HEADER HYDROLASE 27-JUN-06 2HH5
TITLE CRYSTAL STRUCTURE OF CATHEPSIN S IN COMPLEX WITH A ZINC MEDIATED NON-
TITLE 2 COVALENT ARYLAMINOETHYL AMIDE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CATHEPSIN S;
COMPND 3 CHAIN: B, A;
COMPND 4 EC: 3.4.22.27;
COMPND 5 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: CTSS;
SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA;
SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108
KEYWDS CATHEPSIN S, NONCOVALENT, INHIBITION, ZINC, ARYLAMINOETHYL-AMIDES,
KEYWDS 2 HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR G.SPRAGGON,M.HORNSBY,S.A.LESLEY,D.C.TULLY,J.L.HARRIS,D.S.KARENEWSKY
REVDAT 5 20-NOV-24 2HH5 1 REMARK
REVDAT 4 30-AUG-23 2HH5 1 REMARK LINK
REVDAT 3 24-FEB-09 2HH5 1 VERSN
REVDAT 2 05-SEP-06 2HH5 1 JRNL
REVDAT 1 15-AUG-06 2HH5 0
JRNL AUTH D.C.TULLY,H.LIU,A.K.CHATTERJEE,P.B.ALPER,R.EPPLE,
JRNL AUTH 2 J.A.WILLIAMS,M.J.ROBERTS,D.H.WOODMANSEE,B.T.MASICK,
JRNL AUTH 3 C.TUMANUT,J.LI,G.SPRAGGON,M.HORNSBY,J.CHANG,T.TUNTLAND,
JRNL AUTH 4 T.HOLLENBECK,P.GORDON,J.L.HARRIS,D.S.KARANEWSKY
JRNL TITL SYNTHESIS AND SAR OF ARYLAMINOETHYL AMIDES AS NONCOVALENT
JRNL TITL 2 INHIBITORS OF CATHEPSIN S: P3 CYCLIC ETHERS.
JRNL REF BIOORG.MED.CHEM.LETT. V. 16 5112 2006
JRNL REFN ISSN 0960-894X
JRNL PMID 16876402
JRNL DOI 10.1016/J.BMCL.2006.07.033
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH D.C.TULLY,H.LIU,P.B.ALPER,A.K.CHATTERJEE,R.EPPLE,
REMARK 1 AUTH 2 M.J.ROBERTS,J.A.WILLIAMS,K.T.NGUYEN,D.H.WOODMANSEE,
REMARK 1 AUTH 3 C.TUMANUT,J.LI,G.SPRAGGON,J.CHANG,T.TUNTLAND,J.L.HARRIS,
REMARK 1 AUTH 4 D.S.KARANEWSKY
REMARK 1 TITL SYNTHESIS AND EVALUATION OF ARYLAMINOETHYL AMIDES AS
REMARK 1 TITL 2 NONCOVALENT INHIBITORS OF CATHEPSIN S. PART 3: HETEROCYCLIC
REMARK 1 TITL 3 P3.
