HEADER HYDROLASE/HYDROLASE INHIBITOR 25-APR-10 3AHN TITLE PZ PEPTIDASE A WITH INHIBITOR 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: OLIGOPEPTIDASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PZ PEPTIDASE A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS SP. MO-1; SOURCE 3 ORGANISM_TAXID: 295930 KEYWDS HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.NAKANO REVDAT 4 21-FEB-24 3AHN 1 REMARK LINK REVDAT 3 16-DEC-15 3AHN 1 JRNL REVDAT 2 13-JUL-11 3AHN 1 VERSN REVDAT 1 25-AUG-10 3AHN 0 JRNL AUTH A.KAWASAKI,H.NAKANO,A.HOSOKAWA,T.NAKATSU,H.KATO,K.WATANABE JRNL TITL THE EXQUISITE STRUCTURE AND REACTION MECHANISM OF BACTERIAL JRNL TITL 2 PZ-PEPTIDASE A TOWARD COLLAGENOUS PEPTIDES: X-RAY JRNL TITL 3 CRYSTALLOGRAPHIC STRUCTURE ANALYSIS OF PZ-PEPTIDASE A JRNL TITL 4 REVEALS DIFFERENCES FROM MAMMALIAN THIMET OLIGOPEPTIDASE. JRNL REF J.BIOL.CHEM. V. 285 34972 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20817732 JRNL DOI 10.1074/JBC.M110.141838 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 104042 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5511 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7382 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.2900 REMARK 3 BIN FREE R VALUE SET COUNT : 372 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 9384 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 106 REMARK 3 SOLVENT ATOMS : 1414 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.148 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.120 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 9737 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 13137 ; 1.337 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1125 ; 1.313 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 536 ;38.246 ;24.179 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1669 ;10.582 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 60 ;14.888 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1317 ; 0.144 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7646 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 5253 ; 0.221 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 6852 ; 0.325 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 836 ; 0.102 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 38 ; 0.156 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.605 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 5636 ; 0.836 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 9060 ; 1.334 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4101 ; 2.298 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 4077 ; 3.497 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3AHN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000029265. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 104042 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 19.