HEADER HYDROLASE 09-APR-15 4Z97
TITLE CRYSTAL STRUCTURE OF USP7 IN COMPLEX WITH DNMT1(K1115Q)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 544-1067;
COMPND 5 SYNONYM: DEUBIQUITINATING ENZYME 7,HERPESVIRUS-ASSOCIATED UBIQUITIN-
COMPND 6 SPECIFIC PROTEASE,UBIQUITIN THIOESTERASE 7,UBIQUITIN-SPECIFIC-
COMPND 7 PROCESSING PROTEASE 7;
COMPND 8 EC: 3.4.19.12;
COMPND 9 ENGINEERED: YES;
COMPND 10 MOL_ID: 2;
COMPND 11 MOLECULE: DNA (CYTOSINE-5)-METHYLTRANSFERASE 1;
COMPND 12 CHAIN: C;
COMPND 13 FRAGMENT: UNP RESIDUES 1097-1129;
COMPND 14 SYNONYM: DNMT1,CXXC-TYPE ZINC FINGER PROTEIN 9,DNA METHYLTRANSFERASE
COMPND 15 HSAI,M.HSAI,MCMT;
COMPND 16 EC: 2.1.1.37;
COMPND 17 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;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 MOL_ID: 2;
SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 10 ORGANISM_COMMON: HUMAN;
SOURCE 11 ORGANISM_TAXID: 9606;
SOURCE 12 GENE: DNMT1, AIM, CXXC9, DNMT;
SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS COMPLEX, TRANSFERASE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR Z.M.ZHANG,J.SONG
REVDAT 2 06-MAR-24 4Z97 1 REMARK
REVDAT 1 12-OCT-16 4Z97 0
JRNL AUTH Z.M.ZHANG,J.SONG
JRNL TITL CRYSTAL STRUCTURE OF USP7 IN COMPLEX WITH DNMT1(K1115Q)
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 3.00 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.9_1692
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) : 3.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.86
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 3 NUMBER OF REFLECTIONS : 27611
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.212
REMARK 3 R VALUE (WORKING SET) : 0.209
REMARK 3 FREE R VALUE : 0.254
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.300
REMARK 3 FREE R VALUE TEST SET COUNT : 2016
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 43.8655 - 7.2149 1.00 1955 153 0.1994 0.2422
REMARK 3 2 7.2149 - 5.7307 1.00 1858 149 0.2425 0.2584
REMARK 3 3 5.7307 - 5.0075 1.00 1849 146 0.1860 0.2607
REMARK 3 4 5.0075 - 4.5502 1.00 1837 148 0.1546 0.1968
REMARK 3 5 4.5502 - 4.2243 1.00 1826 146 0.1649 0.2130
REMARK 3 6 4.2243 - 3.9754 1.00 1799 143 0.1979 0.2301
REMARK 3 7 3.9754 - 3.7765 1.00 1825 142 0.2088 0.2709
REMARK 3 8 3.7765 - 3.6121 1.00 1815 146 0.2171 0.2598
REMARK 3 9 3.6121 - 3.4731 1.00 1805 140 0.2329 0.2855
REMARK 3 10 3.4731 - 3.3533 1.00 1814 140 0.2523 0.2827
REMARK 3 11 3.3533 - 3.2485 1.00 1791 142 0.2603 0.3191
REMARK 3 12 3.2485 - 3.1557 1.00 1830 142 0.2783 0.3678
REMARK 3 13 3.1557 - 3.0726 1.00 1801 142 0.3177 0.3238
REMARK 3 14 3.0726 - 2.9980 1.00 1790 137 0.3327 0.4104
