PDB Short entry for 3JVZ HEADER LIGASE/SIGNALING PROTEIN 17-SEP-09 3JVZ TITLE E2~UBIQUITIN-HECT COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 D2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: UBIQUITIN-PROTEIN LIGASE D2, UBIQUITIN CARRIER PROTEIN D2, COMPND 5 UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2, E2(17)KB 2; COMPND 6 EC: 6.3.2.19; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE NEDD4-LIKE; COMPND 11 CHAIN: C, D; COMPND 12 FRAGMENT: HECT DOMAIN; COMPND 13 SYNONYM: NEDD4-2, NEDD4.2; COMPND 14 EC: 6.3.2.-; COMPND 15 ENGINEERED: YES; COMPND 16 MUTATION: YES; COMPND 17 MOL_ID: 3; COMPND 18 MOLECULE: UBIQUITIN; COMPND 19 CHAIN: X, Y; COMPND 20 ENGINEERED: YES; COMPND 21 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UBE2D2, UBC4, UBCH5B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: NEDD4L, KIAA0439, NEDL3; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITIN, HECT, E3, UBIQUITIN LIGASE, UBCH5B, NEDD4L, NEDD4-2, KEYWDS 2 LIGASE, UBL CONJUGATION PATHWAY, HOST-VIRUS INTERACTION, LIGASE- KEYWDS 3 SIGNALING PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.SOUPHRON,H.B.KAMADURAI,B.A.SCHULMAN REVDAT 4 06-SEP-23 3JVZ 1 REMARK REVDAT 3 13-OCT-21 3JVZ 1 SEQADV LINK REVDAT 2 21-MAR-12 3JVZ 1 JRNL VERSN REVDAT 1 12-JAN-10 3JVZ 0 JRNL AUTH H.B.KAMADURAI,J.SOUPHRON,D.C.SCOTT,D.M.DUDA,D.J.MILLER, JRNL AUTH 2 D.STRINGER,R.C.PIPER,B.A.SCHULMAN JRNL TITL INSIGHTS INTO UBIQUITIN TRANSFER CASCADES FROM A STRUCTURE JRNL TITL 2 OF A UBCH5B APPROXIMATELY UBIQUITIN-HECT(NEDD4L) COMPLEX. JRNL REF MOL.CELL V. 36 1095 2009 JRNL REFN ISSN 1097-2765 JRNL PMID 20064473 JRNL DOI 10.1016/J.MOLCEL.2009.11.010 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.5 REMARK 3 NUMBER OF REFLECTIONS : 25449 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1234 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 9814 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3JVZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000055228. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 5.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25449 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : 0.09200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.5500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.56800 REMARK 200 R SYM FOR SHELL (I) : 0.56800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.370 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: 2C4O.PDB, 2ONI.PDB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, PH 5.1-5.2, 2.4 REMARK 280 -2.5 M SODIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 54.85350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.85350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 