HEADER SIGNALING PROTEIN/VIRAL PROTEIN 14-JUN-23 8T5Q TITLE SARS-COV-2 ORF3A PEPTIDE IN COMPLEX WITH TRAF2 TRAF DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TNF RECEPTOR-ASSOCIATED FACTOR 2; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 FRAGMENT: TRAF DOMAIN (UNP RESIDUES 315-501); COMPND 5 SYNONYM: E3 UBIQUITIN-PROTEIN LIGASE TRAF2,RING-TYPE E3 UBIQUITIN COMPND 6 TRANSFERASE TRAF2,TUMOR NECROSIS FACTOR TYPE 2 RECEPTOR-ASSOCIATED COMPND 7 PROTEIN 3; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: ORF3A PROTEIN; COMPND 11 CHAIN: G, H, I; COMPND 12 FRAGMENT: UNP RESIDUES 36-40; COMPND 13 SYNONYM: ORF3A,ACCESSORY PROTEIN 3A,PROTEIN 3A,PROTEIN U274,PROTEIN COMPND 14 X1; COMPND 15 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: TRAF2, TRAP3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: RIPL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSMT3; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 14 2; SOURCE 15 ORGANISM_TAXID: 2697049 KEYWDS SIGNALING PROTEIN-VIRAL PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.M.BUSSCHER,T.S.XIAO REVDAT 2 06-DEC-23 8T5Q 1 JRNL REVDAT 1 29-NOV-23 8T5Q 0 JRNL AUTH B.M.BUSSCHER,H.B.BEFEKADU,Z.LIU,T.S.XIAO JRNL TITL SARS-COV-2 ORF3A-MEDIATED NF-KAPPA B ACTIVATION IS NOT JRNL TITL 2 DEPENDENT ON TRAF-BINDING SEQUENCE. JRNL REF VIRUSES V. 15 2023 JRNL REFN ESSN 1999-4915 JRNL PMID 38005906 JRNL DOI 10.3390/V15112229 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 95467 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 4757 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 29.6100 - 5.8800 0.98 3113 152 0.1859 0.2137 REMARK 3 2 5.8800 - 4.6700 0.99 3048 152 0.1659 0.1853 REMARK 3 3 4.6700 - 4.0800 0.99 3082 164 0.1524 0.1821 REMARK 3 4 4.0800 - 3.7100 1.00 3091 148 0.1736 0.1943 REMARK 3 5 3.7100 - 3.4500 1.00 3045 150 0.1840 0.2130 REMARK 3 6 3.4500 - 3.2400 0.99 3044 168 0.1949 0.2381 REMARK 3 7 3.2400 - 3.0800 0.96 2917 176 0.2155 0.2264 REMARK 3 8 3.0800 - 2.9500 0.99 3043 165 0.2208 0.2623 REMARK 3 9 2.9500 - 2.8300 1.00 3040 164 0.2226 0.2666 REMARK 3 10 2.8300 - 2.7400 0.99 3066 156 0.2246 0.2366 REMARK 3 11 2.7400 - 2.6500 0.99 3008 162 0.2221 0.2517 REMARK 3 12 2.6500 - 2.5700 0.99 3026 168 0.2396 0.2472 REMARK 3 13 2.5700 - 2.5100 0.99 3051 163 0.2428 0.2779 REMARK 3 14 2.5100 - 2.4500 0.99 3033 167 0.2386 0.2758 REMARK 3 15 2.4500 - 2.3900 0.99 2966 188 0.2358 0.2776 REMARK 3 16 2.3900 - 2.3400 0.99 3007 145 0.2409 0.2815 REMARK 3 17 2.3400 - 2.2900 0.99 3058 185 0.2322 0.2487 