PDB Short entry for 3CL3 HEADER VIRAL PROTEIN/SIGNALING PROTEIN 18-MAR-08 3CL3 TITLE CRYSTAL STRUCTURE OF A VFLIP-IKKGAMMA COMPLEX: INSIGHTS INTO VIRAL TITLE 2 ACTIVATION OF THE IKK SIGNALOSOME COMPND MOL_ID: 1; COMPND 2 MOLECULE: ORF K13; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 1-178; COMPND 5 SYNONYM: KS-VFLIP; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NF-KAPPA-B ESSENTIAL MODULATOR; COMPND 9 CHAIN: D, E; COMPND 10 FRAGMENT: RESIDUES 150-272; COMPND 11 SYNONYM: NEMO, NF-KAPPA-B ESSENTIAL MODIFIER, INHIBITOR OF NUCLEAR COMPND 12 FACTOR KAPPA-B KINASE SUBUNIT GAMMA, IKB KINASE SUBUNIT GAMMA, I- COMPND 13 KAPPA-B KINASE GAMMA, IKK-GAMMA, IKKG, IKB KINASE-ASSOCIATED PROTEIN COMPND 14 1, IKKAP1, FIP-3; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN GAMMAHERPESVIRUS 8; SOURCE 3 ORGANISM_TAXID: 37296; SOURCE 4 GENE: VFLIP; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B834; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETM442; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: IKBKG, FIP3, NEMO; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: B834; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PETM6T1 KEYWDS DEATH EFFECTOR DOMAIN, COILED-COIL, COILED COIL, CYTOPLASM, DISEASE KEYWDS 2 MUTATION, ECTODERMAL DYSPLASIA, HOST-VIRUS INTERACTION, NUCLEUS, KEYWDS 3 TRANSCRIPTION, TRANSCRIPTION REGULATION, VIRAL PROTEIN-SIGNALING KEYWDS 4 PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.BAGNERIS,A.V.AGEICHIK,N.CRONIN,C.BOSHOFF,G.WAKSMAN,T.BARRETT REVDAT 4 21-FEB-24 3CL3 1 REMARK REVDAT 3 13-JUN-18 3CL3 1 SOURCE DBREF SEQADV REVDAT 2 24-FEB-09 3CL3 1 VERSN REVDAT 1 17-JUN-08 3CL3 0 JRNL AUTH C.BAGNERIS,A.V.AGEICHIK,N.CRONIN,B.WALLACE,M.COLLINS, JRNL AUTH 2 C.BOSHOFF,G.WAKSMAN,T.BARRETT JRNL TITL CRYSTAL STRUCTURE OF A VFLIP-IKKGAMMA COMPLEX: INSIGHTS INTO JRNL TITL 2 VIRAL ACTIVATION OF THE IKK SIGNALOSOME. JRNL REF MOL.CELL V. 30 620 2008 JRNL REFN ISSN 1097-2765 JRNL PMID 18538660 JRNL DOI 10.1016/J.MOLCEL.2008.04.029 REMARK 2 REMARK 2 RESOLUTION. 3.20 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20830 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) : 0.261 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1065 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) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.25 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3600 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 55 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 : 3477 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) : 93.