PDB Short entry for 4DM9 HEADER HYDROLASE, LIGASE/INHIBITOR 07-FEB-12 4DM9 TITLE THE CRYSTAL STRUCTURE OF UBIQUITIN CARBOXY-TERMINAL HYDROLASE L1 TITLE 2 (UCHL1) BOUND TO A TRIPEPTIDE FLUOROMETHYL KETONE Z-VAE(OME)-FMK COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: UCH-L1, NEURON CYTOPLASMIC PROTEIN 9.5, PGP 9.5, PGP9.5, COMPND 5 UBIQUITIN THIOESTERASE L1; COMPND 6 EC: 3.4.19.12, 6.-.-.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: TRIPEPTIDE FLUOROMETHYL KETONE INHIBITOR Z-VAE(OME)-FMK; COMPND 10 CHAIN: X, Y; COMPND 11 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: UCHL1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P1; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS UBIQUITIN HYDROLASE, LIGASE, HYDROLASE, LIGASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.W.DAVIES,J.CHANEY,G.KORBEL,D.RINGE,G.A.PETSKO,H.PLOEGH,C.DAS REVDAT 3 13-SEP-23 4DM9 1 SEQADV LINK REVDAT 2 13-JUN-12 4DM9 1 JRNL REVDAT 1 23-MAY-12 4DM9 0 JRNL AUTH C.W.DAVIES,J.CHANEY,G.KORBEL,D.RINGE,G.A.PETSKO,H.PLOEGH, JRNL AUTH 2 C.DAS JRNL TITL THE CO-CRYSTAL STRUCTURE OF UBIQUITIN CARBOXY-TERMINAL JRNL TITL 2 HYDROLASE L1 (UCHL1) WITH A TRIPEPTIDE FLUOROMETHYL KETONE JRNL TITL 3 (Z-VAE(OME)-FMK). JRNL REF BIOORG.MED.CHEM.LETT. V. 22 3900 2012 JRNL REFN ISSN 0960-894X JRNL PMID 22617491 JRNL DOI 10.1016/J.BMCL.2012.04.124 REMARK 2 REMARK 2 RESOLUTION. 2.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 20267 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120 REMARK 3 FREE R VALUE TEST SET COUNT : 1037 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 34.8766 - 4.4932 0.99 2978 138 0.1788 0.2368 REMARK 3 2 4.4932 - 3.5675 1.00 2842 132 0.1517 0.1803 REMARK 3 3 3.5675 - 3.1169 1.00 2777 168 0.2139 0.2458 REMARK 3 4 3.1169 - 2.8321 1.00 2753 162 0.2403 0.3503 REMARK 3 5 2.8321 - 2.6291 1.00 2747 165 0.2586 0.3077 REMARK 3 6 2.6291 - 2.4742 0.98 2696 138 0.2801 0.3371 REMARK 3 7 2.4742 - 2.3503 0.89 2437 134 0.3369 0.3832 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.36 REMARK 3 B_SOL : 61.66 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.820 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) : 8.91500 REMARK 3 B22 (A**2) : 8.91500 REMARK 3 B33 (A**2) : -17.83010 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.005 3611 REMARK 3 ANGLE : 1.048 4856 REMARK 3 CHIRALITY : 0.088 530 REMARK 3 PLANARITY : 0.004 643 REMARK 3 DIHEDRAL : 16.536 1361 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 1:136) REMARK 3 ORIGIN FOR THE GROUP (A): 36.1751 16.6399 14.5648 REMARK 3 T TENSOR REMARK 3 T11: 0.2131 T22: 0.3525 REMARK 3 T33: 0.2420 T12: 0.0259 REMARK 3 T13: 0.0212 T23: 0.0842 REMARK 3 L TENSOR REMARK 3 L11: 3.5907 L22: 5.6719 REMARK 3 L33: 3.8446 L12: -0.4424 REMARK 3 L13: 0.8571 L23: 1.2130 REMARK 