PDB Short entry for 1M1I
HEADER    HYDROLASE                               19-JUN-02   1M1I              
TITLE     ADAM-10 COMPLEXED WITH A HYPOTHETICAL SUBSTRATE                       
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: ADAM 10;                                                   
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: CATALYTIC DOMAIN;                                          
COMPND   5 SYNONYM: A DISINTEGRIN AND METALLOPROTEINASE DOMAIN 10;              
COMPND   6 ADAM-10;                                                             
COMPND   7 EC: 3.4.24.-;                                                        
COMPND   8 MOL_ID: 2;                                                           
COMPND   9 MOLECULE: EMPIRICAL SUBSTRATE LAGAVMSS;                              
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 MOL_ID: 2;                                                           
SOURCE   5 SYNTHETIC: YES                                                       
KEYWDS    ADAM-10, NATURAL SUBSTRATE, MOLECULAR SIMULATIONS                     
EXPDTA    THEORETICAL MODEL                                                     
AUTHOR    S.MANZETTI,D.R.MCCULLOCH,A.C.HERINGTON                                
REVDAT   2   05-APR-05 1M1I    1       JRNL   REMARK                            
REVDAT   1   05-JUL-02 1M1I    0                                                
JRNL        AUTH   S.MANZETTI,D.R.MCCULLOCH,A.C.HERINGTON,                      
JRNL        AUTH 2 D.VAN DER SPOEL                                              
JRNL        TITL   MODELING OF ENZYME-SUBSTRATE COMPLEXES FOR THE               
JRNL        TITL 2 METALLOPROTEASES MMP-3, ADAM-9 AND ADAM-10                   
JRNL        REF    COMPUT.AIDED DES.             V.  17   551 2003              
JRNL        REFN   ASTM CAIDA5  UK ISSN 0010-4485                               
REMARK   1                                                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : NULL                                                 
REMARK   3   AUTHORS     : NULL                                                 
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1M1I COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998                       
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PRAGUE ON 27-JUN-2002.              
REMARK 100 THE RCSB ID CODE IS RCSB016481.                                      
REMARK 220                                                                      
REMARK 220 EXPERIMENTAL DETAILS                                                 
REMARK 220  EXPERIMENT TYPE                : THEORETICAL MODELLING              
REMARK 220                                                                      
REMARK 220 REMARK: ADAM-10 IN COMPLEX WITH ITS RESPECTIVE SUBSTRATE WAS         
REMARK 220         CONFINED IN A VIRTUAL 125NM3-BOX FILLED WITH ~3200 WATER     
REMARK 220         MOLECULES AND MINIMIZED WITH THE SOLVENT WITH 100 STEPS      
REMARK 220         (SD). THE SIMULATION WAS CARRIED OUT AT 300K IN A 2NS-       
REMARK 220         INTERVAL WITH A TIME-STEP OF 2FS USING THE GROMOS96 43A2     
REMARK 220         DEVELOPMENT FORCE FIELD IN THE GROMACS 3.1.1 PACKAGE.        
REMARK 220         SINGLE POINT CHARGE (SPC) WATER MOLECULES WERE USED. THE     
REMARK 220         POSITIONS OF THE WATER MOLECULES WAS OPTIMISED WITH A        
REMARK 220         100-STEP SD MINIMIZATION ALL WATER MOLECULES WERE            
REMARK 220         CONSTRAINED USING THE SETTLE ALGORITHM . ALL N- AND C-       
REMARK 220         TERMINI WERE ASSIGNED A NEUTRAL STATE AND THE ZN2+-          
REMARK 220         CHELATING HISTIDINE RESIDUES WERE PROTONATED AT THE &#       
REMARK 220         948;-NITROGEN, AS OBSERVED IN CRYSTAL STRUCTURES OF          
REMARK 220         MMPS. DISTANCE RESTRAINTS WERE APPLIED FOR ZN2+- IONS        
REMARK 220         WITH ITS RESPECTIVE CHELATING ATOMS: ZN2+-εN: 2-2.1     
REMARK 220         . BOND WERE SIMULATED USING THE LINCS ALGORITHM.             