86.99000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 99.94400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 86.99000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 99.94400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 54.85350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 86.99000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 99.94400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 54.85350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 86.99000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 99.94400 REMARK 290 SMTRY3 8 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, X 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D, Y 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 GLY C 571 REMARK 465 SER C 572 REMARK 465 PRO C 573 REMARK 465 PHE C 951 REMARK 465 GLU C 952 REMARK 465 GLY C 953 REMARK 465 VAL C 954 REMARK 465 ASP C 955 REMARK 465 GLY D 571 REMARK 465 SER D 572 REMARK 465 PRO D 573 REMARK 465 GLU D 574 REMARK 465 PHE D 575 REMARK 465 GLY D 950 REMARK 465 PHE D 951 REMARK 465 GLU D 952 REMARK 465 GLY D 953 REMARK 465 VAL D 954 REMARK 465 ASP D 955 REMARK 465 GLY X -4 REMARK 465 SER X -3 REMARK 465 GLY X -2 REMARK 465 GLY X -1 REMARK 465 SER X 0 REMARK 465 GLY Y -4 REMARK 465 SER Y -3 REMARK 465 GLY Y -2 REMARK 465 GLY Y -1 REMARK 465 SER Y 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG SER A 85 O GLY X 76 2.18 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 ALA A 14 43.59 -84.43 REMARK 500 ARG A 15 -37.52 -132.86 REMARK 500 ASP A 16 66.71 -152.63 REMARK 500 ARG A 90 -86.54 -121.80 REMARK 500 ASP A 112 77.13 -113.75 REMARK 500 PRO A 113 170.26 -48.62 REMARK 500 ASP A 130 69.43 -100.98 REMARK 500 SER B 3 -81.00 -40.28 REMARK 500 ASP B 16 54.87 -163.33 REMARK 500 ASP B 28 -51.90 -130.57 REMARK 500 PRO B 44 -2.64 -59.21 REMARK 500 PRO B 57 175.04 -59.04 REMARK 500 ASN B 81 24.58 -75.47 REMARK 500 ARG B 90 -79.05 -132.29 REMARK 500 ASP B 117 52.07 -148.23 REMARK 500 LEU B 119 -52.81 -127.18 REMARK 500 THR B 129 -81.39 -63.67 REMARK 500 PHE C 577 -38.12 -34.16 REMARK 500 PRO C 591 176.31 -57.70 REMARK 500 ASP C 593 46.87 -67.11 REMARK 500 PRO C 595 160.35 -43.13 REMARK 500 ASN C 606 45.57 -149.63 REMARK 500 PHE C 608 -74.42 -60.09 REMARK 500 MET C 616 5.68 -65.20 REMARK 500 ALA C 626 -178.89 -66.63 REMARK 500 GLU C 633 14.28 -68.45 REMARK 500 SER C 634 -72.07 -120.79 REMARK 500 ASP C 639 -68.46 -126.14 REMARK 500 PHE C 656 45.52 -99.14 REMARK 500 ASN C 678 36.28 -98.80 REMARK 500 ASP C 685 44.64 -166.83 REMARK 500 ASP C 733 82.00 -152.25 REMARK 500 PRO C 748 30.94 -97.05 REMARK 500 