HEADER LYASE 16-JUL-25 9VVV TITLE CRYSTAL STRUCTURE OF USP15 CATALYTIC DOMAIN IN COMPLEX WITH UB-PA COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 15; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DEUBIQUITINATING ENZYME 15,UBIQUITIN THIOESTERASE 15, COMPND 5 UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 15,UNPH-2,UNPH4; COMPND 6 EC: 3.4.19.12; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: RESIDUES FROM P469 TO F785 ARE DELETED AND A LINKER COMPND 9 CONTAINING RESIDUES ASTSK ARE INSERTED.; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: POLYUBIQUITIN-C; COMPND 12 CHAIN: C, D; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: THE UBIQUITIN MOLECULE, SPECIFICALLY ITS FIRST 75 COMPND 15 AMINO ACIDS, IS CONJUGATED WITH A PA GROUP AT THE 75TH GLYCINE COMPND 16 RESIDUE (75G), FORMING A UNIQUE LINKAGE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: USP15, KIAA0529; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: UBC; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DUB, CYSTEINE PROTEASE, COMPLEX, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR B.LIU,X.XU REVDAT 1 24-JUN-26 9VVV 0 JRNL AUTH B.LIU,T.WANG,H.LUO,L.LANG,X.LIU,Z.GONG,T.WANG,W.CHENG,L.XIE, JRNL AUTH 2 X.ZHANG,X.FANG,X.XU JRNL TITL STRUCTURAL INSIGHTS INTO UBIQUITIN RECOGNITION BY USP15 JRNL TITL 2 REVEALED THROUGH A COVALENT ACTIVITY-BASED PROBE. JRNL REF COMMUN BIOL 2026 JRNL REFN ESSN 2399-3642 JRNL PMID 42259887 JRNL DOI 10.1038/S42003-026-10386-7 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 53365 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.224 REMARK 3 R VALUE (WORKING SET) : 0.222 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 2658 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 8.5040 - 6.1403 0.99 2828 141 0.1988 0.2379 REMARK 3 2 6.1403 - 4.8768 1.00 2759 110 0.1965 0.2365 REMARK 3 3 4.8768 - 4.2612 1.00 2717 115 0.1677 0.1978 REMARK 3 4 4.2612 - 3.8720 1.00 2663 164 0.1936 0.2554 REMARK 3 5 3.8720 - 3.5947 1.00 2710 127 0.2170 0.2734 REMARK 3 6 3.5947 - 3.3829 1.00 2687 142 0.2223 0.2710 REMARK 3 7 3.3829 - 3.2136 1.00 2649 154 0.2314 0.2619 REMARK 3 8 3.2136 - 3.0737 1.00 2696 139 0.2448 0.3160 REMARK 3 9 3.0737 - 2.9554 1.00 2639 158 0.2533 0.2905 REMARK 3 10 2.9554 - 2.8535 1.00 2667 120 0.2485 0.3140 REMARK 3 11 2.8535 - 2.7643 1.00 2653 164 0.2636 0.3298 REMARK 3 12 2.7643 - 2.6853 0.99 2614 164 0.2703 0.3182 REMARK 3 13 2.6853 - 2.6146 1.00 2634 166 0.2860 0.3468 REMARK 3 14 2.6146 - 2.5508 1.00 2678 119 0.2824 0.3905 REMARK 3 15 2.5508 - 2.4929 1.00 2617 155 0.2909 0.3491 REMARK 3 16 2.4929 - 2.4398 0.99 2627 136 0.2895 0.3477 REMARK 3 17 2.4398 - 2.3910 0.99 2643 137 0.2961 0.3100 REMARK 3 18 2.3910 - 2.3459 0.99 2632 123 0.2993 0.3765 REMARK 3 19 2.3459 - 2.3040 0.98 2594 124 0.3165 0.3638 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.99 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 : 0.015 6719 REMARK 3 ANGLE : 1.443 9071 REMARK 3 CHIRALITY : 0.063 983 REMARK 3 PLANARITY : 0.010 1175 REMARK 3 DIHEDRAL : 7.861 4050 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 9VVV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 20-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1300061655. