HEADER HYDROLASE/HYDROLASE INHIBITOR 18-NOV-10 3PMU TITLE ENDOTHIAPEPSIN IN COMPLEX WITH A FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOTHIAPEPSIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ASPARTATE PROTEASE; COMPND 5 EC: 3.4.23.22 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CRYPHONECTRIA PARASITICA; SOURCE 3 ORGANISM_COMMON: CHESNUT BLIGHT FUNGUS; SOURCE 4 ORGANISM_TAXID: 5116 KEYWDS HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.KOESTER,A.HEINE,G.KLEBE REVDAT 5 30-OCT-24 3PMU 1 REMARK REVDAT 4 20-SEP-23 3PMU 1 REMARK REVDAT 3 31-MAY-23 3PMU 1 REMARK REVDAT 2 30-NOV-11 3PMU 1 JRNL REVDAT 1 02-NOV-11 3PMU 0 JRNL AUTH H.KOSTER,T.CRAAN,S.BRASS,C.HERHAUS,M.ZENTGRAF,L.NEUMANN, JRNL AUTH 2 A.HEINE,G.KLEBE JRNL TITL A SMALL NONRULE OF 3 COMPATIBLE FRAGMENT LIBRARY PROVIDES JRNL TITL 2 HIGH HIT RATE OF ENDOTHIAPEPSIN CRYSTAL STRUCTURES WITH JRNL TITL 3 VARIOUS FRAGMENT CHEMOTYPES. JRNL REF J.MED.CHEM. V. 54 7784 2011 JRNL REFN ISSN 0022-2623 JRNL PMID 21972967 JRNL DOI 10.1021/JM200642W REMARK 2 REMARK 2 RESOLUTION. 1.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 56527 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 2856 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 19.7003 - 3.0774 0.96 5563 282 0.1675 0.1745 REMARK 3 2 3.0774 - 2.4441 0.98 5597 326 0.1699 0.2029 REMARK 3 3 2.4441 - 2.1355 0.99 5644 300 0.1570 0.1889 REMARK 3 4 2.1355 - 1.9405 0.99 5572 313 0.1455 0.1666 REMARK 3 5 1.9405 - 1.8015 0.96 5459 291 0.1500 0.1717 REMARK 3 6 1.8015 - 1.6953 0.95 5411 272 0.1501 0.1811 REMARK 3 7 1.6953 - 1.6105 0.94 5355 272 0.1606 0.1946 REMARK 3 8 1.6105 - 1.5404 0.92 5188 293 0.1759 0.2160 REMARK 3 9 1.5404 - 1.4811 0.89 5087 277 0.1978 0.2274 REMARK 3 10 1.4811 - 1.4300 0.85 4795 230 0.2382 0.2819 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.44 REMARK 3 B_SOL : 49.40 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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) : -1.63550 REMARK 3 B22 (A**2) : 0.26660 REMARK 3 B33 (A**2) : 1.36880 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.04260 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 2463 REMARK 3 ANGLE : 1.070 3381 REMARK 3 CHIRALITY : 0.069 405 REMARK 3 PLANARITY : 0.005 429 REMARK 3 DIHEDRAL : 11.117 806 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 3PMU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000062566. