HEADER HYDROLASE/HYDROLASE INHIBITOR 19-SEP-17 6B1X TITLE CRYSTAL STRUCTURE KPC-2 BETA-LACTAMASE COMPLEXED WITH WCK 5153 BY TITLE 2 SOAKING CAVEAT 6B1X THR A 93 HAS WRONG CHIRALITY AT ATOM CB COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARBAPENEM-HYDROLYZING BETA-LACTAMASE KPC; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CARBAPENEM-HYDROLYZING BETA-LACTAMASE KPC-1; COMPND 5 EC: 3.5.2.6; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 573; SOURCE 4 GENE: BLA, KPC, KPC1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR F.VAN DEN AKKER,N.Q.NGUYEN REVDAT 1 01-AUG-18 6B1X 0 JRNL AUTH K.M.PAPP-WALLACE,N.Q.NGUYEN,M.R.JACOBS,C.R.BETHEL, JRNL AUTH 2 M.D.BARNES,V.KUMAR,S.BAJAKSOUZIAN,S.D.RUDIN,P.N.RATHER, JRNL AUTH 3 S.BHAVSAR,T.RAVIKUMAR,P.K.DESHPANDE,V.PATIL,R.YEOLE, JRNL AUTH 4 S.S.BHAGWAT,M.V.PATEL,F.VAN DEN AKKER,R.A.BONOMO JRNL TITL STRATEGIC APPROACHES TO OVERCOME RESISTANCE AGAINST JRNL TITL 2 GRAM-NEGATIVE PATHOGENS USING BETA-LACTAMASE INHIBITORS AND JRNL TITL 3 BETA-LACTAM ENHANCERS: ACTIVITY OF THREE NOVEL JRNL TITL 4 DIAZABICYCLOOCTANES WCK 5153, ZIDEBACTAM (WCK 5107), AND WCK JRNL TITL 5 4234. JRNL REF J. MED. CHEM. V. 61 4067 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 29627985 JRNL DOI 10.1021/ACS.JMEDCHEM.8B00091 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 63748 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) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3375 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3474 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 67.87 REMARK 3 BIN R VALUE (WORKING SET) : 0.1890 REMARK 3 BIN FREE R VALUE SET COUNT : 164 REMARK 3 BIN FREE R VALUE : 0.2360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3977 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 108 REMARK 3 SOLVENT ATOMS : 480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.92 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): 0.071 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.069 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.076 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4250 ; 0.013 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 4052 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5787 ; 2.352 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9302 ; 1.065 ; 3.006 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 543 ; 6.246 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 170 ;34.498 ;23.353 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 648 ;12.092 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;15.065 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 656 ; 0.334 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4844 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 951 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6B1X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1000230150. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.12708 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.8 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67132 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 37.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.18700 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: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: OF 20% PEG 6000, 100 MM CITRATE PH REMARK 280 4.0, 100 MM KSCN, 10 MM CDCL2, AND 10MM WCK 5153., VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 ALA B 22 REMARK 465 THR B 23 REMARK 465 ALA B 24 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 ARG B 266 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG B 266 NE - CZ - NH2 ANGL. DEV. = 5.4 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 CYS A 69 -140.34 50.42 REMARK 500 ARG A 220 -123.76 -116.78 REMARK 500 CYS B 69 -139.78 48.56 REMARK 500 TRP B 105 70.55 52.87 REMARK 500 ARG B 220 -123.12 -113.69 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 residue C9D A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CIT A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CIT B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide C9D B 301 and SER B REMARK 800 70 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6B1J RELATED DB: PDB REMARK 900 6B1J CONTAINS THE SAME PROTEIN BUT COMPLEXED TO A SIMILAR INHIBITOR, REMARK 900 WCK 5107 DBREF 6B1X A 22 291 UNP Q9F663 BLKPC_KLEPN 22 289 DBREF 6B1X B 22 291 UNP Q9F663 BLKPC_KLEPN 22 289 SEQRES 1 A 268 ALA THR ALA LEU THR ASN LEU VAL ALA GLU PRO PHE ALA SEQRES 2 A 268 LYS LEU GLU GLN ASP PHE GLY GLY SER ILE GLY VAL TYR SEQRES 3 A 268 ALA MET ASP THR GLY SER GLY ALA THR VAL SER TYR ARG SEQRES 4 A 268 ALA GLU GLU ARG PHE PRO LEU CYS SER SER PHE LYS GLY SEQRES 5 A 268 PHE LEU ALA ALA ALA VAL LEU ALA ARG SER GLN GLN GLN SEQRES 6 A 268 ALA GLY LEU LEU ASP THR PRO ILE ARG TYR GLY LYS ASN SEQRES 7 A 268 ALA LEU VAL PRO TRP SER PRO ILE SER GLU LYS TYR LEU SEQRES 8 A 268 THR THR GLY MET THR VAL ALA GLU LEU SER ALA ALA ALA SEQRES 9 A 268 VAL GLN TYR SER ASP ASN ALA ALA ALA ASN LEU LEU LEU SEQRES 10 A 268 LYS GLU LEU GLY GLY PRO ALA GLY LEU THR ALA PHE MET SEQRES 11 A 268 ARG SER ILE GLY ASP THR THR PHE ARG LEU ASP ARG TRP SEQRES 12 A 268 GLU LEU GLU LEU ASN SER ALA ILE PRO GLY ASP ALA ARG SEQRES 13 A 268 ASP THR SER SER PRO ARG ALA VAL THR GLU SER LEU GLN SEQRES 14 A 268 LYS LEU THR LEU GLY SER ALA LEU ALA ALA PRO GLN ARG SEQRES 15 A 268 GLN GLN PHE VAL ASP TRP LEU LYS GLY ASN THR THR GLY SEQRES 16 A 268 ASN HIS ARG ILE ARG ALA ALA VAL PRO ALA ASP TRP ALA SEQRES 17 A 268 VAL GLY ASP LYS THR GLY THR CYS GLY VAL TYR GLY THR SEQRES 18 A 268 ALA ASN ASP TYR ALA VAL VAL TRP PRO THR GLY ARG ALA SEQRES 19 A 268 PRO ILE VAL LEU ALA VAL TYR THR ARG ALA PRO ASN LYS SEQRES 20 A 268 ASP ASP LYS HIS SER GLU ALA VAL ILE ALA ALA ALA ALA SEQRES 21 A 268 ARG LEU ALA LEU GLU GLY LEU GLY SEQRES 1 B 268 ALA THR ALA LEU THR ASN LEU VAL