REMARK 3 18 2.2900 - 2.2500 0.98 2966 141 0.2336 0.2771 REMARK 3 19 2.2500 - 2.2100 0.97 2958 126 0.2323 0.2867 REMARK 3 20 2.2100 - 2.1700 0.98 3022 174 0.2447 0.3105 REMARK 3 21 2.1700 - 2.1400 0.98 2999 152 0.2370 0.2834 REMARK 3 22 2.1400 - 2.1000 0.98 3004 155 0.2448 0.3135 REMARK 3 23 2.1000 - 2.0700 0.99 3055 143 0.2434 0.2977 REMARK 3 24 2.0700 - 2.0400 0.99 2965 168 0.2413 0.2955 REMARK 3 25 2.0400 - 2.0200 0.99 3068 163 0.2528 0.2770 REMARK 3 26 2.0200 - 1.9900 0.99 2961 169 0.2631 0.3112 REMARK 3 27 1.9900 - 1.9700 0.99 3075 150 0.2714 0.2940 REMARK 3 28 1.9700 - 1.9400 0.99 2990 148 0.2868 0.3416 REMARK 3 29 1.9400 - 1.9200 0.99 3053 143 0.3060 0.3580 REMARK 3 30 1.9200 - 1.9000 0.97 2956 152 0.3296 0.3557 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.227 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.346 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.34 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 : 0.007 8361 REMARK 3 ANGLE : 0.948 11266 REMARK 3 CHIRALITY : 0.064 1224 REMARK 3 PLANARITY : 0.010 1449 REMARK 3 DIHEDRAL : 8.885 1162 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 8T5Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1000275198. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 95517 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 29.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.490 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: PDB ENTRY 1D01 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, PH 5.0, 20% W/V REMARK 280 PEG8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 67.60000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.11000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.60000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 42.11000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, G, H 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F, I 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 SER A 314 REMARK 465 GLU A 315 REMARK 465 ALA A 316 REMARK 465 LEU A 317 REMARK 465 SER A 318 REMARK 465 SER A 319 REMARK 465 LYS A 320 REMARK 465 VAL A 321 REMARK 465 GLN A 322 REMARK 465 GLN A 323 REMARK 465 LEU A 324 REMARK 465 GLU A 325 REMARK 465 ARG A 326 REMARK 465 SER A 327 REMARK 465 ILE A 328 REMARK 465 GLY A 329 REMARK 465 LEU A 330 REMARK 465 LYS A 331 REMARK 465 ASP A 332 REMARK 465 LEU A 333 REMARK 465 SER B 314 REMARK 465 GLU B 315 REMARK 465 ALA B 316 REMARK 465 LEU B 317 REMARK 465 SER B 318 REMARK 465 SER B 319 REMARK 465 LYS B 320 REMARK 