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.60 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) : 0.62 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : 6.00 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.288 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.436 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.564 ; 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: USED A MAXIMUM LIKELIHOOD TARGET REMARK 4 REMARK 4 3CL3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1000046907. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : CHANNEL CUT ESRF MONOCHROMATOR REMARK 200 OPTICS : WIGGLER REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20877 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 125.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : 0.10500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.50 REMARK 200 R MERGE FOR SHELL (I) : 0.10500 REMARK 200 R SYM FOR SHELL (I) : 0.54300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 225MM TRIS PH 7.5, 4% ETHYLENE GLYCOL, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.69333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.84667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 33.84667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 67.69333 REMARK 290 REMARK 290 REMARK: NULL 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, E 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 A -4 REMARK 465 ALA A -3 REMARK 465 MET A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 HIS A 174 REMARK 465 LEU A 175 REMARK 465 SER A 176 REMARK 465 GLY A 177 REMARK 465 PRO A 178 REMARK 465 GLY B -4 REMARK 465 ALA B -3 REMARK 465 MET B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 LYS B 118 REMARK 465 ASP B 119 REMARK 465 THR B 120 REMARK 465 ILE B 121 REMARK 465 GLY B 122 REMARK 465 SER B 123 REMARK 465 ARG B 124 REMARK 465 HIS B 174 REMARK 465 LEU B 175 REMARK 465 SER B 176 REMARK 465 GLY B 177 REMARK 465 PRO B 178 REMARK 465 GLY D 143 REMARK 465 HIS D 144 REMARK 465 MET D 145 REMARK 465 ALA D 146 REMARK 465 SER D 147 REMARK 465 GLY D 148 REMARK 465 SER D 149 REMARK 465 LEU D 150 REMARK 465 GLY D 151 REMARK 465 GLU D 152 REMARK 465 LEU D 153 REMARK 465 GLN D 154 REMARK 465 GLU D 155 REMARK 465 SER D 156 REMARK 465 GLN D 157 REMARK 465 SER D 158 REMARK 465 ARG D 159 REMARK 465 LEU D 160 REMARK 465 GLU D 161 REMARK 465 ALA D 162 REMARK 465 ALA D 163 REMARK 465 THR D 164 REMARK 465 LYS D 165 REMARK 465 GLU D 166 REMARK 465 CYS D 167 REMARK 465 GLN D 168 REMARK 465 ALA D 169 REMARK 465 LEU D 170 REMARK 465 GLU D 171 REMARK 465 GLY D 172 REMARK 465 ARG D 173 REMARK 465 ALA D 174 REMARK 465 ARG D 175 REMARK 465 ALA D 176 REMARK 465 ALA D 177 REMARK 465 SER D 178 REMARK 465 GLU D 179 REMARK 465 GLN D 180 REMARK 465 ALA D 181 