HEADER LIGASE/INHIBITOR 28-JUN-23 8JVL TITLE IDENTIFICATION AND CHARACTERIZATION OF INHIBITORS COVALENTLY MODIFYING TITLE 2 CATALYTIC CYSTEINE OF UBE2T AND BLOCKING UBIQUITIN TRANSFER COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 T; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: E2 UBIQUITIN-CONJUGATING ENZYME T,UBIQUITIN CARRIER PROTEIN COMPND 5 T,UBIQUITIN-PROTEIN LIGASE T; COMPND 6 EC: 2.3.2.23; COMPND 7 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: UBE2T; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBE2T, STRUCTURE; DRUG DISCOVERY, COVALENT INHIBITOR, FANCONI ANEMIA, KEYWDS 2 LIGASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.ANANTHARAJAN,N.BABURAJENDRAN REVDAT 1 29-NOV-23 8JVL 0 JRNL AUTH J.ANANTHARAJAN,Q.W.TAN,J.FULWOOD,W.SIFANG,Q.HUANG,H.Q.NG, JRNL AUTH 2 X.KOH,W.XU,J.CHERIAN,N.BABURAJENDRAN,C.KANG,Z.KE JRNL TITL IDENTIFICATION AND CHARACTERIZATION OF INHIBITORS COVALENTLY JRNL TITL 2 MODIFYING CATALYTIC CYSTEINE OF UBE2T AND BLOCKING UBIQUITIN JRNL TITL 3 TRANSFER. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 689 49238 2023 JRNL REFN ESSN 1090-2104 JRNL PMID 37979329 JRNL DOI 10.1016/J.BBRC.2023.149238 REMARK 2 REMARK 2 RESOLUTION. 2.06 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 18128 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1813 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 47.1400 - 4.8600 1.00 1402 156 0.1847 0.1856 REMARK 3 2 4.8500 - 3.8500 1.00 1310 146 0.1572 0.1911 REMARK 3 3 3.8500 - 3.3600 1.00 1287 142 0.1947 0.1949 REMARK 3 4 3.3600 - 3.0600 1.00 1251 140 0.2115 0.2581 REMARK 3 5 3.0600 - 2.8400 1.00 1262 140 0.2393 0.2575 REMARK 3 6 2.8400 - 2.6700 1.00 1243 138 0.2387 0.2680 REMARK 3 7 2.6700 - 2.5400 1.00 1248 139 0.2233 0.2649 REMARK 3 8 2.5400 - 2.4300 1.00 1226 135 0.2256 0.2575 REMARK 3 9 2.4300 - 2.3300 1.00 1244 138 0.2343 0.2549 REMARK 3 10 2.3300 - 2.2500 1.00 1231 137 0.2478 0.3072 REMARK 3 11 2.2500 - 2.1800 1.00 1220 135 0.2550 0.2754 REMARK 3 12 2.1800 - 2.1200 1.00 1208 135 0.2441 0.2759 REMARK 3 13 2.1200 - 2.0600 0.96 1183 132 0.2724 0.3005 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.280 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 NULL REMARK 3 ANGLE : 0.855 NULL REMARK 3 CHIRALITY : 0.051 186 REMARK 3 PLANARITY : 0.008 229 REMARK 3 DIHEDRAL : 15.379 171 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 8JVL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300039017. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUL-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95365 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18267 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.060 REMARK 200 RESOLUTION RANGE LOW (A) : 47.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 25.60 REMARK 200 R MERGE (I) : 0.01700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.06 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 24.40 REMARK 200 R MERGE FOR SHELL (I) : 2.05000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.8 M SODIUM FORMATE PH 7.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 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+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 92.03700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.44500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.44500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 138.05550 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.44500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.44500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 46.01850 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.44500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.44500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 138.05550 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.44500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.44500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 46.01850 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 0.00000 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 92.03700 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 352 LIES ON A SPECIAL POSITION. 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 -1 REMARK 465 GLN A 153 REMARK 465 LYS A 154 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 GLN A 2 CG CD OE1 NE2 REMARK 470 LYS A 48 CG CD CE NZ 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 SG CYS A 86 C13 V5L A 201 1.77 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 LYS A 28 -92.75 -148.00 REMARK 500 LYS A 48 -8.52 73.58 REMARK 500 ASN A 135 56.55 -142.85 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 404 DISTANCE = 6.54 ANGSTROMS DBREF 8JVL A 1 154 UNP Q9NPD8 UBE2T_HUMAN 1 154 SEQADV 8JVL GLY A -1 UNP Q9NPD8 EXPRESSION TAG SEQADV 8JVL SER A 0 UNP Q9NPD8 EXPRESSION TAG SEQRES 1 A 156 GLY SER MET GLN ARG ALA SER ARG LEU LYS ARG GLU LEU SEQRES 2 A 156 HIS MET LEU ALA THR GLU PRO PRO PRO GLY ILE THR CYS SEQRES 3 A 156 TRP GLN ASP LYS ASP GLN MET ASP ASP LEU ARG ALA GLN SEQRES 4 A 156 ILE LEU GLY GLY ALA ASN THR PRO TYR GLU LYS GLY VAL SEQRES 5 A 156 PHE LYS LEU GLU VAL ILE ILE PRO GLU ARG TYR PRO PHE SEQRES 6 A 156 GLU PRO PRO GLN ILE ARG PHE LEU THR PRO ILE TYR HIS SEQRES 7 A 156 PRO ASN ILE ASP SER ALA GLY ARG ILE CYS LEU ASP VAL SEQRES 8 A 156 LEU LYS LEU PRO PRO LYS GLY ALA TRP ARG PRO SER LEU SEQRES 9 A 156 ASN ILE ALA THR VAL LEU THR SER ILE GLN LEU LEU MET SEQRES 10 A 156 SER GLU PRO ASN PRO ASP ASP PRO LEU MET ALA ASP ILE SEQRES 11 A 156 SER SER GLU PHE LYS TYR ASN LYS PRO ALA PHE LEU LYS SEQRES 12 A 156 ASN ALA ARG GLN TRP THR GLU LYS HIS ALA ARG GLN LYS HET V5L A 201 13 HET EDO A 202 4 HETNAM V5L 1-(4-METHOXYPHENYL)-1,2,3,4-TETRAZOLE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 V5L C8 H8 N4 O FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *104(H2 O) HELIX 1 AA1 SER A 0 GLU A 17 1 18 HELIX 2 AA2 LEU A 87 LYS A 91 5 5 HELIX 3 AA3 ASN A 103 GLU A 117 1 15 HELIX 4 AA4 MET A 125 ASN A 135 1 11 HELIX 5 AA5 ASN A 135 ALA A 151 1 17 SHEET 1 AA1 4 ILE A 22 GLN A 26 0 SHEET 2 AA1 4 ASP A 33 LEU A 39 -1 O GLN A 37 N THR A 23 SHEET 3 AA1 4 VAL A 50 ILE A 56 -1 O LEU A 53 N ALA A 36 SHEET 4 AA1 4 GLN A 67 PHE A 70 -1 O GLN A 67 N ILE A 56 CISPEP 1 TYR A 61 PRO A 62 0 8.25 CISPEP 2 PRO A 93 PRO A 94 0 8.85 CRYST1 54.890 54.890 184.074 90.00 90.00 90.00 P 43 21 2 8 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 0.018218 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018218 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005433 0.00000