465 VAL B 321 REMARK 465 GLN B 322 REMARK 465 GLN B 323 REMARK 465 LEU B 324 REMARK 465 GLU B 325 REMARK 465 ARG B 326 REMARK 465 SER B 327 REMARK 465 ILE B 328 REMARK 465 GLY B 329 REMARK 465 LEU B 330 REMARK 465 LYS B 331 REMARK 465 ASP B 332 REMARK 465 LEU B 333 REMARK 465 SER C 314 REMARK 465 GLU C 315 REMARK 465 ALA C 316 REMARK 465 LEU C 317 REMARK 465 SER C 318 REMARK 465 SER C 319 REMARK 465 LYS C 320 REMARK 465 VAL C 321 REMARK 465 GLN C 322 REMARK 465 GLN C 323 REMARK 465 LEU C 324 REMARK 465 GLU C 325 REMARK 465 ARG C 326 REMARK 465 SER C 327 REMARK 465 ILE C 328 REMARK 465 GLY C 329 REMARK 465 LEU C 330 REMARK 465 LYS C 331 REMARK 465 ASP C 332 REMARK 465 LEU C 333 REMARK 465 SER D 314 REMARK 465 GLU D 315 REMARK 465 ALA D 316 REMARK 465 LEU D 317 REMARK 465 SER D 318 REMARK 465 SER D 319 REMARK 465 LYS D 320 REMARK 465 VAL D 321 REMARK 465 GLN D 322 REMARK 465 GLN D 323 REMARK 465 LEU D 324 REMARK 465 GLU D 325 REMARK 465 ARG D 326 REMARK 465 SER D 327 REMARK 465 ILE D 328 REMARK 465 GLY D 329 REMARK 465 LEU D 330 REMARK 465 LYS D 331 REMARK 465 ASP D 332 REMARK 465 LEU D 333 REMARK 465 SER E 314 REMARK 465 GLU E 315 REMARK 465 ALA E 316 REMARK 465 LEU E 317 REMARK 465 SER E 318 REMARK 465 SER E 319 REMARK 465 LYS E 320 REMARK 465 VAL E 321 REMARK 465 GLN E 322 REMARK 465 GLN E 323 REMARK 465 LEU E 324 REMARK 465 GLU E 325 REMARK 465 ARG E 326 REMARK 465 SER E 327 REMARK 465 ILE E 328 REMARK 465 GLY E 329 REMARK 465 LEU E 330 REMARK 465 LYS E 331 REMARK 465 ASP E 332 REMARK 465 LEU E 333 REMARK 465 SER F 314 REMARK 465 GLU F 315 REMARK 465 ALA F 316 REMARK 465 LEU F 317 REMARK 465 SER F 318 REMARK 465 SER F 319 REMARK 465 LYS F 320 REMARK 465 VAL F 321 REMARK 465 GLN F 322 REMARK 465 GLN F 323 REMARK 465 LEU F 324 REMARK 465 GLU F 325 REMARK 465 ARG F 326 REMARK 465 SER F 327 REMARK 465 ILE F 328 REMARK 465 GLY F 329 REMARK 465 LEU F 330 REMARK 465 LYS F 331 REMARK 465 ASP F 332 REMARK 465 LEU F 333 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN I 206 C 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 ASN A 427 29.99 -141.37 REMARK 500 LEU A 471 41.88 -103.92 REMARK 500 LEU B 471 40.11 -108.77 REMARK 500 ARG C 440 -158.38 -79.34 REMARK 500 GLU C 441 109.82 -59.32 REMARK 500 LEU C 471 40.73 -109.39 REMARK 500 SER C 483 -5.56 77.05 REMARK 500 ASN D 482 -169.49 -162.43 REMARK 500 ASN E 439 16.06 55.16 REMARK 500 ASN F 427 32.52 -140.52 REMARK 500 LEU F 471 44.28 -107.90 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 ARG E 365 