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR KMC REMARK 200 -2 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59547 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07300 REMARK 200 FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.42900 REMARK 200 FOR SHELL : 2.300 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: PDB ENTRY 1OEW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NH4AC, 0.1M ACETATE BUFFER PH REMARK 280 4.6, 26% PEG 4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 36.87000 REMARK 290 SMTRY3 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 GLU A 47 CG CD OE1 OE2 REMARK 470 LYS A 63 CG CD CE NZ REMARK 470 LYS A 68 CG CD CE NZ REMARK 470 LYS A 149 CG CD CE NZ REMARK 470 LYS A 191 CG CD CE NZ REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE F7L A 2001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PBD RELATED DB: PDB REMARK 900 RELATED ID: 3PBZ RELATED DB: PDB REMARK 900 RELATED ID: 3PB5 RELATED DB: PDB REMARK 900 RELATED ID: 3PGI RELATED DB: PDB REMARK 900 RELATED ID: 3PCW RELATED DB: PDB REMARK 900 RELATED ID: 3PLD RELATED DB: PDB REMARK 900 RELATED ID: 3PCZ RELATED DB: PDB REMARK 900 RELATED ID: 3PI0 RELATED DB: PDB REMARK 900 RELATED ID: 3PLL RELATED DB: PDB REMARK 900 RELATED ID: 3PM4 RELATED DB: PDB REMARK 900 RELATED ID: 3PMY RELATED DB: PDB DBREF 3PMU A 1 330 UNP P11838 CARP_CRYPA 90 419 SEQRES 1 A 330 SER THR GLY SER ALA THR THR THR PRO ILE ASP SER LEU SEQRES 2 A 330 ASP ASP ALA TYR ILE THR PRO VAL GLN ILE GLY THR PRO SEQRES 3 A 330 ALA GLN THR LEU ASN LEU ASP PHE ASP THR GLY SER SER SEQRES 4 A 330 ASP LEU TRP VAL PHE SER SER GLU THR THR ALA SER GLU SEQRES 5 A 330 VAL ASP GLY GLN THR ILE TYR THR PRO SER LYS SER THR SEQRES 6 A 330 THR ALA LYS LEU LEU SER GLY ALA THR TRP SER ILE SER SEQRES 7 A 330 TYR GLY ASP GLY SER SER SER SER GLY ASP VAL TYR THR SEQRES 8 A 330 ASP THR VAL SER VAL GLY GLY LEU THR VAL THR GLY GLN SEQRES 9 A 330 ALA VAL GLU SER ALA LYS LYS VAL SER SER SER PHE THR SEQRES 10 A 330 GLU ASP SER THR ILE ASP GLY LEU LEU GLY LEU ALA PHE SEQRES 11 A 330 SER THR LEU ASN THR VAL SER PRO THR GLN GLN LYS THR SEQRES 12 A 330 PHE PHE ASP ASN ALA LYS ALA SER LEU ASP SER PRO VAL SEQRES 13 A 330 PHE THR ALA ASP LEU GLY TYR HIS ALA PRO GLY THR TYR SEQRES 14 A 330 ASN PHE GLY PHE ILE ASP THR THR ALA TYR THR GLY SER SEQRES 15 A 330 ILE THR TYR THR ALA VAL SER THR LYS GLN GLY PHE TRP SEQRES 16 A 330 GLU TRP THR SER THR GLY TYR ALA VAL GLY SER GLY THR SEQRES 17 A 330 PHE LYS SER THR SER ILE ASP GLY ILE ALA ASP THR GLY SEQRES 18 A 330 THR THR LEU LEU TYR LEU PRO ALA THR VAL VAL SER ALA SEQRES 19 A 330 TYR TRP ALA GLN VAL SER GLY ALA LYS SER SER SER SER SEQRES 20 A 330 VAL GLY GLY TYR VAL PHE PRO CYS SER ALA THR LEU PRO SEQRES 21 A 330 SER PHE THR PHE GLY VAL GLY SER ALA ARG ILE VAL ILE SEQRES 22 A 330 PRO GLY ASP TYR ILE ASP PHE GLY PRO ILE SER THR GLY SEQRES 23 A 330 SER SER SER CYS PHE GLY GLY ILE GLN SER SER ALA GLY SEQRES 24 A 330 ILE GLY ILE ASN ILE PHE GLY ASP VAL ALA LEU LYS ALA SEQRES 25 A 330 ALA PHE VAL VAL PHE ASN GLY ALA THR THR PRO THR LEU SEQRES 26 A 330 GLY PHE