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE PURIFIED PROTEIN SOLUTION, REMARK 280 CONCENTRATED TO ABOUT 20 MG/ML IN 50 MM TRIS-HCL (PH7.5), WAS REMARK 280 INCUBATED IN THE ABSENCE OR PRESENCE OF THE INHIBITOR IN 12% (W/ REMARK 280 V) PEG 4000, 0.5 M MAGNESIUM ACETATE, AND 0.1 M TRIS-HCL (PH 7.0) REMARK 280 FOR FIVE DAYS BY THE HANGING-DROP VAPOR DIFFUSION METHOD AT 293 REMARK 280 K. THE INHIBITOR AT FINAL CONCENTRATIONS WERE 0.5 MM., VAPOR REMARK 280 DIFFUSION, HANGING DROP 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 97.07400 REMARK 290 SMTRY3 2 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: 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 MET B 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 869 O HOH B 846 2545 0.27 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 LYS B 2 CD - CE - NZ ANGL. DEV. = 25.5 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 LYS A 281 41.30 -93.03 REMARK 500 LEU A 314 34.83 -90.96 REMARK 500 LYS A 403 -120.98 54.92 REMARK 500 ASP A 463 50.80 37.13 REMARK 500 TYR A 487 -39.97 -171.04 REMARK 500 LYS B 281 37.94 -86.99 REMARK 500 LEU B 314 40.65 -91.28 REMARK 500 LYS B 403 -116.10 49.93 REMARK 500 ASP B 463 43.20 38.85 REMARK 500 PHE B 485 -0.59 70.57 REMARK 500 TYR B 487 -41.15 -168.78 REMARK 500 ASN B 507 87.02 -151.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 566 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 356 NE2 REMARK 620 2 HIS A 360 NE2 103.7 REMARK 620 3 GLU A 384 OE2 140.3 91.9 REMARK 620 4 GLU A 384 OE1 85.1 97.5 56.5 REMARK 620 5 3A1 A 565 O36 102.9 137.5 88.2 117.3 REMARK 620 6 3A1 A 565 OP3 92.2 85.0 125.8 176.7 61.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 565 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 356 NE2 REMARK 620 2 HIS B 360 NE2 105.5 REMARK 620 3 GLU B 384 OE1 86.0 99.3 REMARK 620 4 GLU B 384 OE2 141.1 89.2 55.8 REMARK 620 5 3A1 B 566 O36 101.8 136.4 116.1 90.3 REMARK 620 6 3A1 B 566 OP3 89.8 85.4 174.4 127.8 61.2 REMARK 620 N 1 2 3 4 5 REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE ENZYME INHIBITOR REMARK 630 MOLECULE NAME: N~2~-{(2S)-3-[(R)-HYDROXY{(1R)-2-PHENYL-1- REMARK 630 [(PHENYLACETYL)AMINO]ETHYL}PHOSPHORYL]-2-METHYLPROPANOYL}-L-LYSYL- REMARK 630 D-SERINE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 3A1 A 565 REMARK 630 3A1 B 566 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: PAC 00F LYS DSN REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3A1 A 565 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 566 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 567 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 568 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 565 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3A1 B 566 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 567 