ALA GLU PRO PHE ALA SEQRES 2 B 268 LYS LEU GLU GLN ASP PHE GLY GLY SER ILE GLY VAL TYR SEQRES 3 B 268 ALA MET ASP THR GLY SER GLY ALA THR VAL SER TYR ARG SEQRES 4 B 268 ALA GLU GLU ARG PHE PRO LEU CYS SER SER PHE LYS GLY SEQRES 5 B 268 PHE LEU ALA ALA ALA VAL LEU ALA ARG SER GLN GLN GLN SEQRES 6 B 268 ALA GLY LEU LEU ASP THR PRO ILE ARG TYR GLY LYS ASN SEQRES 7 B 268 ALA LEU VAL PRO TRP SER PRO ILE SER GLU LYS TYR LEU SEQRES 8 B 268 THR THR GLY MET THR VAL ALA GLU LEU SER ALA ALA ALA SEQRES 9 B 268 VAL GLN TYR SER ASP ASN ALA ALA ALA ASN LEU LEU LEU SEQRES 10 B 268 LYS GLU LEU GLY GLY PRO ALA GLY LEU THR ALA PHE MET SEQRES 11 B 268 ARG SER ILE GLY ASP THR THR PHE ARG LEU ASP ARG TRP SEQRES 12 B 268 GLU LEU GLU LEU ASN SER ALA ILE PRO GLY ASP ALA ARG SEQRES 13 B 268 ASP THR SER SER PRO ARG ALA VAL THR GLU SER LEU GLN SEQRES 14 B 268 LYS LEU THR LEU GLY SER ALA LEU ALA ALA PRO GLN ARG SEQRES 15 B 268 GLN GLN PHE VAL ASP TRP LEU LYS GLY ASN THR THR GLY SEQRES 16 B 268 ASN HIS ARG ILE ARG ALA ALA VAL PRO ALA ASP TRP ALA SEQRES 17 B 268 VAL GLY ASP LYS THR GLY THR CYS GLY VAL TYR GLY THR SEQRES 18 B 268 ALA ASN ASP TYR ALA VAL VAL TRP PRO THR GLY ARG ALA SEQRES 19 B 268 PRO ILE VAL LEU ALA VAL TYR THR ARG ALA PRO ASN LYS SEQRES 20 B 268 ASP ASP LYS HIS SER GLU ALA VAL ILE ALA ALA ALA ALA SEQRES 21 B 268 ARG LEU ALA LEU GLU GLY LEU GLY HET C9D A 301 25 HET CIT A 302 13 HET EDO A 303 4 HET EDO A 304 4 HET EDO A 305 4 HET EDO A 306 4 HET EDO A 307 4 HET C9D B 301 25 HET CIT B 302 13 HET EDO B 303 4 HET EDO B 304 4 HET EDO B 305 4 HETNAM C9D (2S,5R)-1-FORMYL-N'-[(3R)-PYRROLIDINE-3-CARBONYL]-5- HETNAM 2 C9D [(SULFOOXY)AMINO]PIPERIDINE-2-CARBOHYDRAZIDE HETNAM CIT CITRIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN C9D OPEN FORM - WCK 5153 HETSYN EDO ETHYLENE GLYCOL FORMUL 3 C9D 2(C12 H21 N5 O7 S) FORMUL 4 CIT 2(C6 H8 O7) FORMUL 5 EDO 8(C2 H6 O2) FORMUL 15 HOH *480(H2 O) HELIX 1 AA1 LEU A 25 GLY A 41 1 17 HELIX 2 AA2 SER A 71 GLN A 87 1 17 HELIX 3 AA3 GLY A 89 ASP A 92 5 4 HELIX 4 AA4 GLY A 98 LEU A 102 5 5 HELIX 5 AA5 ILE A 108 LEU A 113 5 6 HELIX 6 AA6 VAL A 119 TYR A 129 1 11 HELIX 7 AA7 ASP A 131 LEU A 142 1 12 HELIX 8 AA8 GLY A 143 ILE A 155 1 13 HELIX 9 AA9 LEU A 167 SER A 171 5 5 HELIX 10 AB1 SER A 182 LEU A 195 1 14 HELIX 11 AB2 ALA A 200 GLY A 213 1 14 HELIX 12 AB3 ARG A 220 VAL A 225 5 6 HELIX 13 AB4 SER A 275 GLY A 289 1 15 HELIX 14 AB5 THR B 26 GLY B 41 1 16 HELIX 15 AB6 SER B 71 GLN B 85 1 15 HELIX 16 AB7 GLY B 89 ASP B 92 5 4 HELIX 17 AB8 GLY B 98 LEU B 102 5 5 HELIX 18 AB9 ILE B 108 LEU B 113 5 6 HELIX 19 AC1 VAL B 119 TYR B 129 1 11 HELIX 20 AC2 ASP B 131 LEU B 142 1 12 HELIX 21 AC3 GLY B 144 ILE B 155 1 12 HELIX 22 AC4 LEU B 167 SER B 171 5 5 HELIX 23 AC5 SER B 182 LEU B 195 1 14 HELIX 24 AC6 ALA B 200 GLY B 213 1 14 HELIX 25 AC7 ARG B 220 VAL B 225 5 6 HELIX 26 AC8 SER B 275 GLY B 289 1 15 SHEET 1 AA1 5 THR A 56 TYR A 60 0 SHEET 2 AA1 5 SER A 43 ASP A 50 -1 N VAL A 