REMARK 220         ENERGIES WERE COMPUTED ONCE PER PICOSECOND BY AVERAGING      
REMARK 220         OVER 100FS INTERVALS, AND TEMPERATURE COUPLING WAS           
REMARK 220         SIMULATED USING THE BERENDSEN SCHEME . SHORT- AND LONG-      
REMARK 220         RANGE ELECTROSTATICS WERE SIMULATED USING PARTICLE-MESH      
REMARK 220         EWALD METHOD WITH A DISTANCE TO NEIGHBOURS: OF 1NM; A        
REMARK 220         VAN DER WAAL CUT-OFF OF 1NM; AN ELECTROSTATIC CUT-OFF OF     
REMARK 220         1NM AND A DIELECTRIC CONSTANT OF 1.                          
REMARK 225                                                                      
REMARK 225 THEORETICAL MODEL                                                    
REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE.           
REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND                
REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE                   
REMARK 225 RECORDS ARE MEANINGLESS.                                             
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   1 GLU A    -9                                                      
REMARK 465   1 LEU A    -8                                                      
REMARK 465   1 LEU A    -7                                                      
REMARK 465   1 ARG A    -6                                                      
REMARK 465   1 LYS A    -5                                                      
REMARK 465   1 LYS A    -4                                                      
REMARK 465   1 ARG A    -3                                                      
REMARK 465   1 THR A    -2                                                      
REMARK 465   1 THR A    -1                                                      
REMARK 465   1 SER A     0                                                      
REMARK 465   1 ALA A     1                                                      
REMARK 465   2 GLU A    -9                                                      
REMARK 465   2 LEU A    -8                                                      
REMARK 465   2 LEU A    -7                                                      
REMARK 465   2 ARG A    -6                                                      
REMARK 465   2 LYS A    -5                                                      
REMARK 465   2 LYS A    -4                                                      
REMARK 465   2 ARG A    -3                                                      
REMARK 465   2 THR A    -2                                                      
REMARK 465   2 THR A    -1                                                      
REMARK 465   2 SER A     0                                                      
REMARK 465   2 ALA A     1                                                      
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS                                             
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.                            
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI                             
REMARK 500   O    VAL A   117     O    HIS A   171              1.68            
REMARK 500   O    GLY A   110     N    SER B   245              2.03            
REMARK 500   OE1  GLU A   168     O    GLY B   241              2.16            
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS                                      
REMARK 500                                                                      
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),F6.3)                  
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991                                
REMARK 500                                                                      
REMARK 500  M RES CSSEQI ATM1   RES CSSEQI ATM2   DEVIATION                     
REMARK 500  1 TRP A 116   CG    TRP A 116   CD2   -0.207                        
REMARK 500  1 TRP A 116   CD1   TRP A 116   NE1   -0.117                        
REMARK 500  1 TRP A 116   NE1   TRP A 116   CE2    0.107                        
REMARK 500  1 TRP A 116   CE2   TRP A 116   CZ2   -0.232                        
REMARK 500  1 TRP A 116   CD2   TRP A 116   CE3    0.115                        
REMARK 500  1 TRP A 116   CE3   TRP A 116   CZ3   -0.118                        