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 568 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 569 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3AHM RELATED DB: PDB REMARK 900 RELATED ID: 3AHO RELATED DB: PDB DBREF 3AHN A 1 564 UNP Q4W803 Q4W803_9BACI 1 564 DBREF 3AHN B 1 564 UNP Q4W803 Q4W803_9BACI 1 564 SEQRES 1 A 564 MET LYS PHE SER GLU PHE ARG TYR GLU ARG PRO ASN ILE SEQRES 2 A 564 GLU LYS LEU LYS ALA SER PHE GLN GLN ALA LEU GLN SER SEQRES 3 A 564 PHE GLN LYS ALA SER ASN ALA GLU GLU GLN ASN GLU ALA SEQRES 4 A 564 MET LYS GLU ILE ASN GLN LEU ARG ASN ASP PHE SER THR SEQRES 5 A 564 MET ALA GLN ILE CYS TYR ILE ARG HIS THR ILE ASP THR SEQRES 6 A 564 ASN ASP GLU PHE TYR LYS GLN GLU GLN ASP PHE PHE ASP SEQRES 7 A 564 GLU VAL GLU PRO ILE VAL LYS GLY LEU VAL ASN ASP TYR SEQRES 8 A 564 TYR ARG ALA LEU VAL SER SER PRO PHE ARG SER GLN LEU SEQRES 9 A 564 GLU GLY LYS TRP GLY LYS GLN LEU PHE ALA LEU ALA GLU SEQRES 10 A 564 ALA GLU LEU LYS THR TYR SER PRO ASP ILE VAL GLU ASP SEQRES 11 A 564 LEU GLN LEU GLU ASN LYS LEU THR SER GLU TYR THR LYS SEQRES 12 A 564 LEU VAL ALA SER ALA LYS ILE PHE PHE GLU GLY GLU GLU SEQRES 13 A 564 ARG THR LEU ALA GLN LEU GLN PRO PHE VAL GLU SER PRO SEQRES 14 A 564 ASP ARG ASP MET ARG LYS ARG ALA SER GLU ALA ARG PHE SEQRES 15 A 564 THR PHE PHE GLN GLU HIS GLU GLU LYS PHE ASP GLU ILE SEQRES 16 A 564 TYR ASP GLN LEU VAL LYS VAL ARG THR ALA ILE ALA GLN SEQRES 17 A 564 LYS LEU GLY PHE LYS ASN PHE VAL GLU LEU GLY TYR ALA SEQRES 18 A 564 ARG LEU GLY ARG THR ASP TYR ASN ALA GLU MET VAL ALA SEQRES 19 A 564 LYS PHE ARG LYS GLN VAL GLU LYS HIS ILE VAL PRO ILE SEQRES 20 A 564 ALA VAL LYS LEU ARG GLU ARG GLN ARG GLU ARG ILE GLY SEQRES 21 A 564 VAL GLU LYS LEU LYS TYR TYR ASP GLU ALA PHE VAL PHE SEQRES 22 A 564 PRO THR GLY ASN PRO MET PRO LYS GLY ASP ALA ASN TRP SEQRES 23 A 564 ILE ILE GLU ASN GLY LYS LYS MET TYR GLU GLU LEU SER SEQRES 24 A 564 PRO GLU THR GLY GLU PHE PHE ARG TYR MET ILE GLU HIS SEQRES 25 A 564 GLU LEU MET ASP LEU VAL ALA LYS LYS GLY LYS ALA SER SEQRES 26 A 564 GLY GLY TYR CYS THR TYR ILE GLU ASN TYR LYS ALA PRO SEQRES 27 A 564 PHE ILE PHE SER ASN PHE THR GLY THR SER GLY ASP ILE SEQRES 28 A 564 ASP VAL LEU THR HIS GLU ALA GLY HIS ALA PHE GLN VAL SEQRES 29 A 564 TYR GLU SER ARG HIS TYR GLU ILE PRO GLU TYR ASN TRP SEQRES 30 A 564 PRO THR LEU GLU ALA CYS GLU ILE HIS SER MET SER MET SEQRES 31 A 564 GLU PHE PHE THR TRP PRO TRP MET LYS LEU PHE PHE LYS SEQRES 32 A 564 GLU ASP ALA GLU LYS TYR GLN PHE TYR HIS LEU SER ASP SEQRES 33 A 564 ALA LEU LEU PHE LEU PRO TYR GLY VAL ALA VAL ASP GLU SEQRES 34 A 564 PHE GLN HIS PHE VAL TYR GLU ASN PRO ASN ALA THR PRO SEQRES 35 A 564 ALA GLU ARG LYS GLN ALA TRP ARG ALA ILE GLU ARG LYS SEQRES 36 A 564 TYR MET PRO THR LYS ASP TYR ASP GLY ASN ASP TYR LEU SEQRES 37 A 564 GLU ARG GLY GLY PHE TRP GLN ARG GLN SER HIS ILE TYR SEQRES 38 A 564 THR THR ALA PHE TYR TYR ILE