HEADER HYDROLASE 30-MAY-19 6P5L TITLE CRYSTAL STRUCTURE OF UBL123 WITH AN EZH2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DEUBIQUITINATING ENZYME 7,HERPESVIRUS-ASSOCIATED UBIQUITIN- COMPND 5 SPECIFIC PROTEASE,UBIQUITIN THIOESTERASE 7,UBIQUITIN-SPECIFIC- COMPND 6 PROCESSING PROTEASE 7; COMPND 7 EC: 3.4.19.12; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: PRO-ARG-LYS-LYS-LYS-ARG-LYS-HIS; COMPND 11 CHAIN: D; COMPND 12 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: USP7, HAUSP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET15B; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS COMPLEX DEUBIQUITINASE, NUCLEAR PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.SARIDAKIS REVDAT 2 11-OCT-23 6P5L 1 REMARK REVDAT 1 06-MAY-20 6P5L 0 JRNL AUTH V.GAGARINA,A.BOJAGORA,I.K.LACDAO,N.LUTHRA,R.PFOH,S.MOHSENI, JRNL AUTH 2 D.CHAHARLANGI,N.TAN,V.SARIDAKIS JRNL TITL STRUCTURAL BASIS OF THE INTERACTION BETWEEN UBIQUITIN JRNL TITL 2 SPECIFIC PROTEASE 7 AND ENHANCER OF ZESTE HOMOLOG 2. JRNL REF J.MOL.BIOL. V. 432 897 2020 JRNL REFN ESSN 1089-8638 JRNL PMID 31866294 JRNL DOI 10.1016/J.JMB.2019.12.026 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 23638 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.430 REMARK 3 FREE R VALUE TEST SET COUNT : 1993 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 29.6096 - 7.8975 1.00 1677 154 0.2065 0.2562 REMARK 3 2 7.8975 - 6.2882 1.00 1605 148 0.2545 0.3069 REMARK 3 3 6.2882 - 5.4991 1.00 1574 145 0.2346 0.2774 REMARK 3 4 5.4991 - 4.9989 1.00 1560 144 0.1905 0.2079 REMARK 3 5 4.9989 - 4.6421 1.00 1556 144 0.1869 0.2599 REMARK 3 6 4.6421 - 4.3693 1.00 1546 141 0.1905 0.2584 REMARK 3 7 4.3693 - 4.1511 1.00 1534 141 0.2227 0.2743 REMARK 3 8 4.1511 - 3.9708 1.00 1531 142 0.2306 0.2949 REMARK 3 9 3.9708 - 3.8183 0.97 1490 135 0.3113 0.4382 REMARK 3 10 3.8183 - 3.6868 1.00 1510 139 0.2917 0.3452 REMARK 3 11 3.6868 - 3.5717 0.99 1524 142 0.3055 0.4044 REMARK 3 12 3.5717 - 3.4698 1.00 1523 140 0.2994 0.3792 REMARK 3 13 3.4698 - 3.3786 1.00 1501 139 0.3480 0.4516 REMARK 3 14 3.3786 - 3.2962 0.99 1514 139 0.2828 0.3880 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) : 0.470 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 122.1 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6P5L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1000241920. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23736 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.296 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 28.90 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 49.