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8T5Q A 315 501 UNP Q12933 TRAF2_HUMAN 315 501 DBREF 8T5Q B 315 501 UNP Q12933 TRAF2_HUMAN 315 501 DBREF 8T5Q C 315 501 UNP Q12933 TRAF2_HUMAN 315 501 DBREF 8T5Q D 315 501 UNP Q12933 TRAF2_HUMAN 315 501 DBREF 8T5Q E 315 501 UNP Q12933 TRAF2_HUMAN 315 501 DBREF 8T5Q F 315 501 UNP Q12933 TRAF2_HUMAN 315 501 DBREF 8T5Q G 204 208 UNP P0DTC3 AP3A_SARS2 36 40 DBREF 8T5Q H 204 208 UNP P0DTC3 AP3A_SARS2 36 40 DBREF 8T5Q I 204 208 UNP P0DTC3 AP3A_SARS2 36 40 SEQADV 8T5Q SER A 314 UNP Q12933 EXPRESSION TAG SEQADV 8T5Q SER B 314 UNP Q12933 EXPRESSION TAG SEQADV 8T5Q SER C 314 UNP Q12933 EXPRESSION TAG SEQADV 8T5Q SER D 314 UNP Q12933 EXPRESSION TAG SEQADV 8T5Q SER E 314 UNP Q12933 EXPRESSION TAG SEQADV 8T5Q SER F 314 UNP Q12933 EXPRESSION TAG SEQRES 1 A 188 SER GLU ALA LEU SER SER LYS VAL GLN GLN LEU GLU ARG SEQRES 2 A 188 SER ILE GLY LEU LYS ASP LEU ALA MET ALA ASP LEU GLU SEQRES 3 A 188 GLN LYS VAL LEU GLU MET GLU ALA SER THR TYR ASP GLY SEQRES 4 A 188 VAL PHE ILE TRP LYS ILE SER ASP PHE ALA ARG LYS ARG SEQRES 5 A 188 GLN GLU ALA VAL ALA GLY ARG ILE PRO ALA ILE PHE SER SEQRES 6 A 188 PRO ALA PHE TYR THR SER ARG TYR GLY TYR LYS MET CYS SEQRES 7 A 188 LEU ARG ILE TYR LEU ASN GLY ASP GLY THR GLY ARG GLY SEQRES 8 A 188 THR HIS LEU SER LEU PHE PHE VAL VAL MET LYS GLY PRO SEQRES 9 A 188 ASN ASP ALA LEU LEU ARG TRP PRO PHE ASN GLN LYS VAL SEQRES 10 A 188 THR LEU MET LEU LEU ASP GLN ASN ASN ARG GLU HIS VAL SEQRES 11 A 188 ILE ASP ALA PHE ARG PRO ASP VAL THR SER SER SER PHE SEQRES 12 A 188 GLN ARG PRO VAL ASN ASP MET ASN ILE ALA SER GLY CYS SEQRES 13 A 188 PRO LEU PHE CYS PRO VAL SER LYS MET GLU ALA LYS ASN SEQRES 14 A 188 SER TYR VAL ARG ASP ASP ALA ILE PHE ILE LYS ALA ILE SEQRES 15 A 188 VAL ASP LEU THR GLY LEU SEQRES 1 B 188 SER GLU ALA LEU SER SER LYS VAL GLN GLN LEU GLU ARG SEQRES 2 B 188 SER ILE GLY LEU LYS ASP LEU ALA MET ALA ASP LEU GLU SEQRES 3 B 188 GLN LYS VAL LEU GLU MET GLU ALA SER THR TYR ASP GLY SEQRES 4 B 188 VAL PHE ILE TRP LYS ILE SER ASP PHE ALA ARG LYS ARG SEQRES 5 B 188 GLN GLU ALA VAL ALA GLY ARG ILE PRO ALA ILE PHE SER SEQRES 6 B 188 PRO ALA PHE TYR THR SER ARG TYR GLY TYR LYS MET CYS SEQRES 7 B 188 LEU ARG ILE TYR LEU ASN GLY ASP GLY THR GLY ARG GLY SEQRES 8 B 188 THR HIS LEU SER LEU PHE PHE VAL VAL MET LYS GLY PRO SEQRES 9 B 188 ASN ASP ALA LEU LEU ARG TRP PRO PHE ASN GLN LYS VAL SEQRES 10 B 188 THR LEU MET LEU LEU ASP GLN ASN ASN ARG GLU HIS VAL SEQRES 11 B 188 ILE ASP ALA PHE ARG PRO ASP VAL THR SER SER SER PHE SEQRES 12 B 188 