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Database: PDB
Entry: 1F8Z
LinkDB: 1F8Z
Original site: 1F8Z 
HEADER    LIPID BINDING PROTEIN                   05-JUL-00   1F8Z              
TITLE     NMR STRUCTURE OF THE SIXTH LIGAND-BINDING MODULE OF THE LDL           
TITLE    2 RECEPTOR                                                             
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: LOW-DENSITY LIPOPROTEIN RECEPTOR;                          
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: SIXTH LIGAND-BINDING MODULE;                               
COMPND   5 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES;                                                      
SOURCE   3 OTHER_DETAILS: PEPTIDE SYNTHESIS - BASED ON THE HUMAN                
SOURCE   4 SEQUENCE                                                             
KEYWDS    LDL RECEPTOR, LIGAND-BINDING DOMAIN, CALCIUM-BINDING,                 
KEYWDS   2 FAMILIAL HYPERCHOLESTEROLEMIA, LIPID BINDING PROTEIN                 
EXPDTA    SOLUTION NMR                                                          
NUMMDL    20                                                                    
AUTHOR    D.J.CLAYTON,I.M.BRERETON,P.A.KROON,R.SMITH                            
REVDAT   3   24-FEB-09 1F8Z    1       VERSN                                    
REVDAT   2   01-APR-03 1F8Z    1       JRNL                                     
REVDAT   1   18-OCT-00 1F8Z    0                                                
JRNL        AUTH   D.CLAYTON,I.M.BRERETON,P.A.KROON,R.SMITH                     
JRNL        TITL   THREE-DIMENSIONAL NMR STRUCTURE OF THE SIXTH                 
JRNL        TITL 2 LIGAND-BINDING MODULE OF THE HUMAN LDL RECEPTOR:             
JRNL        TITL 3 COMPARISON OF TWO ADJACENT MODULES WITH DIFFERENT            
JRNL        TITL 4 LIGAND BINDING SPECIFICITIES.                                
JRNL        REF    FEBS LETT.                    V. 479   118 2000              
JRNL        REFN                   ISSN 0014-5793                               
JRNL        PMID   10981718                                                     
JRNL        DOI    10.1016/S0014-5793(00)01842-1                                
REMARK   1                                                                      
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR 3.1                                           
REMARK   3   AUTHORS     : AXEL BRUNGER                                         
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON 552 DISTANCE      
REMARK   3  CONSTRAINTS, 18 BACKBONE ANGLE RESTRAINTS AND 14 SIDECHAIN          
REMARK   3  ANGLE RESTRAINTS                                                    
REMARK   4                                                                      
REMARK   4 1F8Z COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-00.                  
REMARK 100 THE RCSB ID CODE IS RCSB011390.                                      
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 298                                
REMARK 210  PH                             : 5.50                               
REMARK 210  IONIC STRENGTH                 : 10 MM                              
REMARK 210  PRESSURE                       : 1 ATM                              
REMARK 210  SAMPLE CONTENTS                : 3 MM LB6, 10 MM CACL2, 1 MM        
REMARK 210  3,3,3-TRIMETHYLSILYLPROPIONATE; 3 MM LB6, 10 MM CACL2, 1 MM 3,      
REMARK 210  3,3-TRIMETHYLSILYLPROPIONATE                                        
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D NOESY, DQF-COSY, E-COSY         
REMARK 210  SPECTROMETER FIELD STRENGTH    : 750 MHZ                            
REMARK 210  SPECTROMETER MODEL             : DMX                                
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : XWINNMR, AURELIA, XEASY,           
REMARK 210                                   DYANA 1.5, X-PLOR 3.1              
REMARK 210   METHOD USED                   : STRUCTURE DETERMINATION BY         
REMARK 210                                   TORSION ANGLE DYNAMICS,            
REMARK 210                                   MOLECULAR DYNAMICS                 
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 50                                 
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 20                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LEAST          
REMARK 210                                   RESTRAINT VIOLATIONS,              
REMARK 210                                   STRUCTURES WITH THE LOWEST         
REMARK 210                                   ENERGY                             
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL                
REMARK 210                                                                      