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.94000 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: 4WPI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 167 MM NACL, 20MM TRIS, 5MM B-ME, 10MM REMARK 280 BETAINE HYDROCHLORID, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 82.72600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 82.72600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 55.45000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 82.72600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 82.72600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.45000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 82.72600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 82.72600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 55.45000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 82.72600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 82.72600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 55.45000 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 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 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 ASP A 535 REMARK 465 ILE A 536 REMARK 465 PRO A 537 REMARK 465 GLN A 538 REMARK 465 GLN A 539 REMARK 465 LEU A 540 REMARK 465 VAL A 541 REMARK 465 GLU A 542 REMARK 465 LYS A 884 REMARK 465 ILE A 885 REMARK 465 THR A 886 REMARK 465 ASP A 887 REMARK 465 PHE A 888 REMARK 465 GLU A 889 REMARK 465 ASN A 890 REMARK 465 ASP B 535 REMARK 465 ILE B 536 REMARK 465 PRO B 537 REMARK 465 MET B 637 REMARK 465 LEU B 638 REMARK 465 ASP B 639 REMARK 465 ASN B 640 REMARK 465 GLU B 641 REMARK 465 MET B 883 REMARK 465 LYS B 884 REMARK 465 ILE B 885 REMARK 465 THR B 886 REMARK 465 ASP B 887 REMARK 465 PHE B 888 REMARK 465 GLU B 889 REMARK 465 ASN B 890 REMARK 465 PRO D 489 REMARK 465 HIS D 496 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 TYR A 845 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 846 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 780 CG CD1 CD2 REMARK 470 TYR B 845 CG CD1 CD2 CE1 CE2 CZ OH 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 NE2 HIS B 578 O GLY B 580 2.10 REMARK 500 O HIS A 704 NH2 ARG A 723 2.16 REMARK 500 OG SER A 652 O GLU A 655 2.16 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 ASN A 645 OD1 - CG - ND2 ANGL. DEV. = -19.3 DEGREES REMARK 500 ASN A 645 CB - CG - OD1 ANGL. DEV. = 57.2 DEGREES REMARK 500 ASN A 645 CB - CG - ND2 ANGL. DEV. = -40.1 DEGREES REMARK 500 LYS A 784 CD - CE - NZ ANGL. DEV. = 18.4 DEGREES REMARK 500 LEU A 830 CA - CB - CG ANGL. DEV. = 23.0 DEGREES REMARK 500 LEU A 830 CB - CG - CD1 ANGL. DEV. = 10.8 DEGREES REMARK 500 LEU A 865 CB - CG - CD2 ANGL. DEV. = -12.3 DEGREES REMARK 500 LYS A 875 CD - CE - NZ ANGL. DEV. = -16.5 DEGREES REMARK 500 GLN A 880 N - CA - CB ANGL. DEV. = -11.4 DEGREES REMARK 500 GLN A 880 CA - CB - CG ANGL. DEV. = -20.2 DEGREES REMARK 500 GLN A 880 CG - CD - NE2 ANGL. DEV. = -33.6 DEGREES REMARK 500 LEU B 544 CB - CG - CD1 ANGL. DEV. = 14.6 DEGREES REMARK 500 LEU B 544 CB - CG - CD2 ANGL. DEV. = -20.1 DEGREES REMARK 500 LEU B 597 CB - CG - CD1 ANGL. DEV. = 22.4 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 ASP A 582 -156.34 47.38 REMARK 500 TYR A 