HEADER LIGASE/LIGASE INHIBITOR 07-DEC-15 5F6V TITLE CRYSTAL STRUCTURE OF UBC9 (K48/K49A/E54A) COMPLEXED WITH FRAGMENT 1 TITLE 2 (BIPHENOL FROM FRAGMENT COCKTAIL SCREEN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUMO-CONJUGATING ENZYME UBC9; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SUMO-PROTEIN LIGASE,UBIQUITIN CARRIER PROTEIN 9,UBIQUITIN COMPND 5 CARRIER PROTEIN I,UBIQUITIN-CONJUGATING ENZYME E2 I,UBIQUITIN-PROTEIN COMPND 6 LIGASE I,P18; COMPND 7 EC: 6.3.2.-; COMPND 8 ENGINEERED: YES; COMPND 9 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: UBE2I, UBC9, UBCE9; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PDN2405 KEYWDS UBC9, FRAGMENT DRUG DESIGN, SUMOYLATION, LIGASE-LIGASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.T.LOUNTOS,W.M.HEWITT,K.ZLOTKOWSKI,S.DAHLHAUSER,L.B.SAUNDERS, AUTHOR 2 D.NEEDLE,J.E.TROPEA,C.ZHAN,G.WEI,B.MA,R.NUSSINOV,J.S.JR.SCHNEEKLOTH, AUTHOR 3 D.S.WAUGH REVDAT 3 27-SEP-23 5F6V 1 JRNL REMARK REVDAT 2 04-MAY-16 5F6V 1 JRNL REVDAT 1 27-APR-16 5F6V 0 JRNL AUTH W.M.HEWITT,G.T.LOUNTOS,K.ZLOTKOWSKI,S.D.DAHLHAUSER, JRNL AUTH 2 L.B.SAUNDERS,D.NEEDLE,J.E.TROPEA,C.ZHAN,G.WEI,B.MA, JRNL AUTH 3 R.NUSSINOV,D.S.WAUGH,J.S.SCHNEEKLOTH JRNL TITL INSIGHTS INTO THE ALLOSTERIC INHIBITION OF THE SUMO E2 JRNL TITL 2 ENZYME UBC9. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 55 5703 2016 JRNL REFN ESSN 1521-3773 JRNL PMID 27038327 JRNL DOI 10.1002/ANIE.201511351 REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 31105 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1991 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 26.8770 - 3.5927 0.98 2141 148 0.1500 0.1592 REMARK 3 2 3.5927 - 2.8527 1.00 2117 148 0.1592 0.1802 REMARK 3 3 2.8527 - 2.4924 1.00 2091 147 0.1604 0.2010 REMARK 3 4 2.4924 - 2.2646 1.00 2094 142 0.1538 0.1875 REMARK 3 5 2.2646 - 2.1024 1.00 2088 139 0.1472 0.1935 REMARK 3 6 2.1024 - 1.9785 1.00 2081 143 0.1444 0.1850 REMARK 3 7 1.9785 - 1.8794 1.00 2081 145 0.1439 0.1902 REMARK 3 8 1.8794 - 1.7976 1.00 2083 139 0.1352 0.1661 REMARK 3 9 1.7976 - 1.7284 1.00 2095 140 0.1355 0.2006 REMARK 3 10 1.7284 - 1.6688 1.00 2049 143 0.1367 0.1761 REMARK 3 11 1.6688 - 1.6166 1.00 2089 138 0.1376 0.2063 REMARK 3 12 1.6166 - 1.5704 1.00 2057 157 0.1513 0.2176 REMARK 3 13 1.5704 - 1.5291 1.00 2054 124 0.1832 0.2320 REMARK 3 14 1.5291 - 1.4918 0.95 1994 138 0.1980 0.2496 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.820 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 : 0.006 1436 REMARK 3 ANGLE : 1.086 1981 REMARK 3 CHIRALITY : 0.080 205 REMARK 3 PLANARITY : 0.006 263 REMARK 3 DIHEDRAL : 13.039 582 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 5F6V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000216100. