HEADER HYDROLASE/HYDROLASE INHIBITOR 02-APR-06 2DJF TITLE CRYSTAL STRUCTURE OF HUMAN DIPEPTIDYL PEPTIDASE I (CATHEPSIN C) IN TITLE 2 COMPLEX WITH THE INHIBITOR GLY-PHE-CHN2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIPEPTIDYL-PEPTIDASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DIPEPTIDYL-PEPTIDASE 1 EXCLUSION DOMAIN CHAIN; COMPND 5 SYNONYM: CATHEPSIN C; COMPND 6 EC: 3.4.14.1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DIPEPTIDYL-PEPTIDASE 1; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: DIPEPTIDYL-PEPTIDASE 1 HEAVY CHAIN; COMPND 12 SYNONYM: CATHEPSIN C; COMPND 13 EC: 3.4.14.1; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: DIPEPTIDYL-PEPTIDASE 1; COMPND 17 CHAIN: C; COMPND 18 FRAGMENT: DIPEPTIDYL-PEPTIDASE 1 LIGHT CHAIN; COMPND 19 SYNONYM: CATHEPSIN C; COMPND 20 EC: 3.4.14.1; COMPND 21 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: CTSC; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 9 EXPRESSION_SYSTEM_CELL: BTI-TN-5B1-4; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: CTSC; SOURCE 16 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 17 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 19 EXPRESSION_SYSTEM_CELL: BTI-TN-5B1-4; SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 21 MOL_ID: 3; SOURCE 22 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 23 ORGANISM_COMMON: HUMAN; SOURCE 24 ORGANISM_TAXID: 9606; SOURCE 25 GENE: CTSC; SOURCE 26 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 27 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 28 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 29 EXPRESSION_SYSTEM_CELL: BTI-TN-5B1-4; SOURCE 30 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS PROTEIN-INHIBITOR COMPLEX, COVALENTLY BOUND INHIBITOR, DPPI-INHIBITOR KEYWDS 2 COMPLEX, CATHEPSIN C INHIBITOR COMPLEX, HYDROLASE-HYDROLASE KEYWDS 3 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.MOLGAARD,J.ARNAU,C.LAURITZEN,S.LARSEN,G.PETERSEN,J.PEDERSEN REVDAT 7 25-OCT-23 2DJF 1 HETSYN REVDAT 6 29-JUL-20 2DJF 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE REVDAT 5 23-MAY-18 2DJF 1 REMARK REVDAT 4 13-JUL-11 2DJF 1 VERSN REVDAT 3 24-FEB-09 2DJF 1 VERSN REVDAT 2 01-JAN-08 2DJF 1 JRNL REVDAT 1 14-NOV-06 2DJF 0 JRNL AUTH A.MOLGAARD,J.ARNAU,C.LAURITZEN,S.LARSEN,G.PETERSEN, JRNL AUTH 2 J.PEDERSEN JRNL TITL THE CRYSTAL STRUCTURE OF HUMAN DIPEPTIDYL PEPTIDASE I JRNL TITL 2 (CATHEPSIN C) IN COMPLEX WITH THE INHIBITOR GLY-PHE-CHN2 JRNL REF BIOCHEM.J. V. 401 645 2007 JRNL REFN ISSN 0264-6021 JRNL PMID 17020538 JRNL DOI 10.1042/BJ20061389 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 28953 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1549 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2072 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1900 REMARK 3 BIN FREE R VALUE SET COUNT : 101 REMARK 3 BIN FREE R VALUE : 0.2480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2748 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 77 REMARK 3 SOLVENT ATOMS : 246 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.01000 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): 0.141 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.133 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.787 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2914 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2449 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3954 ; 1.486 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5690 ; 0.858 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 345 ; 6.932 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 413 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3232 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 629 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 526 ; 0.204 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2776 ; 0.255 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1543 ; 0.083 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 189 ; 0.161 ; 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): 3 ; 0.118 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 39 ; 0.293 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.185 ; 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): 1725 ; 1.056 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2760 ; 1.928 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1189 ; 2.585 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1194 ; 4.183 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2DJF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000025484. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I711 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.094 REMARK 200 MONOCHROMATOR : PT COATED MIRROR PLUS SI(111) REMARK 200 MONOCHROMATOR CRYSTAL REMARK 200 OPTICS : MIRROR AND MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 143822 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 28.