GenomeNet

Database: PDB
Entry: 2N83
LinkDB: 2N83
Original site: 2N83 
HEADER    SIGNALING PROTEIN/TRANSFERASE           02-OCT-15   2N83              
TITLE     P75NTR DD:RIP2 CARD                                                   
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 16;      
COMPND   3 CHAIN: A;                                                            
COMPND   4 FRAGMENT: UNP RESIDUES 334-427;                                      
COMPND   5 SYNONYM: GP80-LNGFR, LOW AFFINITY NEUROTROPHIN RECEPTOR P75NTR, LOW- 
COMPND   6 AFFINITY NERVE GROWTH FACTOR RECEPTOR, NGF RECEPTOR, P75 ICD;        
COMPND   7 ENGINEERED: YES;                                                     
COMPND   8 MOL_ID: 2;                                                           
COMPND   9 MOLECULE: RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 2;    
COMPND  10 CHAIN: B;                                                            
COMPND  11 FRAGMENT: UNP RESIDUES 435-539;                                      
COMPND  12 SYNONYM: CARD-CONTAINING INTERLEUKIN-1 BETA-CONVERTING ENZYME-       
COMPND  13 ASSOCIATED KINASE, CARD-CONTAINING IL-1 BETA ICE-KINASE, RIP-LIKE-   
COMPND  14 INTERACTING CLARP KINASE, RECEPTOR-INTERACTING PROTEIN 2, RIP-2,     
COMPND  15 TYROSINE-PROTEIN KINASE RIPK2;                                       
COMPND  16 EC: 2.7.11.1, 2.7.10.2;                                              
COMPND  17 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: NGFR, TNFRSF16;                                                
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR;                               
SOURCE   9 EXPRESSION_SYSTEM_VECTOR: PET32A-DERIVED;                            
SOURCE  10 MOL_ID: 2;                                                           
SOURCE  11 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE  12 ORGANISM_COMMON: HUMAN;                                              
SOURCE  13 ORGANISM_TAXID: 9606;                                                
SOURCE  14 GENE: RIPK2, CARDIAK, RICK, RIP2, UNQ277/PRO314/PRO34092;            
SOURCE  15 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE  16 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE  17 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR                                
KEYWDS    RIP2 CARD, P75NTR, DEATH DOMAIN, SIGNALING PROTEIN-TRANSFERASE        
KEYWDS   2 COMPLEX                                                              
EXPDTA    SOLUTION NMR                                                          
NUMMDL    10                                                                    
AUTHOR    Z.LIN,C.F.IBANEZ                                                      
REVDAT   2   27-APR-16 2N83    1       ATOM   DBREF  REMARK SEQRES              
REVDAT   1   23-DEC-15 2N83    0                                                
JRNL        AUTH   Z.LIN,J.Y.TANN,E.T.GOH,C.KELLY,K.B.LIM,J.F.GAO,C.F.IBANEZ    
JRNL        TITL   STRUCTURAL BASIS OF DEATH DOMAIN SIGNALING IN THE P75        
JRNL        TITL 2 NEUROTROPHIN RECEPTOR                                        
JRNL        REF    ELIFE                         V.   4 11692 2015              
JRNL        REFN                   ESSN 2050-084X                               
JRNL        PMID   26646181                                                     
JRNL        DOI    10.7554/ELIFE.11692                                          
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : AMBER                                                
REMARK   3   AUTHORS     : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG,       
REMARK   3                 DUKE, LUO, ... AND KOLLMAN                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 2N83 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-OCT-15.                  
REMARK 100 THE RCSB ID CODE IS RCSB104540.                                      