ASP TYR THR LEU ALA GLN SEQRES 39 A 564 ILE CYS ALA PHE GLN PHE TRP LYS ARG SER ARG GLU ASN SEQRES 40 A 564 TYR LYS GLU ALA TRP ASN ASP TYR LEU THR LEU CYS ARG SEQRES 41 A 564 GLN GLY GLY SER LYS PRO PHE THR GLU LEU VAL ARG VAL SEQRES 42 A 564 ALA ASN LEU ILE SER PRO PHE GLU ASP GLY CYS VAL GLN SEQRES 43 A 564 SER VAL VAL GLY GLY ILE GLU GLY TRP LEU ASN SER VAL SEQRES 44 A 564 ASP ASP GLN SER LEU SEQRES 1 B 564 MET LYS PHE SER GLU PHE ARG TYR GLU ARG PRO ASN ILE SEQRES 2 B 564 GLU LYS LEU LYS ALA SER PHE GLN GLN ALA LEU GLN SER SEQRES 3 B 564 PHE GLN LYS ALA SER ASN ALA GLU GLU GLN ASN GLU ALA SEQRES 4 B 564 MET LYS GLU ILE ASN GLN LEU ARG ASN ASP PHE SER THR SEQRES 5 B 564 MET ALA GLN ILE CYS TYR ILE ARG HIS THR ILE ASP THR SEQRES 6 B 564 ASN ASP GLU PHE TYR LYS GLN GLU GLN ASP PHE PHE ASP SEQRES 7 B 564 GLU VAL GLU PRO ILE VAL LYS GLY LEU VAL ASN ASP TYR SEQRES 8 B 564 TYR ARG ALA LEU VAL SER SER PRO PHE ARG SER GLN LEU SEQRES 9 B 564 GLU GLY LYS TRP GLY LYS GLN LEU PHE ALA LEU ALA GLU SEQRES 10 B 564 ALA GLU LEU LYS THR TYR SER PRO ASP ILE VAL GLU ASP SEQRES 11 B 564 LEU GLN LEU GLU ASN LYS LEU THR SER GLU TYR THR LYS SEQRES 12 B 564 LEU VAL ALA SER ALA LYS ILE PHE PHE GLU GLY GLU GLU SEQRES 13 B 564 ARG THR LEU ALA GLN LEU GLN PRO PHE VAL GLU SER PRO SEQRES 14 B 564 ASP ARG ASP MET ARG LYS ARG ALA SER GLU ALA ARG PHE SEQRES 15 B 564 THR PHE PHE GLN GLU HIS GLU GLU LYS PHE ASP GLU ILE SEQRES 16 B 564 TYR ASP GLN LEU VAL LYS VAL ARG THR ALA ILE ALA GLN SEQRES 17 B 564 LYS LEU GLY PHE LYS ASN PHE VAL GLU LEU GLY TYR ALA SEQRES 18 B 564 ARG LEU GLY ARG THR ASP TYR ASN ALA GLU MET VAL ALA SEQRES 19 B 564 LYS PHE ARG LYS GLN VAL GLU LYS HIS ILE VAL PRO ILE SEQRES 20 B 564 ALA VAL LYS LEU ARG GLU ARG GLN ARG GLU ARG ILE GLY SEQRES 21 B 564 VAL GLU LYS LEU LYS TYR TYR ASP GLU ALA PHE VAL PHE SEQRES 22 B 564 PRO THR GLY ASN PRO MET PRO LYS GLY ASP ALA ASN TRP SEQRES 23 B 564 ILE ILE GLU ASN GLY LYS LYS MET TYR GLU GLU LEU SER SEQRES 24 B 564 PRO GLU THR GLY GLU PHE PHE ARG TYR MET ILE GLU HIS SEQRES 25 B 564 GLU LEU MET ASP LEU VAL ALA LYS LYS GLY LYS ALA SER SEQRES 26 B 564 GLY GLY TYR CYS THR TYR ILE GLU ASN TYR LYS ALA PRO SEQRES 27 B 564 PHE ILE PHE SER ASN PHE THR GLY THR SER GLY ASP ILE SEQRES 28 B 564 ASP VAL LEU THR HIS GLU ALA GLY HIS ALA PHE GLN VAL SEQRES 29 B 564 TYR GLU SER ARG HIS TYR GLU ILE PRO GLU TYR ASN TRP SEQRES 30 B 564 PRO THR LEU GLU ALA CYS GLU ILE HIS SER MET SER MET SEQRES 31 B 564 GLU PHE PHE THR TRP PRO TRP MET LYS LEU PHE PHE LYS SEQRES 32 B 564 GLU ASP ALA GLU LYS TYR GLN PHE TYR HIS LEU SER ASP SEQRES 33 B 564 ALA LEU LEU PHE LEU PRO TYR GLY VAL ALA VAL ASP GLU SEQRES 34 B 564 PHE GLN HIS PHE VAL TYR GLU ASN PRO ASN ALA THR PRO SEQRES 35 B 564 ALA GLU ARG LYS GLN ALA TRP ARG ALA ILE GLU ARG LYS SEQRES 36 B 564 TYR MET PRO THR LYS ASP TYR ASP GLY ASN ASP TYR LEU SEQRES 37 B 564 GLU