HEADER HYDROLASE 23-NOV-22 8HJE TITLE VISMODEGIB BINDS TO THE CATALYTICAL DOMAIN OF HUMAN UBIQUITIN-SPECIFIC TITLE 2 PROTEASE 28 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 28; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DEUBIQUITINATING ENZYME 28,UBIQUITIN THIOESTERASE 28, COMPND 5 UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 28; COMPND 6 EC: 3.4.19.12; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: THE PROTEIN IS EXPRESSED AS AN INSERT DELETION, AND COMPND 9 THE CATALYTICAL DOMAIN OF UBIQUITIN-SPECIFIC PROTEASE 28 IS LINKED BY COMPND 10 A FLEXIBLE GSGSGS LINKER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: USP28, KIAA1515; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI, ESCHERICHIA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562, 561 KEYWDS VISMODEGIB, USP28, CATALYTICAL DOMAIN, INHIBITOR, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.SHI,H.WANG,Z.XU,B.XIONG,N.ZHANG REVDAT 1 03-MAY-23 8HJE 0 JRNL AUTH D.ZHOU,Z.XU,Y.HUANG,H.WANG,X.ZHU,W.ZHANG,W.SONG,T.GAO,T.LIU, JRNL AUTH 2 M.WANG,L.SHI,N.ZHANG,B.XIONG JRNL TITL STRUCTURE-BASED DISCOVERY OF POTENT USP28 INHIBITORS DERIVED JRNL TITL 2 FROM VISMODEGIB. JRNL REF EUR.J.MED.CHEM. V. 254 15369 2023 JRNL REFN ISSN 0223-5234 JRNL PMID 37075624 JRNL DOI 10.1016/J.EJMECH.2023.115369 REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 1.16 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15881 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 + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 825 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2411 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 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) : 66.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.58000 REMARK 3 B22 (A**2) : 1.58000 REMARK 3 B33 (A**2) : -5.14000 REMARK 3 B12 (A**2) : 0.79000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.405 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.289 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.226 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.840 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8HJE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1300033723. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16695 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.850 REMARK 200 RESOLUTION RANGE LOW (A) : 43.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.7600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PROPANE PH 6.4, 0.2 M REMARK 280 POTASSIUM THIOCYANATE, 20% PEG3350 AND 3% SUCROSE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-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 0.00000 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 0.00000 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 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 52.54950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 30.33947 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 109.14067 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 52.54950 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 30.33947 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 