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JAN-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 : 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) : 0.97919 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53563 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.304 REMARK 200 RESOLUTION RANGE LOW (A) : 77.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.95500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.600 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 (%): 60.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% MPD, 0.1M IMIDAZOLE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.86650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 69.86650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 65.43650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 65.92550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 65.43650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 65.92550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 69.86650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 65.43650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 65.92550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 69.86650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 65.43650 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 65.92550 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 3920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 350 REMARK 350 BIOMOLECULE: 2 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: 4040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 283 REMARK 465 THR A 783 REMARK 465 THR A 935 REMARK 465 PHE A 936 REMARK 465 SER A 937 REMARK 465 GLY A 938 REMARK 465 THR A 939 REMARK 465 GLY A 940 REMARK 465 PHE A 941 REMARK 465 SER B 283 REMARK 465 ARG B 400 REMARK 465 LYS B 401 REMARK 465 LYS B 402 REMARK 465 PRO B 403 REMARK 465 TYR B 404 REMARK 465 ILE B 405 REMARK 465 GLN B 406 REMARK 465 THR B 783 REMARK 465 THR B 935 REMARK 465 PHE B 936 REMARK 465 SER B 937 REMARK 465 GLY B 938 REMARK 465 THR B 939 REMARK 465 GLY B 940 REMARK 465 PHE B 941 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 ARG A 400 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 401 CG CD CE NZ REMARK 470 LYS A 402 CG CD CE NZ REMARK 470 GLU A 804 CG CD OE1 OE2 REMARK 470 ARG B 842 CG CD NE CZ NH1 NH2 REMARK 470 MET B 844 CG SD CE 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 HD22 ASN A 301 OD1 ASP A 909 1.33 REMARK 500 O SER C 57 H ASN C 60 1.52 REMARK 500 HH TYR A 316 OE1 GLU A 325 1.55 REMARK 500 SG CYS B 298 N1 AYE D 76 2.15 REMARK 500 OG SER A 470 N SER A 784 2.17 REMARK 500 ND2 ASN A 301 OD1 ASP A 909 2.17 REMARK 500 SG CYS B 298 C1 AYE D 76 2.19 