REMARK 500  1 TRP A 116   CH2   TRP A 116   CZ2    0.143                        
REMARK 500  1 TRP A 116   C     VAL A 117   N     -0.110                        
REMARK 500  1 VAL A 117   C     GLY A 118   N     -0.519                        
REMARK 500  1 GLU A 129   C     LYS A 130   N     -0.114                        
REMARK 500  2 VAL A 237   C     VAL A 237   O      0.133                        
REMARK 500  2 SER B 246   C     SER B 246   O      0.126                        
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES                                       
REMARK 500                                                                      
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)              
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991                                
REMARK 500                                                                      
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3                                     
REMARK 500  1 TRP A 116   CA  -  C   -  N   ANGL. DEV. = 40.0 DEGREES           
REMARK 500  1 TRP A 116   O   -  C   -  N   ANGL. DEV. =-39.7 DEGREES           
REMARK 500  1 VAL A 117   CA  -  C   -  N   ANGL. DEV. = 60.0 DEGREES           
REMARK 500  1 VAL A 117   O   -  C   -  N   ANGL. DEV. =-59.7 DEGREES           
REMARK 500  1 GLY A 118   C   -  N   -  CA  ANGL. DEV. = 24.6 DEGREES           
REMARK 500  1 LEU A 142   CB  -  CG  -  CD2 ANGL. DEV. =-29.8 DEGREES           
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  M RES CSSEQI        PSI       PHI                                   
REMARK 500  1 ILE A  49       91.54    120.72                                   
REMARK 500  1 CYS A  97      -51.40    132.70                                   
REMARK 500  1 VAL A 117     -140.95    119.58                                   
REMARK 500  1 SER A 123      172.71     92.04                                   
REMARK 500  1 ASN A 143     -119.05    167.92                                   
REMARK 500  2 ASN A  78      -65.15     47.21                                   
REMARK 500  2 ASP A 109     -110.94      5.48                                   
REMARK 500  2 SER A 207      -62.09     73.16                                   
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS                                         
REMARK 500                                                                      
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH          
REMARK 500 CIS AND TRANS CONFORMATION.  CIS BONDS, IF ANY, ARE LISTED           
REMARK 500 ON CISPEP RECORDS.  TRANS IS DEFINED AS 180 +/- 30 AND               
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.                                  
REMARK 500                                 MODEL     OMEGA                      
REMARK 500 GLU A   24    ALA A   25          1      -115.19                     
REMARK 500 ILE A   79    GLY A   80          1      -141.28                     
REMARK 500 TRP A  116    VAL A  117          1       108.20                     
REMARK 500 THR A  181    GLU A  182          1        50.57                     
REMARK 500 LYS A  194    GLU A  195          1        68.37                     
REMARK 500 LEU B  239    ALA B  240          1        36.70                     
REMARK 500 ALA B  240    GLY B  241          1       143.83                     
REMARK 500 GLY B  241    ALA B  242          1      -110.92                     
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 1KNH   RELATED DB: PDB                                   
REMARK 900 ADAM-9 COMPLEXED WITH A HYPOTHETICAL SUBSTRATE                       
REMARK 900 RELATED ID: 1KN8   RELATED DB: PDB                                   
REMARK 900 MMP-3 COMPLEXED WITH A HYPOTHETICAL SUBSTRATE                        
DBREF  1M1I A   -9   237  GB     2393947  AAC51766       207    453             
SEQRES   1 A  247  GLU LEU LEU ARG LYS LYS ARG THR THR SER ALA GLU LYS          
SEQRES   2 A  247  ASN THR CYS GLN LEU TYR ILE GLN THR ASP HIS LEU PHE          
SEQRES   3 A  247  PHE LYS TYR TYR GLY THR ARG GLU ALA VAL ILE ALA GLN          
SEQRES   4 A  247  ILE SER SER HIS VAL LYS ALA ILE ASP THR ILE TYR GLN          
SEQRES   5 A  247  THR THR ASP PHE SER GLY ILE ARG ASN ILE SER PHE MET          