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 301                                
REMARK 210  PH                             : NULL                               
REMARK 210  IONIC STRENGTH                 : NULL                               
REMARK 210  PRESSURE                       : AMBIENT ATM                        
REMARK 210  SAMPLE CONTENTS                : 0.5 MM [U-99% 13C; U-99% 15N]      
REMARK 210                                   P75NTR DD-1, 10 MM [U-98% 2H] DTT  
REMARK 210                                   -2, 1 MM RIP2 CARD-3, 95% H2O/5%   
REMARK 210                                   D2O; 0.5 MM [U-99% 13C; U-99%      
REMARK 210                                   15N] RIP2 CARD-4, 1 MM P75NTR DD-  
REMARK 210                                   5, 10 MM [U-98% 2H] DTT-6, 95%     
REMARK 210                                   H2O/5% D2O                         
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : 2D 1H-15N HSQC; 2D 1H-13C HSQC     
REMARK 210                                   ALIPHATIC; 2D 1H-13C HSQC          
REMARK 210                                   AROMATIC; 3D HNCACB; 3D CBCA(CO)   
REMARK 210                                   NH; 3D HCCH-TOCSY; 3D 13C,15N-     
REMARK 210                                   FILTERED NOESY; 3D 13C, 15N-       
REMARK 210                                   EDITED NOESY; 3D HN(CO)CA; 4D      
REMARK 210                                   13C, 15N-EDITED NOESY              
REMARK 210  SPECTROMETER FIELD STRENGTH    : 800 MHZ                            
REMARK 210  SPECTROMETER MODEL             : AVANCE                             
REMARK 210  SPECTROMETER MANUFACTURER      : BRUKER                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : NMRPIPE, NMRVIEW, CYANA            
REMARK 210   METHOD USED                   : MOLECULAR DYNAMICS                 
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 100                                
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 10                                 
REMARK 210 CONFORMERS, SELECTION CRITERIA  : STRUCTURES WITH THE LOWEST ENERGY  
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1                   
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 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 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;                   
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                            
REMARK 465   MODELS 1-10                                                        
REMARK 465     RES C SSSEQI                                                     
REMARK 465     LYS A   330                                                      
REMARK 465     GLY A   331                                                      
REMARK 465     ASP A   332                                                      
REMARK 465     GLY A   333                                                      
REMARK 465     GLY B   434                                                      
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  4 ARG A 360   NE  -  CZ  -  NH1 ANGL. DEV. =   3.2 DEGREES          
REMARK 500  6 ARG A 360   NE  -  CZ  -  NH1 ANGL. DEV. =   3.0 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 ALA A 396       26.08    -67.25                                   
REMARK 500  1 GLN A 409       11.98     91.05                                   
REMARK 500  1 ARG A 410       55.66    -92.47                                   
REMARK 500  1 ALA A 423      106.15   -160.51                                   
REMARK 500  1 THR B 452      -76.95    -57.13                                   
REMARK 500  1 GLU B 453      -46.46   -159.67                                   
REMARK 500  1 ASP B 467       25.82     49.89                                   
REMARK 500  1 LYS B 513       58.58     38.24                                   
REMARK 500  1 LEU B 517       27.47   -146.94                                   
REMARK 500  1 ARG B 528       39.36   -162.85                                   
REMARK 500  1 SER B 531      -63.16   -101.07                                   
REMARK 500  1 LEU B 535      -38.02   -159.50                                   
REMARK 500  2 SER A 354       49.28   -149.16                                   
REMARK 500  2 ALA A 355      -74.57    -78.68                                   
REMARK 500  2 ARG A 410       47.00    -95.00                                   
REMARK 500  2 ASN B 512      -85.52    -88.02                                   
REMARK 500  2 LYS B 513       24.31    179.49                                   
REMARK 500  2 LEU B 517       22.54   -144.86                                   
REMARK 500  2 LEU B 524       51.05     75.97                                   
REMARK 500  2 VAL B 526      102.65    -41.19                                   
REMARK 500  2 SER B 531      -80.76   -142.93                                   
REMARK 500  2 LEU B 535       28.22   -159.60                                   
REMARK 500  3 ALA A 355       32.54   -144.20                                   
REMARK 500  3 ASP A 357       -2.96   -140.84                                   
REMARK 500  3 ALA A 396       30.83    -69.07                                   
REMARK 500  3 ARG A 410       37.84    -88.09                                   
REMARK 500  3 THR A 422       53.10    -91.89                                   
REMARK 500  3 SER A 425       78.49   -156.83                                   
REMARK 500  3 THR B 452      -81.71    -74.58                                   
REMARK 500  3 GLU B 453      -35.10   -157.61                                   
REMARK 500  3 GLU B 500      -70.24    -78.53                                   
REMARK 500  3 ASN B 512      -90.21    -88.58                                   
REMARK 500  3 LYS B 513       25.32   -177.37                                   
REMARK 500  3 GLN B 518      -48.60    -26.49                                   
REMARK 500  3 VAL B 525        7.58    -67.65                                   
REMARK 500  3 SER B 527      -85.34   -111.97                                   
REMARK 500  3 ARG B 528       31.87   -158.73                                   
REMARK 500  3 SER B 531      -69.62   -157.02                                   
REMARK 500  3 LEU B 532       33.21    -93.10                                   
REMARK 500  3 LYS B 538       82.58     40.34                                   
REMARK 500  4 ALA A 355      -76.58    -84.42                                   
REMARK 500  4 ALA A 396       42.98    -70.48                                   
REMARK 500  4 ARG A 410       45.36    -91.89                                   
REMARK 500  4 SER A 425       74.57   -162.73                                   
REMARK 500  4 SER B 442      -56.21   -139.56                                   
REMARK 500  4 GLU B 500      -71.03    -70.13                                   
REMARK 500  4 MET B 515       10.41     56.39                                   
REMARK 500  4 GLN B 518      -51.26    -21.59                                   
REMARK 500  4 LEU B 524      128.15     74.31                                   
REMARK 500  4 VAL B 525       14.04   -148.83                                   
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS     139 RAMACHANDRAN OUTLIERS.                        