ARG GLY GLY PHE TRP GLN ARG GLN SER HIS ILE TYR SEQRES 38 B 564 THR THR ALA PHE TYR TYR ILE ASP TYR THR LEU ALA GLN SEQRES 39 B 564 ILE CYS ALA PHE GLN PHE TRP LYS ARG SER ARG GLU ASN SEQRES 40 B 564 TYR LYS GLU ALA TRP ASN ASP TYR LEU THR LEU CYS ARG SEQRES 41 B 564 GLN GLY GLY SER LYS PRO PHE THR GLU LEU VAL ARG VAL SEQRES 42 B 564 ALA ASN LEU ILE SER PRO PHE GLU ASP GLY CYS VAL GLN SEQRES 43 B 564 SER VAL VAL GLY GLY ILE GLU GLY TRP LEU ASN SER VAL SEQRES 44 B 564 ASP ASP GLN SER LEU HET 3A1 A 565 42 HET ZN A 566 1 HET ACT A 567 4 HET ACT A 568 4 HET ZN B 565 1 HET 3A1 B 566 42 HET ACT B 567 4 HET ACT B 568 4 HET ACT B 569 4 HETNAM 3A1 N~2~-{(2S)-3-[(R)-HYDROXY{(1R)-2-PHENYL-1- HETNAM 2 3A1 [(PHENYLACETYL)AMINO]ETHYL}PHOSPHORYL]-2- HETNAM 3 3A1 METHYLPROPANOYL}-L-LYSYL-D-SERINE HETNAM ZN ZINC ION HETNAM ACT ACETATE ION FORMUL 3 3A1 2(C29 H41 N4 O8 P) FORMUL 4 ZN 2(ZN 2+) FORMUL 5 ACT 5(C2 H3 O2 1-) FORMUL 12 HOH *1414(H2 O) HELIX 1 1 LYS A 2 PHE A 6 5 5 HELIX 2 2 ASN A 12 LYS A 29 1 18 HELIX 3 3 ASN A 32 ASP A 64 1 33 HELIX 4 4 ASP A 67 SER A 97 1 31 HELIX 5 5 PHE A 100 GLY A 109 1 10 HELIX 6 6 LYS A 110 LYS A 121 1 12 HELIX 7 7 THR A 122 TYR A 123 5 2 HELIX 8 8 SER A 124 ASP A 126 5 3 HELIX 9 9 ILE A 127 SER A 147 1 21 HELIX 10 10 LEU A 159 GLN A 161 5 3 HELIX 11 11 LEU A 162 GLU A 167 1 6 HELIX 12 12 ASP A 170 HIS A 188 1 19 HELIX 13 13 HIS A 188 LEU A 210 1 23 HELIX 14 14 ASN A 214 LEU A 223 1 10 HELIX 15 15 ASN A 229 ILE A 244 1 16 HELIX 16 16 ILE A 244 GLY A 260 1 17 HELIX 17 17 ASP A 283 SER A 299 1 17 HELIX 18 18 SER A 299 HIS A 312 1 14 HELIX 19 19 GLU A 333 LYS A 336 5 4 HELIX 20 20 THR A 347 SER A 367 1 21 HELIX 21 21 ILE A 372 ASN A 376 5 5 HELIX 22 22 THR A 379 THR A 394 1 16 HELIX 23 23 TRP A 397 LYS A 403 1 7 HELIX 24 24 ASP A 405 ASN A 437 1 33 HELIX 25 25 THR A 441 MET A 457 1 17 HELIX 26 26 ASN A 465 ARG A 470 1 6 HELIX 27 27 GLY A 472 ARG A 476 5 5 HELIX 28 28 GLN A 477 THR A 483 1 7 HELIX 29 29 TYR A 487 ASN A 507 1 21 HELIX 30 30 ASN A 507 ARG A 520 1 14 HELIX 31 31 PRO A 526 ALA A 534 1 9 HELIX 32 32 GLY A 543 ASN A 557 1 15 HELIX 33 33 SER A 558 VAL A 559 5 2 HELIX 34 34 ASP A 560 LEU A 564 5 5 HELIX 35 35 LYS B 2 PHE B 6 5 5 HELIX 36 36 ASN B 12 LYS B 29 1 18 HELIX 37 37 ASN B 32 ASP B 64 1 33 HELIX 38 38 ASP B 67 SER B 97 1 31 HELIX 39 39 PHE B 100 GLY B 109 1 10 HELIX 40 40 GLY B 109 LYS B 121 1 13 HELIX 41 41 THR B 122 TYR B 123 5 2 HELIX 42 42 SER B 124 ASP B 126 5 3 HELIX 43 43 ILE B 127 SER B 147 1 21 HELIX 44 44 LEU B 159 GLN B 161 5 3 HELIX 45 45 LEU B 162 GLU B 167 1 6 HELIX 46 46 ASP B 170 HIS B 188 1 19 HELIX 47 47 HIS B 188 LEU B 210 1 23 HELIX 48 48 ASN B 214 LEU B 223 1 10 HELIX 49 49 ASN B 229 ILE B 244 1 16 HELIX 50 50 ILE B 244 GLY B 260 1 17 HELIX 51 51 ASP B 283 SER B 299 1 17 HELIX 52 52 SER B 299 HIS B 312 1 14 HELIX 53 53 GLU B 333 LYS B 336 5 4 HELIX 54 54 SER