REMARK 1 REF BIOORG.MED.CHEM.LETT. V. 16 1975 2006
REMARK 1 REFN ISSN 0960-894X
REMARK 1 PMID 16446091
REMARK 1 DOI 10.1016/J.BMCL.2005.12.095
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0005
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) : 34.20
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 3 NUMBER OF REFLECTIONS : 38549
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) : 0.176
REMARK 3 R VALUE (WORKING SET) : 0.173
REMARK 3 FREE R VALUE : 0.220
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 2048
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) : 2803
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.24
REMARK 3 BIN R VALUE (WORKING SET) : 0.2870
REMARK 3 BIN FREE R VALUE SET COUNT : 156
REMARK 3 BIN FREE R VALUE : 0.3360
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3372
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 86
REMARK 3 SOLVENT ATOMS : 289
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.91
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.72000
REMARK 3 B22 (A**2) : -0.72000
REMARK 3 B33 (A**2) : 1.08000
REMARK 3 B12 (A**2) : -0.36000
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): 0.127
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.126
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.101
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.355
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3554 ; 0.014 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): 2996 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4818 ; 1.511 ; 1.972
REMARK 3 BOND ANGLES OTHERS (DEGREES): 7016 ; 0.765 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 432 ; 6.018 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 160 ;38.744 ;24.375
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 558 ;12.197 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;12.584 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 486 ; 0.134 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4006 ; 0.006 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 752 ; 0.001 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 861 ; 0.201 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3424 ; 0.180 ; 0.200
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1820 ; 0.191 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): 1967 ; 0.087 ; 0.200
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 267 ; 0.149 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 9 ; 0.114 ; 0.200
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 16 ; 0.283 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): 39 ; 0.234 ; 0.200
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.166 ; 0.200
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 1 ; 0.109 ; 0.200
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): 2738 ; 1.425 ; 2.000
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 904 ; 0.300 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3432 ; 1.713 ; 3.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1729 ; 3.349 ; 5.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1386 ; 4.303 ; 8.000
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 : BABINET MODEL WITH MASK
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
REMARK 4
REMARK 4 2HH5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-06.
REMARK 100 THE DEPOSITION ID IS D_1000038342.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 28-SEP-03
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 : ALS
REMARK 200 BEAMLINE : 5.0.3
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 : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PROCESS
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38549
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 34.200
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 200 DATA REDUNDANCY : 2.700
REMARK 200 R MERGE (I) : 0.06400
REMARK 200 R SYM (I) : 0.06400
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.7000
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) : 1.86
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2
REMARK 200 DATA REDUNDANCY IN SHELL : 2.50
REMARK 200 R MERGE FOR SHELL (I) : 0.76300
REMARK 200 R SYM FOR SHELL (I) : 0.76300
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300
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: 2F1G
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 47.24
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M ZNACETATE, 20% PEG-3350, 150MM
REMARK 280 SODIUM CHLORIDE, PH 7.0, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z
REMARK 290 3555 -X+Y,-X,Z
REMARK 290 4555 X+2/3,Y+1/3,Z+1/3
REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3
REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3
REMARK 290 7555 X+1/3,Y+2/3,Z+2/3
REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3
REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 54.77100
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.62205
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 32.84300
REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 54.77100
REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 31.62205
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 32.84300
REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 54.77100
REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 31.62205
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.84300
REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 63.24410
REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 65.68600
REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 63.24410
REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 65.68600
REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 63.24410
REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 65.68600
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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER - THERE ARE TWO
REMARK 300 MONOMERS IN THE ASYMMETRIC UNIT.
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 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 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
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 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 B 934 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 941 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 942 LIES ON A SPECIAL POSITION.