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 CYS A 306 CA - CB - SG ANGL. DEV. = 8.7 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 ASN A 296 47.09 33.06 REMARK 500 PRO A 359 45.43 -83.34 REMARK 500 TYR A 376 45.10 -140.14 REMARK 500 TYR A 404 69.20 61.97 REMARK 500 LYS A 813 41.00 -107.12 REMARK 500 ASP A 909 -118.18 55.17 REMARK 500 TYR A 926 -47.82 -132.37 REMARK 500 LEU C 71 -156.65 -98.84 REMARK 500 MET B 334 57.78 -145.99 REMARK 500 TYR B 376 36.13 -155.64 REMARK 500 LYS B 408 -168.94 -102.35 REMARK 500 ALA B 469 68.40 -104.40 REMARK 500 TYR B 840 44.97 -156.96 REMARK 500 ARG B 842 -73.43 -87.15 REMARK 500 TYR B 843 9.44 -153.23 REMARK 500 ASN B 869 40.25 -103.13 REMARK 500 ASP B 909 -117.95 58.13 REMARK 500 PRO D 38 3.74 -66.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 874 0.30 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLY B 295 -10.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 448 SG REMARK 620 2 CYS A 451 SG 111.5 REMARK 620 3 CYS A 809 SG 103.5 104.6 REMARK 620 4 CYS A 812 SG 96.9 124.0 114.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 448 SG REMARK 620 2 CYS B 451 SG 126.7 REMARK 620 3 CYS B 809 SG 120.7 94.7 REMARK 620 4 CYS B 812 SG 101.4 91.5 119.8 REMARK 620 N 1 2 3 DBREF 9VVV A 284 468 UNP Q9Y4E8 UBP15_HUMAN 284 468 DBREF 9VVV A 786 941 UNP Q9Y4E8 UBP15_HUMAN 786 941 DBREF 9VVV C 1 76 UNP P0CG48 UBC_HUMAN 1 76 DBREF 9VVV B 284 468 UNP Q9Y4E8 UBP15_HUMAN 284 468 DBREF 9VVV B 786 941 UNP Q9Y4E8 UBP15_HUMAN 786 941 DBREF 9VVV D 1 76 UNP P0CG48 UBC_HUMAN 1 76 SEQADV 9VVV SER A 283 UNP Q9Y4E8 EXPRESSION TAG SEQADV 9VVV ALA A 469 UNP Q9Y4E8 LINKER SEQADV 9VVV SER A 470 UNP Q9Y4E8 LINKER SEQADV 9VVV THR A 783 UNP Q9Y4E8 LINKER SEQADV 9VVV SER A 784 UNP Q9Y4E8 LINKER SEQADV 9VVV LYS A 785 UNP Q9Y4E8 LINKER SEQADV 9VVV AYE C 76 UNP P0CG48 GLY 76 ENGINEERED MUTATION SEQADV 9VVV SER B 283 UNP Q9Y4E8 EXPRESSION TAG SEQADV 9VVV ALA B 469 UNP Q9Y4E8 LINKER SEQADV 9VVV SER B 470 UNP Q9Y4E8 LINKER SEQADV 9VVV THR B 783 UNP Q9Y4E8 LINKER SEQADV 9VVV SER B 784 UNP Q9Y4E8 LINKER SEQADV 9VVV LYS B 785 UNP Q9Y4E8 LINKER SEQADV 9VVV AYE D 76 UNP P0CG48 GLY 76 ENGINEERED MUTATION SEQRES 1 A 347 SER GLU GLN PRO GLY LEU CYS GLY LEU SER ASN LEU GLY SEQRES 2 A 347 ASN THR CYS PHE MET ASN SER ALA ILE GLN CYS LEU SER SEQRES 3 A 347 ASN THR PRO PRO LEU THR GLU TYR PHE LEU ASN ASP LYS SEQRES 4 A 347 TYR GLN GLU GLU LEU ASN PHE ASP ASN PRO LEU GLY MET SEQRES 5 A 347 ARG GLY GLU ILE ALA LYS SER TYR ALA GLU LEU ILE LYS SEQRES 6 A 347 GLN MET TRP SER GLY LYS PHE SER TYR VAL THR PRO ARG SEQRES 7 A 347 ALA PHE LYS THR GLN VAL GLY ARG PHE ALA PRO GLN PHE SEQRES 8 A 347 SER GLY TYR GLN GLN GLN ASP CYS GLN GLU LEU LEU ALA SEQRES 9 A 347 PHE LEU LEU ASP GLY LEU HIS GLU ASP LEU ASN ARG ILE SEQRES 10 A 347 ARG LYS LYS PRO TYR ILE GLN LEU LYS ASP ALA ASP GLY SEQRES 11 A 347 ARG PRO ASP LYS VAL VAL ALA GLU GLU ALA TRP GLU ASN SEQRES 12 A 347 HIS LEU LYS ARG ASN ASP SER ILE ILE VAL ASP ILE PHE SEQRES 13 A 347 