3 S TENSOR REMARK 3 S11: -0.1107 S12: -0.0529 S13: -0.0454 REMARK 3 S21: 0.0049 S22: 0.2731 S23: 0.2469 REMARK 3 S31: -0.1560 S32: -0.4633 S33: -0.1397 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 137:159) REMARK 3 ORIGIN FOR THE GROUP (A): 47.4842 11.0402 23.1044 REMARK 3 T TENSOR REMARK 3 T11: 0.5280 T22: 0.5180 REMARK 3 T33: 0.4218 T12: 0.1397 REMARK 3 T13: 0.0035 T23: 0.0267 REMARK 3 L TENSOR REMARK 3 L11: 6.5915 L22: 1.5880 REMARK 3 L33: 9.0049 L12: 3.0473 REMARK 3 L13: -6.6302 L23: -3.5284 REMARK 3 S TENSOR REMARK 3 S11: -0.8111 S12: -0.5419 S13: -0.8537 REMARK 3 S21: -0.0751 S22: 0.4172 S23: -0.2754 REMARK 3 S31: 0.8797 S32: 0.6685 S33: 0.3267 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 160:207) REMARK 3 ORIGIN FOR THE GROUP (A): 33.0017 13.3556 3.4491 REMARK 3 T TENSOR REMARK 3 T11: 0.3822 T22: 0.4472 REMARK 3 T33: 0.2619 T12: 0.0236 REMARK 3 T13: 0.0059 T23: 0.0383 REMARK 3 L TENSOR REMARK 3 L11: 9.0015 L22: 8.0962 REMARK 3 L33: 7.4248 L12: -1.4749 REMARK 3 L13: 5.4123 L23: -2.0489 REMARK 3 S TENSOR REMARK 3 S11: 0.0420 S12: 0.5642 S13: -0.2451 REMARK 3 S21: -0.7443 S22: 0.1874 S23: 0.4170 REMARK 3 S31: 0.1659 S32: -0.2229 S33: -0.2159 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 208:223) REMARK 3 ORIGIN FOR THE GROUP (A): 37.9014 3.8756 9.5624 REMARK 3 T TENSOR REMARK 3 T11: 0.4350 T22: 0.5138 REMARK 3 T33: 0.5501 T12: -0.1347 REMARK 3 T13: 0.0280 T23: 0.0346 REMARK 3 L TENSOR REMARK 3 L11: 3.5202 L22: 8.1477 REMARK 3 L33: 4.8391 L12: -5.2664 REMARK 3 L13: -2.7472 L23: 4.9500 REMARK 3 S TENSOR REMARK 3 S11: -0.1862 S12: 0.2716 S13: 0.0443 REMARK 3 S21: -0.1999 S22: 0.5389 S23: -0.2362 REMARK 3 S31: 0.0577 S32: -0.1825 S33: -0.2875 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 1:45) REMARK 3 ORIGIN FOR THE GROUP (A): 54.8744 22.0824 44.8497 REMARK 3 T TENSOR REMARK 3 T11: 0.4388 T22: 0.4528 REMARK 3 T33: 0.4536 T12: 0.0288 REMARK 3 T13: 0.1567 T23: 0.0054 REMARK 3 L TENSOR REMARK 3 L11: 8.5730 L22: 6.4432 REMARK 3 L33: 7.8430 L12: -0.9465 REMARK 3 L13: 2.9828 L23: 2.4268 REMARK 3 S TENSOR REMARK 3 S11: 0.1544 S12: 0.2524 S13: 0.4820 REMARK 3 S21: -0.4520 S22: 0.2010 S23: -0.9860 REMARK 3 S31: -0.8570 S32: 0.6289 S33: -0.3269 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 46:69) REMARK 3 ORIGIN FOR THE GROUP (A): 44.4992 15.6694 61.6965 REMARK 3 T TENSOR REMARK 3 T11: 0.4745 T22: 0.7314 REMARK 3 T33: 0.3201 T12: -0.0556 REMARK 3 T13: 0.0121 T23: -0.0587 REMARK 3 L TENSOR REMARK 3 L11: 6.2654 L22: 8.2477 REMARK 3 L33: 4.1422 L12: 1.4365 REMARK 3 L13: -0.4841 L23: -0.2635 REMARK 3 S TENSOR REMARK 3 S11: 0.2031 S12: -0.5834 S13: -0.4085 REMARK 3 S21: 1.0916 S22: -0.1353 S23: 0.3504 REMARK 3 S31: -0.0759 S32: -1.3217 S33: -0.0368 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 