ASP C 752 72.56 49.35 REMARK 500 CYS C 756 122.88 -176.41 REMARK 500 ASN C 761 126.90 179.81 REMARK 500 ILE C 777 137.05 -39.24 REMARK 500 VAL C 797 -72.68 -128.04 REMARK 500 ASN C 798 -64.16 -24.44 REMARK 500 VAL C 800 17.86 -140.21 REMARK 500 LEU C 814 -30.48 -140.64 REMARK 500 PRO C 902 129.62 -39.52 REMARK 500 ASN C 924 50.45 38.59 REMARK 500 PRO C 930 74.88 -66.88 REMARK 500 GLU C 946 -72.50 -57.72 REMARK 500 GLN C 949 26.50 87.77 REMARK 500 PHE D 577 -39.10 -38.38 REMARK 500 LYS D 636 56.55 -116.52 REMARK 500 PRO D 658 -33.78 -34.11 REMARK 500 ASP D 708 76.81 -111.09 REMARK 500 REMARK 500 THIS ENTRY HAS 79 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3JW0 RELATED DB: PDB DBREF 3JVZ A 2 147 UNP P62837 UB2D2_HUMAN 2 147 DBREF 3JVZ B 2 147 UNP P62837 UB2D2_HUMAN 2 147 DBREF 3JVZ C 576 955 UNP Q96PU5 NED4L_HUMAN 596 975 DBREF 3JVZ D 576 955 UNP Q96PU5 NED4L_HUMAN 596 975 DBREF 3JVZ X 1 76 UNP P62988 UBIQ_HUMAN 1 76 DBREF 3JVZ Y 1 76 UNP P62988 UBIQ_HUMAN 1 76 SEQADV 3JVZ SER A 3 UNP P62837 LEU 3 ENGINEERED MUTATION SEQADV 3JVZ SER A 85 UNP P62837 CYS 85 ENGINEERED MUTATION SEQADV 3JVZ LYS A 98 UNP P62837 THR 98 ENGINEERED MUTATION SEQADV 3JVZ SER B 3 UNP P62837 LEU 3 ENGINEERED MUTATION SEQADV 3JVZ SER B 85 UNP P62837 CYS 85 ENGINEERED MUTATION SEQADV 3JVZ LYS B 98 UNP P62837 THR 98 ENGINEERED MUTATION SEQADV 3JVZ GLY C 571 UNP Q96PU5 EXPRESSION TAG SEQADV 3JVZ SER C 572 UNP Q96PU5 EXPRESSION TAG SEQADV 3JVZ PRO C 573 UNP Q96PU5 EXPRESSION TAG SEQADV 3JVZ GLU C 574 UNP Q96PU5 EXPRESSION TAG SEQADV 3JVZ PHE C 575 UNP Q96PU5 EXPRESSION TAG SEQADV 3JVZ ALA C 922 UNP Q96PU5 CYS 942 ENGINEERED MUTATION SEQADV 3JVZ GLY D 571 UNP Q96PU5 EXPRESSION TAG SEQADV 3JVZ SER D 572 UNP Q96PU5 EXPRESSION TAG SEQADV 3JVZ PRO D 573 UNP Q96PU5 EXPRESSION TAG SEQADV 3JVZ GLU D 574 UNP Q96PU5 EXPRESSION TAG SEQADV 3JVZ PHE D 575 UNP Q96PU5 EXPRESSION TAG SEQADV 3JVZ ALA D 922 UNP Q96PU5 CYS 942 ENGINEERED MUTATION SEQADV 3JVZ GLY X -4 UNP P62988 EXPRESSION TAG SEQADV 3JVZ SER X -3 UNP P62988 EXPRESSION TAG SEQADV 3JVZ GLY X -2 UNP P62988 EXPRESSION TAG SEQADV 3JVZ GLY X -1 UNP P62988 EXPRESSION TAG SEQADV 3JVZ SER X 0 UNP P62988 EXPRESSION TAG SEQADV 3JVZ GLY Y -4 UNP P62988 EXPRESSION TAG SEQADV 3JVZ SER Y -3 UNP P62988 EXPRESSION TAG SEQADV 3JVZ GLY Y -2 UNP P62988 EXPRESSION TAG SEQADV 3JVZ GLY Y -1 UNP P62988 EXPRESSION TAG SEQADV 3JVZ SER Y 0 UNP P62988 EXPRESSION TAG SEQRES 1 A 146 ALA SER LYS ARG ILE HIS LYS GLU LEU ASN ASP LEU ALA SEQRES 2 A 146 ARG ASP PRO PRO ALA GLN CYS SER ALA GLY PRO VAL GLY SEQRES 3 A 146 ASP ASP MET PHE HIS TRP GLN ALA THR ILE MET GLY PRO SEQRES 4 A 146 ASN ASP SER PRO TYR GLN GLY GLY VAL PHE PHE LEU THR