109.14067 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 52.54950 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 30.33947 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 109.14067 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 52.54950 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 30.33947 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 109.14067 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 52.54950 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 30.33947 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 109.14067 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 52.54950 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 30.33947 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 109.14067 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 60.67894 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 218.28133 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 60.67894 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 218.28133 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 60.67894 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 218.28133 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 60.67894 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 218.28133 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 60.67894 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 218.28133 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 60.67894 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 218.28133 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 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 GLN A 197 REMARK 465 ASN A 198 REMARK 465 VAL A 199 REMARK 465 LEU A 200 REMARK 465 GLU A 201 REMARK 465 ASN A 202 REMARK 465 CYS A 203 REMARK 465 ARG A 204 REMARK 465 LYS A 243 REMARK 465 GLY A 244 REMARK 465 ALA A 245 REMARK 465 PHE A 246 REMARK 465 ARG A 247 REMARK 465 SER A 248 REMARK 465 SER A 249 REMARK 465 GLU A 250 REMARK 465 GLU A 251 REMARK 465 GLN A 252 REMARK 465 GLN A 253 REMARK 465 GLN A 254 REMARK 465 PRO A 280 REMARK 465 ARG A 281 REMARK 465 ASN A 282 REMARK 465 GLU A 336 REMARK 465 GLY A 337 REMARK 465 ASP A 338 REMARK 465 VAL A 339 REMARK 465 GLU A 340 REMARK 465 LEU A 341 REMARK 465 LEU A 342 REMARK 465 PRO A 343 REMARK 465 SER A 344 REMARK 465 ASP A 345 REMARK 465 HIS A 346 REMARK 465 SER A 347 REMARK 465 VAL A 348 REMARK 465 LYS A 349 REMARK 465 TYR A 350 REMARK 465 GLY A 351 REMARK 465 LEU A 376 REMARK 465 GLY A 377 REMARK 465 SER A 575 REMARK 465 GLY A 576 REMARK 465 SER A 577 REMARK 465 GLY A 578 REMARK 465 SER A 579 REMARK 465 PRO A 653 REMARK 465 TYR A 654 REMARK 465 ALA A 657 REMARK 465 GLU A 658 REMARK 465 ALA A 659 REMARK 465 ALA A 660 REMARK 465 PRO A 661 REMARK 465 THR A 662 REMARK 465 GLU A 663 REMARK 465 SER A 664 REMARK 465 ASP A 665 REMARK 465 GLN A 666 REMARK 465 GLU A 694 REMARK 465 TRP A 695 REMARK 465 GLU A 696 REMARK 465 GLU A 697 REMARK 465 GLU A 698 REMARK 465 GLN A 699 REMARK 465 SER A 700 REMARK 465 CYS A 701 REMARK 465 LYS A 702 REMARK 465 ILE A 703 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 ASN A 150 CB CG OD1 