70:136) REMARK 3 ORIGIN FOR THE GROUP (A): 38.5733 26.7631 47.3766 REMARK 3 T TENSOR REMARK 3 T11: 0.6049 T22: 0.6702 REMARK 3 T33: 0.4736 T12: 0.2618 REMARK 3 T13: -0.0808 T23: -0.0306 REMARK 3 L TENSOR REMARK 3 L11: 5.0121 L22: 4.8274 REMARK 3 L33: 4.9971 L12: -0.2953 REMARK 3 L13: -0.7897 L23: 2.9375 REMARK 3 S TENSOR REMARK 3 S11: 0.1364 S12: 0.2842 S13: 0.5280 REMARK 3 S21: -0.5247 S22: -0.1766 S23: 0.4168 REMARK 3 S31: -1.2450 S32: -1.0133 S33: 0.0176 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 137:159) REMARK 3 ORIGIN FOR THE GROUP (A): 46.7575 10.6179 40.4082 REMARK 3 T TENSOR REMARK 3 T11: 0.6567 T22: 0.5312 REMARK 3 T33: 0.4898 T12: 0.2428 REMARK 3 T13: 0.1002 T23: -0.0172 REMARK 3 L TENSOR REMARK 3 L11: 5.1641 L22: 3.0443 REMARK 3 L33: 4.1343 L12: 3.9454 REMARK 3 L13: -4.6078 L23: -3.4781 REMARK 3 S TENSOR REMARK 3 S11: -0.0984 S12: 0.1664 S13: -0.8112 REMARK 3 S21: -0.6641 S22: -0.5297 S23: -0.0365 REMARK 3 S31: 0.3441 S32: 0.2036 S33: 0.5282 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 160:189) REMARK 3 ORIGIN FOR THE GROUP (A): 45.1064 25.5604 58.7128 REMARK 3 T TENSOR REMARK 3 T11: 0.5241 T22: 0.4365 REMARK 3 T33: 0.3941 T12: 0.0657 REMARK 3 T13: -0.0564 T23: -0.0175 REMARK 3 L TENSOR REMARK 3 L11: 8.1196 L22: 3.5896 REMARK 3 L33: 8.0553 L12: -4.5360 REMARK 3 L13: -0.6193 L23: 2.4615 REMARK 3 S TENSOR REMARK 3 S11: -0.0316 S12: -0.1922 S13: 0.7677 REMARK 3 S21: 0.6923 S22: -0.1819 S23: 0.0167 REMARK 3 S31: -0.7578 S32: -0.5968 S33: 0.1190 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 190:207) REMARK 3 ORIGIN FOR THE GROUP (A): 55.2659 24.7432 62.7919 REMARK 3 T TENSOR REMARK 3 T11: 0.5265 T22: 0.6773 REMARK 3 T33: 0.6273 T12: 0.0300 REMARK 3 T13: -0.0594 T23: -0.1117 REMARK 3 L TENSOR REMARK 3 L11: 3.8676 L22: 2.9590 REMARK 3 L33: 7.4628 L12: 2.3223 REMARK 3 L13: 1.6934 L23: -0.7324 REMARK 3 S TENSOR REMARK 3 S11: 0.3846 S12: -0.9621 S13: 0.3042 REMARK 3 S21: 1.6720 S22: 0.2097 S23: -0.2050 REMARK 3 S31: 0.1403 S32: -0.0337 S33: -0.4778 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'B' AND (RESSEQ 208:223) REMARK 3 ORIGIN FOR THE GROUP (A): 56.6024 17.7255 53.7477 REMARK 3 T TENSOR REMARK 3 T11: 0.3839 T22: 0.5043 REMARK 3 T33: 0.4467 T12: -0.0803 REMARK 3 T13: -0.0738 T23: -0.0300 REMARK 3 L TENSOR REMARK 3 L11: 9.5371 L22: 4.1077 REMARK 3 L33: 9.0101 L12: -5.7101 REMARK 3 L13: 3.9145 L23: -1.0637 REMARK 3 S TENSOR REMARK 3 S11: 0.0020 S12: -0.5052 S13: -0.0865 REMARK 3 S21: 0.5219 S22: 0.3936 S23: -0.5478 REMARK 3 S31: -0.6031 S32: 0.3883 S33: -0.3503 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 4DM9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070506. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-FEB-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20326 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 48.