SEQRES 5 A 146 ILE HIS PHE PRO THR ASP TYR PRO PHE LYS PRO PRO LYS SEQRES 6 A 146 VAL ALA PHE THR THR ARG ILE TYR HIS PRO ASN ILE ASN SEQRES 7 A 146 SER ASN GLY SER ILE SER LEU ASP ILE LEU ARG SER GLN SEQRES 8 A 146 TRP SER PRO ALA LEU LYS ILE SER LYS VAL LEU LEU SER SEQRES 9 A 146 ILE CYS SER LEU LEU CYS ASP PRO ASN PRO ASP ASP PRO SEQRES 10 A 146 LEU VAL PRO GLU ILE ALA ARG ILE TYR LYS THR ASP ARG SEQRES 11 A 146 GLU LYS TYR ASN ARG ILE ALA ARG GLU TRP THR GLN LYS SEQRES 12 A 146 TYR ALA MET SEQRES 1 B 146 ALA SER LYS ARG ILE HIS LYS GLU LEU ASN ASP LEU ALA SEQRES 2 B 146 ARG ASP PRO PRO ALA GLN CYS SER ALA GLY PRO VAL GLY SEQRES 3 B 146 ASP ASP MET PHE HIS TRP GLN ALA THR ILE MET GLY PRO SEQRES 4 B 146 ASN ASP SER PRO TYR GLN GLY GLY VAL PHE PHE LEU THR SEQRES 5 B 146 ILE HIS PHE PRO THR ASP TYR PRO PHE LYS PRO PRO LYS SEQRES 6 B 146 VAL ALA PHE THR THR ARG ILE TYR HIS PRO ASN ILE ASN SEQRES 7 B 146 SER ASN GLY SER ILE SER LEU ASP ILE LEU ARG SER GLN SEQRES 8 B 146 TRP SER PRO ALA LEU LYS ILE SER LYS VAL LEU LEU SER SEQRES 9 B 146 ILE CYS SER LEU LEU CYS ASP PRO ASN PRO ASP ASP PRO SEQRES 10 B 146 LEU VAL PRO GLU ILE ALA ARG ILE TYR LYS THR ASP ARG SEQRES 11 B 146 GLU LYS TYR ASN ARG ILE ALA ARG GLU TRP THR GLN LYS SEQRES 12 B 146 TYR ALA MET SEQRES 1 C 385 GLY SER PRO GLU PHE GLU PHE LYS GLN LYS TYR ASP TYR SEQRES 2 C 385 PHE ARG LYS LYS LEU LYS LYS PRO ALA ASP ILE PRO ASN SEQRES 3 C 385 ARG PHE GLU MET LYS LEU HIS ARG ASN ASN ILE PHE GLU SEQRES 4 C 385 GLU SER TYR ARG ARG ILE MET SER VAL LYS ARG PRO ASP SEQRES 5 C 385 VAL LEU LYS ALA ARG LEU TRP ILE GLU PHE GLU SER GLU SEQRES 6 C 385 LYS GLY LEU ASP TYR GLY GLY VAL ALA ARG GLU TRP PHE SEQRES 7 C 385 PHE LEU LEU SER LYS GLU MET PHE ASN PRO TYR TYR GLY SEQRES 8 C 385 LEU PHE GLU TYR SER ALA THR ASP ASN TYR THR LEU GLN SEQRES 9 C 385 ILE ASN PRO ASN SER GLY LEU CYS ASN GLU ASP HIS LEU SEQRES 10 C 385 SER TYR PHE THR PHE ILE GLY ARG VAL ALA GLY LEU ALA SEQRES 11 C 385 VAL PHE HIS GLY LYS LEU LEU ASP GLY PHE PHE ILE ARG SEQRES 12 C 385 PRO PHE TYR LYS MET MET LEU GLY LYS GLN ILE THR LEU SEQRES 13 C 385 ASN ASP MET GLU SER VAL ASP SER GLU TYR TYR ASN SER SEQRES 14 C 385 LEU LYS TRP ILE LEU GLU ASN ASP PRO THR GLU LEU ASP SEQRES 15 C 385 LEU MET PHE CYS ILE ASP GLU GLU ASN PHE GLY GLN THR SEQRES 16 C 385 TYR GLN VAL ASP LEU LYS PRO ASN GLY SER GLU ILE MET SEQRES 17 C 385 VAL THR ASN GLU ASN LYS ARG GLU TYR ILE ASP LEU VAL SEQRES 18 C 385 ILE GLN TRP ARG PHE VAL ASN ARG VAL GLN LYS GLN MET SEQRES 19 C 385 ASN ALA PHE LEU GLU GLY PHE THR GLU LEU LEU PRO ILE SEQRES 20 C 385 ASP LEU ILE LYS ILE PHE ASP GLU ASN GLU LEU GLU LEU SEQRES 21 C 385 LEU MET CYS GLY LEU GLY ASP VAL ASP VAL ASN