B 348 SER B 367 1 20 HELIX 55 55 ILE B 372 ASN B 376 5 5 HELIX 56 56 THR B 379 THR B 394 1 16 HELIX 57 57 TRP B 397 LYS B 403 1 7 HELIX 58 58 ASP B 405 ASN B 437 1 33 HELIX 59 59 THR B 441 MET B 457 1 17 HELIX 60 60 ASN B 465 ARG B 470 1 6 HELIX 61 61 GLY B 472 ARG B 476 5 5 HELIX 62 62 GLN B 477 THR B 483 1 7 HELIX 63 63 TYR B 487 ASN B 507 1 21 HELIX 64 64 ASN B 507 ARG B 520 1 14 HELIX 65 65 PRO B 526 ALA B 534 1 9 HELIX 66 66 GLY B 543 SER B 558 1 16 HELIX 67 67 VAL B 559 LEU B 564 5 6 SHEET 1 A 2 ILE A 150 PHE A 152 0 SHEET 2 A 2 GLU A 155 ARG A 157 -1 O ARG A 157 N ILE A 150 SHEET 1 B 3 MET A 315 VAL A 318 0 SHEET 2 B 3 ALA A 337 PHE A 344 1 O PHE A 344 N LEU A 317 SHEET 3 B 3 TYR A 328 ILE A 332 -1 N ILE A 332 O ALA A 337 SHEET 1 C 2 ILE B 150 PHE B 152 0 SHEET 2 C 2 GLU B 155 ARG B 157 -1 O ARG B 157 N ILE B 150 SHEET 1 D 3 MET B 315 VAL B 318 0 SHEET 2 D 3 ALA B 337 PHE B 344 1 O PHE B 344 N LEU B 317 SHEET 3 D 3 TYR B 328 ILE B 332 -1 N TYR B 328 O PHE B 341 LINK NE2 HIS A 356 ZN ZN A 566 1555 1555 2.17 LINK NE2 HIS A 360 ZN ZN A 566 1555 1555 2.11 LINK OE2 GLU A 384 ZN ZN A 566 1555 1555 2.32 LINK OE1 GLU A 384 ZN ZN A 566 1555 1555 2.32 LINK O36 3A1 A 565 ZN ZN A 566 1555 1555 2.16 LINK OP3 3A1 A 565 ZN ZN A 566 1555 1555 2.58 LINK NE2 HIS B 356 ZN ZN B 565 1555 1555 2.23 LINK NE2 HIS B 360 ZN ZN B 565 1555 1555 2.17 LINK OE1 GLU B 384 ZN ZN B 565 1555 1555 2.26 LINK OE2 GLU B 384 ZN ZN B 565 1555 1555 2.41 LINK ZN ZN B 565 O36 3A1 B 566 1555 1555 2.15 LINK ZN ZN B 565 OP3 3A1 B 566 1555 1555 2.61 SITE 1 AC1 24 GLY A 327 TYR A 328 CYS A 329 HIS A 356 SITE 2 AC1 24 GLU A 357 HIS A 360 CYS A 383 GLU A 384 SITE 3 AC1 24 PHE A 420 ARG A 476 GLN A 477 HIS A 479 SITE 4 AC1 24 THR A 483 TYR A 486 TYR A 487 TYR A 490 SITE 5 AC1 24 ZN A 566 HOH A 582 HOH A 620 HOH A 630 SITE 6 AC1 24 HOH A 833 HOH A 928 HOH A 970 HOH A1217 SITE 1 AC2 5 HIS A 356 HIS A 360 GLU A 384 SER A 387 SITE 2 AC2 5 3A1 A 565 SITE 1 AC3 5 ARG A 47 VAL A 88 HOH A 715 HOH A 939 SITE 2 AC3 5 HOH A1022 SITE 1 AC4 4 GLU A 257 ARG A 258 GLN A 562 HOH A1293 SITE 1 AC5 5 HIS B 356 HIS B 360 GLU B 384 SER B 387 SITE 2 AC5 5 3A1 B 566 SITE 1 AC6 24 GLY B 327 TYR B 328 CYS B 329 HIS B 356 SITE 2 AC6 24 GLU B 357 HIS B 360 TRP B 377 GLU B 384 SITE 3 AC6 24 MET B 388 PHE B 420 ARG B 476 GLN B 477 SITE 4 AC6 24 HIS B 479 THR B 483 TYR B 486 TYR B 487 SITE 5 AC6 24 TYR B 490 GLN B 494 ZN B 565 HOH B 622 SITE 6 AC6 24 HOH B 902 HOH B 924 HOH B1012 HOH B1083 SITE 1 AC7 2 ILE B 259 HOH B1122 SITE 1 AC8 4 ARG B 47 VAL B 88 HOH B 575 HOH B 743 SITE 1 AC9 5 ARG B 171 LYS B 265 TYR B 267 HOH B 779 SITE 2 AC9 5 HOH B 958 CRYST1 56.379 194.148 59.924 90.00 106.22 90.00 P 1 21 1 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 0.017737 0.000000 0.005161 0.00000 SCALE2 0.000000 0.005151 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017380 0.00000