GLN ARG PRO VAL ASN ASP MET ASN ILE ALA SER GLY CYS SEQRES 13 B 188 PRO LEU PHE CYS PRO VAL SER LYS MET GLU ALA LYS ASN SEQRES 14 B 188 SER TYR VAL ARG ASP ASP ALA ILE PHE ILE LYS ALA ILE SEQRES 15 B 188 VAL ASP LEU THR GLY LEU SEQRES 1 C 188 SER GLU ALA LEU SER SER LYS VAL GLN GLN LEU GLU ARG SEQRES 2 C 188 SER ILE GLY LEU LYS ASP LEU ALA MET ALA ASP LEU GLU SEQRES 3 C 188 GLN LYS VAL LEU GLU MET GLU ALA SER THR TYR ASP GLY SEQRES 4 C 188 VAL PHE ILE TRP LYS ILE SER ASP PHE ALA ARG LYS ARG SEQRES 5 C 188 GLN GLU ALA VAL ALA GLY ARG ILE PRO ALA ILE PHE SER SEQRES 6 C 188 PRO ALA PHE TYR THR SER ARG TYR GLY TYR LYS MET CYS SEQRES 7 C 188 LEU ARG ILE TYR LEU ASN GLY ASP GLY THR GLY ARG GLY SEQRES 8 C 188 THR HIS LEU SER LEU PHE PHE VAL VAL MET LYS GLY PRO SEQRES 9 C 188 ASN ASP ALA LEU LEU ARG TRP PRO PHE ASN GLN LYS VAL SEQRES 10 C 188 THR LEU MET LEU LEU ASP GLN ASN ASN ARG GLU HIS VAL SEQRES 11 C 188 ILE ASP ALA PHE ARG PRO ASP VAL THR SER SER SER PHE SEQRES 12 C 188 GLN ARG PRO VAL ASN ASP MET ASN ILE ALA SER GLY CYS SEQRES 13 C 188 PRO LEU PHE CYS PRO VAL SER LYS MET GLU ALA LYS ASN SEQRES 14 C 188 SER TYR VAL ARG ASP ASP ALA ILE PHE ILE LYS ALA ILE SEQRES 15 C 188 VAL ASP LEU THR GLY LEU SEQRES 1 D 188 SER GLU ALA LEU SER SER LYS VAL GLN GLN LEU GLU ARG SEQRES 2 D 188 SER ILE GLY LEU LYS ASP LEU ALA MET ALA ASP LEU GLU SEQRES 3 D 188 GLN LYS VAL LEU GLU MET GLU ALA SER THR TYR ASP GLY SEQRES 4 D 188 VAL PHE ILE TRP LYS ILE SER ASP PHE ALA ARG LYS ARG SEQRES 5 D 188 GLN GLU ALA VAL ALA GLY ARG ILE PRO ALA ILE PHE SER SEQRES 6 D 188 PRO ALA PHE TYR THR SER ARG TYR GLY TYR LYS MET CYS SEQRES 7 D 188 LEU ARG ILE TYR LEU ASN GLY ASP GLY THR GLY ARG GLY SEQRES 8 D 188 THR HIS LEU SER LEU PHE PHE VAL VAL MET LYS GLY PRO SEQRES 9 D 188 ASN ASP ALA LEU LEU ARG TRP PRO PHE ASN GLN LYS VAL SEQRES 10 D 188 THR LEU MET LEU LEU ASP GLN ASN ASN ARG GLU HIS VAL SEQRES 11 D 188 ILE ASP ALA PHE ARG PRO ASP VAL THR SER SER SER PHE SEQRES 12 D 188 GLN ARG PRO VAL ASN ASP MET ASN ILE ALA SER GLY CYS SEQRES 13 D 188 PRO LEU PHE CYS PRO VAL SER LYS MET GLU ALA LYS ASN SEQRES 14 D 188 SER TYR VAL ARG ASP ASP ALA ILE PHE ILE LYS ALA ILE SEQRES 15 D 188 VAL ASP LEU THR GLY LEU SEQRES 1 E 188 SER GLU ALA LEU SER SER LYS VAL GLN GLN LEU GLU ARG SEQRES 2 E 188 SER ILE GLY LEU LYS ASP LEU ALA MET ALA ASP LEU GLU SEQRES 3 E 188 GLN LYS VAL LEU GLU MET GLU ALA SER THR TYR ASP GLY SEQRES 4 E 188 VAL PHE ILE TRP LYS ILE SER ASP PHE ALA ARG LYS ARG SEQRES 5 E 188 GLN GLU ALA VAL ALA GLY ARG ILE PRO ALA