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 ASN B -2
REMARK 465 ARG B -1
REMARK 465 ILE B 0
REMARK 465 ASN A -2
REMARK 465 ARG A -1
REMARK 465 ILE A 0
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 A 149 NE - CZ - NH2 ANGL. DEV. = -3.1 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 SER B 21 42.57 -89.27
REMARK 500 THR B 58 -128.70 -115.42
REMARK 500 THR A 58 -130.61 -117.16
REMARK 500 ASN A 163 2.66 -151.24
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 B 603 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU B 15 OE2
REMARK 620 2 HIS B 188 ND1 104.8
REMARK 620 3 GLU B 193 OE2 114.1 116.0
REMARK 620 4 ASP A 173 OD2 107.2 118.9 95.9
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B 601 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS B 25 SG
REMARK 620 2 HIS B 164 ND1 104.6
REMARK 620 3 GNQ B 501 N1 120.1 112.2
REMARK 620 4 CL B 801 CL 110.2 103.7 104.9
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B 602 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP B 139 OD1
REMARK 620 2 ASP B 139 OD2 56.1
REMARK 620 3 HIS B 142 NE2 95.4 111.7
REMARK 620 4 HOH B 882 O 156.0 101.6 102.0
REMARK 620 5 HOH B 933 O 85.6 113.9 124.9 97.6
REMARK 620 N 1 2 3 4
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 703 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 3 OD1
REMARK 620 2 HOH A 864 O 90.7
REMARK 620 3 HOH A 926 O 100.4 90.2
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 701 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 25 SG
REMARK 620 2 HIS A 164 ND1 107.6
REMARK 620 3 GNQ A 401 N1 120.2 112.5
REMARK 620 4 CL A 802 CL 110.6 104.1 100.5
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 702 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 139 OD2
REMARK 620 2 ASP A 139 OD1 56.3
REMARK 620 3 HIS A 142 NE2 115.6 102.9
REMARK 620 4 HOH A 803 O 116.0 81.5 119.5
REMARK 620 5 HOH A 940 O 105.6 158.7 95.2 99.5
REMARK 620 N 1 2 3 4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 601
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 602
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 603
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 701
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 702
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 703
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 801
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 802
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNQ A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNQ B 501