REMARK 210 REMARK: NULL                                                         
REMARK 215                                                                      
REMARK 215 NMR STUDY                                                            
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION           
REMARK 215 NMR DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT                
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON              
REMARK 215 THESE RECORDS ARE MEANINGLESS.                                       
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 PROTEIN: ENGH AND HUBER, 1999                        
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996                     
REMARK 500                                                                      
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3                                     
REMARK 500  1 CYS A  15   CA  -  CB  -  SG  ANGL. DEV. =   6.7 DEGREES          
REMARK 500  1 CYS A  22   CA  -  CB  -  SG  ANGL. DEV. =   7.7 DEGREES          
REMARK 500  2 CYS A  22   CA  -  CB  -  SG  ANGL. DEV. =   7.8 DEGREES          
REMARK 500  3 CYS A  15   CA  -  CB  -  SG  ANGL. DEV. =   6.8 DEGREES          
REMARK 500  3 CYS A  22   CA  -  CB  -  SG  ANGL. DEV. =   7.2 DEGREES          
REMARK 500  4 CYS A  22   CA  -  CB  -  SG  ANGL. DEV. =   6.8 DEGREES          
REMARK 500  6 ARG A  20   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.0 DEGREES          
REMARK 500  7 CYS A  22   CA  -  CB  -  SG  ANGL. DEV. =   7.8 DEGREES          
REMARK 500  8 CYS A  22   CA  -  CB  -  SG  ANGL. DEV. =   7.5 DEGREES          
REMARK 500  9 CYS A  22   CA  -  CB  -  SG  ANGL. DEV. =   7.3 DEGREES          
REMARK 500 11 CYS A  22   CA  -  CB  -  SG  ANGL. DEV. =   7.5 DEGREES          
REMARK 500 12 CYS A  22   CA  -  CB  -  SG  ANGL. DEV. =   7.3 DEGREES          
REMARK 500 13 CYS A  15   CA  -  CB  -  SG  ANGL. DEV. =   7.0 DEGREES          
REMARK 500 13 CYS A  22   CA  -  CB  -  SG  ANGL. DEV. =   6.9 DEGREES          
REMARK 500 14 CYS A  22   CA  -  CB  -  SG  ANGL. DEV. =   7.8 DEGREES          
REMARK 500 15 CYS A  15   CA  -  CB  -  SG  ANGL. DEV. =   7.2 DEGREES          
REMARK 500 15 CYS A  22   CA  -  CB  -  SG  ANGL. DEV. =   8.3 DEGREES          
REMARK 500 16 CYS A  22   CA  -  CB  -  SG  ANGL. DEV. =   7.4 DEGREES          
REMARK 500 17 CYS A  22   CA  -  CB  -  SG  ANGL. DEV. =   8.3 DEGREES          
REMARK 500 18 CYS A  22   CA  -  CB  -  SG  ANGL. DEV. =   7.7 DEGREES          
REMARK 500 19 CYS A  15   CA  -  CB  -  SG  ANGL. DEV. =   6.7 DEGREES          
REMARK 500 19 CYS A  22   CA  -  CB  -  SG  ANGL. DEV. =   7.3 DEGREES          
REMARK 500 20 CYS A  22   CA  -  CB  -  SG  ANGL. DEV. =   7.7 DEGREES          
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
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  1 ASP A  23        3.39   -150.33                                   
REMARK 500  1 GLU A  25       38.03    -92.60                                   
REMARK 500  1 TYR A  26       75.85     -2.20                                   
REMARK 500  1 MET A  31       17.15     56.81                                   
REMARK 500  2 CYS A  22       63.86     68.06                                   
REMARK 500  2 ASP A  23        9.97   -150.42                                   
REMARK 500  2 ARG A  24       28.23     43.10                                   
REMARK 500  2 GLU A  25       41.38   -101.65                                   
REMARK 500  2 TYR A  26       80.39      1.07                                   
REMARK 500  2 MET A  31       17.41     55.80                                   
REMARK 500  3 ASP A  23        3.64   -150.61                                   
REMARK 500  3 GLU A  25       39.82    -93.95                                   
REMARK 500  3 TYR A  26       79.06     -3.96                                   
REMARK 500  3 MET A  31       11.17     51.23                                   
REMARK 500  4 ASP A  23       -5.07   -141.70                                   
REMARK 500  4 GLU A  25       44.71    -98.48                                   
REMARK 500  4 TYR A  26       82.95     -2.60                                   
REMARK 500  4 MET A  31       16.46     46.11                                   
REMARK 500  5 CYS A  22       65.00     67.67                                   
REMARK 500  5 ASP A  23        1.11   -150.48                                   
REMARK 500  5 GLU A  25       40.48    -89.99                                   
REMARK 500  5 TYR A  26       76.31      1.40                                   
REMARK 500  5 MET A  31       12.54     57.51                                   
REMARK 500  5 VAL A  38       46.80   -102.93                                   
REMARK 500  6 ASP A  23        2.49   -150.18                                   