584 -153.66 -139.65 REMARK 500 GLN A 617 -6.57 -31.92 REMARK 500 ASP A 639 109.66 -59.35 REMARK 500 GLU A 641 -38.43 -137.82 REMARK 500 ASP A 643 27.64 -67.95 REMARK 500 ASN A 645 12.64 -56.00 REMARK 500 SER A 672 -3.27 -37.41 REMARK 500 ASN A 741 -23.56 75.34 REMARK 500 ASP A 750 29.74 -57.88 REMARK 500 ASP A 771 59.83 -90.41 REMARK 500 LYS A 784 -53.93 -28.04 REMARK 500 ARG A 829 -15.01 -47.28 REMARK 500 MET A 835 -3.00 -50.69 REMARK 500 LYS A 841 179.00 -58.63 REMARK 500 TYR A 845 -71.08 -107.15 REMARK 500 LYS A 869 -155.32 -138.73 REMARK 500 PRO A 870 -108.31 -53.00 REMARK 500 ARG A 871 -38.77 -36.87 REMARK 500 GLN A 872 101.37 -58.27 REMARK 500 LYS A 874 118.37 -35.26 REMARK 500 LYS A 882 -165.73 -74.68 REMARK 500 LEU B 540 -108.02 -113.29 REMARK 500 VAL B 541 -97.87 -39.99 REMARK 500 GLU B 542 -97.85 37.88 REMARK 500 ARG B 543 -59.94 -0.14 REMARK 500 GLU B 557 -0.72 -37.30 REMARK 500 HIS B 578 139.57 -31.35 REMARK 500 ASN B 581 126.53 40.67 REMARK 500 ASP B 582 -156.23 71.08 REMARK 500 ASN B 599 77.87 -58.69 REMARK 500 SER B 608 -65.90 -29.78 REMARK 500 GLN B 617 -23.30 -14.35 REMARK 500 ARG B 621 137.42 -173.44 REMARK 500 THR B 647 -158.45 -72.35 REMARK 500 MET B 648 -96.31 -84.56 REMARK 500 ILE B 649 -34.91 -36.79 REMARK 500 SER B 652 -1.84 -42.57 REMARK 500 ASN B 654 97.26 59.06 REMARK 500 ASP B 666 127.70 -37.12 REMARK 500 GLU B 668 -74.86 -54.56 REMARK 500 LEU B 669 -14.49 -47.99 REMARK 500 SER B 672 28.38 -63.14 REMARK 500 ALA B 674 94.80 24.85 REMARK 500 CYS B 702 32.82 -141.52 REMARK 500 GLU B 737 85.05 -66.35 REMARK 500 VAL B 738 -74.37 -62.55 REMARK 500 ASN B 741 -46.14 72.57 REMARK 500 THR B 743 53.70 -158.66 REMARK 500 GLU B 744 106.37 -42.25 REMARK 500 REMARK 500 THIS ENTRY HAS 58 RAMACHANDRAN OUTLIERS. 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 GLN B 607 SER B 608 149.23 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 GLN A 880 0.18 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 6P5L A 535 890 UNP Q93009 UBP7_HUMAN 535 890 DBREF 6P5L B 535 890 UNP Q93009 UBP7_HUMAN 535 890 DBREF 6P5L D 489 496 PDB 6P5L 6P5L 489 496 SEQRES 1 A 356 ASP ILE PRO GLN GLN LEU VAL GLU ARG LEU GLN GLU GLU SEQRES 2 A 356 LYS ARG ILE GLU ALA GLN LYS ARG LYS GLU ARG GLN GLU SEQRES 3 A 356 ALA HIS LEU TYR MET GLN VAL GLN ILE VAL ALA GLU ASP SEQRES 4 A 356 GLN PHE CYS GLY HIS GLN GLY ASN ASP MET TYR ASP GLU SEQRES 5 A 356 GLU LYS VAL LYS TYR THR VAL PHE LYS VAL LEU LYS ASN SEQRES 6 A 356 SER SER LEU ALA GLU PHE VAL GLN SER LEU SER GLN THR SEQRES 7 A 356 MET GLY PHE PRO GLN ASP GLN ILE ARG LEU TRP PRO MET SEQRES 8 A 356 GLN ALA ARG SER ASN GLY THR LYS ARG PRO ALA MET LEU SEQRES 9 A 356 ASP ASN GLU ALA ASP GLY ASN LYS THR MET ILE GLU LEU SEQRES 10 A 356 SER ASP ASN GLU ASN PRO TRP THR ILE PHE LEU GLU THR SEQRES 11 A 356 VAL ASP PRO GLU LEU ALA ALA SER GLY ALA THR LEU PRO SEQRES 12 A 356 LYS PHE ASP LYS ASP HIS ASP VAL MET LEU PHE LEU LYS SEQRES 