HEADER TRANSFERASE 18-APR-18 6D4P TITLE UBE2D1 IN COMPLEX WITH UBIQUITIN VARIANT UBV.D1.1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 D1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: (E3-INDEPENDENT) E2 UBIQUITIN-CONJUGATING ENZYME D1,E2 COMPND 5 UBIQUITIN-CONJUGATING ENZYME D1,STIMULATOR OF FE TRANSPORT,SFT,UBC4/5 COMPND 6 HOMOLOG,UBCH5,UBIQUITIN CARRIER PROTEIN D1,UBIQUITIN-CONJUGATING COMPND 7 ENZYME E2(17)KB 1,UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 1,UBIQUITIN- COMPND 8 PROTEIN LIGASE D1; COMPND 9 EC: 2.3.2.23,2.3.2.24; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: UBIQUITIN VARIANT UBV.D1.1; COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UBE2D1, SFT, UBC5A, UBCH5, UBCH5A; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS UBIQUITIN, UBIQUITIN CONJUGATING ENZYME, UBIQUITIN VARIANT, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.F.CECCARELLI,P.GARG,S.SIDHU,F.SICHERI REVDAT 5 04-OCT-23 6D4P 1 REMARK REVDAT 4 11-MAR-20 6D4P 1 JRNL REVDAT 3 08-JAN-20 6D4P 1 REMARK REVDAT 2 06-NOV-19 6D4P 1 JRNL REVDAT 1 17-JUL-19 6D4P 0 JRNL AUTH P.GARG,D.F.CECCARELLI,A.F.A.KESZEI,I.KURINOV,F.SICHERI, JRNL AUTH 2 S.S.SIDHU JRNL TITL STRUCTURAL AND FUNCTIONAL ANALYSIS OF UBIQUITIN-BASED JRNL TITL 2 INHIBITORS THAT TARGET THE BACKSIDES OF E2 ENZYMES. JRNL REF J.MOL.BIOL. V. 432 952 2020 JRNL REFN ESSN 1089-8638 JRNL PMID 31634471 JRNL DOI 10.1016/J.JMB.2019.09.024 REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX PHENIX.REFINE: 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) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 15521 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 787 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 48.3900 - 3.8300 1.00 2607 136 0.1873 0.2054 REMARK 3 2 3.8300 - 3.0400 1.00 2446 151 0.2105 0.2249 REMARK 3 3 3.0400 - 2.6600 1.00 2456 134 0.2313 0.2330 REMARK 3 4 2.6600 - 2.4200 1.00 2443 129 0.2446 0.2743 REMARK 3 5 2.4200 - 2.2400 1.00 2425 117 0.2663 0.3284 REMARK 3 6 2.2400 - 2.1100 0.98 2357 120 0.3081 0.3089 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) : 0.233 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.242 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.99 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 : 0.002 1783 REMARK 3 ANGLE : 0.599 2435 REMARK 3 CHIRALITY : 0.044 269 REMARK 3 PLANARITY : 0.003 316 REMARK 3 DIHEDRAL : 11.388 1068 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -1 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.0160 2.9201 -13.6240 REMARK 3 T TENSOR REMARK 3 T11: 0.4831 T22: 0.4423 REMARK 3 T33: 0.4543 T12: -0.0617 REMARK 3 T13: -0.0861 T23: -0.0430 REMARK 3 L TENSOR REMARK 3 L11: 1.3340 L22: 4.2208 REMARK 3 L33: 1.4055 L12: -0.4693 REMARK 3 L13: -0.1781 L23: -0.8908 REMARK 3 S TENSOR REMARK 3 S11: -0.3142 S12: 0.0030 S13: 0.2084 REMARK 3 S21: -0.0829 S22: 0.1168 S23: -0.2301 REMARK 3 S31: -0.2731 S32: -0.0391 S33: 0.2066 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 16 THROUGH 38 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.6500 -3.9994 -15.2383 REMARK 3 T TENSOR REMARK 3 T11: 0.4315 T22: 0.4703 REMARK 3 T33: 0.4685 T12: -0.0683 REMARK 3 T13: -0.0534 T23: 0.0357 REMARK 3 L TENSOR REMARK 3 L11: 1.4863 L22: 2.3659 REMARK 3 L33: 1.6589 L12: -0.4028 REMARK 3 L13: 0.2532 L23: 0.4526 REMARK 3 S TENSOR REMARK 3 S11: -0.0449 