ILE PHE SER SEQRES 6 E 188 PRO ALA PHE TYR THR SER ARG TYR GLY TYR LYS MET CYS SEQRES 7 E 188 LEU ARG ILE TYR LEU ASN GLY ASP GLY THR GLY ARG GLY SEQRES 8 E 188 THR HIS LEU SER LEU PHE PHE VAL VAL MET LYS GLY PRO SEQRES 9 E 188 ASN ASP ALA LEU LEU ARG TRP PRO PHE ASN GLN LYS VAL SEQRES 10 E 188 THR LEU MET LEU LEU ASP GLN ASN ASN ARG GLU HIS VAL SEQRES 11 E 188 ILE ASP ALA PHE ARG PRO ASP VAL THR SER SER SER PHE SEQRES 12 E 188 GLN ARG PRO VAL ASN ASP MET ASN ILE ALA SER GLY CYS SEQRES 13 E 188 PRO LEU PHE CYS PRO VAL SER LYS MET GLU ALA LYS ASN SEQRES 14 E 188 SER TYR VAL ARG ASP ASP ALA ILE PHE ILE LYS ALA ILE SEQRES 15 E 188 VAL ASP LEU THR GLY LEU SEQRES 1 F 188 SER GLU ALA LEU SER SER LYS VAL GLN GLN LEU GLU ARG SEQRES 2 F 188 SER ILE GLY LEU LYS ASP LEU ALA MET ALA ASP LEU GLU SEQRES 3 F 188 GLN LYS VAL LEU GLU MET GLU ALA SER THR TYR ASP GLY SEQRES 4 F 188 VAL PHE ILE TRP LYS ILE SER ASP PHE ALA ARG LYS ARG SEQRES 5 F 188 GLN GLU ALA VAL ALA GLY ARG ILE PRO ALA ILE PHE SER SEQRES 6 F 188 PRO ALA PHE TYR THR SER ARG TYR GLY TYR LYS MET CYS SEQRES 7 F 188 LEU ARG ILE TYR LEU ASN GLY ASP GLY THR GLY ARG GLY SEQRES 8 F 188 THR HIS LEU SER LEU PHE PHE VAL VAL MET LYS GLY PRO SEQRES 9 F 188 ASN ASP ALA LEU LEU ARG TRP PRO PHE ASN GLN LYS VAL SEQRES 10 F 188 THR LEU MET LEU LEU ASP GLN ASN ASN ARG GLU HIS VAL SEQRES 11 F 188 ILE ASP ALA PHE ARG PRO ASP VAL THR SER SER SER PHE SEQRES 12 F 188 GLN ARG PRO VAL ASN ASP MET ASN ILE ALA SER GLY CYS SEQRES 13 F 188 PRO LEU PHE CYS PRO VAL SER LYS MET GLU ALA LYS ASN SEQRES 14 F 188 SER TYR VAL ARG ASP ASP ALA ILE PHE ILE LYS ALA ILE SEQRES 15 F 188 VAL ASP LEU THR GLY LEU SEQRES 1 G 5 PRO ILE GLN ALA SER SEQRES 1 H 5 PRO ILE GLN ALA SER SEQRES 1 I 5 PRO ILE GLN ALA SER HET PG4 A 601 13 HET PG4 B 601 13 HET PEG C 601 7 HET PEG C 602 7 HET PG4 D 601 13 HET PEG E 601 7 HET PEG E 602 7 HET PG4 F 601 13 HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 10 PG4 4(C8 H18 O5) FORMUL 12 PEG 4(C4 H10 O3) FORMUL 18 HOH *316(H2 O) HELIX 1 AA1 ALA A 334 SER A 348 1 15 HELIX 2 AA2 ASP A 360 ALA A 370 1 11 HELIX 3 AA3 ASP A 399 ARG A 403 5 5 HELIX 4 AA4 ASN A 418 LEU A 422 5 5 HELIX 5 AA5 SER A 453 GLN A 457 5 5 HELIX 6 AA6 VAL A 475 ALA A 480 1 6 HELIX 7 AA7 MET B 335 SER B 348 1 14 HELIX 8 AA8 ASP B 360 ALA B 370 1 11 HELIX 9 AA9 ASP B 399 ARG B 403 5 5 HELIX 10 AB1 ASN B 418 LEU B 422 5 5 HELIX 11 AB2 SER B 453 GLN B 457 5 5 HELIX 12 AB3 SER B 476 GLU B 479 5 4 HELIX 13 AB4 MET C 335 SER C 348 1 14 HELIX 14 AB5 ASP C 360 ALA C 370 1 11 