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) : 0.450
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.510
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 : 0.008 4221
REMARK 3 ANGLE : 1.154 5719
REMARK 3 CHIRALITY : 0.044 628
REMARK 3 PLANARITY : 0.005 755
REMARK 3 DIHEDRAL : 14.820 1531
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 555 THROUGH 800 )
REMARK 3 ORIGIN FOR THE GROUP (A): -60.2038 -33.4089 -2.5777
REMARK 3 T TENSOR
REMARK 3 T11: 0.6866 T22: 0.8287
REMARK 3 T33: 0.6368 T12: -0.1047
REMARK 3 T13: 0.2406 T23: -0.1944
REMARK 3 L TENSOR
REMARK 3 L11: 1.5880 L22: 2.9944
REMARK 3 L33: 2.3888 L12: -0.7646
REMARK 3 L13: 1.7533 L23: -0.4804
REMARK 3 S TENSOR
REMARK 3 S11: -0.0237 S12: 0.2354 S13: -0.4956
REMARK 3 S21: 0.1484 S22: 0.4621 S23: -0.0113
REMARK 3 S31: 0.0783 S32: 0.1356 S33: -0.4652
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 801 THROUGH 1083 )
REMARK 3 ORIGIN FOR THE GROUP (A): -36.8084 26.1051 20.7742
REMARK 3 T TENSOR
REMARK 3 T11: 0.7129 T22: 0.6575
REMARK 3 T33: 0.7151 T12: -0.1616
REMARK 3 T13: -0.0482 T23: -0.1900
REMARK 3 L TENSOR
REMARK 3 L11: 0.8116 L22: 4.7287
REMARK 3 L33: 1.6768 L12: 0.1446
REMARK 3 L13: -0.6434 L23: 1.3183
REMARK 3 S TENSOR
REMARK 3 S11: 0.1911 S12: -0.1860 S13: 0.2137
REMARK 3 S21: -0.5263 S22: 0.2178 S23: -0.5031
REMARK 3 S31: -0.3501 S32: 0.4182 S33: -0.3418
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1110 THROUGH 1117 )
REMARK 3 ORIGIN FOR THE GROUP (A): -64.0763 -36.8178 11.1483
REMARK 3 T TENSOR
REMARK 3 T11: 0.9938 T22: 0.6122
REMARK 3 T33: 0.7684 T12: -0.1735
REMARK 3 T13: 0.4320 T23: 0.1436
REMARK 3 L TENSOR
REMARK 3 L11: 5.9307 L22: 2.0712
REMARK 3 L33: 3.2146 L12: -2.1282
REMARK 3 L13: -2.1354 L23: 1.5336
REMARK 3 S TENSOR
REMARK 3 S11: -0.2465 S12: -0.0067 S13: -0.3487
REMARK 3 S21: -0.2748 S22: 0.1340 S23: -0.8603
REMARK 3 S31: 0.1863 S32: 0.1706 S33: 0.1144
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 4Z97 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-APR-15.
REMARK 100 THE DEPOSITION ID IS D_1000208843.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 17-DEC-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ALS
REMARK 200 BEAMLINE : 5.0.1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9774
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 : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27615
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.998
REMARK 200 RESOLUTION RANGE LOW (A) : 43.861
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 5.100
REMARK 200 R MERGE (I) : 0.07200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9
REMARK 200 DATA REDUNDANCY IN SHELL : 4.80