HIS GLY LEU PHE LYS SER THR LEU VAL CYS PRO GLU CYS SEQRES 14 A 347 ALA LYS ILE SER VAL THR PHE ASP PRO PHE CYS TYR LEU SEQRES 15 A 347 THR LEU PRO LEU ALA SER THR SER LYS VAL LYS LEU LYS SEQRES 16 A 347 ASP CYS ILE GLU LEU PHE THR THR LYS GLU LYS LEU GLY SEQRES 17 A 347 ALA GLU ASP PRO TRP TYR CYS PRO ASN CYS LYS GLU HIS SEQRES 18 A 347 GLN GLN ALA THR LYS LYS LEU ASP LEU TRP SER LEU PRO SEQRES 19 A 347 PRO VAL LEU VAL VAL HIS LEU LYS ARG PHE SER TYR SER SEQRES 20 A 347 ARG TYR MET ARG ASP LYS LEU ASP THR LEU VAL ASP PHE SEQRES 21 A 347 PRO ILE ASN ASP LEU ASP MET SER GLU PHE LEU ILE ASN SEQRES 22 A 347 PRO ASN ALA GLY PRO CYS ARG TYR ASN LEU ILE ALA VAL SEQRES 23 A 347 SER ASN HIS TYR GLY GLY MET GLY GLY GLY HIS TYR THR SEQRES 24 A 347 ALA PHE ALA LYS ASN LYS ASP ASP GLY LYS TRP TYR TYR SEQRES 25 A 347 PHE ASP ASP SER SER VAL SER THR ALA SER GLU ASP GLN SEQRES 26 A 347 ILE VAL SER LYS ALA ALA TYR VAL LEU PHE TYR GLN ARG SEQRES 27 A 347 GLN ASP THR PHE SER GLY THR GLY PHE SEQRES 1 C 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY AYE SEQRES 1 B 347 SER GLU GLN PRO GLY LEU CYS GLY LEU SER ASN LEU GLY SEQRES 2 B 347 ASN THR CYS PHE MET ASN SER ALA ILE GLN CYS LEU SER SEQRES 3 B 347 ASN THR PRO PRO LEU THR GLU TYR PHE LEU ASN ASP LYS SEQRES 4 B 347 TYR GLN GLU GLU LEU ASN PHE ASP ASN PRO LEU GLY MET SEQRES 5 B 347 ARG GLY GLU ILE ALA LYS SER TYR ALA GLU LEU ILE LYS SEQRES 6 B 347 GLN MET TRP SER GLY LYS PHE SER TYR VAL THR PRO ARG SEQRES 7 B 347 ALA PHE LYS THR GLN VAL GLY ARG PHE ALA PRO GLN PHE SEQRES 8 B 347 SER GLY TYR GLN GLN GLN ASP CYS GLN GLU LEU LEU ALA SEQRES 9 B 347 PHE LEU LEU ASP GLY LEU HIS GLU ASP LEU ASN ARG ILE SEQRES 10 B 347 ARG LYS LYS PRO TYR ILE GLN LEU LYS ASP ALA ASP GLY SEQRES 11 B 347 ARG PRO ASP LYS VAL VAL ALA GLU GLU ALA TRP GLU ASN SEQRES 12 B 347 HIS LEU LYS ARG ASN ASP SER ILE ILE VAL ASP ILE PHE SEQRES 13 B 347 HIS GLY LEU PHE LYS SER THR LEU VAL CYS PRO GLU CYS SEQRES 14 B 347 ALA LYS ILE SER VAL THR PHE ASP PRO PHE CYS TYR LEU SEQRES 15 B 347 THR LEU PRO LEU ALA SER THR SER LYS VAL LYS LEU LYS SEQRES 16 B 347 ASP CYS ILE GLU LEU PHE THR THR LYS GLU LYS LEU GLY SEQRES 17 B 347 ALA GLU ASP PRO TRP TYR CYS PRO ASN CYS LYS GLU HIS SEQRES 18 B 347 GLN GLN ALA THR LYS LYS LEU ASP LEU TRP SER LEU PRO SEQRES 19 B 347 PRO VAL LEU VAL VAL HIS LEU LYS ARG PHE SER TYR SER SEQRES 20 B 347 ARG TYR MET ARG ASP LYS LEU ASP THR LEU VAL ASP PHE SEQRES 21 B 347 PRO ILE ASN ASP LEU ASP MET SER GLU PHE LEU ILE ASN SEQRES 22 B 347 PRO ASN ALA GLY PRO CYS ARG TYR ASN LEU ILE ALA VAL SEQRES 23 B 347 SER ASN HIS TYR GLY GLY MET GLY GLY GLY HIS TYR THR SEQRES 24 B 347 ALA PHE ALA LYS ASN LYS ASP ASP GLY LYS TRP TYR TYR SEQRES 25 B 347 PHE ASP ASP SER SER VAL SER THR ALA SER GLU ASP GLN SEQRES 26 B 347 ILE VAL SER LYS ALA ALA TYR VAL LEU PHE TYR GLN ARG SEQRES 27 B 347 GLN ASP THR PHE SER GLY THR GLY PHE SEQRES 1 D 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 D 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 