10 20 30 40 50 60 70 80 2OP3 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 26-JAN-07 2OP3
TITLE THE STRUCTURE OF CATHEPSIN S WITH A NOVEL 2- TITLE 2 ARYLPHENOXYACETALDEHYDE INHIBITOR DERIVED BY THE SUBSTRATE TITLE 3 ACTIVITY SCREENING (SAS) METHOD
COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHEPSIN S; COMPND 3 CHAIN: A, B; 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: CATHS; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS
KEYWDS CATHEPSIN S, NONPEPTIDIC, SUBSTRATE ACTIVITY SCREENING, KEYWDS 2 HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR G.SPRAGGON,H.INAGAKI,H.TSURUOKA,M.HORNSBY,S.A.LESLEY, AUTHOR 2 J.A.ELLMAN
REVDAT 3 24-FEB-09 2OP3 1 VERSN REVDAT 2 21-AUG-07 2OP3 1 JRNL REVDAT 1 22-MAY-07 2OP3 0
JRNL AUTH H.INAGAKI,H.TSURUOKA,M.HORNSBY,S.A.LESLEY, JRNL AUTH 2 G.SPRAGGON,J.A.ELLMAN JRNL TITL CHARACTERIZATION AND OPTIMIZATION OF SELECTIVE, JRNL TITL 2 NONPEPTIDIC INHIBITORS OF CATHEPSIN S WITH AN JRNL TITL 3 UNPRECEDENTED BINDING MODE. JRNL REF J.MED.CHEM. V. 50 2693 2007 JRNL REFN ISSN 0022-2623 JRNL PMID 17469812 JRNL DOI 10.1021/JM070111+
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 70645 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) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3738 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5169 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.1780 REMARK 3 BIN FREE R VALUE SET COUNT : 262 REMARK 3 BIN FREE R VALUE : 0.2170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3417 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 475 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : 0.06000 REMARK 3 B33 (A**2) : -0.12000 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): 0.069 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.070 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.040 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.098 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3580 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2430 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4846 ; 1.367 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5895 ; 0.833 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 444 ; 5.536 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 167 ;37.146 ;24.371 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 570 ;10.528 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;13.293 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 484 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4047 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 752 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 756 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2753 ; 0.195 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1839 ; 0.195 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1868 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 356 ; 0.146 ; 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): 13 ; 0.731 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 37 ; 0.202 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 26 ; 0.133 ; 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): 2223 ; 0.983 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 914 ; 0.231 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3462 ; 1.472 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1603 ; 2.464 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1378 ; 3.625 ; 4.500 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 REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 2OP3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-FEB-07. REMARK 100 THE RCSB ID CODE IS RCSB041411.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-AUG-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74679 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 43.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.300 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : 0.08200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 45.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.20 REMARK 200 R MERGE FOR SHELL (I) : 0.72500 REMARK 200 R SYM FOR SHELL (I) : 0.72500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: FFT REMARK 200 STARTING MODEL: PDB ENTRY 2F1G REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NAACETATE, 20% PEG-8000 AND REMARK 280 2.0M LI2SO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z+1/2 REMARK 290 7555 Y,X,-Z+3/4 REMARK 290 8555 -Y,-X,-Z+1/4 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.60000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.80000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 113.40000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 75.60000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 113.40000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 37.80000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 85.38400 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 75.60000 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 85.38400 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 75.60000