S12: -0.1863 S13: 0.1958 REMARK 3 S21: 0.0114 S22: 0.0053 S23: -0.1155 REMARK 3 S31: -0.3789 S32: 0.2278 S33: 0.0248 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 39 THROUGH 74 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.9537 -7.7093 -23.9951 REMARK 3 T TENSOR REMARK 3 T11: 0.3722 T22: 0.3653 REMARK 3 T33: 0.3525 T12: -0.0656 REMARK 3 T13: 0.0112 T23: 0.0170 REMARK 3 L TENSOR REMARK 3 L11: 1.9339 L22: 1.4123 REMARK 3 L33: 1.3787 L12: -0.1419 REMARK 3 L13: 0.6754 L23: 0.0393 REMARK 3 S TENSOR REMARK 3 S11: 0.1253 S12: 0.1418 S13: 0.1839 REMARK 3 S21: -0.0921 S22: -0.1337 S23: -0.2132 REMARK 3 S31: -0.1408 S32: 0.3481 S33: -0.0175 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 75 THROUGH 111 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.0689 -8.8617 -28.7479 REMARK 3 T TENSOR REMARK 3 T11: 0.4836 T22: 0.4575 REMARK 3 T33: 0.3899 T12: -0.0986 REMARK 3 T13: -0.0196 T23: 0.0177 REMARK 3 L TENSOR REMARK 3 L11: 1.3998 L22: 1.7588 REMARK 3 L33: 2.1937 L12: -1.4793 REMARK 3 L13: -0.3554 L23: 0.8139 REMARK 3 S TENSOR REMARK 3 S11: 0.0239 S12: 0.3782 S13: 0.0964 REMARK 3 S21: -0.3265 S22: -0.0248 S23: 0.0459 REMARK 3 S31: -0.1296 S32: 0.0452 S33: -0.0652 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 112 THROUGH 130 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.6654 -19.8716 -38.3968 REMARK 3 T TENSOR REMARK 3 T11: 0.8888 T22: 0.7165 REMARK 3 T33: 0.4992 T12: 0.0105 REMARK 3 T13: -0.0570 T23: -0.0498 REMARK 3 L TENSOR REMARK 3 L11: 4.8237 L22: 1.2586 REMARK 3 L33: 3.7825 L12: 0.1048 REMARK 3 L13: -1.3051 L23: -0.4137 REMARK 3 S TENSOR REMARK 3 S11: 0.6362 S12: 1.0020 S13: -0.2511 REMARK 3 S21: -0.8467 S22: -0.1392 S23: 0.2946 REMARK 3 S31: 0.0246 S32: 0.2084 S33: -0.4124 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 131 THROUGH 147 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.2694 -22.9935 -27.0210 REMARK 3 T TENSOR REMARK 3 T11: 0.5709 T22: 0.5823 REMARK 3 T33: 0.5509 T12: 0.0702 REMARK 3 T13: -0.0128 T23: -0.0245 REMARK 3 L TENSOR REMARK 3 L11: 1.7545 L22: 2.8280 REMARK 3 L33: 3.1319 L12: 0.1321 REMARK 3 L13: 0.3810 L23: 1.9234 REMARK 3 S TENSOR REMARK 3 S11: 0.0885 S12: -0.4947 S13: -0.5134 REMARK 3 S21: -0.4938 S22: 0.2058 S23: -0.2900 REMARK 3 S31: 0.3212 S32: 0.4911 S33: -0.1305 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID -1 THROUGH 7 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.4904 -12.2034 1.9363 REMARK 3 T TENSOR REMARK 3 T11: 0.4618 T22: 0.5049 REMARK 3 T33: 0.4464 T12: -0.1280 REMARK 3 T13: 0.0593 T23: -0.0670 REMARK 3 L TENSOR REMARK 3 L11: 5.7361 L22: 0.4211 REMARK 3 L33: 1.4218 L12: -0.2770 REMARK 3 L13: 2.3396 L23: -0.5830 REMARK 3 S TENSOR REMARK 3 S11: 0.1820 S12: -0.0330 S13: 0.5226 REMARK 3 S21: 0.4820 S22: -0.4611 S23: 0.7731 REMARK 3 S31: 1.0191 S32: -0.5644 S33: 0.2028 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 8 THROUGH 17 ) REMARK 3 ORIGIN FOR THE GROUP (A): 8.7698 -16.9536 -3.5002 REMARK 3 T TENSOR REMARK 3 T11: 0.4335 T22: 0.5046 REMARK 3 T33: 0.4192 T12: -0.0479 REMARK 3 T13: -0.0057 T23: 0.0196 REMARK 3 L TENSOR REMARK 3 L11: 0.7041 L22: 1.0406 REMARK 3 L33: 2.3085 L12: -0.0559 REMARK 3 L13: -0.9435 L23: -0.8858 REMARK 3 S TENSOR REMARK 3 S11: 0.0102 S12: -0.3945 S13: 0.2172 REMARK 3 S21: 0.3676 S22: 0.2073 S23: 0.2786 REMARK 3 S31: 0.8843 S32: 0.2916 S33: -0.0634 