13 A 356 MET TYR ASP PRO LYS THR ARG SER LEU ASN TYR CYS GLY SEQRES 14 A 356 HIS ILE TYR THR PRO ILE SER CYS LYS ILE ARG ASP LEU SEQRES 15 A 356 LEU PRO VAL MET CYS ASP ARG ALA GLY PHE ILE GLN ASP SEQRES 16 A 356 THR SER LEU ILE LEU TYR GLU GLU VAL LYS PRO ASN LEU SEQRES 17 A 356 THR GLU ARG ILE GLN ASP TYR ASP VAL SER LEU ASP LYS SEQRES 18 A 356 ALA LEU ASP GLU LEU MET ASP GLY ASP ILE ILE VAL PHE SEQRES 19 A 356 GLN LYS ASP ASP PRO GLU ASN ASP ASN SER GLU LEU PRO SEQRES 20 A 356 THR ALA LYS GLU TYR PHE ARG ASP LEU TYR HIS ARG VAL SEQRES 21 A 356 ASP VAL ILE PHE CYS ASP LYS THR ILE PRO ASN ASP PRO SEQRES 22 A 356 GLY PHE VAL VAL THR LEU SER ASN ARG MET ASN TYR PHE SEQRES 23 A 356 GLN VAL ALA LYS THR VAL ALA GLN ARG LEU ASN THR ASP SEQRES 24 A 356 PRO MET LEU LEU GLN PHE PHE LYS SER GLN GLY TYR ARG SEQRES 25 A 356 ASP GLY PRO GLY ASN PRO LEU ARG HIS ASN TYR GLU GLY SEQRES 26 A 356 THR LEU ARG ASP LEU LEU GLN PHE PHE LYS PRO ARG GLN SEQRES 27 A 356 PRO LYS LYS LEU TYR TYR GLN GLN LEU LYS MET LYS ILE SEQRES 28 A 356 THR ASP PHE GLU ASN SEQRES 1 B 356 ASP ILE PRO GLN GLN LEU VAL GLU ARG LEU GLN GLU GLU SEQRES 2 B 356 LYS ARG ILE GLU ALA GLN LYS ARG LYS GLU ARG GLN GLU SEQRES 3 B 356 ALA HIS LEU TYR MET GLN VAL GLN ILE VAL ALA GLU ASP SEQRES 4 B 356 GLN PHE CYS GLY HIS GLN GLY ASN ASP MET TYR ASP GLU SEQRES 5 B 356 GLU LYS VAL LYS TYR THR VAL PHE LYS VAL LEU LYS ASN SEQRES 6 B 356 SER SER LEU ALA GLU PHE VAL GLN SER LEU SER GLN THR SEQRES 7 B 356 MET GLY PHE PRO GLN ASP GLN ILE ARG LEU TRP PRO MET SEQRES 8 B 356 GLN ALA ARG SER ASN GLY THR LYS ARG PRO ALA MET LEU SEQRES 9 B 356 ASP ASN GLU ALA ASP GLY ASN LYS THR MET ILE GLU LEU SEQRES 10 B 356 SER ASP ASN GLU ASN PRO TRP THR ILE PHE LEU GLU THR SEQRES 11 B 356 VAL ASP PRO GLU LEU ALA ALA SER GLY ALA THR LEU PRO SEQRES 12 B 356 LYS PHE ASP LYS ASP HIS ASP VAL MET LEU PHE LEU LYS SEQRES 13 B 356 MET TYR ASP PRO LYS THR ARG SER LEU ASN TYR CYS GLY SEQRES 14 B 356 HIS ILE TYR THR PRO ILE SER CYS LYS ILE ARG ASP LEU SEQRES 15 B 356 LEU PRO VAL MET CYS ASP ARG ALA GLY PHE ILE GLN ASP SEQRES 16 B 356 THR SER LEU ILE LEU TYR GLU GLU VAL LYS PRO ASN LEU SEQRES 17 B 356 THR GLU ARG ILE GLN ASP TYR ASP VAL SER LEU ASP LYS SEQRES 18 B 356 ALA LEU ASP GLU LEU MET ASP GLY ASP ILE ILE VAL PHE SEQRES 19 B 356 GLN LYS ASP ASP PRO GLU ASN ASP ASN SER GLU LEU PRO SEQRES 20 B 356 THR ALA LYS GLU TYR PHE ARG ASP LEU TYR HIS ARG VAL SEQRES 21 B 356 ASP VAL ILE PHE CYS ASP LYS THR ILE PRO ASN ASP PRO SEQRES 22 B 356 GLY PHE VAL VAL THR LEU SER ASN ARG MET ASN TYR PHE SEQRES 23 B 356 GLN VAL ALA LYS THR VAL ALA GLN ARG LEU ASN THR ASP SEQRES 24 B 356 PRO MET LEU LEU GLN PHE PHE LYS SER GLN GLY TYR ARG SEQRES 25 B 356 ASP GLY PRO GLY ASN PRO LEU ARG HIS ASN TYR GLU GLY SEQRES 26 B 356 THR LEU ARG ASP LEU LEU GLN PHE PHE LYS PRO ARG GLN SEQRES 27 B 356 PRO LYS LYS LEU TYR TYR GLN GLN LEU LYS MET LYS ILE SEQRES 28 B 356 THR ASP PHE GLU