REMARK 465 ARG D 182 REMARK 465 GLN D 183 REMARK 465 LEU D 184 REMARK 465 GLU D 185 REMARK 465 SER D 186 REMARK 465 GLU D 187 REMARK 465 ARG D 188 REMARK 465 GLU D 189 REMARK 465 ALA D 190 REMARK 465 LEU D 191 REMARK 465 GLN D 192 REMARK 465 SER D 252 REMARK 465 GLU D 253 REMARK 465 ARG D 254 REMARK 465 LYS D 255 REMARK 465 ARG D 256 REMARK 465 GLY D 257 REMARK 465 MET D 258 REMARK 465 GLN D 259 REMARK 465 LEU D 260 REMARK 465 GLU D 261 REMARK 465 ASP D 262 REMARK 465 LEU D 263 REMARK 465 LYS D 264 REMARK 465 GLN D 265 REMARK 465 GLN D 266 REMARK 465 LEU D 267 REMARK 465 GLN D 268 REMARK 465 GLN D 269 REMARK 465 ALA D 270 REMARK 465 GLU D 271 REMARK 465 GLU D 272 REMARK 465 GLY E 143 REMARK 465 HIS E 144 REMARK 465 MET E 145 REMARK 465 ALA E 146 REMARK 465 SER E 147 REMARK 465 GLY E 148 REMARK 465 SER E 149 REMARK 465 LEU E 150 REMARK 465 GLY E 151 REMARK 465 GLU E 152 REMARK 465 LEU E 153 REMARK 465 GLN E 154 REMARK 465 GLU E 155 REMARK 465 SER E 156 REMARK 465 GLN E 157 REMARK 465 SER E 158 REMARK 465 ARG E 159 REMARK 465 LEU E 160 REMARK 465 GLU E 161 REMARK 465 ALA E 162 REMARK 465 ALA E 163 REMARK 465 THR E 164 REMARK 465 LYS E 165 REMARK 465 GLU E 166 REMARK 465 CYS E 167 REMARK 465 GLN E 168 REMARK 465 ALA E 169 REMARK 465 LEU E 170 REMARK 465 GLU E 171 REMARK 465 GLY E 172 REMARK 465 ARG E 173 REMARK 465 ALA E 174 REMARK 465 ARG E 175 REMARK 465 ALA E 176 REMARK 465 ALA E 177 REMARK 465 SER E 178 REMARK 465 GLU E 179 REMARK 465 GLN E 180 REMARK 465 ALA E 181 REMARK 465 ARG E 182 REMARK 465 GLN E 183 REMARK 465 LEU E 184 REMARK 465 GLU E 185 REMARK 465 SER E 186 REMARK 465 GLU E 187 REMARK 465 ARG E 188 REMARK 465 GLU E 189 REMARK 465 ALA E 190 REMARK 465 LEU E 191 REMARK 465 GLN E 192 REMARK 465 GLN E 193 REMARK 465 GLN E 194 REMARK 465 HIS E 195 REMARK 465 ARG E 254 REMARK 465 LYS E 255 REMARK 465 ARG E 256 REMARK 465 GLY E 257 REMARK 465 MET E 258 REMARK 465 GLN E 259 REMARK 465 LEU E 260 REMARK 465 GLU E 261 REMARK 465 ASP E 262 REMARK 465 LEU E 263 REMARK 465 LYS E 264 REMARK 465 GLN E 265 REMARK 465 GLN E 266 REMARK 465 LEU E 267 REMARK 465 GLN E 268 REMARK 465 GLN E 269 REMARK 465 ALA E 270 REMARK 465 GLU E 271 REMARK 465 GLU E 272 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 35 CG CD1 CD2 REMARK 470 LYS A 46 CG CD CE NZ REMARK 470 LEU A 96 CG CD1 CD2 REMARK 470 LEU A 99 CG CD1 CD2 REMARK 470 ARG A 124 CG CD NE CZ NH1 NH2 REMARK 470 MET A 154 CG SD CE REMARK 470 GLN A 164 CG CD OE1 NE2 REMARK 470 ARG A 165 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 173 CG CD1 CD2 REMARK 470 TYR B 4 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU B 20 CG CD OE1 OE2 REMARK 470 LYS B 46 CG CD CE NZ REMARK 470 ARG B 78 