ND2 REMARK 470 ASN A 152 CG OD1 ND2 REMARK 470 ARG A 155 CB CG CD NE CZ NH1 NH2 REMARK 470 ASP A 158 CB CG OD1 OD2 REMARK 470 LYS A 165 CG CD CE NZ REMARK 470 VAL A 167 CG1 CG2 REMARK 470 THR A 170 CB OG1 CG2 REMARK 470 LEU A 180 CD1 CD2 REMARK 470 SER A 205 CB OG REMARK 470 HIS A 206 CB CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 208 CB CG CD OE1 OE2 REMARK 470 LYS A 209 CB CG CD CE NZ REMARK 470 ARG A 210 CB CG CD NE CZ NH1 NH2 REMARK 470 ILE A 212 CG1 CG2 CD1 REMARK 470 GLN A 216 CG CD OE1 NE2 REMARK 470 LEU A 239 CD1 CD2 REMARK 470 ASP A 255 CB CG OD1 OD2 REMARK 470 SER A 257 OG REMARK 470 PHE A 259 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 262 CB CG CD CE NZ REMARK 470 VAL A 275 CG1 CG2 REMARK 470 VAL A 277 CG1 CG2 REMARK 470 LYS A 283 CG CD CE NZ REMARK 470 SER A 284 OG REMARK 470 GLU A 285 CG CD OE1 OE2 REMARK 470 ARG A 302 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 303 CB CG CD OE1 OE2 REMARK 470 LYS A 305 CB CG CD CE NZ REMARK 470 ASN A 321 CB CG OD1 ND2 REMARK 470 GLU A 353 CB CG CD OE1 OE2 REMARK 470 ASN A 373 CB CG OD1 ND2 REMARK 470 GLN A 378 CB CG CD OE1 NE2 REMARK 470 GLU A 380 CB CG CD OE1 OE2 REMARK 470 MET A 394 CE REMARK 470 GLN A 581 CG CD OE1 NE2 REMARK 470 GLN A 595 CB CG CD OE1 NE2 REMARK 470 ALA A 596 CB REMARK 470 HIS A 600 CB CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 618 CG OD1 OD2 REMARK 470 LYS A 651 CB CG CD CE NZ REMARK 470 LEU A 652 CB CG CD1 CD2 REMARK 470 PHE A 655 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 MET A 667 CG SD CE REMARK 470 GLU A 669 CG CD OE1 OE2 REMARK 470 VAL A 670 CG1 CG2 REMARK 470 GLU A 671 CB CG CD OE1 OE2 REMARK 470 GLU A 676 CD OE1 OE2 REMARK 470 GLN A 682 CB CG CD OE1 NE2 REMARK 470 GLU A 683 CD OE1 OE2 REMARK 470 VAL A 692 CG1 CG2 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 ASP A 158 -134.39 43.08 REMARK 500 VAL A 167 -75.49 -57.36 REMARK 500 THR A 170 53.23 -95.90 REMARK 500 ASN A 321 111.18 -32.43 REMARK 500 ALA A 596 -77.28 -32.18 REMARK 500 ASN A 597 51.61 -94.83 REMARK 500 ALA A 598 -155.32 -159.77 REMARK 500 ASP A 618 -123.55 54.75 REMARK 500 REMARK 500 REMARK: NULL DBREF 8HJE A 150 399 UNP Q96RU2 UBP28_HUMAN 150 399 DBREF 8HJE A 580 703 UNP Q96RU2 UBP28_HUMAN 580 703 SEQADV 8HJE GLY A 400 UNP Q96RU2 LINKER SEQADV 8HJE SER A 575 UNP Q96RU2 LINKER SEQADV 8HJE GLY A 576 UNP Q96RU2 LINKER SEQADV 8HJE SER A 577 UNP Q96RU2 LINKER SEQADV 8HJE GLY A 578 UNP Q96RU2 LINKER SEQADV 8HJE SER A 579 UNP Q96RU2 LINKER SEQRES 1 A 380 ASN PRO ASN ASP TRP ARG ARG VAL ASP GLY TRP PRO VAL SEQRES 2 A 380 GLY LEU LYS ASN VAL GLY ASN THR CYS TRP PHE SER ALA SEQRES 3 A 380 VAL ILE GLN SER LEU PHE GLN LEU PRO GLU PHE ARG ARG SEQRES 4 A 380 LEU VAL LEU SER TYR SER LEU PRO GLN ASN VAL LEU GLU SEQRES 5 A 380 ASN CYS ARG SER HIS THR GLU LYS ARG ASN ILE MET PHE SEQRES 6 A 380 MET GLN GLU LEU GLN TYR LEU PHE ALA LEU MET MET GLY SEQRES 7 A 380 SER ASN ARG LYS PHE VAL ASP PRO SER ALA ALA LEU ASP SEQRES 8 A 380 LEU LEU LYS GLY ALA PHE ARG SER SER GLU GLU GLN GLN SEQRES 9 A 380 GLN ASP VAL SER GLU PHE THR HIS LYS LEU LEU ASP TRP SEQRES 10 A 380 LEU GLU ASP ALA PHE GLN LEU ALA VAL ASN VAL ASN SER