ASP TRP SEQRES 22 C 385 ARG GLN HIS SER ILE TYR LYS ASN GLY TYR CYS PRO ASN SEQRES 23 C 385 HIS PRO VAL ILE GLN TRP PHE TRP LYS ALA VAL LEU LEU SEQRES 24 C 385 MET ASP ALA GLU LYS ARG ILE ARG LEU LEU GLN PHE VAL SEQRES 25 C 385 THR GLY THR SER ARG VAL PRO MET ASN GLY PHE ALA GLU SEQRES 26 C 385 LEU TYR GLY SER ASN GLY PRO GLN LEU PHE THR ILE GLU SEQRES 27 C 385 GLN TRP GLY SER PRO GLU LYS LEU PRO ARG ALA HIS THR SEQRES 28 C 385 ALA PHE ASN ARG LEU ASP LEU PRO PRO TYR GLU THR PHE SEQRES 29 C 385 GLU ASP LEU ARG GLU LYS LEU LEU MET ALA VAL GLU ASN SEQRES 30 C 385 ALA GLN GLY PHE GLU GLY VAL ASP SEQRES 1 D 385 GLY SER PRO GLU PHE GLU PHE LYS GLN LYS TYR ASP TYR SEQRES 2 D 385 PHE ARG LYS LYS LEU LYS LYS PRO ALA ASP ILE PRO ASN SEQRES 3 D 385 ARG PHE GLU MET LYS LEU HIS ARG ASN ASN ILE PHE GLU SEQRES 4 D 385 GLU SER TYR ARG ARG ILE MET SER VAL LYS ARG PRO ASP SEQRES 5 D 385 VAL LEU LYS ALA ARG LEU TRP ILE GLU PHE GLU SER GLU SEQRES 6 D 385 LYS GLY LEU ASP TYR GLY GLY VAL ALA ARG GLU TRP PHE SEQRES 7 D 385 PHE LEU LEU SER LYS GLU MET PHE ASN PRO TYR TYR GLY SEQRES 8 D 385 LEU PHE GLU TYR SER ALA THR ASP ASN TYR THR LEU GLN SEQRES 9 D 385 ILE ASN PRO ASN SER GLY LEU CYS ASN GLU ASP HIS LEU SEQRES 10 D 385 SER TYR PHE THR PHE ILE GLY ARG VAL ALA GLY LEU ALA SEQRES 11 D 385 VAL PHE HIS GLY LYS LEU LEU ASP GLY PHE PHE ILE ARG SEQRES 12 D 385 PRO PHE TYR LYS MET MET LEU GLY LYS GLN ILE THR LEU SEQRES 13 D 385 ASN ASP MET GLU SER VAL ASP SER GLU TYR TYR ASN SER SEQRES 14 D 385 LEU LYS TRP ILE LEU GLU ASN ASP PRO THR GLU LEU ASP SEQRES 15 D 385 LEU MET PHE CYS ILE ASP GLU GLU ASN PHE GLY GLN THR SEQRES 16 D 385 TYR GLN VAL ASP LEU LYS PRO ASN GLY SER GLU ILE MET SEQRES 17 D 385 VAL THR ASN GLU ASN LYS ARG GLU TYR ILE ASP LEU VAL SEQRES 18 D 385 ILE GLN TRP ARG PHE VAL ASN ARG VAL GLN LYS GLN MET SEQRES 19 D 385 ASN ALA PHE LEU GLU GLY PHE THR GLU LEU LEU PRO ILE SEQRES 20 D 385 ASP LEU ILE LYS ILE PHE ASP GLU ASN GLU LEU GLU LEU SEQRES 21 D 385 LEU MET CYS GLY LEU GLY ASP VAL ASP VAL ASN ASP TRP SEQRES 22 D 385 ARG GLN HIS SER ILE TYR LYS ASN GLY TYR CYS PRO ASN SEQRES 23 D 385 HIS PRO VAL ILE GLN TRP PHE TRP LYS ALA VAL LEU LEU SEQRES 24 D 385 MET ASP ALA GLU LYS ARG ILE ARG LEU LEU GLN PHE VAL SEQRES 25 D 385 THR GLY THR SER ARG VAL PRO MET ASN GLY PHE ALA GLU SEQRES 26 D 385 LEU TYR GLY SER ASN GLY PRO GLN LEU PHE THR ILE GLU SEQRES 27 D 385 GLN TRP GLY SER PRO GLU LYS LEU PRO ARG ALA HIS THR SEQRES 28 D 385 ALA PHE ASN ARG LEU ASP LEU PRO PRO TYR GLU THR PHE SEQRES 29 D 385 GLU ASP LEU ARG GLU LYS LEU LEU MET ALA VAL GLU ASN SEQRES 30 D 385 ALA GLN GLY PHE GLU GLY VAL ASP SEQRES 1 X 81 GLY SER GLY GLY SER MET GLN ILE PHE VAL LYS THR