D 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 D 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 D 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 D 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY AYE HET AYE C 76 4 HET AYE D 76 4 HET ZN A1001 1 HET IMD A1002 10 HET ZN B1001 1 HETNAM AYE PROP-2-EN-1-AMINE HETNAM ZN ZINC ION HETNAM IMD IMIDAZOLE HETSYN AYE ALLYLAMINE FORMUL 2 AYE 2(C3 H7 N) FORMUL 5 ZN 2(ZN 2+) FORMUL 6 IMD C3 H5 N2 1+ FORMUL 8 HOH *149(H2 O) HELIX 1 AA1 THR A 297 ASN A 309 1 13 HELIX 2 AA2 THR A 310 ASN A 319 1 10 HELIX 3 AA3 TYR A 322 LEU A 326 5 5 HELIX 4 AA4 GLY A 336 GLY A 352 1 17 HELIX 5 AA5 PRO A 359 ALA A 370 1 12 HELIX 6 AA6 CYS A 381 LEU A 396 1 16 HELIX 7 AA7 PRO A 414 LYS A 428 1 15 HELIX 8 AA8 SER A 432 HIS A 439 1 8 HELIX 9 AA9 LEU A 788 THR A 796 1 9 HELIX 10 AB1 SER A 862 LEU A 865 5 4 HELIX 11 AB2 THR C 22 GLY C 35 1 14 HELIX 12 AB3 PRO C 37 GLN C 41 5 5 HELIX 13 AB4 LEU C 56 ASN C 60 5 5 HELIX 14 AB5 THR B 297 ASN B 309 1 13 HELIX 15 AB6 THR B 310 ASN B 319 1 10 HELIX 16 AB7 LYS B 321 LEU B 326 1 6 HELIX 17 AB8 GLY B 336 TRP B 350 1 15 HELIX 18 AB9 PRO B 359 ALA B 370 1 12 HELIX 19 AC1 ASP B 380 LEU B 396 1 17 HELIX 20 AC2 PRO B 414 LYS B 428 1 15 HELIX 21 AC3 SER B 432 HIS B 439 1 8 HELIX 22 AC4 LEU B 788 THR B 796 1 9 HELIX 23 AC5 SER B 862 LEU B 865 5 4 HELIX 24 AC6 SER B 916 ILE B 920 5 5 HELIX 25 AC7 THR D 22 GLY D 35 1 14 HELIX 26 AC8 THR D 55 ASN D 60 5 6 SHEET 1 AA1 2 GLY A 290 LEU A 291 0 SHEET 2 AA1 2 TYR A 356 VAL A 357 1 O VAL A 357 N GLY A 290 SHEET 1 AA2 2 GLN A 379 ASP A 380 0 SHEET 2 AA2 2 ARG C 74 GLY C 75 -1 O GLY C 75 N GLN A 379 SHEET 1 AA3 4 ILE A 454 PHE A 461 0 SHEET 2 AA3 4 GLY A 440 VAL A 447 -1 N PHE A 442 O ASP A 459 SHEET 3 AA3 4 THR A 819 SER A 826 -1 O ASP A 823 N LYS A 443 SHEET 4 AA3 4 GLU A 799 LYS A 800 -1 N GLU A 799 O LYS A 820 SHEET 1 AA4 5 TYR A 463 LEU A 466 0 SHEET 2 AA4 5 VAL A 830 LEU A 835 1 O HIS A 834 N LEU A 464 SHEET 3 AA4 5 ALA A 925 ARG A 932 -1 O LEU A 928 N VAL A 833 SHEET 4 AA4 5 ARG A 874 GLY A 885 -1 N ALA A 879 O PHE A 929 SHEET 5 AA4 5 LEU A 859 ASP A 860 -1 N LEU A 859 O TYR A 875 SHEET 1 AA5 7 TYR A 463 LEU A 466 0 SHEET 2 AA5 7 VAL A 830 LEU A 835 1 O HIS A 834 N LEU A 464 SHEET 3 AA5 7 ALA A 925 ARG A 932 -1 O LEU A 928 N VAL A 833 SHEET 4 AA5 7 ARG A 874 GLY A 885 -1 N ALA A 879 O PHE A 929 SHEET 5 AA5 7 GLY A 890 LYS A 897 -1 O HIS A 891 N TYR A 884 SHEET 6 AA5 7 TRP A 904 ASP A 908 -1 O TYR A 905 N ALA A 896 SHEET 7 AA5 7 SER A 911 ALA A 915 -1 O ALA A 915 N TRP A 904 SHEET 1 AA6 2 LYS A 785 LYS A 787 0 SHEET 2 AA6 2 LEU A 851 ASP A 853 1 O ASP A 853 N VAL A 786 SHEET 1 AA7 2 TRP A 807 TYR A 808 0 SHEET 2 AA7 2 HIS A 815 GLN A 816 -1 O GLN A 816 N TRP A 807 SHEET 1 AA8 5 THR C 12 GLU C 16 0 SHEET 2 AA8 5 GLN C 2 LYS C 6 -1 N ILE C 3 O LEU C 15 SHEET 3 AA8 5 THR C 66 VAL C 70 1 O LEU C 67 N PHE C 4 SHEET 4 AA8 5 ARG C 42 PHE C 45 -1 N ILE C 44 O HIS C 68 SHEET 5 AA8 