1 AA1 ASP A  172  GLY A  192  1                                  21    
HELIX    2 AA2 SER A  202  HIS A  224  1                                  23    
HELIX    3 AA3 HIS A  224  ASP A  236  1                                  13    
HELIX    4 AA4 ASN A  239  SER A  245  1                                   7    
HELIX    5 AA5 LEU A  246  ILE A  251  1                                   6    
HELIX    6 AA6 HIS A  252  SER A  255  5                                   4    
HELIX    7 AA7 ASN A  260  ILE A  281  1                                  22    
HELIX    8 AA8 ASN A  282  SER A  285  5                                   4    
HELIX    9 AA9 CYS A  286  GLN A  309  1                                  24    
HELIX   10 AB1 ARG A  310  PHE A  319  1                                  10    
HELIX   11 AB2 LYS B    2  LYS B   20  1                                  19    
SITE     1 AC1  4 PRO A 198  MET A 199  ARG A 207  PHE A 318                    
CRYST1   80.758   80.758   57.950  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      0.012383  0.007149  0.000000        0.00000                         
SCALE2      0.000000  0.014298  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.017256        0.00000                         
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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