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.49900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2ETL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4M AMMONIUM SULFATE, 0.1M HEPES, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 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 REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z 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 55.00550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 55.00550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 55.00550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 55.00550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 55.00550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 55.00550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 55.00550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 55.00550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 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, X 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 APPLY THE FOLLOWING TO CHAINS: B, Y 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 308 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE TRIPEPTIDE FLUOROMETHYL KETONE INHIBITOR Z-VAE(OME)-FMK IS REMARK 400 PEPTIDE-LIKE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: TRIPEPTIDE FLUOROMETHYL KETONE INHIBITOR Z-VAE(OME)-FMK REMARK 400 CHAIN: X, Y REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 A -4 REMARK 465 PRO A -3 REMARK 465 LEU A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 GLY B -4 REMARK 465 PRO B -3 REMARK 465 LEU B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 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 LYS A 71 -3.02 69.40 REMARK 500 CYS A 152 120.24 107.76 REMARK 500 ASP A 155 -69.25 46.72 REMARK 500 CYS B 152 121.72 110.21 REMARK 500 VAL B 154 -4.06 81.65 REMARK 500 LYS B 157 33.48 -63.01 REMARK 500 ALA B 222 118.67 -37.96 REMARK 500 ALA Y 3 -60.99 54.69 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 CHAIN X OF TRIPEPTIDE REMARK 800 FLUOROMETHYL KETONE INHIBITOR Z-VAE(OME)-FMK REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN Y OF TRIPEPTIDE REMARK 800 FLUOROMETHYL KETONE INHIBITOR Z-VAE(OME)-FMK REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ETL RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITHOUT FLUOROMETHYL KETONE INHBITOR DBREF 4DM9 A 1 223 UNP P09936 UCHL1_HUMAN 1 223 DBREF 4DM9 B 1 223 UNP P09936 UCHL1_HUMAN 1 223 DBREF 4DM9 X 1 5 PDB 4DM9 4DM9 1 5 DBREF 4DM9 Y 1 5 PDB 4DM9 4DM9 1 5 SEQADV 4DM9 GLY A -4 UNP P09936 EXPRESSION TAG SEQADV 4DM9 PRO A -3 UNP P09936 EXPRESSION TAG SEQADV 4DM9 LEU A -2 UNP P09936 EXPRESSION TAG SEQADV 4DM9 GLY A -1 UNP P09936 EXPRESSION TAG SEQADV 4DM9 