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 82 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 99 CG CD1 CD2 REMARK 470 LEU B 116 CG CD1 CD2 REMARK 470 GLN B 128 CG CD OE1 NE2 REMARK 470 LEU B 140 CG CD1 CD2 REMARK 470 LEU B 142 CG CD1 CD2 REMARK 470 LEU B 143 CG CD1 CD2 REMARK 470 GLN B 164 CG CD OE1 NE2 REMARK 470 ARG B 165 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 173 CG CD1 CD2 REMARK 470 GLN D 194 CG CD OE1 NE2 REMARK 470 SER D 196 OG REMARK 470 GLN D 198 CG CD OE1 NE2 REMARK 470 GLN D 201 CG CD OE1 NE2 REMARK 470 LEU D 202 CG CD1 CD2 REMARK 470 SER D 208 OG REMARK 470 GLU D 210 CG CD OE1 OE2 REMARK 470 LEU D 213 CG CD1 CD2 REMARK 470 VAL D 250 CG1 CG2 REMARK 470 GLN E 201 CG CD OE1 NE2 REMARK 470 ARG E 203 CG CD NE CZ NH1 NH2 REMARK 470 GLN E 205 CG CD OE1 NE2 REMARK 470 GLN E 207 CG CD OE1 NE2 REMARK 470 ARG E 214 CG CD NE CZ NH1 NH2 REMARK 470 ARG E 225 CG CD NE CZ NH1 NH2 REMARK 470 LYS E 246 CG CD CE NZ REMARK 470 SER E 247 OG REMARK 470 SER E 248 OG REMARK 470 VAL E 249 CG1 CG2 REMARK 470 VAL E 250 CG1 CG2 REMARK 470 SER E 252 OG REMARK 470 GLU E 253 CG CD OE1 OE2 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 O SER A 117 N ASP A 119 2.06 REMARK 500 REMARK 500 REMARK: NULL 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 PRO B 127 C - N - CA ANGL. DEV. = 14.3 DEGREES REMARK 500 PRO B 127 C - N - CD ANGL. DEV. = -21.9 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 LEU A 14 -117.52 -61.31 REMARK 500 GLN A 32 67.31 31.60 REMARK 500 ARG A 65 55.41 -91.77 REMARK 500 ASP A 71 -35.80 -130.16 REMARK 500 LEU A 116 -19.69 -37.10 REMARK 500 SER A 117 -77.43 -105.13 REMARK 500 LYS A 118 -28.40 30.28 REMARK 500 SER A 125 -9.51 172.04 REMARK 500 THR A 126 145.71 63.45 REMARK 500 ASN A 139 11.55 -59.99 REMARK 500 LEU A 143 -164.99 -114.21 REMARK 500 ASP A 147 110.16 -164.77 REMARK 500 ARG A 160 64.76 -107.88 REMARK 500 PHE B 29 142.02 -36.55 REMARK 500 GLN B 32 60.99 27.21 REMARK 500 HIS B 74 39.35 71.18 REMARK 500 ALA B 85 24.26 -77.80 REMARK 500 THR B 87 -162.61 -122.44 REMARK 500 SER B 89 121.44 69.81 REMARK 500 ASP B 102 -39.28 -35.35 REMARK 500 LEU B 116 -15.70 -44.78 REMARK 500 GLN B 128 1.50 -169.59 REMARK 500 MET B 171 -97.35 -130.03 REMARK 500 ASP E 242 -70.47 -56.84 REMARK 500 VAL E 250 128.99 -171.12 REMARK 500 SER E 252 -132.95 -138.23 REMARK 500 REMARK 500 REMARK: NULL DBREF 3CL3 A 1 178 UNP P88961 P88961_HHV8 1 178 DBREF 3CL3 B 1 178 UNP P88961 P88961_HHV8 1 178 DBREF 3CL3 D 150 252 UNP Q9Y6K9 NEMO_HUMAN 150 272 DBREF 3CL3 E 150 252 UNP Q9Y6K9 NEMO_HUMAN 150 272 SEQADV 3CL3 GLY A -4 UNP P88961 EXPRESSION TAG SEQADV 3CL3 ALA A -3 UNP P88961 EXPRESSION TAG SEQADV 3CL3 MET A -2 UNP