REMARK 200 R MERGE FOR SHELL (I) : 0.74400
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
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 (%): 76.19
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.17
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, PH5.5, 10%
REMARK 280 PEG6000, 15% GLYCEROL, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 297K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+2/3
REMARK 290 3555 -X+Y,-X,Z+1/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+1/3
REMARK 290 6555 -X,-X+Y,-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 101.95200
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 50.97600
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 50.97600
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 101.95200
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1610 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 28390 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 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 554
REMARK 465 LYS A 984
REMARK 465 HIS A 1012
REMARK 465 GLN A 1013
REMARK 465 GLU A 1032
REMARK 465 LYS A 1033
REMARK 465 GLU A 1034
REMARK 465 VAL A 1058
REMARK 465 ASN A 1069
REMARK 465 SER C 1097
REMARK 465 ASP C 1098
REMARK 465 TRP C 1099
REMARK 465 PRO C 1100
REMARK 465 ASN C 1101
REMARK 465 HIS C 1102
REMARK 465 ALA C 1103
REMARK 465 ARG C 1104
REMARK 465 SER C 1105
REMARK 465 PRO C 1106
REMARK 465 GLY C 1107
REMARK 465 ASN C 1108
REMARK 465 LYS C 1109
REMARK 465 GLY C 1118
REMARK 465 LYS C 1119
REMARK 465 PRO C 1120
REMARK 465 LYS C 1121
REMARK 465 SER C 1122
REMARK 465 GLN C 1123
REMARK 465 ALA C 1124
REMARK 465 CYS C 1125
REMARK 465 GLU C 1126
REMARK 465 PRO C 1127
REMARK 465 SER C 1128
REMARK 465 GLU C 1129
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 LYS A 590 CG CD CE NZ
REMARK 470 GLU A 641 CG CD OE1 OE2
REMARK 470 ASN A 645 CG OD1 ND2
REMARK 470 LYS A 646 CG CD CE NZ
REMARK 470 ASP A 666 CG OD1 OD2
REMARK 470 GLU A 668 CG CD OE1 OE2
REMARK 470 LEU A 669 CG CD1 CD2
REMARK 470 LYS A 678 CG CD CE NZ
REMARK 470 LYS A 695 CG CD CE NZ
REMARK 470 ILE A 727 CG1 CG2 CD1
REMARK 470 ASP A 729 CG OD1 OD2
REMARK 470 ASP A 772 CG OD1 OD2
REMARK 470 GLU A 774 CG CD OE1 OE2
REMARK 470 LYS A 801 CG CD CE NZ
REMARK 470 ASN A 805 CG OD1 ND2
REMARK 470 PHE A 820 CG CD1 CD2 CE1 CE2 CZ
REMARK 470 LYS A 824 CG CD CE NZ
REMARK 470 GLN A 828 CG CD OE1 NE2
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 ASP A 847 CG OD1 OD2
REMARK 470 ARG A 854 CG CD NE CZ NH1 NH2
REMARK 470 LYS A 869 CG CD CE NZ
REMARK 470 ARG A 871 CG CD NE CZ NH1 NH2
REMARK 470 LYS A 875 CG CD CE NZ
