HEADER HYDROLASE/HYDROLASE INHIBITOR 19-SEP-17 6B1Y TITLE CRYSTAL STRUCTURE KPC-2 BETA-LACTAMASE COMPLEXED WITH WCK 5153 BY CO- TITLE 2 CRYSTALLIZATION 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 6B1Y 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 34166 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) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1799 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) : 2461 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.42 REMARK 3 BIN R VALUE (WORKING SET) : 0.2190 REMARK 3 BIN FREE R VALUE SET COUNT : 137 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3975 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 77 REMARK 3 SOLVENT ATOMS : 335 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : 0.01000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.142 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.131 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.860 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4133 ; 0.015 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3913 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5632 ; 1.694 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8973 ; 1.097 ; 3.005 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 531 ; 6.369 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 164 ;36.202 ;23.537 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 623 ;13.920 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;16.043 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 647 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4715 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 925 ; 0.005 ; 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 6B1Y 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_1000230152. 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 : 4.4 - 4.6 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 : 35965 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 37.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.27200 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 (%): 33.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200MM LITHIUM SULFATE, 100MM SODIUM REMARK 280 ACETATE PH 4.4-4.6, AND 28-31% PEG8000. PROTEIN TO INHIBITOR REMARK 280 MOLAR RATIO OF 1 IS TO 10 AND KPC-2 CONCENTRATION WAS 10 MG/ML, REMARK 280 VAPOR 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2 SO4 B 306 O HOH B 401 1.99 REMARK 500 OG SER A 70 OAB CD7 A 301 2.13 REMARK 500 OG SER B 70 OAB CD7 B 301 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 OD2 ASP A 92 NH1 ARG A 161 1545 2.01 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 ARG B 178 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 204 NE - CZ - NH1 ANGL. DEV. = 3.3 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 -139.16 51.49 REMARK 500 SER A 197 30.24 -98.84 REMARK 500 ARG A 220 -124.21 -111.03 REMARK 500 CYS B 69 -138.36 46.57 REMARK 500 GLN B 87 79.79 -162.72 REMARK 500 ARG B 220 -121.66 -113.