P88961 EXPRESSION TAG SEQADV 3CL3 GLY A -1 UNP P88961 EXPRESSION TAG SEQADV 3CL3 SER A 0 UNP P88961 EXPRESSION TAG SEQADV 3CL3 GLY B -4 UNP P88961 EXPRESSION TAG SEQADV 3CL3 ALA B -3 UNP P88961 EXPRESSION TAG SEQADV 3CL3 MET B -2 UNP P88961 EXPRESSION TAG SEQADV 3CL3 GLY B -1 UNP P88961 EXPRESSION TAG SEQADV 3CL3 SER B 0 UNP P88961 EXPRESSION TAG SEQADV 3CL3 GLY D 143 UNP Q9Y6K9 EXPRESSION TAG SEQADV 3CL3 HIS D 144 UNP Q9Y6K9 EXPRESSION TAG SEQADV 3CL3 MET D 145 UNP Q9Y6K9 EXPRESSION TAG SEQADV 3CL3 ALA D 146 UNP Q9Y6K9 EXPRESSION TAG SEQADV 3CL3 SER D 147 UNP Q9Y6K9 EXPRESSION TAG SEQADV 3CL3 GLY D 148 UNP Q9Y6K9 EXPRESSION TAG SEQADV 3CL3 SER D 149 UNP Q9Y6K9 EXPRESSION TAG SEQADV 3CL3 GLY E 143 UNP Q9Y6K9 EXPRESSION TAG SEQADV 3CL3 HIS E 144 UNP Q9Y6K9 EXPRESSION TAG SEQADV 3CL3 MET E 145 UNP Q9Y6K9 EXPRESSION TAG SEQADV 3CL3 ALA E 146 UNP Q9Y6K9 EXPRESSION TAG SEQADV 3CL3 SER E 147 UNP Q9Y6K9 EXPRESSION TAG SEQADV 3CL3 GLY E 148 UNP Q9Y6K9 EXPRESSION TAG SEQADV 3CL3 SER E 149 UNP Q9Y6K9 EXPRESSION TAG SEQRES 1 A 183 GLY ALA MET GLY SER MET ALA THR TYR GLU VAL LEU CYS SEQRES 2 A 183 GLU VAL ALA ARG LYS LEU GLY THR ASP ASP ARG GLU VAL SEQRES 3 A 183 VAL LEU PHE LEU LEU ASN VAL PHE ILE PRO GLN PRO THR SEQRES 4 A 183 LEU ALA GLN LEU ILE GLY ALA LEU ARG ALA LEU LYS GLU SEQRES 5 A 183 GLU GLY ARG LEU THR PHE PRO LEU LEU ALA GLU CYS LEU SEQRES 6 A 183 PHE ARG ALA GLY ARG ARG ASP LEU LEU ARG ASP LEU LEU SEQRES 7 A 183 HIS LEU ASP PRO ARG PHE LEU GLU ARG HIS LEU ALA GLY SEQRES 8 A 183 THR MET SER TYR PHE SER PRO TYR GLN LEU THR VAL LEU SEQRES 9 A 183 HIS VAL ASP GLY GLU LEU CYS ALA ARG ASP ILE ARG SER SEQRES 10 A 183 LEU ILE PHE LEU SER LYS ASP THR ILE GLY SER ARG SER SEQRES 11 A 183 THR PRO GLN THR PHE LEU HIS TRP VAL TYR CYS MET GLU SEQRES 12 A 183 ASN LEU ASP LEU LEU GLY PRO THR ASP VAL ASP ALA LEU SEQRES 13 A 183 MET SER MET LEU ARG SER LEU SER ARG VAL ASP LEU GLN SEQRES 14 A 183 ARG GLN VAL GLN THR LEU MET GLY LEU HIS LEU SER GLY SEQRES 15 A 183 PRO SEQRES 1 B 183 GLY ALA MET GLY SER MET ALA THR TYR GLU VAL LEU CYS SEQRES 2 B 183 GLU VAL ALA ARG LYS LEU GLY THR ASP ASP ARG GLU VAL SEQRES 3 B 183 VAL LEU PHE LEU LEU ASN VAL PHE ILE PRO GLN PRO THR SEQRES 4 B 183 LEU ALA GLN LEU ILE GLY ALA LEU ARG ALA LEU LYS GLU SEQRES 5 B 183 GLU GLY ARG LEU THR PHE PRO LEU LEU ALA GLU CYS LEU SEQRES 6 B 183 PHE ARG ALA GLY ARG ARG ASP LEU LEU ARG ASP LEU LEU SEQRES 7 B 183 HIS LEU ASP PRO ARG PHE LEU GLU ARG HIS LEU ALA GLY SEQRES 8 B 183 THR MET SER TYR PHE SER PRO TYR GLN LEU THR VAL LEU SEQRES 9 B 183 HIS VAL ASP GLY GLU LEU CYS ALA ARG ASP ILE ARG SER SEQRES 10 B 183 LEU ILE PHE LEU SER LYS ASP THR ILE GLY SER ARG SER SEQRES 11 B 183 THR PRO GLN THR