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2F1G RELATED DB: PDB
REMARK 900 RELATED ID: 2HHN RELATED DB: PDB
REMARK 900 CATHEPSIN S IN COMPLEX WITH NON COVALENT ARYLAMINOETHYL AMIDE.
DBREF 2HH5 A -2 217 UNP P25774 CATS_HUMAN 112 331
DBREF 2HH5 B -2 217 UNP P25774 CATS_HUMAN 112 331
SEQRES 1 B 220 ASN ARG ILE LEU PRO ASP SER VAL ASP TRP ARG GLU LYS
SEQRES 2 B 220 GLY CYS VAL THR GLU VAL LYS TYR GLN GLY SER CYS GLY
SEQRES 3 B 220 ALA CYS TRP ALA PHE SER ALA VAL GLY ALA LEU GLU ALA
SEQRES 4 B 220 GLN LEU LYS LEU LYS THR GLY LYS LEU VAL SER LEU SER
SEQRES 5 B 220 ALA GLN ASN LEU VAL ASP CYS SER THR GLU LYS TYR GLY
SEQRES 6 B 220 ASN LYS GLY CYS ASN GLY GLY PHE MET THR THR ALA PHE
SEQRES 7 B 220 GLN TYR ILE ILE ASP ASN LYS GLY ILE ASP SER ASP ALA
SEQRES 8 B 220 SER TYR PRO TYR LYS ALA MET ASP GLN LYS CYS GLN TYR
SEQRES 9 B 220 ASP SER LYS TYR ARG ALA ALA THR CYS SER LYS TYR THR
SEQRES 10 B 220 GLU LEU PRO TYR GLY ARG GLU ASP VAL LEU LYS GLU ALA
SEQRES 11 B 220 VAL ALA ASN LYS GLY PRO VAL SER VAL GLY VAL ASP ALA
SEQRES 12 B 220 ARG HIS PRO SER PHE PHE LEU TYR ARG SER GLY VAL TYR
SEQRES 13 B 220 TYR GLU PRO SER CYS THR GLN ASN VAL ASN HIS GLY VAL
SEQRES 14 B 220 LEU VAL VAL GLY TYR GLY ASP LEU ASN GLY LYS GLU TYR
SEQRES 15 B 220 TRP LEU VAL LYS ASN SER TRP GLY HIS ASN PHE GLY GLU
SEQRES 16 B 220 GLU GLY TYR ILE ARG MET ALA ARG ASN LYS GLY ASN HIS
SEQRES 17 B 220 CYS GLY ILE ALA SER PHE PRO SER TYR PRO GLU ILE
SEQRES 1 A 220 ASN ARG ILE LEU PRO ASP SER VAL ASP TRP ARG GLU LYS
SEQRES 2 A 220 GLY CYS VAL THR GLU VAL LYS TYR GLN GLY SER CYS GLY
SEQRES 3 A 220 ALA CYS TRP ALA PHE SER ALA VAL GLY ALA LEU GLU ALA
SEQRES 4 A 220 GLN LEU LYS LEU LYS THR GLY LYS LEU VAL SER LEU SER
SEQRES 5 A 220 ALA GLN ASN LEU VAL ASP CYS SER THR GLU LYS TYR GLY
SEQRES 6 A 220 ASN LYS GLY CYS ASN GLY GLY PHE MET THR THR ALA PHE
SEQRES 7 A 220 GLN TYR ILE ILE ASP ASN LYS GLY ILE ASP SER ASP ALA
SEQRES 8 A 220 SER TYR PRO TYR LYS ALA MET ASP GLN LYS CYS GLN TYR
SEQRES 9 A 220 ASP SER LYS TYR ARG ALA ALA THR CYS SER LYS TYR THR
SEQRES 10 A 220 GLU LEU PRO TYR GLY ARG GLU ASP VAL LEU LYS GLU ALA
SEQRES 11 A 220 VAL ALA ASN LYS GLY PRO VAL SER VAL GLY VAL ASP ALA
SEQRES 12 A 220 ARG HIS PRO SER PHE PHE LEU TYR ARG SER GLY VAL TYR
SEQRES 13 A 220 TYR GLU PRO SER CYS THR GLN ASN VAL ASN HIS GLY VAL
SEQRES 14 A 220 LEU VAL VAL GLY TYR GLY ASP LEU ASN GLY LYS GLU TYR
SEQRES 15 A 220 TRP LEU VAL LYS ASN SER TRP GLY HIS ASN PHE GLY GLU
SEQRES 16 A 220 GLU GLY TYR ILE ARG MET ALA ARG ASN LYS GLY ASN HIS
SEQRES 17 A 220 CYS GLY ILE ALA SER PHE PRO SER TYR PRO GLU ILE