LEU SEQRES 2 X 81 THR GLY LYS THR ILE THR LEU GLU VAL GLU PRO SER ASP SEQRES 3 X 81 THR ILE GLU ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU SEQRES 4 X 81 GLY ILE PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY SEQRES 5 X 81 LYS GLN LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN SEQRES 6 X 81 ILE GLN LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU SEQRES 7 X 81 ARG GLY GLY SEQRES 1 Y 81 GLY SER GLY GLY SER MET GLN ILE PHE VAL LYS THR LEU SEQRES 2 Y 81 THR GLY LYS THR ILE THR LEU GLU VAL GLU PRO SER ASP SEQRES 3 Y 81 THR ILE GLU ASN VAL LYS ALA LYS ILE GLN ASP LYS GLU SEQRES 4 Y 81 GLY ILE PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY SEQRES 5 Y 81 LYS GLN LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN SEQRES 6 Y 81 ILE GLN LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU SEQRES 7 Y 81 ARG GLY GLY HELIX 1 1 ALA A 2 ASP A 12 1 11 HELIX 2 2 LEU A 13 ASP A 16 5 4 HELIX 3 3 LEU A 86 ARG A 90 5 5 HELIX 4 4 LYS A 98 ASP A 112 1 15 HELIX 5 5 VAL A 120 THR A 129 1 10 HELIX 6 6 ASP A 130 ALA A 146 1 17 HELIX 7 7 ALA B 2 ASP B 16 1 15 HELIX 8 8 LEU B 86 ARG B 90 5 5 HELIX 9 9 LYS B 98 ASP B 112 1 15 HELIX 10 10 VAL B 120 THR B 129 1 10 HELIX 11 11 ASP B 130 ALA B 146 1 17 HELIX 12 12 GLU C 574 LEU C 588 1 15 HELIX 13 13 HIS C 603 ASN C 605 5 3 HELIX 14 14 ASN C 606 MET C 616 1 11 HELIX 15 15 ASP C 622 ALA C 626 5 5 HELIX 16 16 GLY C 642 PHE C 656 1 15 HELIX 17 17 ASP C 685 HIS C 703 1 19 HELIX 18 18 ILE C 712 GLY C 721 1 10 HELIX 19 19 THR C 725 ASN C 727 5 3 HELIX 20 20 ASP C 728 ASP C 733 1 6 HELIX 21 21 ASP C 733 ASN C 746 1 14 HELIX 22 22 ASN C 783 VAL C 797 1 15 HELIX 23 23 VAL C 800 THR C 812 1 13 HELIX 24 24 PRO C 816 LYS C 821 5 6 HELIX 25 25 ASP C 824 GLY C 834 1 11 HELIX 26 26 ASP C 839 GLN C 845 1 7 HELIX 27 27 HIS C 857 MET C 870 1 14 HELIX 28 28 ASP C 871 GLY C 884 1 14 HELIX 29 29 GLY C 892 GLU C 895 5 4 HELIX 30 30 THR C 933 ASN C 947 1 15 HELIX 31 31 GLU D 576 LEU D 588 1 13 HELIX 32 32 ASN D 606 SER D 617 1 12 HELIX 33 33 ARG D 620 LYS D 625 5 6 HELIX 34 34 VAL D 643 PHE D 656 1 14 HELIX 35 35 ASN D 657 GLY D 661 5 5 HELIX 36 36 ASN D 678 ASN D 683 1 6 HELIX 37 37 ASP D 685 GLY D 704 1 20 HELIX 38 38 ILE D 712 GLY D 721 1 10 HELIX 39 39 THR D 725 ASN D 727 5 3 HELIX 40 40 ASP D 728 ASP D 733 1 6 HELIX 41 41 ASP D 733 ASN D 746 1 14 HELIX 42 42 PRO D 748 ASP D 752 5 5 HELIX 43 43 ASN D 773 ILE D 777 5 5 HELIX 44 44 ASN D 783 VAL D 797 1 15 HELIX 45 45 VAL D 800 THR D 812 1 13 HELIX 46 46 PRO D 816 LYS D 821 1 6 HELIX 47 47 ASN D 826 CYS D 833 1 8 HELIX 48 48 ASP D 839 HIS D 846 1 8 HELIX 49 49 HIS D 857 MET D 870 1 14 HELIX 50 50 ASP D 871 GLY D 884 1 14 HELIX 