HELIX 15 AB6 ASP C 399 ARG C 403 5 5 HELIX 16 AB7 ASN C 418 LEU C 422 5 5 HELIX 17 AB8 SER C 453 GLN C 457 5 5 HELIX 18 AB9 SER C 476 MET C 478 5 3 HELIX 19 AC1 MET D 335 SER D 348 1 14 HELIX 20 AC2 ASP D 360 ALA D 370 1 11 HELIX 21 AC3 ASP D 399 ARG D 403 5 5 HELIX 22 AC4 ASN D 418 LEU D 422 5 5 HELIX 23 AC5 SER D 453 GLN D 457 5 5 HELIX 24 AC6 SER D 476 GLU D 479 5 4 HELIX 25 AC7 MET E 335 SER E 348 1 14 HELIX 26 AC8 ASP E 360 ALA E 370 1 11 HELIX 27 AC9 ASP E 399 ARG E 403 5 5 HELIX 28 AD1 ASN E 418 LEU E 422 5 5 HELIX 29 AD2 SER E 453 GLN E 457 5 5 HELIX 30 AD3 SER E 476 GLU E 479 5 4 HELIX 31 AD4 MET F 335 SER F 348 1 14 HELIX 32 AD5 ASP F 360 ALA F 370 1 11 HELIX 33 AD6 ASP F 399 ARG F 403 5 5 HELIX 34 AD7 ASN F 418 LEU F 422 5 5 HELIX 35 AD8 SER F 453 GLN F 457 5 5 HELIX 36 AD9 SER F 476 GLU F 479 5 4 SHEET 1 AA1 4 VAL A 353 SER A 359 0 SHEET 2 AA1 4 ALA A 489 VAL A 496 -1 O ILE A 492 N TRP A 356 SHEET 3 AA1 4 VAL A 430 LEU A 434 -1 N MET A 433 O LYS A 493 SHEET 4 AA1 4 VAL A 443 PHE A 447 -1 O VAL A 443 N LEU A 434 SHEET 1 AA2 3 ILE A 376 PHE A 377 0 SHEET 2 AA2 3 LYS A 389 TYR A 395 -1 O ILE A 394 N ILE A 376 SHEET 3 AA2 3 PHE A 381 TYR A 382 -1 N PHE A 381 O MET A 390 SHEET 1 AA3 5 ILE A 376 PHE A 377 0 SHEET 2 AA3 5 LYS A 389 TYR A 395 -1 O ILE A 394 N ILE A 376 SHEET 3 AA3 5 HIS A 406 MET A 414 -1 O PHE A 410 N ARG A 393 SHEET 4 AA3 5 SER A 467 PRO A 474 -1 O CYS A 473 N LEU A 407 SHEET 5 AA3 5 ILE G 205 GLN G 206 -1 O ILE G 205 N GLY A 468 SHEET 1 AA4 4 VAL B 353 ILE B 358 0 SHEET 2 AA4 4 ILE B 490 VAL B 496 -1 O ILE B 492 N TRP B 356 SHEET 3 AA4 4 VAL B 430 LEU B 434 -1 N THR B 431 O ILE B 495 SHEET 4 AA4 4 VAL B 443 PHE B 447 -1 O ASP B 445 N LEU B 432 SHEET 1 AA5 3 ILE B 376 PHE B 377 0 SHEET 2 AA5 3 LYS B 389 TYR B 395 -1 O ILE B 394 N ILE B 376 SHEET 3 AA5 3 PHE B 381 TYR B 382 -1 N PHE B 381 O MET B 390 SHEET 1 AA6 5 ILE B 376 PHE B 377 0 SHEET 2 AA6 5 LYS B 389 TYR B 395 -1 O ILE B 394 N ILE B 376 SHEET 3 AA6 5 HIS B 406 MET B 414 -1 O PHE B 410 N ARG B 393 SHEET 4 AA6 5 SER B 467 PRO B 474 -1 O CYS B 473 N LEU B 407 SHEET 5 AA6 5 ILE H 205 GLN H 206 -1 O ILE H 205 N GLY B 468 SHEET 1 AA7 4 VAL C 353 SER C 359 0 SHEET 2 AA7 4 ALA C 489 VAL C 496 -1 O ILE C 492 N TRP C 356 SHEET 3 AA7 4 VAL C 430 LEU C 434 -1 N MET C 433 O LYS C 493 SHEET 4 AA7 4 VAL C 443 PHE C 447 -1 O ASP C 445 N LEU C 432 SHEET 1 AA8 3 ILE C 376 PHE C 377 0 SHEET 2 AA8 3 LYS C 389 TYR C 395 -1 O ILE C 394 N ILE C 376 SHEET 3 AA8 3 PHE C 381 TYR C 382 -1 N PHE C 381 O MET C 390 SHEET 1 