PDB Short entry for 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