REMARK 500  6 GLU A  25       43.65    -98.37                                   
REMARK 500  6 TYR A  26       83.97     -3.66                                   
REMARK 500  6 MET A  31       14.48     53.72                                   
REMARK 500  6 CYS A  37      -75.50    -52.57                                   
REMARK 500  7 ASP A  23        6.44   -150.45                                   
REMARK 500  7 ARG A  24       29.96     48.95                                   
REMARK 500  7 GLU A  25       41.92    -92.29                                   
REMARK 500  7 TYR A  26       79.79     -5.74                                   
REMARK 500  7 MET A  31       15.90     59.42                                   
REMARK 500  8 ASP A  23        6.64   -150.60                                   
REMARK 500  8 GLU A  25       41.76    -92.12                                   
REMARK 500  8 TYR A  26       76.96     -6.52                                   
REMARK 500  8 MET A  31       13.40     54.65                                   
REMARK 500  8 VAL A  38       43.16    -95.19                                   
REMARK 500  9 ASP A  23        9.32   -150.43                                   
REMARK 500  9 GLU A  25       45.38    -97.83                                   
REMARK 500  9 TYR A  26       85.73    -11.39                                   
REMARK 500  9 MET A  31       15.65     52.17                                   
REMARK 500 10 ASP A  23       12.17   -150.56                                   
REMARK 500 10 ARG A  24       33.62     39.90                                   
REMARK 500 10 GLU A  25       40.15    -96.73                                   
REMARK 500 10 TYR A  26       76.82      1.36                                   
REMARK 500 10 CYS A  37      -73.42    -68.87                                   
REMARK 500 11 CYS A  22       61.59     63.48                                   
REMARK 500 11 ASP A  23       -0.20   -143.53                                   
REMARK 500 11 ARG A  24       26.95     45.09                                   
REMARK 500 11 GLU A  25       46.36   -100.53                                   
REMARK 500 11 TYR A  26       76.68      4.29                                   
REMARK 500 11 MET A  31       13.17     58.40                                   
REMARK 500 12 ASP A  23        3.58   -150.64                                   
REMARK 500 12 GLU A  25       39.62    -92.16                                   
REMARK 500 12 TYR A  26       76.68     -2.35                                   
REMARK 500 12 MET A  31       16.26     54.76                                   
REMARK 500 13 ASP A  23        6.45   -150.37                                   
REMARK 500 13 GLU A  25       40.16    -94.34                                   
REMARK 500 13 TYR A  26       77.92     -3.44                                   
REMARK 500 13 MET A  31       13.28     57.21                                   
REMARK 500 14 CYS A  22       60.04     65.18                                   
REMARK 500 14 ASP A  23        8.03   -150.28                                   
REMARK 500 14 ARG A  24       29.93     44.39                                   
REMARK 500 14 GLU A  25       42.91    -94.76                                   
REMARK 500 14 TYR A  26       78.90     -2.94                                   
REMARK 500 14 MET A  31       13.62     55.99                                   
REMARK 500 15 CYS A  22       60.85     67.70                                   
REMARK 500 15 ASP A  23       -5.38   -142.34                                   
REMARK 500 15 GLU A  25       41.58    -99.93                                   
REMARK 500 15 TYR A  26       70.78      9.76                                   
REMARK 500 15 CYS A  37      -74.32    -77.36                                   
REMARK 500 15 VAL A  38       45.94   -101.35                                   
REMARK 500 16 ASP A  23        2.85   -150.52                                   
REMARK 500 16 GLU A  25       42.76    -94.19                                   
REMARK 500 16 TYR A  26       82.72     -6.25                                   
REMARK 500 16 MET A  31       13.45     51.23                                   
REMARK 500 17 CYS A  22       60.08     65.39                                   
REMARK 500 17 ASP A  23       -4.39   -147.49                                   
REMARK 500 17 GLU A  25       36.00    -96.77                                   
REMARK 500 17 TYR A  26       73.87      5.84                                   
REMARK 500 17 MET A  31       14.72     59.13                                   
REMARK 500 17 CYS A  37      -71.94    -59.53                                   
REMARK 500 17 VAL A  38       43.35    -96.40                                   
REMARK 500 18 ASP A  23        5.47   -150.39                                   