AA9 4 ILE C 376 PHE C 377 0 SHEET 2 AA9 4 LYS C 389 TYR C 395 -1 O ILE C 394 N ILE C 376 SHEET 3 AA9 4 HIS C 406 MET C 414 -1 O MET C 414 N LYS C 389 SHEET 4 AA9 4 SER C 467 PRO C 474 -1 O CYS C 473 N LEU C 407 SHEET 1 AB1 4 VAL D 353 SER D 359 0 SHEET 2 AB1 4 ALA D 489 VAL D 496 -1 O ILE D 492 N TRP D 356 SHEET 3 AB1 4 VAL D 430 LEU D 434 -1 N MET D 433 O LYS D 493 SHEET 4 AB1 4 VAL D 443 PHE D 447 -1 O PHE D 447 N VAL D 430 SHEET 1 AB2 3 ILE D 376 PHE D 377 0 SHEET 2 AB2 3 LYS D 389 TYR D 395 -1 O ILE D 394 N ILE D 376 SHEET 3 AB2 3 PHE D 381 TYR D 382 -1 N PHE D 381 O MET D 390 SHEET 1 AB3 5 ILE D 376 PHE D 377 0 SHEET 2 AB3 5 LYS D 389 TYR D 395 -1 O ILE D 394 N ILE D 376 SHEET 3 AB3 5 HIS D 406 MET D 414 -1 O MET D 414 N LYS D 389 SHEET 4 AB3 5 SER D 467 PRO D 474 -1 O CYS D 473 N LEU D 407 SHEET 5 AB3 5 ILE I 205 GLN I 206 -1 O ILE I 205 N GLY D 468 SHEET 1 AB4 4 VAL E 353 ILE E 358 0 SHEET 2 AB4 4 ILE E 490 VAL E 496 -1 O ILE E 492 N TRP E 356 SHEET 3 AB4 4 VAL E 430 LEU E 434 -1 N MET E 433 O LYS E 493 SHEET 4 AB4 4 VAL E 443 PHE E 447 -1 O ASP E 445 N LEU E 432 SHEET 1 AB5 3 ILE E 376 PHE E 377 0 SHEET 2 AB5 3 LYS E 389 TYR E 395 -1 O ILE E 394 N ILE E 376 SHEET 3 AB5 3 PHE E 381 TYR E 382 -1 N PHE E 381 O MET E 390 SHEET 1 AB6 4 ILE E 376 PHE E 377 0 SHEET 2 AB6 4 LYS E 389 TYR E 395 -1 O ILE E 394 N ILE E 376 SHEET 3 AB6 4 HIS E 406 MET E 414 -1 O MET E 414 N LYS E 389 SHEET 4 AB6 4 SER E 467 PRO E 474 -1 O CYS E 473 N LEU E 407 SHEET 1 AB7 4 VAL F 353 ILE F 358 0 SHEET 2 AB7 4 ILE F 490 VAL F 496 -1 O ILE F 492 N TRP F 356 SHEET 3 AB7 4 VAL F 430 LEU F 434 -1 N MET F 433 O LYS F 493 SHEET 4 AB7 4 VAL F 443 PHE F 447 -1 O ASP F 445 N LEU F 432 SHEET 1 AB8 3 ALA F 375 PHE F 377 0 SHEET 2 AB8 3 LYS F 389 TYR F 395 -1 O ILE F 394 N ILE F 376 SHEET 3 AB8 3 PHE F 381 TYR F 382 -1 N PHE F 381 O MET F 390 SHEET 1 AB9 4 ALA F 375 PHE F 377 0 SHEET 2 AB9 4 LYS F 389 TYR F 395 -1 O ILE F 394 N ILE F 376 SHEET 3 AB9 4 HIS F 406 MET F 414 -1 O PHE F 410 N ARG F 393 SHEET 4 AB9 4 SER F 467 PRO F 474 -1 O CYS F 473 N LEU F 407 CISPEP 1 TRP A 424 PRO A 425 0 1.74 CISPEP 2 TRP B 424 PRO B 425 0 1.56 CISPEP 3 TRP C 424 PRO C 425 0 4.07 CISPEP 4 TRP D 424 PRO D 425 0 1.72 CISPEP 5 TRP E 424 PRO E 425 0 2.04 CISPEP 6 TRP F 424 PRO F 425 0 -4.06 CRYST1 135.200 84.220 124.390 90.00 118.82 90.00 C 1 2 1 24 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 0.007396 0.000000 0.004070 0.00000 SCALE2 0.000000 0.011874 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009176 0.00000