ALA SER LYS HET F7L A2001 18 HETNAM F7L (2S)-1-[(2-FLUOROBENZYL)OXY]-3-(PYRROLIDIN-1-YL)PROPAN- HETNAM 2 F7L 2-OL FORMUL 2 F7L C14 H20 F N O2 FORMUL 3 HOH *264(H2 O) HELIX 1 1 THR A 49 VAL A 53 5 5 HELIX 2 2 THR A 60 SER A 64 5 5 HELIX 3 3 SER A 113 GLU A 118 1 6 HELIX 4 4 PHE A 130 ASN A 134 5 5 HELIX 5 5 THR A 143 LYS A 149 1 7 HELIX 6 6 ALA A 150 LEU A 152 5 3 HELIX 7 7 PRO A 228 ALA A 237 1 10 HELIX 8 8 PRO A 274 TYR A 277 5 4 HELIX 9 9 GLY A 306 LYS A 311 1 6 SHEET 1 A 9 LYS A 68 SER A 78 0 SHEET 2 A 9 SER A 84 VAL A 96 -1 O VAL A 89 N LEU A 70 SHEET 3 A 9 TYR A 17 ILE A 23 -1 N GLN A 22 O SER A 95 SHEET 4 A 9 GLY A 3 PRO A 9 -1 N THR A 8 O ILE A 18 SHEET 5 A 9 GLY A 167 PHE A 171 -1 O GLY A 167 N THR A 7 SHEET 6 A 9 VAL A 156 ASP A 160 -1 N THR A 158 O ASN A 170 SHEET 7 A 9 PHE A 314 ASN A 318 -1 O PHE A 317 N PHE A 157 SHEET 8 A 9 THR A 324 ALA A 328 -1 O GLY A 326 N VAL A 316 SHEET 9 A 9 THR A 184 ALA A 187 -1 N THR A 184 O PHE A 327 SHEET 1 B13 LYS A 68 SER A 78 0 SHEET 2 B13 SER A 84 VAL A 96 -1 O VAL A 89 N LEU A 70 SHEET 3 B13 LEU A 99 VAL A 112 -1 O VAL A 106 N TYR A 90 SHEET 4 B13 LEU A 41 VAL A 43 1 N LEU A 41 O GLU A 107 SHEET 5 B13 GLY A 124 GLY A 127 -1 O LEU A 125 N TRP A 42 SHEET 6 B13 GLN A 28 ASP A 35 1 N ASP A 33 O GLY A 124 SHEET 7 B13 TYR A 17 ILE A 23 -1 N ILE A 23 O GLN A 28 SHEET 8 B13 GLY A 3 PRO A 9 -1 N THR A 8 O ILE A 18 SHEET 9 B13 GLY A 167 PHE A 171 -1 O GLY A 167 N THR A 7 SHEET 10 B13 VAL A 156 ASP A 160 -1 N THR A 158 O ASN A 170 SHEET 11 B13 PHE A 314 ASN A 318 -1 O PHE A 317 N PHE A 157 SHEET 12 B13 THR A 324 ALA A 328 -1 O GLY A 326 N VAL A 316 SHEET 13 B13 THR A 184 ALA A 187 -1 N THR A 184 O PHE A 327 SHEET 1 C 7 ALA A 269 ILE A 273 0 SHEET 2 C 7 PHE A 262 VAL A 266 -1 N PHE A 262 O ILE A 273 SHEET 3 C 7 GLU A 196 VAL A 204 -1 N ALA A 203 O THR A 263 SHEET 4 C 7 LYS A 210 ALA A 218 -1 O LYS A 210 N TYR A 202 SHEET 5 C 7 ASN A 303 PHE A 305 1 O PHE A 305 N ILE A 217 SHEET 6 C 7 LEU A 225 LEU A 227 -1 N TYR A 226 O ILE A 304 SHEET 7 C 7 ILE A 294 SER A 296 1 O GLN A 295 N LEU A 225 SHEET 1 D 4 LYS A 243 SER A 245 0 SHEET 2 D 4 GLY A 250 PRO A 254 -1 O VAL A 252 N LYS A 243 SHEET 3 D 4 SER A 289 GLY A 292 -1 O CYS A 290 N PHE A 253 SHEET 4 D 4 ASP A 279 PRO A 282 -1 N GLY A 281 O PHE A 291 SSBOND 1 CYS A 255 CYS A 290 1555 1555 2.04 CISPEP 1 THR A 25 PRO A 26 0 -6.10 CISPEP 2 SER A 137 PRO A 138 0 4.76 SITE 1 AC1 9 ASP A 35 TYR A 79 GLY A 80 ASP A 81 SITE 2 AC1 9 LEU A 125 GLY A 221 THR A 222 TYR A 226 SITE 3 AC1 9 ILE A 304 CRYST1 45.190 73.740 52.480 90.00 109.32 90.00 P 1 21 1 2 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 0.022129 0.000000 0.007758 0.00000 SCALE2 0.000000 0.013561 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020192 0.00000