SEQRES   6 A  247  VAL LYS ARG ILE ARG ILE ASN THR THR ALA ASP GLU LYS          
SEQRES   7 A  247  ASP PRO THR ASN PRO PHE ARG PHE PRO ASN ILE GLY VAL          
SEQRES   8 A  247  GLU LYS PHE LEU GLU LEU ASN SER GLU GLN ASN HIS ASP          
SEQRES   9 A  247  ASP TYR CYS LEU ALA TYR VAL PHE THR ASP ARG ASP PHE          
SEQRES  10 A  247  ASP ASP GLY VAL LEU GLY LEU ALA TRP VAL GLY ALA PRO          
SEQRES  11 A  247  SER GLY SER SER GLY GLY ILE CYS GLU LYS SER LYS LEU          
SEQRES  12 A  247  TYR SER ASP GLY LYS LYS LYS SER LEU ASN THR GLY ILE          
SEQRES  13 A  247  ILE THR VAL GLN ASN TYR GLY SER HIS VAL PRO PRO LYS          
SEQRES  14 A  247  VAL SER HIS ILE THR PHE ALA HIS GLU VAL GLY HIS ASN          
SEQRES  15 A  247  PHE GLY SER PRO HIS ASP SER GLY THR GLU CYS THR PRO          
SEQRES  16 A  247  GLY GLU SER LYS ASN LEU GLY GLN LYS GLU ASN GLY ASN          
SEQRES  17 A  247  TYR ILE MET TYR ALA ARG ALA THR SER GLY ASP LYS LEU          
SEQRES  18 A  247  ASN ASN ASN LYS PHE SER LEU CYS SER ILE ARG ASN ILE          
SEQRES  19 A  247  SER GLN VAL LEU GLU LYS LYS ARG ASN ASN CYS PHE VAL          
SEQRES   1 B    8  LEU ALA GLY ALA VAL MET SER SER                              
HET     ZN  A   1       1                                                       
HETNAM      ZN ZINC ION                                                         
FORMUL   3   ZN    ZN 2+                                                        
HELIX    1   1 ASP A   13  LYS A   18  1                                   6    
HELIX    2   2 ALA A   25  THR A   44  1                                  20    
HELIX    3   3 GLY A   80  ASN A   92  1                                  13    
HELIX    4   4 PHE A  107  ASP A  109  5                                   3    
HELIX    5   5 PRO A  157  PHE A  173  1                                  17    
HELIX    6   6 LYS A  210  LYS A  215  5                                   6    
HELIX    7   7 SER A  217  PHE A  236  1                                  20    
SHEET    1   A 6 SER A  53  ILE A  61  0                                        
SHEET    2   A 6 THR A   5  THR A  12  1  N  LEU A   8   O  LYS A  57           
SHEET    3   A 6 CYS A  97  THR A 103  1  O  PHE A 102   N  GLN A  11           
SHEET    4   A 6 GLY A 145  THR A 148  1  O  ILE A 147   N  THR A 103           
SHEET    5   A 6 VAL A 111  ALA A 115 -1  N  LEU A 114   O  ILE A 146           
SHEET    6   A 6 GLY B 241  MET B 244 -1  O  GLY B 241   N  ALA A 115           
SHEET    1   B 2 LYS A 132  TYR A 134  0                                        
SHEET    2   B 2 LYS A 139  SER A 141 -1  O  LYS A 139   N  TYR A 134           
SHEET    1   C 2 GLN A 150  ASN A 151  0                                        
SHEET    2   C 2 SER A 154  HIS A 155 -1  O  SER A 154   N  ASN A 151           
SSBOND   1 CYS A    6    CYS A   97                                             
SSBOND   2 CYS A  128    CYS A  235                                             
SSBOND   3 CYS A  183    CYS A  219                                             
CISPEP   1 GLY A   48    ILE A   49          1        -0.99                     
CISPEP   2 VAL A  117    GLY A  118          1         2.15                     
CISPEP   3 GLY A  122    SER A  123          1        -8.59                     
CISPEP   4 ASN A  143    THR A  144          1        -5.87                     
CISPEP   5 GLY A   48    ILE A   49          2        16.40                     
CISPEP   6 VAL A  117    GLY A  118          2       -12.04                     
CISPEP   7 GLY A  122    SER A  123          2         0.86                     
CISPEP   8 ASN A  143    THR A  144          2       -20.15                     
CISPEP   9 THR A  181    GLU A  182          2         2.96                     
CISPEP  10 LYS A  194    GLU A  195          2        -2.62                     
CISPEP  11 LEU B  239    ALA B  240          2        10.49                     
CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1          
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      1.000000  0.000000  0.000000        0.00000                         
SCALE2      0.000000  1.000000  0.000000        0.00000                         
SCALE3      0.000000  0.000000  1.000000        0.00000