HEADER PROTEIN BINDING 25-MAR-20 6YEK TITLE CRYSTAL STRUCTURE OF HUMAN NEMO APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: INHIBITOR OF KAPPA LIGHT POLYPEPTIDE GENE ENHANCER IN B- COMPND 3 CELLS, KINASE GAMMA, ISOFORM CRA_B; COMPND 4 CHAIN: A, B; COMPND 5 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: IKBKG, HCG_2003089; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CELL SIGNALING, NF-KB PATHWAY, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.GARCIA-PARDO,M.AKUTSU,P.BUSSE,A.SKENDEROVIC,T.MACULINS,I.DIKIC REVDAT 2 24-JAN-24 6YEK 1 REMARK REVDAT 1 03-MAR-21 6YEK 0 JRNL AUTH T.MACULINS,J.GARCIA-PARDO,A.SKENDEROVIC,J.GEBEL,M.PUTYRSKI, JRNL AUTH 2 A.VOROBYOV,P.BUSSE,G.VARGA,M.KUZIKOV,A.ZALIANI,S.RAHIGHI, JRNL AUTH 3 V.SCHAEFFER,M.J.PARNHAM,S.S.SIDHU,A.ERNST,V.DOTSCH,M.AKUTSU, JRNL AUTH 4 I.DIKIC JRNL TITL DISCOVERY OF PROTEIN-PROTEIN INTERACTION INHIBITORS BY JRNL TITL 2 INTEGRATING PROTEIN ENGINEERING AND CHEMICAL SCREENING JRNL TITL 3 PLATFORMS. JRNL REF CELL CHEM BIOL V. 27 1441 2020 JRNL REFN ESSN 2451-9456 JRNL PMID 32726587 JRNL DOI 10.1016/J.CHEMBIOL.2020.07.010 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 85.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 6464 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.295 REMARK 3 R VALUE (WORKING SET) : 0.291 REMARK 3 FREE R VALUE : 0.336 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 646 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 85.7600 - 5.4800 0.99 1241 138 0.2451 0.2612 REMARK 3 2 5.4800 - 4.3500 1.00 1166 130 0.2942 0.3599 REMARK 3 3 4.3500 - 3.8000 1.00 1151 128 0.2996 0.3734 REMARK 3 4 3.8000 - 3.4500 1.00 1138 125 0.3527 0.4087 REMARK 3 5 3.4500 - 3.2000 1.00 1122 125 0.4230 0.4769 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.608 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.569 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 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 : 0.014 1390 REMARK 3 ANGLE : 1.859 1858 REMARK 3 CHIRALITY : 0.088 210 REMARK 3 PLANARITY : 0.012 246 REMARK 3 DIHEDRAL : 20.327 177 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 6YEK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292107493. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6469 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 85.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.8000 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) : 3.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.200 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: 3F89 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 45% (V/V) ETHYLENE GLYCOL 50MM ACETATE REMARK 280 (PH 4.0), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 2 2 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 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+1/4 REMARK 290 8555 -Y,-X,-Z+3/4 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 49.50500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 74.25750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.75250 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 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 49.50500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 24.75250 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 74.25750 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL 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. (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 256 REMARK 465 PRO A 257 REMARK 465 MET A 258 REMARK 465 LYS A 344 REMARK 465 GLY B 256 REMARK 465 PRO B 257 REMARK 465 MET B 258 REMARK 465 GLN B 259 REMARK 465 LEU B 260 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 LEU A 263 CA - CB - CG ANGL. DEV. = 16.6 DEGREES REMARK 500 MET B 295 CB - CG - SD ANGL. DEV. = 18.4 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 260 82.17 -168.52 REMARK 500 ALA A 276 15.75 -68.32 REMARK 500 LEU B 263 87.39 -52.34 REMARK 500 LYS B 264 78.97 -57.02 REMARK 500 THR B 297 -7.45 -57.56 REMARK 500 LEU B 343 -100.91 -115.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 275 ALA A 276 147.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6XX0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NEMO IN COMPLEX WITH UBV-LIN DBREF 6YEK A 258 344 UNP D3DWY0 D3DWY0_HUMAN 124 210 DBREF 6YEK B 258 344 UNP D3DWY0 D3DWY0_HUMAN 124 210 SEQADV 6YEK GLY A 256 UNP D3DWY0 EXPRESSION TAG SEQADV 6YEK PRO A 257 UNP D3DWY0 EXPRESSION TAG SEQADV 6YEK ALA A 289 UNP D3DWY0 GLU 155 CONFLICT SEQADV 6YEK ALA A 292 UNP D3DWY0 LYS 158 CONFLICT SEQADV 6YEK GLY B 256 UNP D3DWY0 EXPRESSION TAG SEQADV 6YEK PRO B 257 UNP D3DWY0 EXPRESSION TAG SEQADV 6YEK ALA B 289 UNP D3DWY0 GLU 155 CONFLICT SEQADV 6YEK ALA B 292 UNP D3DWY0 LYS 158 CONFLICT SEQRES 1 A 89 GLY PRO MET GLN LEU GLU ASP LEU LYS GLN GLN LEU GLN SEQRES 2 A 89 GLN ALA GLU GLU ALA LEU VAL ALA LYS GLN GLU VAL ILE SEQRES 3 A 89 ASP LYS LEU LYS GLU GLU ALA ALA GLN HIS ALA ILE VAL SEQRES 4 A 89 MET GLU THR VAL PRO VAL LEU LYS ALA GLN ALA ASP ILE SEQRES 5 A 89 TYR LYS ALA ASP PHE GLN ALA GLU ARG GLN ALA ARG GLU SEQRES 6 A 89 LYS LEU ALA GLU LYS LYS GLU LEU LEU GLN GLU GLN LEU SEQRES 7 A 89 GLU GLN LEU GLN ARG GLU TYR SER LYS LEU LYS SEQRES 1 B 89 GLY PRO MET GLN LEU GLU ASP LEU LYS GLN GLN LEU GLN SEQRES 2 B 89 GLN ALA GLU GLU ALA LEU VAL ALA LYS GLN GLU VAL ILE SEQRES 3 B 89 ASP LYS LEU LYS GLU GLU ALA ALA GLN HIS ALA ILE VAL SEQRES 4 B 89 MET GLU THR VAL PRO VAL LEU LYS ALA GLN ALA ASP ILE SEQRES 5 B 89 TYR LYS ALA ASP PHE GLN ALA GLU ARG GLN ALA ARG GLU SEQRES 6 B 89 LYS LEU ALA GLU LYS LYS GLU LEU LEU GLN GLU GLN LEU SEQRES 7 B 89 GLU GLN LEU GLN ARG GLU TYR SER LYS LEU LYS FORMUL 3 HOH *45(H2 O) HELIX 1 AA1 GLN A 266 MET A 295 1 30 HELIX 2 AA2 GLU A 296 GLN A 337 1 42 HELIX 3 AA3 GLU B 271 MET B 295 1 25 HELIX 4 AA4 GLU B 296 SER B 341 1 46 CRYST1 85.760 85.760 99.010 90.00 90.00 90.00 P 43 2 2 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 0.011660 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011660 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010100 0.00000