46 O TYR A 60 SHEET 3 AA1 5 ILE A 259 ARG A 266 -1 O TYR A 264 N GLY A 45 SHEET 4 AA1 5 ALA A 244 TRP A 251 -1 N VAL A 250 O ILE A 259 SHEET 5 AA1 5 ALA A 230 THR A 237 -1 N ALA A 230 O TRP A 251 SHEET 1 AA2 2 PHE A 66 PRO A 67 0 SHEET 2 AA2 2 THR A 180 SER A 181 -1 O SER A 181 N PHE A 66 SHEET 1 AA3 2 PRO A 94 ILE A 95 0 SHEET 2 AA3 2 MET A 117 THR A 118 -1 O MET A 117 N ILE A 95 SHEET 1 AA4 5 THR B 56 TYR B 60 0 SHEET 2 AA4 5 SER B 43 ASP B 50 -1 N VAL B 46 O TYR B 60 SHEET 3 AA4 5 ILE B 259 ARG B 266 -1 O TYR B 264 N GLY B 45 SHEET 4 AA4 5 ALA B 244 TRP B 251 -1 N ASP B 246 O VAL B 263 SHEET 5 AA4 5 ALA B 230 THR B 237 -1 N GLY B 236 O ASN B 245 SHEET 1 AA5 2 PHE B 66 PRO B 67 0 SHEET 2 AA5 2 THR B 180 SER B 181 -1 O SER B 181 N PHE B 66 SHEET 1 AA6 2 PRO B 94 ILE B 95 0 SHEET 2 AA6 2 MET B 117 THR B 118 -1 O MET B 117 N ILE B 95 SSBOND 1 CYS A 69 CYS A 238 1555 1555 2.08 SSBOND 2 CYS B 69 CYS B 238 1555 1555 2.10 LINK SD AMET A 49 OE1AGLN A 191 1555 1555 1.78 LINK OG SER A 70 CAG C9D A 301 1555 1555 1.44 LINK OG SER B 70 CAG C9D B 301 1555 1555 1.49 CISPEP 1 GLU A 166 LEU A 167 0 9.10 CISPEP 2 GLU B 166 LEU B 167 0 8.04 SITE 1 AC1 18 CYS A 69 SER A 70 TRP A 105 SER A 130 SITE 2 AC1 18 ASN A 132 ASN A 170 THR A 216 LYS A 234 SITE 3 AC1 18 THR A 235 GLY A 236 THR A 237 CYS A 238 SITE 4 AC1 18 HOH A 405 HOH A 424 HOH A 537 HOH A 538 SITE 5 AC1 18 HOH A 572 HOH A 580 SITE 1 AC2 14 TYR A 97 GLY A 98 ASN A 100 ALA A 101 SITE 2 AC2 14 HOH A 401 HOH A 404 HOH A 493 ARG B 96 SITE 3 AC2 14 ARG B 164 ARG B 178 EDO B 304 HOH B 420 SITE 4 AC2 14 HOH B 428 HOH B 483 SITE 1 AC3 6 ALA A 124 ALA A 125 GLN A 128 TYR A 129 SITE 2 AC3 6 PRO A 174 HOH A 505 SITE 1 AC4 7 ALA A 82 GLN A 85 GLN A 86 VAL A 103 SITE 2 AC4 7 PRO A 104 HOH A 414 HOH A 484 SITE 1 AC5 6 ARG A 96 THR A 115 ASN B 136 TRP B 165 SITE 2 AC5 6 CIT B 302 HOH B 497 SITE 1 AC6 5 GLN A 205 VAL A 208 LYS A 212 TRP A 251 SITE 2 AC6 5 HOH A 586 SITE 1 AC7 3 PRO A 107 ARG A 204 HOH A 403 SITE 1 AC8 13 PRO A 94 ARG A 96 THR A 115 GLY A 116 SITE 2 AC8 13 MET A 117 THR A 118 ARG A 178 EDO A 305 SITE 3 AC8 13 ASN B 100 ALA B 101 LYS B 140 HOH B 491 SITE 4 AC8 13 HOH B 537 SITE 1 AC9 7 ALA B 124 ALA B 125 GLN B 128 TYR B 129 SITE 2 AC9 7 ILE B 173 PRO B 174 HOH B 492 SITE 1 AD1 6 CIT A 302 PRO B 94 THR B 115 ARG B 178 SITE 2 AD1 6 EDO B 305 HOH B 420 SITE 1 AD2 6 TYR B 112 THR B 115 GLU B 121 ARG B 178 SITE 2 AD2 6 EDO B 304 HOH B 407 SITE 1 AD3 22 LEU B 68 CYS B 69 SER B 71 PHE B 72 SITE 2 AD3 22 LYS B 73 TRP B 105 SER B 130 ASN B 132 SITE 3 AD3 22 LEU B 167 ASN B 170 THR B 216 LYS B 234 SITE 4 AD3 22 THR B 235 GLY B 236 THR B 237 CYS B 238 SITE 5 AD3 22 HOH B 412 HOH B 425 HOH B 495 HOH B 514 SITE 6 AD3 22 HOH B 526 HOH B 554 CRYST1 34.493 37.436 82.235 92.30 90.21 95.08 P 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 0.028991 0.002579 0.000209 0.00000 SCALE2 0.000000 0.026818 0.001091 0.00000 SCALE3 0.000000 0.000000 0.012170 0.00000