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE COVALENTLY BOUND INHIBITOR BECOMES DESULFATED DURING THE CO- REMARK 600 CRYSTALLIZATION PROCESS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 CD7 A 301 REMARK 610 CD7 B 301 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD7 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide CD7 B 301 and SER B REMARK 800 70 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6B1X RELATED DB: PDB REMARK 900 6B1X CONTAINS THE SAME PROTEIN COMPLEX WITH WCK 5153 BUT IS REMARK 900 OBTAINED BY SOAKING DBREF 6B1Y A 22 291 UNP Q9F663 BLKPC_KLEPN 22 289 DBREF 6B1Y 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 CD7 A 301 20 HET SO4 A 302 5 HET SO4 A 303 5 HET CL A 304 1 HET CD7 B 301 20 HET SO4 B 302 5 HET SO4 B 303 5 HET SO4 B 304 5 HET SO4 B 305 5 HET SO4 B 306 5 HET CL B 307 1 HETNAM CD7 (2S,5Z)-1-FORMYL-5-IMINO-N'-[(3R)-1-(SULFOOXY) HETNAM 2 CD7 PYRROLIDINE-3-CARBONYL]PIPERIDINE-2-CARBOHYDRAZIDE HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION HETSYN CD7 OPEN FORM - WCK 5153 FORMUL 3 CD7 2(C12 H19 N5 O7 S) FORMUL 4 SO4 7(O4 S 2-) FORMUL 6 CL 2(CL 1-) FORMUL 14 HOH *335(H2 O) HELIX 1 AA1 LEU A 25 GLY A 41 1 17 HELIX 2 AA2 SER A 71 GLN A 86 1 16 HELIX 3 AA3 GLY A 98 LEU A 102 5 5 HELIX 4 AA4 SER A 106 TYR A 112 1 7 HELIX 5 AA5 VAL A 119 TYR A 129 1 11 HELIX 6 AA6 ASP A 131 LEU A 142 1 12 HELIX 7 AA7 GLY A 143 ILE A 155 1 13 HELIX 8 AA8 LEU A 167 SER A 171 5 5 HELIX 9 AA9 SER A 182 LEU A 195 1 14 HELIX 10 AB1 ALA A 200 GLY A 213 1 14 HELIX 11 AB2 ARG A 220 VAL A 225 5 6 HELIX 12 AB3 SER A 275 GLY A 289 1 15 HELIX 13 AB4 THR B 26 GLY B 41 1 16 HELIX 14 AB5 SER B 71 GLN B 87 1 17 HELIX 15 AB6 GLY B 89 ASP B 92 5 4 HELIX 16 AB7 GLY B 98 LEU B 102 5 5 HELIX 17 AB8 SER B 106 TYR B 112 1 7 HELIX 18 AB9 VAL B 119 SER B 130 1 12 HELIX 19 AC1 ASP B 131 LEU B 142 1 12 HELIX 20 AC2 GLY B 144 ILE B 155 1 12 HELIX 21 AC3 LEU B 167 SER B 171 5 5 HELIX 22 AC4 SER B 182 LEU B 195 1 14 HELIX 23 AC5 ALA B 200 GLY B 213 1 14 HELIX 24 AC6 ARG B 220 VAL B 225 5 6 HELIX 25 AC7 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 2.06 SSBOND 2 CYS B 69 CYS B 238 1555 1555 2.07 LINK OG SER A 70 CAE CD7 A 301 1555 1555 1.34 LINK OG SER B 70 CAE CD7 B 301 1555 1555 1.36 CISPEP 1 GLU A 166 LEU A 167 0 6.24 CISPEP 2 GLU B 166 LEU B 167 0 3.73 SITE 1 AC1 17 SER A 70 LYS A 73 TRP A 105 SER A 130 SITE 2 AC1 17 ASN A 132 ILE A 155 ASN A 170 SER A 197 SITE 3 AC1 17 GLY A 236 THR A 237 CYS A 238 SO4 A 302 SITE 4 AC1 17 HOH A 406 HOH A 416 HOH A 474 HOH A 524 SITE 5 AC1 17 HOH A 545 SITE 1 AC2 10 SER A 70 SER A 130 THR A 216 LYS A 234 SITE 2 AC2 10 THR A 235 GLY A 236 THR A 237 CD7 A 301 SITE 3 AC2 10 HOH A 487 HOH A 501 SITE 1 AC3 5 ARG A 96 ARG A 164 ARG A 178 HOH A 516 SITE 2 AC3 5 LYS B 140 SITE 1 AC4 2 ASN A 100 ARG B 178 SITE 1 AC5 6 LYS A 140 ARG B 96 ARG B 178 HOH B 411 SITE 2 AC5 6 HOH B 519 HOH B 528 SITE 1 AC6 4 SER B 275 GLU B 276 ALA B 277 HOH B 465 SITE 1 AC7 8 SER B 70 SER B 130 THR B 216 THR B 235 SITE 2 AC7 8 GLY B 236 THR B 237 CD7 B 301 HOH B 515 SITE 1 AC8 5 LYS B 111 ALA B 200 ALA B 201 TYR B 241 SITE 2 AC8 5 LYS B 270 SITE 1 AC9 5 ARG B 61 LYS B 212 ALA B 230 VAL B 231 SITE 2 AC9 5 HOH B 401 SITE 1 AD1 3 ARG A 178 GLY B 98 ASN B 100 SITE 1 AD2 19 LEU B 68 CYS B 69 SER B 71 PHE B 72 SITE 2 AD2 19 LYS B 73 TRP B 105 SER B 130 ASN B 132 SITE 3 AD2 19 ASN B 170 LYS B 234 THR B 235 GLY B 236 SITE 4 AD2 19 THR B 237 CYS B 238 SO4 B 304 HOH B 406 SITE 5 AD2 19 HOH B 425 HOH B 506 HOH B 531 CRYST1 34.529 37.349 82.070 87.66 89.71 84.31 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 0.028961 -0.002888 -0.000032 0.00000 SCALE2 0.000000 0.026907 -0.001091 0.00000 SCALE3 0.000000 0.000000 0.012195 0.00000