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: PLANAR GROUPS                                              
REMARK 500                                                                      
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL                 
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE                    
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN                    
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS                        
REMARK 500 AN RMSD GREATER THAN THIS VALUE                                      
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
REMARK 500                                                                      
REMARK 500  M RES CSSEQI        RMS     TYPE                                    
REMARK 500  4 ARG B 466         0.08    SIDE CHAIN                              
REMARK 500  8 TYR A 336         0.07    SIDE CHAIN                              
REMARK 500  9 TYR A 336         0.09    SIDE CHAIN                              
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 25833   RELATED DB: BMRB                                 
REMARK 900 RELATED ID: 2N7Z   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 2N80   RELATED DB: PDB                                   
REMARK 900 RELATED ID: 2N97   RELATED DB: PDB                                   
DBREF  2N83 A  330   427  UNP    P08138   TNR16_HUMAN    330    427             
DBREF  2N83 B  434   539  UNP    O43353   RIPK2_HUMAN    434    539             
SEQRES   1 A   98  LYS GLY ASP GLY GLY LEU TYR SER SER LEU PRO PRO ALA          
SEQRES   2 A   98  LYS ARG GLU GLU VAL GLU LYS LEU LEU ASN GLY SER ALA          
SEQRES   3 A   98  GLY ASP THR TRP ARG HIS LEU ALA GLY GLU LEU GLY TYR          
SEQRES   4 A   98  GLN PRO GLU HIS ILE ASP SER PHE THR HIS GLU ALA CYS          
SEQRES   5 A   98  PRO VAL ARG ALA LEU LEU ALA SER TRP ALA THR GLN ASP          
SEQRES   6 A   98  SER ALA THR LEU ASP ALA LEU LEU ALA ALA LEU ARG ARG          
SEQRES   7 A   98  ILE GLN ARG ALA ASP LEU VAL GLU SER LEU CYS SER GLU          
SEQRES   8 A   98  SER THR ALA THR SER PRO VAL                                  
SEQRES   1 B  106  GLY ILE ALA GLN GLN TRP ILE GLN SER LYS ARG GLU ASP          
SEQRES   2 B  106  ILE VAL ASN GLN MET THR GLU ALA CYS LEU ASN GLN SER          
SEQRES   3 B  106  LEU ASP ALA LEU LEU SER ARG ASP LEU ILE MET LYS GLU          
SEQRES   4 B  106  ASP TYR GLU LEU VAL SER THR LYS PRO THR ARG THR SER          
SEQRES   5 B  106  LYS VAL ARG GLN LEU LEU ASP THR THR ASP ILE GLN GLY          
SEQRES   6 B  106  GLU GLU PHE ALA LYS VAL ILE VAL GLN LYS LEU LYS ASP          
SEQRES   7 B  106  ASN LYS GLN MET GLY LEU GLN PRO TYR PRO GLU ILE LEU          
SEQRES   8 B  106  VAL VAL SER ARG SER PRO SER LEU ASN LEU LEU GLN ASN          
SEQRES   9 B  106  LYS SER                                                      
HELIX    1   1 LEU A  335  LEU A  339  5                                   5    
HELIX    2   2 PRO A  340  ALA A  355  1                                  16    
HELIX    3   3 ASP A  357  GLY A  367  1                                  11    
HELIX    4   4 GLN A  369  THR A  377  1                                   9    
HELIX    5   5 CYS A  381  THR A  392  1                                  12    
HELIX    6   6 THR A  397  GLN A  409  1                                  13    
HELIX    7   7 ARG A  410  GLU A  420  1                                  11    
HELIX    8   8 ALA B  436  LYS B  443  1                                   8    
HELIX    9   9 LYS B  443  MET B  451  1                                   9    
HELIX   10  10 GLU B  453  SER B  465  1                                  13    
HELIX   11  11 MET B  470  LYS B  480  1                                  11    
HELIX   12  12 THR B  482  GLY B  498  1                                  17    
HELIX   13  13 GLU B  499  LYS B  513  1                                  15    
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                                                                             
DBGET integrated database retrieval system