ASN SEQRES 1 D 8 PRO ARG LYS LYS LYS ARG LYS HIS HELIX 1 AA1 LEU A 544 LYS A 548 5 5 HELIX 2 AA2 ARG A 555 ALA A 561 1 7 HELIX 3 AA3 ASP A 573 CYS A 576 5 4 HELIX 4 AA4 SER A 601 GLY A 614 1 14 HELIX 5 AA5 THR A 647 SER A 652 1 6 HELIX 6 AA6 LYS A 712 ASP A 715 5 4 HELIX 7 AA7 LEU A 716 ALA A 724 1 9 HELIX 8 AA8 SER A 752 LEU A 757 1 6 HELIX 9 AA9 ASP A 772 SER A 778 5 7 HELIX 10 AB1 THR A 782 HIS A 792 1 11 HELIX 11 AB2 ASN A 818 ARG A 829 1 12 HELIX 12 AB3 ASP A 833 MET A 835 5 3 HELIX 13 AB4 THR A 860 GLN A 866 1 7 HELIX 14 AB5 GLU B 542 GLU B 560 1 19 HELIX 15 AB6 ASP B 573 CYS B 576 5 4 HELIX 16 AB7 SER B 601 MET B 613 1 13 HELIX 17 AB8 ASP B 666 SER B 672 1 7 HELIX 18 AB9 LYS B 712 ASP B 715 5 4 HELIX 19 AC1 LEU B 716 GLY B 725 1 10 HELIX 20 AC2 SER B 752 LEU B 757 1 6 HELIX 21 AC3 ASP B 772 ASN B 777 5 6 HELIX 22 AC4 THR B 782 HIS B 792 1 11 HELIX 23 AC5 ASN B 818 ASN B 831 1 14 HELIX 24 AC6 ASP B 833 MET B 835 5 3 HELIX 25 AC7 ARG B 862 GLN B 866 5 5 SHEET 1 AA1 5 THR A 592 LEU A 597 0 SHEET 2 AA1 5 TYR A 564 ALA A 571 -1 N MET A 565 O VAL A 596 SHEET 3 AA1 5 TRP A 658 THR A 664 1 O LEU A 662 N VAL A 570 SHEET 4 AA1 5 ILE A 620 ALA A 627 -1 N ARG A 621 O GLU A 663 SHEET 5 AA1 5 LYS A 633 PRO A 635 -1 O ARG A 634 N GLN A 626 SHEET 1 AA2 5 SER A 698 PRO A 708 0 SHEET 2 AA2 5 ASP A 684 ASP A 693 -1 N MET A 691 O ASN A 700 SHEET 3 AA2 5 ILE A 765 LYS A 770 1 O PHE A 768 N TYR A 692 SHEET 4 AA2 5 LEU A 732 LYS A 739 -1 N TYR A 735 O VAL A 767 SHEET 5 AA2 5 LEU A 742 ARG A 745 -1 O GLU A 744 N GLU A 736 SHEET 1 AA3 5 PHE A 809 SER A 814 0 SHEET 2 AA3 5 ARG A 793 ASP A 800 -1 N VAL A 796 O VAL A 811 SHEET 3 AA3 5 LYS A 875 GLN A 880 1 O LEU A 876 N ILE A 797 SHEET 4 AA3 5 LEU A 837 SER A 842 -1 N GLN A 838 O GLN A 879 SHEET 5 AA3 5 PRO A 849 LEU A 853 -1 O LEU A 853 N PHE A 839 SHEET 1 AA4 5 THR B 592 LEU B 597 0 SHEET 2 AA4 5 TYR B 564 ALA B 571 -1 N MET B 565 O VAL B 596 SHEET 3 AA4 5 TRP B 658 THR B 664 1 O TRP B 658 N GLN B 568 SHEET 4 AA4 5 ILE B 620 ALA B 627 -1 N TRP B 623 O PHE B 661 SHEET 5 AA4 5 LYS B 633 PRO B 635 -1 O ARG B 634 N GLN B 626 SHEET 1 AA5 4 SER B 698 PRO B 708 0 SHEET 2 AA5 4 ASP B 684 ASP B 693 -1 N MET B 691 O ASN B 700 SHEET 3 AA5 4 ILE B 765 LYS B 770 1 O PHE B 768 N LYS B 690 SHEET 4 AA5 4 LEU B 732 GLU B 736 -1 N TYR B 735 O VAL B 767 SHEET 1 AA6 5 VAL B 810 SER B 814 0 SHEET 2 AA6 5 ARG B 793 ASP B 800 -1 N VAL B 794 O LEU B 813 SHEET 3 AA6 5 LYS B 875 GLN B 880 1 O LEU B 876 N ILE B 797 SHEET 4 AA6 5 LEU B 837 SER B 842 -1 N PHE B 840 O TYR B 877 SHEET 5 AA6 5 PRO B 849 LEU B 853 -1 O GLY B 850 N LYS B 841 CISPEP 1 ASN A 656 PRO A 657 0 7.11 CISPEP 2 ASN B 656 PRO B 657 0 5.37 CRYST1 165.452 165.452 110.900 90.00 90.00 90.00 P 42 21 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 0.006044 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006044 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009017 0.00000