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31125 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.77800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 1U9B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH 8.5, 8% (W/V) REMARK 280 POLYETHYLENE GLYCOL 8000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 17.61650 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 158 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 OE2 GLU A 98 O HOH A 301 2.05 REMARK 500 O ILE A 125 OH TYR A 134 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 308 O HOH A 328 2849 2.17 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 HIS A 83 139.67 -172.72 REMARK 500 LYS A 101 -103.39 -108.83 REMARK 500 ASN A 140 93.72 -161.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 528 DISTANCE = 6.13 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5VL A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5F6D RELATED DB: PDB REMARK 900 RELATED ID: 5F6E RELATED DB: PDB REMARK 900 RELATED ID: 5F6U RELATED DB: PDB REMARK 900 RELATED ID: 5F6W RELATED DB: PDB REMARK 900 RELATED ID: 5F6X RELATED DB: PDB REMARK 900 RELATED ID: 5F6Y RELATED DB: PDB DBREF 5F6V A 2 158 UNP P63279 UBC9_HUMAN 2 158 SEQADV 5F6V ALA A 48 UNP P63279 LYS 48 ENGINEERED MUTATION SEQADV 5F6V ALA A 49 UNP P63279 LYS 49 ENGINEERED MUTATION SEQADV 5F6V ALA A 54 UNP P63279 GLU 54 ENGINEERED MUTATION SEQRES 1 A 157 SER GLY ILE ALA LEU SER ARG LEU ALA GLN GLU ARG LYS SEQRES 2 A 157 ALA TRP ARG LYS ASP HIS PRO PHE GLY PHE VAL ALA VAL SEQRES 3 A 157 PRO THR LYS ASN PRO ASP GLY THR MET ASN LEU MET ASN SEQRES 4 A 157 TRP GLU CYS ALA ILE PRO GLY ALA ALA GLY THR PRO TRP SEQRES 5 A 157 ALA GLY GLY LEU PHE LYS LEU ARG MET LEU PHE LYS ASP SEQRES 6 A 157 ASP TYR PRO SER SER PRO PRO LYS CYS LYS PHE GLU PRO SEQRES 7 A 157 PRO LEU PHE HIS PRO ASN VAL TYR PRO SER GLY THR VAL SEQRES 8 A 157 CYS LEU SER ILE LEU GLU GLU ASP LYS ASP TRP ARG PRO SEQRES 9 A 157 ALA ILE THR ILE LYS GLN ILE LEU LEU GLY ILE GLN GLU SEQRES 10 A 157 LEU LEU ASN GLU PRO ASN ILE GLN ASP PRO ALA GLN ALA SEQRES 11 A 157 GLU ALA TYR THR ILE TYR CYS GLN ASN ARG VAL GLU TYR SEQRES 12 A 157 GLU LYS ARG VAL ARG ALA GLN ALA LYS LYS PHE ALA PRO SEQRES 13 A 157 SER HET 5VL A 201 14 HETNAM 5VL 2-(2-HYDROXYPHENYL)PHENOL FORMUL 2 5VL C12 H10 O2 FORMUL 3 HOH *228(H2 O) HELIX 1 AA1 SER A 2 ASP A 19 1 18 HELIX 2 AA2 LEU A 94 GLU A 98 5 5 HELIX 3 AA3 THR A 108 GLU A 122 1 15 HELIX 4 AA4 GLN A 130 ASN A 140 1 11 HELIX 5 AA5 ASN A 140 PHE A 155 1 16 SHEET 1 AA1 4 VAL A 25 LYS A 30 0 SHEET 2 AA1 4 MET A 36 PRO A 46 -1 O GLU A 42 N VAL A 27 SHEET 3 AA1 4 LEU A 57 LEU A 63 -1 O LEU A 60 N CYS A 43 SHEET 4 AA1 4 LYS A 74 PHE A 77 -1 O LYS A 76 N ARG A 61 CISPEP 1 TYR A 68 PRO A 69 0 7.04 CISPEP 2 GLU A 78 PRO A 79 0 0.91 SITE 1 AC1 9 GLU A 42 CYS A 43 ALA A 44 LYS A 59 SITE 2 AC1 9 LEU A 60 ARG A 61 GLU A 78 HOH A 412 SITE 3 AC1 9 HOH A 457 CRYST1 50.757 35.233 57.951 90.00 111.96 90.00 P 1 21 1 2 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 0.019702 0.000000 0.007945 0.00000 SCALE2 0.000000 0.028382 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018606 0.00000