REMARK 470 LYS A 882 CG CD CE NZ
REMARK 470 LYS A 884 CD CE NZ
REMARK 470 LYS A 914 CG CD CE NZ
REMARK 470 GLU A 930 CG CD OE1 OE2
REMARK 470 LYS A 934 CG CD CE NZ
REMARK 470 ASP A 981 CG OD1 OD2
REMARK 470 ILE A 982 CG1 CG2 CD1
REMARK 470 GLU A 985 CG CD OE1 OE2
REMARK 470 LYS A 997 CG CD CE NZ
REMARK 470 GLU A 998 CD OE1 OE2
REMARK 470 ILE A1011 CG1 CG2 CD1
REMARK 470 GLU A1015 CG CD OE1 OE2
REMARK 470 ARG A1018 CG CD NE CZ NH1 NH2
REMARK 470 GLU A1019 CG CD OE1 OE2
REMARK 470 MET A1021 CG SD CE
REMARK 470 LYS A1022 CG CD CE NZ
REMARK 470 SER A1026 OG
REMARK 470 LEU A1028 CG CD1 CD2
REMARK 470 ASP A1029 CG OD1 OD2
REMARK 470 ILE A1030 CG1 CG2 CD1
REMARK 470 GLN A1031 CG CD OE1 NE2
REMARK 470 GLU A1036 CG CD OE1 OE2
REMARK 470 PHE A1038 CG CD1 CD2 CE1 CE2 CZ
REMARK 470 LYS A1039 CG CD CE NZ
REMARK 470 ILE A1042 CG1 CG2 CD1
REMARK 470 ILE A1051 CG1 CG2 CD1
REMARK 470 ASN A1052 CG OD1 ND2
REMARK 470 ASP A1054 CG OD1 OD2
REMARK 470 GLU A1055 CG CD OE1 OE2
REMARK 470 TYR A1056 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 470 ASN A1059 CG OD1 ND2
REMARK 470 LEU A1060 CG CD1 CD2
REMARK 470 LYS A1061 CG CD CE NZ
REMARK 470 GLU A1064 CG CD OE1 OE2
REMARK 470 ARG A1074 CG CD NE CZ NH1 NH2
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 -160.20 53.58
REMARK 500 ASN A 640 0.62 -68.08
REMARK 500 ASP A 666 102.10 -50.29
REMARK 500 ASP A 750 37.57 -95.66
REMARK 500 ASP A 771 48.79 -96.50
REMARK 500 ASN A 815 -43.54 -25.72
REMARK 500 ARG A 829 -6.02 75.98
REMARK 500 GLN A 843 -53.77 -123.73
REMARK 500 ASP A 847 105.31 61.30
REMARK 500 ASN A 900 171.64 -59.52
REMARK 500 ALA A 935 -157.90 -87.02
REMARK 500 GLN A 979 54.08 -94.32
REMARK 500 VAL A 980 -31.44 -157.59
REMARK 500 ASP A 981 50.73 -93.77
REMARK 500 ASN A 986 -29.85 99.83
REMARK 500 LYS A 997 -98.10 61.32
REMARK 500 HIS A1016 -162.89 -177.73
REMARK 500 PHE A1017 -84.25 -146.69
REMARK 500 ARG A1018 -35.23 -28.61
REMARK 500 ILE A1030 -151.47 -82.49
REMARK 500 LYS A1037 -130.20 -71.77
REMARK 500 PHE A1038 101.65 61.66
REMARK 500 MET A1044 -161.77 -121.17
REMARK 500 LEU A1060 -137.29 175.09
REMARK 500 PRO A1067 75.64 -66.74
REMARK 500 LYS C1113 -70.90 -98.40
REMARK 500 GLN C1115 -76.69 -32.78
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1101
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4Z96 RELATED DB: PDB
DBREF 4Z97 A 560 1083 UNP Q93009 UBP7_HUMAN 544 1067
DBREF 4Z97 C 1097 1129 PDB 4Z97 4Z97 1097 1129
SEQADV 4Z97 SER A 554 UNP Q93009 EXPRESSION TAG
SEQADV 4Z97 GLY A 555 UNP Q93009 EXPRESSION TAG
SEQADV 4Z97 PRO A 556 UNP Q93009 EXPRESSION TAG
SEQADV 4Z97 LEU A 557 UNP Q93009 EXPRESSION TAG
SEQADV 4Z97 GLY A 558 UNP Q93009 EXPRESSION TAG