PHE LEU HIS TRP VAL TYR CYS MET GLU SEQRES 12 B 183 ASN LEU ASP LEU LEU GLY PRO THR ASP VAL ASP ALA LEU SEQRES 13 B 183 MET SER MET LEU ARG SER LEU SER ARG VAL ASP LEU GLN SEQRES 14 B 183 ARG GLN VAL GLN THR LEU MET GLY LEU HIS LEU SER GLY SEQRES 15 B 183 PRO SEQRES 1 D 130 GLY HIS MET ALA SER GLY SER LEU GLY GLU LEU GLN GLU SEQRES 2 D 130 SER GLN SER ARG LEU GLU ALA ALA THR LYS GLU CYS GLN SEQRES 3 D 130 ALA LEU GLU GLY ARG ALA ARG ALA ALA SER GLU GLN ALA SEQRES 4 D 130 ARG GLN LEU GLU SER GLU ARG GLU ALA LEU GLN GLN GLN SEQRES 5 D 130 HIS SER VAL GLN VAL ASP GLN LEU ARG MET GLN GLY GLN SEQRES 6 D 130 SER VAL GLU ALA ALA LEU ARG MET GLU ARG GLN ALA ALA SEQRES 7 D 130 SER GLU GLU LYS ARG LYS LEU ALA GLN LEU GLN VAL ALA SEQRES 8 D 130 TYR HIS GLN LEU PHE GLN GLU TYR ASP ASN HIS ILE LYS SEQRES 9 D 130 SER SER VAL VAL GLY SER GLU ARG LYS ARG GLY MET GLN SEQRES 10 D 130 LEU GLU ASP LEU LYS GLN GLN LEU GLN GLN ALA GLU GLU SEQRES 1 E 130 GLY HIS MET ALA SER GLY SER LEU GLY GLU LEU GLN GLU SEQRES 2 E 130 SER GLN SER ARG LEU GLU ALA ALA THR LYS GLU CYS GLN SEQRES 3 E 130 ALA LEU GLU GLY ARG ALA ARG ALA ALA SER GLU GLN ALA SEQRES 4 E 130 ARG GLN LEU GLU SER GLU ARG GLU ALA LEU GLN GLN GLN SEQRES 5 E 130 HIS SER VAL GLN VAL ASP GLN LEU ARG MET GLN GLY GLN SEQRES 6 E 130 SER VAL GLU ALA ALA LEU ARG MET GLU ARG GLN ALA ALA SEQRES 7 E 130 SER GLU GLU LYS ARG LYS LEU ALA GLN LEU GLN VAL ALA SEQRES 8 E 130 TYR HIS GLN LEU PHE GLN GLU TYR ASP ASN HIS ILE LYS SEQRES 9 E 130 SER SER VAL VAL GLY SER GLU ARG LYS ARG GLY MET GLN SEQRES 10 E 130 LEU GLU ASP LEU LYS GLN GLN LEU GLN GLN ALA GLU GLU HELIX 1 1 THR A 3 ARG A 12 1 10 HELIX 2 2 GLY A 15 LEU A 26 1 12 HELIX 3 3 THR A 34 GLU A 47 1 14 HELIX 4 4 THR A 52 ALA A 63 1 12 HELIX 5 5 ARG A 65 ARG A 70 1 6 HELIX 6 6 ASP A 76 ALA A 85 1 10 HELIX 7 7 SER A 92 LEU A 105 1 14 HELIX 8 8 CYS A 106 LYS A 118 1 13 HELIX 9 9 THR A 129 ASN A 139 1 11 HELIX 10 10 VAL A 148 LEU A 158 1 11 HELIX 11 11 ARG A 160 GLY A 172 1 13 HELIX 12 12 THR B 3 LEU B 14 1 12 HELIX 13 13 GLY B 15 LEU B 26 1 12 HELIX 14 14 THR B 34 GLU B 48 1 15 HELIX 15 15 THR B 52 ALA B 63 1 12 HELIX 16 16 ARG B 65 LEU B 73 1 9 HELIX 17 17 ASP B 76 ALA B 85 1 10 HELIX 18 18 SER B 92 LEU B 105 1 14 HELIX 19 19 CYS B 106 SER B 117 1 12 HELIX 20 20 THR B 129 LEU B 140 1 12 HELIX 21 21 VAL B 148 LEU B 155 1 8 HELIX 22 22 ARG B 160 LEU B 170 1 11 HELIX 23 23 SER D 196 VAL D 250 1 55 HELIX 24 24 SER E 196 SER E 248 1 53 CRYST1 145.670 145.670 101.540 90.00 90.00 120.00 P 32 2 1 12 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 0.006865 0.003963 0.000000 0.00000 SCALE2 0.000000 0.007927 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009848 0.00000