HET ZN B 601 1
HET ZN B 602 1
HET ZN B 603 1
HET CL B 801 1
HET GNQ B 501 44
HET ZN A 701 1
HET ZN A 702 1
HET ZN A 703 1
HET CL A 802 1
HET GNQ A 401 44
HETNAM ZN ZINC ION
HETNAM CL CHLORIDE ION
HETNAM GNQ N-[(1R)-1-[(BENZYLSULFONYL)METHYL]-2-{[(1S)-1-METHYL-2-
HETNAM 2 GNQ {[4-(TRIFLUOROMETHOXY)PHENYL]AMINO}ETHYL]AMINO}-2-
HETNAM 3 GNQ OXOETHYL]MORPHOLINE-4-CARBOXAMIDE
FORMUL 3 ZN 6(ZN 2+)
FORMUL 6 CL 2(CL 1-)
FORMUL 7 GNQ 2(C25 H31 F3 N4 O6 S)
FORMUL 13 HOH *289(H2 O)
HELIX 1 1 ARG B 8 GLY B 11 5 4
HELIX 2 2 ALA B 24 GLY B 43 1 20
HELIX 3 3 SER B 49 SER B 57 1 9
HELIX 4 4 THR B 58 GLY B 62 5 5
HELIX 5 5 LYS B 64 GLY B 68 5 5
HELIX 6 6 PHE B 70 LYS B 82 1 13
HELIX 7 7 ASP B 102 LYS B 104 5 3
HELIX 8 8 ARG B 120 LYS B 131 1 12
HELIX 9 9 HIS B 142 LEU B 147 1 6
HELIX 10 10 ASN B 204 ILE B 208 5 5
HELIX 11 11 ARG A 8 GLY A 11 5 4
HELIX 12 12 ALA A 24 GLY A 43 1 20
HELIX 13 13 SER A 49 SER A 57 1 9
HELIX 14 14 THR A 58 GLY A 62 5 5
HELIX 15 15 LYS A 64 GLY A 68 5 5
HELIX 16 16 PHE A 70 ASN A 81 1 12
HELIX 17 17 ASP A 102 LYS A 104 5 3
HELIX 18 18 ARG A 120 LYS A 131 1 12
HELIX 19 19 HIS A 142 LEU A 147 1 6
HELIX 20 20 ASN A 204 ILE A 208 5 5
SHEET 1 A 3 VAL B 5 ASP B 6 0
SHEET 2 A 3 HIS B 164 LEU B 174 -1 O TYR B 171 N VAL B 5
SHEET 3 A 3 VAL B 134 VAL B 138 -1 N VAL B 134 O VAL B 168
SHEET 1 B 5 VAL B 5 ASP B 6 0
SHEET 2 B 5 HIS B 164 LEU B 174 -1 O TYR B 171 N VAL B 5
SHEET 3 B 5 LYS B 177 LYS B 183 -1 O LYS B 183 N LEU B 167
SHEET 4 B 5 TYR B 195 ALA B 199 -1 O MET B 198 N TRP B 180
SHEET 5 B 5 VAL B 152 TYR B 153 1 N TYR B 153 O ARG B 197
SHEET 1 C 2 ILE B 84 ASP B 85 0
SHEET 2 C 2 ARG B 106 ALA B 108 -1 O ALA B 107 N ILE B 84
SHEET 1 D 2 LYS B 112 GLU B 115 0
SHEET 2 D 2 SER B 213 GLU B 216 -1 O TYR B 214 N THR B 114
SHEET 1 E 3 VAL A 5 ASP A 6 0
SHEET 2 E 3 HIS A 164 LEU A 174 -1 O TYR A 171 N VAL A 5
SHEET 3 E 3 VAL A 134 VAL A 138 -1 N VAL A 136 O VAL A 166
SHEET 1 F 5 VAL A 5 ASP A 6 0
SHEET 2 F 5 HIS A 164 LEU A 174 -1 O TYR A 171 N VAL A 5
SHEET 3 F 5 LYS A 177 LYS A 183 -1 O LYS A 183 N LEU A 167
SHEET 4 F 5 TYR A 195 ALA A 199 -1 O MET A 198 N TRP A 180
SHEET 5 F 5 VAL A 152 TYR A 153 1 N TYR A 153 O ARG A 197
SHEET 1 G 2 ILE A 84 ASP A 85 0
SHEET 2 G 2 ARG A 106 ALA A 108 -1 O ALA A 107 N ILE A 84
SHEET 1 H 2 LYS A 112 GLU A 115 0
SHEET 2 H 2 SER A 213 GLU A 216 -1 O TYR A 214 N THR A 114
SSBOND 1 CYS B 22 CYS B 66 1555 1555 2.06
SSBOND 2 CYS B 56 CYS B 99 1555 1555 2.08
SSBOND 3 CYS B 158 CYS B 206 1555 1555 2.05
SSBOND 4 CYS A 22 CYS A 66 1555 1555 2.07
SSBOND 5 CYS A 56 CYS A 99 1555 1555 2.10