SER A 0 UNP P09936 EXPRESSION TAG SEQADV 4DM9 GLY B -4 UNP P09936 EXPRESSION TAG SEQADV 4DM9 PRO B -3 UNP P09936 EXPRESSION TAG SEQADV 4DM9 LEU B -2 UNP P09936 EXPRESSION TAG SEQADV 4DM9 GLY B -1 UNP P09936 EXPRESSION TAG SEQADV 4DM9 SER B 0 UNP P09936 EXPRESSION TAG SEQRES 1 A 228 GLY PRO LEU GLY SER MET GLN LEU LYS PRO MET GLU ILE SEQRES 2 A 228 ASN PRO GLU MET LEU ASN LYS VAL LEU SER ARG LEU GLY SEQRES 3 A 228 VAL ALA GLY GLN TRP ARG PHE VAL ASP VAL LEU GLY LEU SEQRES 4 A 228 GLU GLU GLU SER LEU GLY SER VAL PRO ALA PRO ALA CYS SEQRES 5 A 228 ALA LEU LEU LEU LEU PHE PRO LEU THR ALA GLN HIS GLU SEQRES 6 A 228 ASN PHE ARG LYS LYS GLN ILE GLU GLU LEU LYS GLY GLN SEQRES 7 A 228 GLU VAL SER PRO LYS VAL TYR PHE MET LYS GLN THR ILE SEQRES 8 A 228 GLY ASN SER CYS GLY THR ILE GLY LEU ILE HIS ALA VAL SEQRES 9 A 228 ALA ASN ASN GLN ASP LYS LEU GLY PHE GLU ASP GLY SER SEQRES 10 A 228 VAL LEU LYS GLN PHE LEU SER GLU THR GLU LYS MET SER SEQRES 11 A 228 PRO GLU ASP ARG ALA LYS CYS PHE GLU LYS ASN GLU ALA SEQRES 12 A 228 ILE GLN ALA ALA HIS ASP ALA VAL ALA GLN GLU GLY GLN SEQRES 13 A 228 CYS ARG VAL ASP ASP LYS VAL ASN PHE HIS PHE ILE LEU SEQRES 14 A 228 PHE ASN ASN VAL ASP GLY HIS LEU TYR GLU LEU ASP GLY SEQRES 15 A 228 ARG MET PRO PHE PRO VAL ASN HIS GLY ALA SER SER GLU SEQRES 16 A 228 ASP THR LEU LEU LYS ASP ALA ALA LYS VAL CYS ARG GLU SEQRES 17 A 228 PHE THR GLU ARG GLU GLN GLY GLU VAL ARG PHE SER ALA SEQRES 18 A 228 VAL ALA LEU CYS LYS ALA ALA SEQRES 1 B 228 GLY PRO LEU GLY SER MET GLN LEU LYS PRO MET GLU ILE SEQRES 2 B 228 ASN PRO GLU MET LEU ASN LYS VAL LEU SER ARG LEU GLY SEQRES 3 B 228 VAL ALA GLY GLN TRP ARG PHE VAL ASP VAL LEU GLY LEU SEQRES 4 B 228 GLU GLU GLU SER LEU GLY SER VAL PRO ALA PRO ALA CYS SEQRES 5 B 228 ALA LEU LEU LEU LEU PHE PRO LEU THR ALA GLN HIS GLU SEQRES 6 B 228 ASN PHE ARG LYS LYS GLN ILE GLU GLU LEU LYS GLY GLN SEQRES 7 B 228 GLU VAL SER PRO LYS VAL TYR PHE MET LYS GLN THR ILE SEQRES 8 B 228 GLY ASN SER CYS GLY THR ILE GLY LEU ILE HIS ALA VAL SEQRES 9 B 228 ALA ASN ASN GLN ASP LYS LEU GLY PHE GLU ASP GLY SER SEQRES 10 B 228 VAL LEU LYS GLN PHE LEU SER GLU THR GLU LYS MET SER SEQRES 11 B 228 PRO GLU ASP ARG ALA LYS CYS PHE GLU LYS ASN GLU ALA SEQRES 12 B 228 ILE GLN ALA ALA HIS ASP ALA VAL ALA GLN GLU GLY GLN SEQRES 13 B 228 CYS ARG VAL ASP ASP LYS VAL ASN PHE HIS PHE ILE LEU SEQRES 14 B 228 PHE ASN ASN VAL ASP GLY HIS LEU TYR GLU LEU ASP GLY SEQRES 15 B 228 ARG MET PRO PHE PRO VAL ASN HIS GLY ALA SER SER GLU SEQRES 16 B 228 ASP THR LEU LEU LYS ASP ALA ALA LYS VAL CYS ARG GLU SEQRES 17 B 228 PHE THR GLU ARG GLU GLN GLY GLU VAL ARG PHE SER ALA SEQRES 18 B 228 VAL ALA LEU CYS LYS ALA ALA SEQRES 1 X 5 PHQ VAL ALA GME CF0 SEQRES 1 Y 5 PHQ VAL ALA GME CF0 MODRES 4DM9 GME X 4 GLU 5-O-METHYL-GLUTAMIC ACID MODRES 4DM9 GME Y 4 