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 SHEET 1 AA9 2 GLY B 290 LEU B 291 0 SHEET 2 AA9 2 TYR B 356 VAL B 357 1 O VAL B 357 N GLY B 290 SHEET 1 AB1 4 ILE B 454 PHE B 461 0 SHEET 2 AB1 4 GLY B 440 VAL B 447 -1 N PHE B 442 O ASP B 459 SHEET 3 AB1 4 THR B 819 SER B 826 -1 O ASP B 823 N LYS B 443 SHEET 4 AB1 4 GLU B 799 LYS B 800 -1 N GLU B 799 O LYS B 820 SHEET 1 AB2 5 TYR B 463 LEU B 466 0 SHEET 2 AB2 5 VAL B 830 LEU B 835 1 O HIS B 834 N LEU B 464 SHEET 3 AB2 5 ALA B 925 ARG B 932 -1 O LEU B 928 N VAL B 833 SHEET 4 AB2 5 ARG B 874 GLY B 885 -1 N ASN B 876 O GLN B 931 SHEET 5 AB2 5 LEU B 859 ASP B 860 -1 N LEU B 859 O TYR B 875 SHEET 1 AB3 7 TYR B 463 LEU B 466 0 SHEET 2 AB3 7 VAL B 830 LEU B 835 1 O HIS B 834 N LEU B 464 SHEET 3 AB3 7 ALA B 925 ARG B 932 -1 O LEU B 928 N VAL B 833 SHEET 4 AB3 7 ARG B 874 GLY B 885 -1 N ASN B 876 O GLN B 931 SHEET 5 AB3 7 GLY B 890 LYS B 897 -1 O HIS B 891 N TYR B 884 SHEET 6 AB3 7 TRP B 904 ASP B 908 -1 O TYR B 905 N ALA B 896 SHEET 7 AB3 7 SER B 911 THR B 914 -1 O SER B 911 N ASP B 908 SHEET 1 AB4 2 LYS B 785 LYS B 787 0 SHEET 2 AB4 2 LEU B 851 ASP B 853 1 O ASP B 853 N VAL B 786 SHEET 1 AB5 2 TRP B 807 CYS B 809 0 SHEET 2 AB5 2 GLU B 814 GLN B 816 -1 O GLN B 816 N TRP B 807 SHEET 1 AB6 5 THR D 12 GLU D 16 0 SHEET 2 AB6 5 GLN D 2 LYS D 6 -1 N VAL D 5 O ILE D 13 SHEET 3 AB6 5 THR D 66 VAL D 70 1 O LEU D 67 N PHE D 4 SHEET 4 AB6 5 ARG D 42 PHE D 45 -1 N ILE D 44 O HIS D 68 SHEET 5 AB6 5 LYS D 48 GLN D 49 -1 O LYS D 48 N PHE D 45 LINK SG CYS A 298 C2 AYE C 76 1555 1555 1.72 LINK C GLY C 75 N1 AYE C 76 1555 1555 1.45 LINK SG CYS B 298 C2 AYE D 76 1555 1555 1.71 LINK C GLY D 75 N1 AYE D 76 1555 1555 1.41 LINK SG CYS A 448 ZN ZN A1001 1555 1555 2.19 LINK SG CYS A 451 ZN ZN A1001 1555 1555 2.17 LINK SG CYS A 809 ZN ZN A1001 1555 1555 2.26 LINK SG CYS A 812 ZN ZN A1001 1555 1555 2.21 LINK SG CYS B 448 ZN ZN B1001 1555 1555 2.38 LINK SG CYS B 451 ZN ZN B1001 1555 1555 2.67 LINK SG CYS B 809 ZN ZN B1001 1555 1555 2.23 LINK SG CYS B 812 ZN ZN B1001 1555 1555 2.56 CRYST1 130.873 131.851 139.733 90.00 90.00 90.00 C 2 2 21 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 0.007641 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007584 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007157 0.00000 CONECT 193 6528 CONECT 256712956 CONECT 260612956 CONECT 332012956 CONECT 335812956 CONECT 6523 6531 CONECT 6528 193 6529 6530 CONECT 6529 6528 CONECT 6530 6528 6531 CONECT 6531 6523 6530 CONECT 672512951 CONECT 900912967 CONECT 904812967 CONECT 977012967 CONECT 980812967 CONECT1294612954 CONECT12951 67251295212953 CONECT1295212951 CONECT129531295112954 CONECT129541294612953 CONECT12956 2567 2606 3320 3358 CONECT12957129581296112962 CONECT12958129571295912963 CONECT12959129581296012964 CONECT12960129591296112965 CONECT12961129571296012966 CONECT1296212957 CONECT1296312958 CONECT1296412959 CONECT1296512960 CONECT1296612961 CONECT12967 9009 9048 9770 9808 MASTER 404 0 5 26 56 0 0 6 6704 4 32 66 END