REMARK 500 18 GLU A  25       41.45    -93.98                                   
REMARK 500 18 TYR A  26       77.35     -5.40                                   
REMARK 500 18 MET A  31       15.89     55.44                                   
REMARK 500 19 ASP A  23        4.65   -150.36                                   
REMARK 500 19 GLU A  25       39.35    -93.93                                   
REMARK 500 19 TYR A  26       76.89      0.35                                   
REMARK 500 19 MET A  31       14.36     56.49                                   
REMARK 500 20 GLU A  25       44.69    -98.49                                   
REMARK 500 20 TYR A  26       80.12    -11.66                                   
REMARK 500 20 MET A  31        6.67     57.42                                   
REMARK 500 20 CYS A  37      -70.49    -69.01                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 620                                                                      
REMARK 620 METAL COORDINATION                                                   
REMARK 620  (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;              
REMARK 620  SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                            
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                           1  CA A  40  CA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1 ARG A  20   O                                                      
REMARK 620 2 ASP A  33   OD2  87.2                                              
REMARK 620 3 TYR A  26   N   179.5  93.3                                        
REMARK 620 4 ASP A  27   OD2  62.9  65.0 117.3                                  
REMARK 620 5 GLU A  25   O   138.9 101.2  41.0  84.2                            
REMARK 620 6 GLU A  34   OE2  70.2  82.1 109.8 122.7 150.4                      
REMARK 620 7 ASP A  23   OD1  61.5 140.9 118.0 113.1 117.7  66.2                
REMARK 620 8 GLU A  25   N   129.9 134.6  49.7 148.8  69.3  87.3  68.5          
REMARK 620 N                    1     2     3     4     5     6     7           
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 40                   
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 1LDL   RELATED DB: PDB                                   
REMARK 900 1LDL CONTAINS THE FIRST LIGAND-BINDING MODULE OF THE LDL             
REMARK 900 RECEPTOR                                                             
REMARK 900 RELATED ID: 1LDR   RELATED DB: PDB                                   
REMARK 900 1LDR CONTAINS THE SECOND LIGAND-BINDING MODULE OF THE LDL            
REMARK 900 RECEPTOR                                                             
DBREF  1F8Z A    1    39  UNP    P01130   LDLR_HUMAN     234    272             
SEQRES   1 A   39  ALA THR CYS ARG PRO ASP GLU PHE GLN CYS SER ASP GLY          
SEQRES   2 A   39  ASN CYS ILE HIS GLY SER ARG GLN CYS ASP ARG GLU TYR          
SEQRES   3 A   39  ASP CYS LYS ASP MET SER ASP GLU VAL GLY CYS VAL ASN          
HET     CA  A  40       1                                                       
HETNAM      CA CALCIUM ION                                                      
FORMUL   2   CA    CA 2+                                                        
HELIX    1   1 MET A   31  VAL A   35  5                                   5    
SHEET    1   A 2 GLU A   7  GLN A   9  0                                        
SHEET    2   A 2 CYS A  15  HIS A  17 -1  O  ILE A  16   N  PHE A   8           
SSBOND   1 CYS A    3    CYS A   15                          1555   1555  2.02  
SSBOND   2 CYS A   10    CYS A   28                          1555   1555  2.02  
SSBOND   3 CYS A   22    CYS A   37                          1555   1555  2.02  
LINK        CA    CA A  40                 O   ARG A  20     1555   1555  2.79  
LINK        CA    CA A  40                 OD2 ASP A  33     1555   1555  2.63  
LINK        CA    CA A  40                 N   TYR A  26     1555   1555  3.25  
LINK        CA    CA A  40                 OD2 ASP A  27     1555   1555  2.64  
LINK        CA    CA A  40                 O   GLU A  25     1555   1555  3.19  
LINK        CA    CA A  40                 OE2 GLU A  34     1555   1555  2.62  
LINK        CA    CA A  40                 OD1 ASP A  23     1555   1555  2.65  
LINK        CA    CA A  40                 N   GLU A  25     1555   1555  3.02  
SITE     1 AC1  7 ARG A  20  ASP A  23  GLU A  25  TYR A  26                    
SITE     2 AC1  7 ASP A  27  ASP A  33  GLU A  34                               
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                         
MODEL        1                                                                  
(ATOM LINES ARE NOT SHOWN.)
END                                                                             
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