GLU 5-O-METHYL-GLUTAMIC ACID HET PHQ X 1 10 HET GME X 4 10 HET CF0 X 5 1 HET PHQ Y 1 10 HET GME Y 4 10 HET CF0 Y 5 1 HETNAM PHQ BENZYL CHLOROCARBONATE HETNAM GME 5-O-METHYL-GLUTAMIC ACID HETNAM CF0 FLUOROMETHANE HETSYN GME (2S)-2-AMINO-5-METHOXY-5-OXOPENTANOIC ACID HETSYN CF0 FLUORO METHYL GROUP FORMUL 3 PHQ 2(C8 H7 CL O2) FORMUL 3 GME 2(C6 H11 N O4) FORMUL 3 CF0 2(C H3 F) FORMUL 5 HOH *42(H2 O) HELIX 1 1 ASN A 9 LEU A 20 1 12 HELIX 2 2 GLU A 35 SER A 41 1 7 HELIX 3 3 THR A 56 LYS A 71 1 16 HELIX 4 4 SER A 89 ASN A 101 1 13 HELIX 5 5 SER A 112 THR A 121 1 10 HELIX 6 6 SER A 125 LYS A 135 1 11 HELIX 7 7 ASN A 136 GLN A 148 1 13 HELIX 8 8 SER A 189 ASP A 191 5 3 HELIX 9 9 THR A 192 GLU A 208 1 17 HELIX 10 10 ASN B 9 LEU B 20 1 12 HELIX 11 11 GLU B 35 SER B 41 1 7 HELIX 12 12 THR B 56 LEU B 70 1 15 HELIX 13 13 SER B 89 ASN B 101 1 13 HELIX 14 14 SER B 112 THR B 121 1 10 HELIX 15 15 SER B 125 LYS B 135 1 11 HELIX 16 16 ASN B 136 GLN B 148 1 13 HELIX 17 17 SER B 189 ASP B 191 5 3 HELIX 18 18 THR B 192 GLU B 208 1 17 SHEET 1 A 6 TRP A 26 VAL A 31 0 SHEET 2 A 6 SER A 215 LYS A 221 -1 O CYS A 220 N ARG A 27 SHEET 3 A 6 ALA A 46 PRO A 54 -1 N LEU A 52 O SER A 215 SHEET 4 A 6 PHE A 160 VAL A 168 -1 O ILE A 163 N LEU A 51 SHEET 5 A 6 HIS A 171 LEU A 175 -1 O TYR A 173 N ASN A 166 SHEET 6 A 6 VAL A 183 ALA A 187 -1 O HIS A 185 N LEU A 172 SHEET 1 B 6 TRP B 26 VAL B 31 0 SHEET 2 B 6 SER B 215 LYS B 221 -1 O CYS B 220 N ARG B 27 SHEET 3 B 6 ALA B 46 PRO B 54 -1 N LEU B 52 O SER B 215 SHEET 4 B 6 PHE B 160 VAL B 168 -1 O ILE B 163 N LEU B 51 SHEET 5 B 6 HIS B 171 LEU B 175 -1 O TYR B 173 N ASN B 166 SHEET 6 B 6 VAL B 183 ALA B 187 -1 O HIS B 185 N LEU B 172 LINK SG CYS A 90 C1 CF0 X 5 1555 1555 1.80 LINK SG CYS B 90 C1 CF0 Y 5 1555 1555 1.80 LINK C1 PHQ X 1 N VAL X 2 1555 1555 1.43 LINK C ALA X 3 N GME X 4 1555 1555 1.33 LINK C GME X 4 C1 CF0 X 5 1555 1555 1.54 LINK C1 PHQ Y 1 N VAL Y 2 1555 1555 1.43 LINK C ALA Y 3 N GME Y 4 1555 1555 1.33 LINK C GME Y 4 C1 CF0 Y 5 1555 1555 1.54 CISPEP 1 ALA A 44 PRO A 45 0 -2.35 CISPEP 2 ALA B 44 PRO B 45 0 -2.39 SITE 1 AC1 18 MET A 6 VAL A 31 LEU A 32 GLY A 33 SITE 2 AC1 18 LEU A 34 GLN A 84 GLY A 87 ASN A 88 SITE 3 AC1 18 SER A 89 CYS A 90 ARG A 153 ASN A 159 SITE 4 AC1 18 PHE A 160 ARG A 178 PHE A 214 SER A 215 SITE 5 AC1 18 ALA A 216 HOH X 101 SITE 1 AC2 17 VAL B 31 LEU B 32 GLY B 33 LEU B 34 SITE 2 AC2 17 GLN B 84 GLY B 87 ASN B 88 SER B 89 SITE 3 AC2 17 CYS B 90 ARG B 153 LYS B 157 VAL B 158 SITE 4 AC2 17 ASN B 159 PHE B 160 ARG B 178 PHE B 214 SITE 5 AC2 17 HOH Y 101 CRYST1 110.011 110.011 78.745 90.00 90.00 90.00 P 4 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 0.009090 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009090 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012699 0.00000