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 18 THROUGH 44 ) REMARK 3 ORIGIN FOR THE GROUP (A): 18.8398 -17.9575 -0.6557 REMARK 3 T TENSOR REMARK 3 T11: 0.4474 T22: 0.4456 REMARK 3 T33: 0.4200 T12: 0.0147 REMARK 3 T13: -0.0193 T23: 0.0344 REMARK 3 L TENSOR REMARK 3 L11: 5.6858 L22: 3.0225 REMARK 3 L33: 4.2764 L12: -0.2092 REMARK 3 L13: 1.2067 L23: -1.2384 REMARK 3 S TENSOR REMARK 3 S11: 0.2704 S12: -0.1300 S13: -0.1682 REMARK 3 S21: 0.4247 S22: -0.2925 S23: -0.5162 REMARK 3 S31: 0.5306 S32: 0.9205 S33: -0.1251 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 45 THROUGH 72 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.2336 -8.3313 -3.9147 REMARK 3 T TENSOR REMARK 3 T11: 0.3246 T22: 0.3314 REMARK 3 T33: 0.4900 T12: -0.0118 REMARK 3 T13: 0.0129 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 5.1896 L22: 0.5673 REMARK 3 L33: 3.8765 L12: -0.3250 REMARK 3 L13: -1.3137 L23: -0.0859 REMARK 3 S TENSOR REMARK 3 S11: 0.1740 S12: 0.1299 S13: 0.3949 REMARK 3 S21: 0.1736 S22: 0.0129 S23: 0.1855 REMARK 3 S31: -0.2713 S32: -0.0426 S33: -0.3785 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 6D4P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-APR-18. REMARK 100 THE DEPOSITION ID IS D_1000233942. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 2.3.12 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15572 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 1.00000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.460 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.2 REMARK 200 STARTING MODEL: 3PTF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% PEG2000-MME, 0.2M TRIMETHYLAMINE N REMARK 280 -OXIDE, 0.1M TRIS-HCL, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 25.56000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.37400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.28250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.37400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.56000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.28250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 1560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 GLY C -11 REMARK 465 ALA C -10 REMARK 465 GLY C -9 REMARK 465 GLY C -8 REMARK 465 ASP C -7 REMARK 465 TYR C -6 REMARK 465 LYS C -5 REMARK 465 ASP C -4 REMARK 465 ASP C -3 REMARK 465 ASP C -2 REMARK 465 LEU C 73 REMARK 465 ARG C 74 REMARK 465 ALA C 75 REMARK 465 GLY C 76 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 4 CG CD CE NZ REMARK 470 ASP A 28 CG OD1 OD2 REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 ARG A 90 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 101 CG CD CE NZ REMARK 470 ASP A 122 CG OD1 OD2 REMARK 470 GLN A 125 CG CD OE1 NE2 REMARK 470 LYS A 131 CG CD CE NZ REMARK 470 GLU A 132 CG CD OE1 OE2 REMARK 470 LYS A 133 CG CD CE NZ REMARK 470 ARG A 136 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 143 CG CD OE1 NE2 REMARK 470 LYS C 0 CG CD CE NZ REMARK 470 LYS C 11 CG CD CE NZ 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 ARG A 90 -95.09 -127.68 REMARK 500 REMARK 500 REMARK: NULL DBREF 6D4P A 1 147 UNP P51668 UB2D1_HUMAN 1 147 DBREF 6D4P C 1 76 UNP Q59EM9 Q59EM9_HUMAN 17 92 SEQADV 6D4P GLY A -1 UNP P51668 EXPRESSION TAG SEQADV 6D4P ALA A 0 UNP P51668 EXPRESSION TAG SEQADV 6D4P GLY C -11 UNP Q59EM9 EXPRESSION TAG SEQADV 6D4P ALA C -10 UNP Q59EM9 EXPRESSION TAG SEQADV 