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 A -2 REMARK 465 ARG A -1 REMARK 465 ILE A 0 REMARK 465 ASN B -2 REMARK 465 ARG B -1 REMARK 465 ILE B 0
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 OD1 ASP A 173 O HOH A 908 1.94 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 O1 SO4 A 701 O4 SO4 A 701 6565 1.31 REMARK 500 S SO4 A 701 O4 SO4 A 701 6565 1.39 REMARK 500 S SO4 A 701 O1 SO4 A 701 6565 1.45 REMARK 500 O1 SO4 A 701 O3 SO4 A 701 6565 1.78 REMARK 500 O2 SO4 A 701 O4 SO4 A 701 6565 1.78 REMARK 500 S SO4 A 701 O2 SO4 A 701 6565 1.80 REMARK 500 O1 SO4 A 701 O2 SO4 A 701 6565 1.97 REMARK 500 O4 SO4 A 701 O4 SO4 A 701 6565 1.98 REMARK 500 O2 SO4 A 701 O3 SO4 A 701 6565 2.04 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 A 21 41.31 -91.15 REMARK 500 THR A 58 -128.57 -113.23 REMARK 500 THR B 58 -128.39 -115.01 REMARK 500 ARG B 141 46.38 -88.67 REMARK 500 REMARK 500 REMARK: NULL
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 PEU A 601
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 701 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TF5 A 501 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TF5 B 502 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEU A 601
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HXZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CATHEPSIN S IN COMPLEX WITH A REMARK 900 NONPEPTIDIC INHIBITOR (HEXAGONAL SPACEGROUP) REMARK 900 RELATED ID: 2H7J RELATED DB: PDB REMARK 900 CATHEPSIN S IN COMPLEX WITH A NONPEPTIDIC INHIBITOR
DBREF 2OP3 A -2 217 UNP P25774 CATS_HUMAN 112 331 DBREF 2OP3 B -2 217 UNP P25774 CATS_HUMAN 112 331
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 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
HET SO4 A 701 5 HET TF5 A 501 19 HET TF5 B 502 19 HET PEU A 601 20
HETNAM SO4 SULFATE ION HETNAM TF5 2-[(2',3',4'-TRIFLUOROBIPHENYL-2-YL)OXY]ETHANOL HETNAM PEU 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56, HETNAM 2 PEU 59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL
HETSYN PEU PEG 8000
FORMUL 3 SO4 O4 S 2- FORMUL 4 TF5 2(C14 H11 F3 O2) FORMUL 6 PEU C55 H112 O28 FORMUL 7 HOH *475(H2 O)
HELIX 1 1 ARG A 8 GLY A 11 5 4 HELIX 2 2 ALA A 24 GLY A 43 1 20 HELIX 3 3 SER A 49 SER A 57 1 9 HELIX 4 4 THR A 58 GLY A 62 5 5 HELIX 5 5 LYS A 64 GLY A 68 5 5 HELIX 6 6 PHE A 70 LYS A 82 1 13 HELIX 7 7 ASP A 102 LYS A 104 5 3 HELIX 8 8 ARG A 120 LYS A 131 1 12 HELIX 9 9 HIS A 142 LEU A 147 1 6 HELIX 10 10 ASN A 204 ILE A 208 5 5 HELIX 11 11 ARG B 8 GLY B 11 5 4 HELIX 12 12 ALA B 24 GLY B 43 1 20 HELIX 13 13 SER B 49 SER B 57 1 9 HELIX 14 14 THR B 58 GLY B 62 5 5 HELIX 15 15 LYS B 64 GLY B 68 5 5 HELIX 16 16 PHE B 70 LYS B 82 1 13 HELIX 17 17 ASP B 102 LYS B 104 5 3 HELIX 18 18 ARG B 120 LYS B 131 1 12 HELIX 19 19 HIS B 142 LEU B 147 1 6 HELIX 20 20 ASN B 204 ILE B 208 5 5
SHEET 1 A 3 VAL A 5 ASP A 6 0 SHEET 2 A 3 HIS A 164 LEU A 174 -1 O TYR A 171 N VAL A 5 SHEET 3 A 3 VAL A 134 VAL A 138 -1 N VAL A 134 O VAL A 168 SHEET 1 B 4 VAL A 5 ASP A 6 0 SHEET 2 B 4 HIS A 164 LEU A 174 -1 O TYR A 171 N VAL A 5 SHEET 3 B 4 LYS A 177 LYS A 183 -1 O LYS A 183 N LEU A 167 SHEET 4 B 4 TYR A 195 ALA A 199 -1 O MET A 198 N TRP A 180 SHEET 1 C 2 ILE A 84 ASP A 85 0 SHEET 2 C 2 ARG A 106 ALA A 108 -1 O ALA A 107 N ILE A 84 SHEET 1 D 2 LYS A 112 GLU A 115 0 SHEET 2 D 2 SER A 213 GLU A 216 -1 O TYR A 214 N THR A 114 SHEET 1 E 3 VAL B 5 ASP B 6 0 SHEET 2 E 3 HIS B 164 LEU B 174 -1 O TYR B 171 N VAL B 5 SHEET 3 E 3 VAL B 134 VAL B 138 -1 N VAL B 134 O VAL B 168 SHEET 1 F 5 VAL B 5 ASP B 6 0 SHEET 2 F 5 HIS B 164 LEU B 174 -1 O TYR B 171 N VAL B 5 SHEET 3 F 5 LYS B 177 LYS B 183 -1 O LYS B 183 N LEU B 167 SHEET 4 F 5 TYR B 195 ALA B 199 -1 O MET B 198 N TRP B 180 SHEET 5 F 5 VAL B 152 TYR B 153 1 N TYR B 153 O ARG B 197 SHEET 1 G 2 ILE B 84 ASP B 85 0 SHEET 2 G 2 ARG B 106 ALA B 108 -1 O ALA B 107 N ILE B 84 SHEET 1 H 2 LYS B 112 GLU B 115 0 SHEET 2 H 2 SER B 213 GLU B 216 -1 O TYR B 214 N THR B 114
SSBOND 1 CYS A 22 CYS A 66 1555 1555 2.07 SSBOND 2 CYS A 56 CYS A 99 1555 1555 2.11 SSBOND 3 CYS A 158 CYS A 206 1555 1555 2.04 SSBOND 4 CYS B 22 CYS B 66 1555 1555 2.07 SSBOND 5 CYS B 56 CYS B 99 1555 1555 2.15 SSBOND 6 CYS B 158 CYS B 206 1555 1555 2.03
LINK SG CYS A 25 C17 TF5 A 501 1555 1555 1.64 LINK SG CYS B 25 C17 TF5 B 502 1555 1555 1.63
SITE 1 AC1 6 SER A 103 ARG A 106 HOH A 734 HOH A 861 SITE 2 AC1 6 HOH A 892 HOH A 925 SITE 1 AC2 15 GLN A 19 GLY A 23 ALA A 24 CYS A 25 SITE 2 AC2 15 TRP A 26 ASN A 67 GLY A 68 GLY A 69 SITE 3 AC2 15 MET A 71 GLY A 137 ASN A 163 HIS A 164 SITE 4 AC2 15 GLY A 165 PEU A 601 HOH A 912 SITE 1 AC3 14 PEU A 601 GLN B 19 GLY B 23 ALA B 24 SITE 2 AC3 14 CYS B 25 TRP B 26 ASN B 67 GLY B 68 SITE 3 AC3 14 GLY B 69 MET B 71 GLY B 137 ASN B 163 SITE 4 AC3 14 HIS B 164 GLY B 165 SITE 1 AC4 7 PHE A 70 TF5 A 501 HOH A 891 HOH A 940 SITE 2 AC4 7 GLY B 69 PHE B 70 TF5 B 502
CRYST1 85.384 85.384 151.200 90.00 90.00 90.00 P 41 2 2 16
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 0.011712 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011712 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006614 0.00000