SEQADV 4Z97 SER A 559 UNP Q93009 EXPRESSION TAG
SEQRES 1 A 530 SER GLY PRO LEU GLY SER GLU ALA HIS LEU TYR MET GLN
SEQRES 2 A 530 VAL GLN ILE VAL ALA GLU ASP GLN PHE CYS GLY HIS GLN
SEQRES 3 A 530 GLY ASN ASP MET TYR ASP GLU GLU LYS VAL LYS TYR THR
SEQRES 4 A 530 VAL PHE LYS VAL LEU LYS ASN SER SER LEU ALA GLU PHE
SEQRES 5 A 530 VAL GLN SER LEU SER GLN THR MET GLY PHE PRO GLN ASP
SEQRES 6 A 530 GLN ILE ARG LEU TRP PRO MET GLN ALA ARG SER ASN GLY
SEQRES 7 A 530 THR LYS ARG PRO ALA MET LEU ASP ASN GLU ALA ASP GLY
SEQRES 8 A 530 ASN LYS THR MET ILE GLU LEU SER ASP ASN GLU ASN PRO
SEQRES 9 A 530 TRP THR ILE PHE LEU GLU THR VAL ASP PRO GLU LEU ALA
SEQRES 10 A 530 ALA SER GLY ALA THR LEU PRO LYS PHE ASP LYS ASP HIS
SEQRES 11 A 530 ASP VAL MET LEU PHE LEU LYS MET TYR ASP PRO LYS THR
SEQRES 12 A 530 ARG SER LEU ASN TYR CYS GLY HIS ILE TYR THR PRO ILE
SEQRES 13 A 530 SER CYS LYS ILE ARG ASP LEU LEU PRO VAL MET CYS ASP
SEQRES 14 A 530 ARG ALA GLY PHE ILE GLN ASP THR SER LEU ILE LEU TYR
SEQRES 15 A 530 GLU GLU VAL LYS PRO ASN LEU THR GLU ARG ILE GLN ASP
SEQRES 16 A 530 TYR ASP VAL SER LEU ASP LYS ALA LEU ASP GLU LEU MET
SEQRES 17 A 530 ASP GLY ASP ILE ILE VAL PHE GLN LYS ASP ASP PRO GLU
SEQRES 18 A 530 ASN ASP ASN SER GLU LEU PRO THR ALA LYS GLU TYR PHE
SEQRES 19 A 530 ARG ASP LEU TYR HIS ARG VAL ASP VAL ILE PHE CYS ASP
SEQRES 20 A 530 LYS THR ILE PRO ASN ASP PRO GLY PHE VAL VAL THR LEU
SEQRES 21 A 530 SER ASN ARG MET ASN TYR PHE GLN VAL ALA LYS THR VAL
SEQRES 22 A 530 ALA GLN ARG LEU ASN THR ASP PRO MET LEU LEU GLN PHE
SEQRES 23 A 530 PHE LYS SER GLN GLY TYR ARG ASP GLY PRO GLY ASN PRO
SEQRES 24 A 530 LEU ARG HIS ASN TYR GLU GLY THR LEU ARG ASP LEU LEU
SEQRES 25 A 530 GLN PHE PHE LYS PRO ARG GLN PRO LYS LYS LEU TYR TYR
SEQRES 26 A 530 GLN GLN LEU LYS MET LYS ILE THR ASP PHE GLU ASN ARG
SEQRES 27 A 530 ARG SER PHE LYS CYS ILE TRP LEU ASN SER GLN PHE ARG
SEQRES 28 A 530 GLU GLU GLU ILE THR LEU TYR PRO ASP LYS HIS GLY CYS
SEQRES 29 A 530 VAL ARG ASP LEU LEU GLU GLU CYS LYS LYS ALA VAL GLU
SEQRES 30 A 530 LEU GLY GLU LYS ALA SER GLY LYS LEU ARG LEU LEU GLU
SEQRES 31 A 530 ILE VAL SER TYR LYS ILE ILE GLY VAL HIS GLN GLU ASP
SEQRES 32 A 530 GLU LEU LEU GLU CYS LEU SER PRO ALA THR SER ARG THR
SEQRES 33 A 530 PHE ARG ILE GLU GLU ILE PRO LEU ASP GLN VAL ASP ILE
SEQRES 34 A 530 ASP LYS GLU ASN GLU MET LEU VAL THR VAL ALA HIS PHE
SEQRES 35 A 530 HIS LYS GLU VAL PHE GLY THR PHE GLY ILE PRO PHE LEU
SEQRES 36 A 530 LEU ARG ILE HIS GLN GLY GLU HIS PHE ARG GLU VAL MET
SEQRES 37 A 530 LYS ARG ILE GLN SER LEU LEU ASP ILE GLN GLU LYS GLU
SEQRES 38 A 530 PHE GLU LYS PHE LYS PHE ALA ILE VAL MET MET GLY ARG