6D4P GLY C -9 UNP Q59EM9 EXPRESSION TAG SEQADV 6D4P GLY C -8 UNP Q59EM9 EXPRESSION TAG SEQADV 6D4P ASP C -7 UNP Q59EM9 EXPRESSION TAG SEQADV 6D4P TYR C -6 UNP Q59EM9 EXPRESSION TAG SEQADV 6D4P LYS C -5 UNP Q59EM9 EXPRESSION TAG SEQADV 6D4P ASP C -4 UNP Q59EM9 EXPRESSION TAG SEQADV 6D4P ASP C -3 UNP Q59EM9 EXPRESSION TAG SEQADV 6D4P ASP C -2 UNP Q59EM9 EXPRESSION TAG SEQADV 6D4P ASP C -1 UNP Q59EM9 EXPRESSION TAG SEQADV 6D4P LYS C 0 UNP Q59EM9 EXPRESSION TAG SEQADV 6D4P LYS C 7 UNP Q59EM9 THR 23 ENGINEERED MUTATION SEQADV 6D4P PHE C 8 UNP Q59EM9 LEU 24 ENGINEERED MUTATION SEQADV 6D4P TRP C 9 UNP Q59EM9 THR 25 ENGINEERED MUTATION SEQADV 6D4P LYS C 64 UNP Q59EM9 GLU 80 ENGINEERED MUTATION SEQADV 6D4P PHE C 65 UNP Q59EM9 SER 81 ENGINEERED MUTATION SEQADV 6D4P TYR C 68 UNP Q59EM9 HIS 84 ENGINEERED MUTATION SEQADV 6D4P ALA C 70 UNP Q59EM9 VAL 86 ENGINEERED MUTATION SEQADV 6D4P TYR C 71 UNP Q59EM9 LEU 87 ENGINEERED MUTATION SEQADV 6D4P GLY C 72 UNP Q59EM9 ARG 88 ENGINEERED MUTATION SEQADV 6D4P ALA C 75 UNP Q59EM9 GLY 91 ENGINEERED MUTATION SEQRES 1 A 149 GLY ALA MET ALA LEU LYS ARG ILE GLN LYS GLU LEU SER SEQRES 2 A 149 ASP LEU GLN ARG ASP PRO PRO ALA HIS CYS SER ALA GLY SEQRES 3 A 149 PRO VAL GLY ASP ASP LEU PHE HIS TRP GLN ALA THR ILE SEQRES 4 A 149 MET GLY PRO PRO ASP SER ALA TYR GLN GLY GLY VAL PHE SEQRES 5 A 149 PHE LEU THR VAL HIS PHE PRO THR ASP TYR PRO PHE LYS SEQRES 6 A 149 PRO PRO LYS ILE ALA PHE THR THR LYS ILE TYR HIS PRO SEQRES 7 A 149 ASN ILE ASN SER ASN GLY SER ILE CYS LEU ASP ILE LEU SEQRES 8 A 149 ARG SER GLN TRP SER PRO ALA LEU THR VAL SER LYS VAL SEQRES 9 A 149 LEU LEU SER ILE CYS SER LEU LEU CYS ASP PRO ASN PRO SEQRES 10 A 149 ASP ASP PRO LEU VAL PRO ASP ILE ALA GLN ILE TYR LYS SEQRES 11 A 149 SER ASP LYS GLU LYS TYR ASN ARG HIS ALA ARG GLU TRP SEQRES 12 A 149 THR GLN LYS TYR ALA MET SEQRES 1 C 88 GLY ALA GLY GLY ASP TYR LYS ASP ASP ASP ASP LYS MET SEQRES 2 C 88 GLN ILE PHE VAL LYS LYS PHE TRP GLY LYS THR ILE THR SEQRES 3 C 88 LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL LYS SEQRES 4 C 88 ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP GLN SEQRES 5 C 88 GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP GLY SEQRES 6 C 88 ARG THR LEU SER ASP TYR ASN ILE GLN LYS LYS PHE THR SEQRES 7 C 88 LEU TYR LEU ALA TYR GLY LEU ARG ALA GLY FORMUL 3 HOH *24(H2 O) HELIX 1 AA1 GLY A -1 ASP A 16 1 18 HELIX 2 AA2 LEU A 86 ARG A 90 5 5 HELIX 3 AA3 THR A 98 ASP A 112 1 15 HELIX 4 AA4 VAL A 120 ASP A 130 1 11 HELIX 5 AA5 ASP A 130 ALA A 146 1 17 HELIX 6 AA6 THR C 22 GLY C 35 1 14 HELIX 7 AA7 PRO C 37 ASP C 39 5 3 HELIX 8 AA8 LEU C 56 ASN C 60 5 5 SHEET 1 AA1 4 SER A 22 PRO A 25 0 SHEET 2 AA1 4 HIS A 32 MET A 38 -1 O THR A 36 N SER A 22 SHEET 3 AA1 4 VAL A 49 HIS A 55 -1 O PHE A 50 N ILE A 37 SHEET 4 AA1 4 LYS A 66 PHE A 69 -1 O LYS A 66 N HIS A 55 SHEET 1 AA2 5 THR C 12 VAL C 17 0 SHEET 2 AA2 5 MET C 1 LYS C 7 -1 N VAL C 5 O ILE C 13 SHEET 3 AA2 5 THR C 66 TYR C 71 1 O LEU C 67 N LYS C 6 SHEET 4 AA2 5 GLN C 41 PHE C 45 -1 N ARG C 42 O ALA C 70 SHEET 5 AA2 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 CISPEP 1 TYR A 60 PRO A 61 0 3.25 CRYST1 51.120 52.565 96.748 90.00 90.00 90.00 P 21 21 21 4 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 0.019562 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019024 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010336 0.00000