51 51 GLY D 892 GLU D 895 5 4 HELIX 52 52 ASP D 936 GLU D 946 1 11 HELIX 53 53 THR X 22 GLN X 31 1 10 HELIX 54 54 PRO X 37 GLN X 41 5 5 HELIX 55 55 THR Y 22 ILE Y 30 1 9 HELIX 56 56 ILE Y 30 GLY Y 35 1 6 HELIX 57 57 PRO Y 37 ASP Y 39 5 3 SHEET 1 A 4 CYS A 21 PRO A 25 0 SHEET 2 A 4 HIS A 32 MET A 38 -1 O GLN A 34 N GLY A 24 SHEET 3 A 4 VAL A 49 HIS A 55 -1 O ILE A 54 N TRP A 33 SHEET 4 A 4 LYS A 66 PHE A 69 -1 O LYS A 66 N HIS A 55 SHEET 1 B 4 CYS B 21 PRO B 25 0 SHEET 2 B 4 HIS B 32 MET B 38 -1 O GLN B 34 N GLY B 24 SHEET 3 B 4 VAL B 49 HIS B 55 -1 O PHE B 50 N ILE B 37 SHEET 4 B 4 LYS B 66 PHE B 69 -1 O ALA B 68 N THR B 53 SHEET 1 C 2 ARG C 597 LYS C 601 0 SHEET 2 C 2 ARG C 627 GLU C 631 1 O ARG C 627 N PHE C 598 SHEET 1 D 2 PHE C 663 TYR C 665 0 SHEET 2 D 2 LEU C 673 ILE C 675 -1 O GLN C 674 N GLU C 664 SHEET 1 E 2 CYS C 756 ASP C 758 0 SHEET 2 E 2 GLN C 767 ASP C 769 -1 O VAL C 768 N ILE C 757 SHEET 1 F 4 ILE C 848 LYS C 850 0 SHEET 2 F 4 THR C 906 GLN C 909 1 O ILE C 907 N ILE C 848 SHEET 3 F 4 ARG C 925 LEU C 928 1 O LEU C 926 N GLU C 908 SHEET 4 F 4 ARG C 918 HIS C 920 -1 N ARG C 918 O ASP C 927 SHEET 1 G 2 TYR C 897 GLY C 898 0 SHEET 2 G 2 GLY C 901 PRO C 902 -1 O GLY C 901 N GLY C 898 SHEET 1 H 3 ARG D 597 HIS D 603 0 SHEET 2 H 3 ARG D 627 GLU D 633 1 O TRP D 629 N MET D 600 SHEET 3 H 3 ASP D 639 GLY D 641 -1 O TYR D 640 N PHE D 632 SHEET 1 I 2 PHE D 663 TYR D 665 0 SHEET 2 I 2 LEU D 673 ILE D 675 -1 O GLN D 674 N GLU D 664 SHEET 1 J 2 CYS D 756 ASN D 761 0 SHEET 2 J 2 GLN D 764 ASP D 769 -1 O VAL D 768 N ILE D 757 SHEET 1 K 4 ILE D 848 LYS D 850 0 SHEET 2 K 4 THR D 906 GLN D 909 1 O ILE D 907 N ILE D 848 SHEET 3 K 4 ARG D 925 LEU D 928 1 O LEU D 926 N THR D 906 SHEET 4 K 4 ARG D 918 ALA D 919 -1 N ARG D 918 O ASP D 927 SHEET 1 L 2 TYR D 897 GLY D 898 0 SHEET 2 L 2 GLY D 901 PRO D 902 -1 O GLY D 901 N GLY D 898 SHEET 1 M 4 THR X 12 GLU X 16 0 SHEET 2 M 4 GLN X 2 THR X 7 -1 N VAL X 5 O ILE X 13 SHEET 3 M 4 THR X 66 LEU X 69 1 O LEU X 69 N LYS X 6 SHEET 4 M 4 LEU X 43 ILE X 44 -1 N ILE X 44 O HIS X 68 SHEET 1 N 3 THR Y 12 LEU Y 15 0 SHEET 2 N 3 ILE Y 3 LYS Y 6 -1 N ILE Y 3 O LEU Y 15 SHEET 3 N 3 SER Y 65 THR Y 66 1 O SER Y 65 N PHE Y 4 SHEET 1 O 2 GLN Y 41 ILE Y 44 0 SHEET 2 O 2 HIS Y 68 LEU Y 71 -1 O HIS Y 68 N ILE Y 44 LINK OG SER A 85 C GLY X 76 1555 1555 1.31 LINK OG SER B 85 C GLY Y 76 1555 1555 1.32 CISPEP 1 TYR A 60 PRO A 61 0 1.62 CISPEP 2 TYR B 60 PRO B 61 0 -2.05 CRYST1 173.980 199.888 109.707 90.00 90.00 90.00 C 2 2 21 16 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 0.005748 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005003 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009115 0.00000