SEQRES 11 A 380 PRO ARG ASN LYS SER GLU ASN PRO MET VAL GLN LEU PHE SEQRES 12 A 380 TYR GLY THR PHE LEU THR GLU GLY VAL ARG GLU GLY LYS SEQRES 13 A 380 PRO PHE CYS ASN ASN GLU THR PHE GLY GLN TYR PRO LEU SEQRES 14 A 380 GLN VAL ASN GLY TYR ARG ASN LEU ASP GLU CYS LEU GLU SEQRES 15 A 380 GLY ALA MET VAL GLU GLY ASP VAL GLU LEU LEU PRO SER SEQRES 16 A 380 ASP HIS SER VAL LYS TYR GLY GLN GLU ARG TRP PHE THR SEQRES 17 A 380 LYS LEU PRO PRO VAL LEU THR PHE GLU LEU SER ARG PHE SEQRES 18 A 380 GLU PHE ASN GLN SER LEU GLY GLN PRO GLU LYS ILE HIS SEQRES 19 A 380 ASN LYS LEU GLU PHE PRO GLN ILE ILE TYR MET ASP ARG SEQRES 20 A 380 TYR MET TYR GLY SER GLY SER GLY SER ARG GLN VAL PRO SEQRES 21 A 380 TYR ARG LEU HIS ALA VAL LEU VAL HIS GLU GLY GLN ALA SEQRES 22 A 380 ASN ALA GLY HIS TYR TRP ALA TYR ILE TYR ASN GLN PRO SEQRES 23 A 380 ARG GLN SER TRP LEU LYS TYR ASN ASP ILE SER VAL THR SEQRES 24 A 380 GLU SER SER TRP GLU GLU VAL GLU ARG ASP SER TYR GLY SEQRES 25 A 380 GLY LEU ARG ASN VAL SER ALA TYR CYS LEU MET TYR ILE SEQRES 26 A 380 ASN ASP LYS LEU PRO TYR PHE ASN ALA GLU ALA ALA PRO SEQRES 27 A 380 THR GLU SER ASP GLN MET SER GLU VAL GLU ALA LEU SER SEQRES 28 A 380 VAL GLU LEU LYS HIS TYR ILE GLN GLU ASP ASN TRP ARG SEQRES 29 A 380 PHE GLU GLN GLU VAL GLU GLU TRP GLU GLU GLU GLN SER SEQRES 30 A 380 CYS LYS ILE HET VIS A 801 27 HETNAM VIS 2-CHLORANYL-~{N}-(4-CHLORANYL-3-PYRIDIN-2-YL-PHENYL)-4- HETNAM 2 VIS METHYLSULFONYL-BENZAMIDE FORMUL 2 VIS C19 H14 CL2 N2 O3 S HELIX 1 AA1 THR A 170 GLN A 182 1 13 HELIX 2 AA2 LEU A 183 SER A 192 1 10 HELIX 3 AA3 HIS A 206 SER A 228 1 23 HELIX 4 AA4 PRO A 235 LEU A 242 1 8 HELIX 5 AA5 VAL A 256 ASN A 278 1 23 HELIX 6 AA6 ASN A 286 TYR A 293 1 8 HELIX 7 AA7 ASN A 325 VAL A 335 1 11 HELIX 8 AA8 ASP A 395 MET A 398 5 4 HELIX 9 AA9 SER A 625 TYR A 634 1 10 HELIX 10 AB1 SER A 668 ALA A 672 1 5 HELIX 11 AB2 SER A 674 GLU A 693 1 20 SHEET 1 AA1 2 GLY A 163 LEU A 164 0 SHEET 2 AA1 2 PHE A 232 VAL A 233 1 O VAL A 233 N GLY A 163 SHEET 1 AA2 3 LYS A 305 PHE A 313 0 SHEET 2 AA2 3 GLY A 294 ARG A 302 -1 N GLY A 294 O PHE A 313 SHEET 3 AA2 3 GLU A 353 LYS A 358 -1 O THR A 357 N THR A 295 SHEET 1 AA3 5 TYR A 316 GLN A 319 0 SHEET 2 AA3 5 VAL A 362 SER A 368 1 O SER A 368 N LEU A 318 SHEET 3 AA3 5 VAL A 640 ASN A 649 -1 O TYR A 647 N LEU A 363 SHEET 4 AA3 5 PRO A 583 GLU A 593 -1 N HIS A 587 O MET A 646 SHEET 5 AA3 5 ILE A 391 TYR A 393 -1 N ILE A 392 O TYR A 584 SHEET 1 AA4 7 TYR A 316 GLN A 319 0 SHEET 2 AA4 7 VAL A 362 SER A 368 1 O SER A 368 N LEU A 318 SHEET 3 AA4 7 VAL A 640 ASN A 649 -1 O TYR A 647 N LEU A 363 SHEET 4 AA4 7 PRO A 583 GLU A 593 -1 N HIS A 587 O MET A 646 SHEET 5 AA4 7 HIS A 600 ASN A 607 -1 O HIS A 600 N GLU A 593 SHEET 6 AA4 7 SER A 612 ASN A 617 -1 O TYR A 616 N ALA A 603 SHEET 7 AA4 7 SER A 620 GLU A 623 -1 O SER A 620 N ASN A 617 SHEET 1 AA5 2 PHE A 370 PHE A 372 0 SHEET 2 AA5 2 PRO A 379 LYS A 381 -1 O GLU A 380 N GLU A 371 CRYST1 105.099 105.099 327.422 90.00 90.00 120.00 H 3 2 18 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 0.009515 0.005493 0.000000 0.00000 SCALE2 0.000000 0.010987 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003054 0.00000