SEQRES 39 A 530 HIS GLN TYR ILE ASN GLU ASP GLU TYR GLU VAL ASN LEU
SEQRES 40 A 530 LYS ASP PHE GLU PRO GLN PRO GLY ASN MET SER HIS PRO
SEQRES 41 A 530 ARG PRO TRP LEU GLY LEU ASP HIS PHE ASN
SEQRES 1 C 33 SER ASP TRP PRO ASN HIS ALA ARG SER PRO GLY ASN LYS
SEQRES 2 C 33 GLY LYS GLY LYS GLY GLN GLY LYS GLY LYS PRO LYS SER
SEQRES 3 C 33 GLN ALA CYS GLU PRO SER GLU
HET GOL A1101 6
HETNAM GOL GLYCEROL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 3 GOL C3 H8 O3
HELIX 1 AA1 ASP A 573 CYS A 576 5 4
HELIX 2 AA2 SER A 601 GLY A 614 1 14
HELIX 3 AA3 PRO A 616 ASP A 618 5 3
HELIX 4 AA4 THR A 647 ASP A 653 1 7
HELIX 5 AA5 GLU A 668 GLY A 673 5 6
HELIX 6 AA6 LYS A 712 ASP A 715 5 4
HELIX 7 AA7 LEU A 716 GLY A 725 1 10
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 GLN A 828 1 11
HELIX 12 AB3 ASP A 833 MET A 835 5 3
HELIX 13 AB4 THR A 860 LEU A 865 1 6
HELIX 14 AB5 LYS A 884 ASN A 890 1 7
HELIX 15 AB6 CYS A 917 VAL A 929 1 13
HELIX 16 AB7 ARG A 1018 ASP A 1029 1 12
SHEET 1 AA1 5 THR A 592 LEU A 597 0
SHEET 2 AA1 5 TYR A 564 ALA A 571 -1 N VAL A 567 O PHE A 594
SHEET 3 AA1 5 TRP A 658 THR A 664 1 O TRP A 658 N GLN A 568
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 LEU A 689 O GLY A 703
SHEET 3 AA2 5 ASP A 764 LYS A 770 1 O ASP A 764 N PHE A 688
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 4 PHE A 809 SER A 814 0
SHEET 2 AA3 4 ARG A 793 ASP A 800 -1 N PHE A 798 O PHE A 809
SHEET 3 AA3 4 LYS A 874 GLN A 880 1 O LYS A 874 N ILE A 797
SHEET 4 AA3 4 LEU A 837 PHE A 840 -1 N GLN A 838 O GLN A 879
SHEET 1 AA4 5 GLU A 905 LEU A 910 0
SHEET 2 AA4 5 PHE A 894 LEU A 899 -1 N TRP A 898 O GLU A 906
SHEET 3 AA4 5 THR A 969 GLU A 974 1 O ILE A 972 N ILE A 897
SHEET 4 AA4 5 LEU A 939 VAL A 945 -1 N LEU A 942 O ARG A 971
SHEET 5 AA4 5 LYS A 948 HIS A 953 -1 O LYS A 948 N VAL A 945
SHEET 1 AA5 5 THR A1002 ILE A1011 0
SHEET 2 AA5 5 MET A 988 PHE A 995 -1 N MET A 988 O ILE A1011
SHEET 3 AA5 5 TRP A1076 ASP A1080 1 O LEU A1077 N THR A 991
SHEET 4 AA5 5 LYS A1039 MET A1044 -1 N ALA A1041 O GLY A1078
SHEET 5 AA5 5 ARG A1047 TYR A1050 -1 O GLN A1049 N ILE A1042
CISPEP 1 GLY A 555 PRO A 556 0 -9.51
CISPEP 2 ASN A 656 PRO A 657 0 7.91
CISPEP 3 GLY A 848 PRO A 849 0 1.23
CISPEP 4 HIS A 1072 PRO A 1073 0 8.56
CISPEP 5 GLY C 1110 LYS C 1111 0 -4.23
SITE 1 AC1 7 GLN A 626 ALA A 636 MET A 637 MET A 761
SITE 2 AC1 7 ASP A 762 GLN C1115 LYS C1117
CRYST1 123.659 123.659 152.928 90.00 90.00 120.00 P 32 2 1 6
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 0.008087 0.004669 0.000000 0.00000
SCALE2 0.000000 0.009338 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006539 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