SSBOND 6 CYS A 158 CYS A 206 1555 1555 2.06
LINK F1 BGNQ B 501 F3 BGNQ A 401 1555 1555 1.73
LINK OE2 GLU B 15 ZN ZN B 603 1555 1555 2.01
LINK SG CYS B 25 ZN ZN B 601 1555 1555 2.26
LINK OD1 ASP B 139 ZN ZN B 602 1555 1555 2.62
LINK OD2 ASP B 139 ZN ZN B 602 1555 1555 1.95
LINK NE2 HIS B 142 ZN ZN B 602 1555 1555 1.89
LINK ND1 HIS B 164 ZN ZN B 601 1555 1555 2.01
LINK ND1 HIS B 188 ZN ZN B 603 1555 1555 2.13
LINK OE2 GLU B 193 ZN ZN B 603 1555 1555 1.96
LINK N1 GNQ B 501 ZN ZN B 601 1555 1555 2.14
LINK ZN ZN B 601 CL CL B 801 1555 1555 2.21
LINK ZN ZN B 602 O HOH B 882 1555 1555 2.09
LINK ZN ZN B 602 O HOH B 933 1555 1555 2.18
LINK ZN ZN B 603 OD2 ASP A 173 1555 6555 2.18
LINK OD1 ASP A 3 ZN ZN A 703 1555 1555 1.91
LINK SG CYS A 25 ZN ZN A 701 1555 1555 2.20
LINK OD2 ASP A 139 ZN ZN A 702 1555 1555 1.90
LINK OD1 ASP A 139 ZN ZN A 702 1555 1555 2.59
LINK NE2 HIS A 142 ZN ZN A 702 1555 1555 2.08
LINK ND1 HIS A 164 ZN ZN A 701 1555 1555 2.00
LINK N1 GNQ A 401 ZN ZN A 701 1555 1555 2.11
LINK ZN ZN A 701 CL CL A 802 1555 1555 2.28
LINK ZN ZN A 702 O HOH A 803 1555 1555 2.30
LINK ZN ZN A 702 O HOH A 940 1555 1555 2.15
LINK ZN ZN A 703 O HOH A 864 1555 1555 2.38
LINK ZN ZN A 703 O HOH A 926 1555 1555 2.36
SITE 1 AC1 4 CYS B 25 HIS B 164 GNQ B 501 CL B 801
SITE 1 AC2 4 ASP B 139 HIS B 142 HOH B 882 HOH B 933
SITE 1 AC3 4 ASP A 173 GLU B 15 HIS B 188 GLU B 193
SITE 1 AC4 4 CYS A 25 HIS A 164 GNQ A 401 CL A 802
SITE 1 AC5 4 ASP A 139 HIS A 142 HOH A 803 HOH A 940
SITE 1 AC6 3 ASP A 3 HOH A 864 HOH A 926
SITE 1 AC7 6 GLN B 19 CYS B 25 HIS B 164 TRP B 186
SITE 2 AC7 6 GNQ B 501 ZN B 601
SITE 1 AC8 6 GLN A 19 CYS A 25 HIS A 164 TRP A 186
SITE 2 AC8 6 GNQ A 401 ZN A 701
SITE 1 AC9 24 CYS A 25 TRP A 26 GLY A 62 LYS A 64
SITE 2 AC9 24 GLY A 68 GLY A 69 PHE A 70 ALA A 140
SITE 3 AC9 24 ARG A 141 HIS A 142 TYR A 154 VAL A 162
SITE 4 AC9 24 ASN A 163 HIS A 164 GLY A 165 TRP A 186
SITE 5 AC9 24 PHE A 211 ZN A 701 CL A 802 HOH A 892
SITE 6 AC9 24 HIS B 142 PRO B 143 PHE B 146 GNQ B 501
SITE 1 BC1 24 HIS A 142 PRO A 143 PHE A 146 GNQ A 401
SITE 2 BC1 24 CYS B 25 TRP B 26 GLY B 62 LYS B 64
SITE 3 BC1 24 ASN B 67 GLY B 68 GLY B 69 PHE B 70
SITE 4 BC1 24 ALA B 140 ARG B 141 HIS B 142 TYR B 154
SITE 5 BC1 24 VAL B 162 ASN B 163 HIS B 164 GLY B 165
SITE 6 BC1 24 TRP B 186 PHE B 211 ZN B 601 CL B 801
CRYST1 109.542 109.542 98.529 90.00 90.00 120.00 H 3 18
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 0.009129 0.005271 0.000000 0.00000
SCALE2 0.000000 0.010541 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010149 0.00000