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1K3B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23% PEG 4000, 0.22M AMMONIUM ACETATE REMARK 280 AND 0.1M MES, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 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 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 43.50000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.51500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 57.78500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 43.50000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.51500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 57.78500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 43.50000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.51500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 57.78500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 43.50000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.51500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 57.78500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: DODECAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 87.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 87.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 GLY A 119 REMARK 465 GLY B 368 REMARK 465 LEU B 369 REMARK 465 ARG B 370 REMARK 465 ASP C 371 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 N LEU B 207 O HOH B 913 2.03 REMARK 500 OD1 ASP A 53 O HOH A 736 2.11 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 O HOH B 918 O HOH B 918 3655 2.16 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 ASP A 52 CB - CG - OD1 ANGL. DEV. = 5.7 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 ASP A 48 27.25 -154.18 REMARK 500 ASP A 53 42.40 -76.51 REMARK 500 LEU A 54 0.95 -155.88 REMARK 500 TYR A 64 -117.57 51.78 REMARK 500 SER A 88 -53.31 93.35 REMARK 500 ALA B 229 -148.34 63.94 REMARK 500 SER B 230 46.24 -96.41 REMARK 500 ILE B 282 -65.37 -106.60 REMARK 500 PHE B 298 77.83 -155.04 REMARK 500 HIS B 358 59.17 -94.40 REMARK 500 PHE C 373 110.21 -32.10 REMARK 500 ILE C 429 40.01 -148.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 117 VAL A 118 145.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1K3B RELATED DB: PDB REMARK 900 FIRST NATIVE STRUCTURE OF HUMAN DIPEPTIDYL PEPTIDASE I (CATHEPSIN C) REMARK 900 RELATED ID: 2DJG RELATED DB: PDB REMARK 900 RE-REFINED NATIVE STRUCTURE OF HUMAN DIPEPTIDYL PEPTIDASE I REMARK 900 (CATHEPSIN C) REMARK 900 RELATED ID: 1JQP RELATED DB: PDB REMARK 900 NATIVE STRUCTURE OF RAT DIPEPTIDYL PEPTIDASE I (CATHEPSIN C) DBREF 2DJF A 1 119 UNP P53634 CATC_HUMAN 25 143 DBREF 2DJF B 207 370 UNP P53634 CATC_HUMAN 231 394 DBREF 2DJF C 371 439 UNP P53634 CATC_HUMAN 395 463 SEQRES 1 A 119 ASP THR PRO ALA ASN CYS THR TYR LEU ASP LEU LEU GLY SEQRES 2 A 119 THR TRP VAL PHE GLN VAL GLY SER SER GLY SER GLN ARG SEQRES 3 A 119 ASP VAL ASN CYS SER VAL MET GLY PRO GLN GLU LYS LYS SEQRES 4 A 119 VAL VAL VAL TYR LEU GLN LYS LEU ASP THR ALA TYR ASP SEQRES 5 A 119 ASP LEU GLY ASN SER GLY HIS PHE THR ILE ILE TYR ASN SEQRES 6 A 119 GLN GLY PHE GLU ILE VAL LEU ASN ASP TYR LYS TRP PHE SEQRES 7 A 119 ALA PHE PHE LYS TYR LYS GLU GLU GLY SER LYS VAL THR SEQRES 8 A 119 THR TYR CYS ASN GLU THR MET THR GLY TRP VAL HIS ASP SEQRES 9 A 119 VAL LEU GLY ARG ASN TRP ALA CYS PHE THR GLY LYS LYS SEQRES 10 A 119 VAL GLY SEQRES 1 B 164 LEU PRO THR SER TRP ASP TRP ARG ASN VAL HIS GLY ILE SEQRES 2 B 164 ASN PHE VAL SER PRO VAL ARG ASN GLN ALA SER CYS GLY SEQRES 3 B 164 SER CYS TYR SER PHE ALA SER MET GLY MET LEU GLU ALA SEQRES 4 B 164 ARG ILE ARG ILE LEU THR ASN ASN SER GLN THR PRO ILE SEQRES 5 B 164 LEU SER PRO GLN GLU VAL VAL SER CYS SER GLN TYR ALA SEQRES 6 B 164 GLN GLY CYS GLU GLY GLY PHE PRO TYR LEU ILE ALA GLY SEQRES 7 B 164 LYS TYR ALA GLN ASP PHE GLY LEU VAL GLU GLU ALA CYS SEQRES 8 B 164 PHE PRO TYR THR GLY THR ASP SER PRO CYS LYS MET LYS SEQRES 9 B 164 GLU ASP CYS PHE ARG TYR TYR SER SER GLU TYR HIS TYR SEQRES 10 B 164 VAL GLY GLY PHE TYR GLY GLY CYS ASN GLU ALA LEU MET SEQRES 11 B 164 LYS LEU GLU LEU VAL HIS HIS GLY PRO MET ALA VAL ALA SEQRES 12 B 164 PHE GLU VAL TYR ASP ASP PHE LEU HIS TYR LYS LYS GLY SEQRES 13 B 164 ILE TYR HIS HIS THR GLY LEU ARG SEQRES 1 C 69 ASP PRO PHE ASN PRO PHE GLU LEU THR ASN HIS ALA VAL SEQRES 2 C 69 LEU LEU VAL GLY TYR GLY THR ASP SER ALA SER GLY MET SEQRES 3 C 69 ASP TYR TRP ILE VAL LYS ASN SER TRP GLY THR GLY TRP SEQRES 4 C 69 GLY GLU ASN GLY TYR PHE ARG ILE ARG ARG GLY THR ASP SEQRES 5 C 69 GLU CYS ALA ILE GLU SER ILE ALA VAL ALA ALA THR PRO SEQRES 6 C 69 ILE PRO LYS LEU MODRES 2DJF ASN A 5 ASN GLYCOSYLATION SITE MODRES 2DJF ASN A 29 ASN GLYCOSYLATION SITE MODRES 2DJF ASN A 95 ASN GLYCOSYLATION SITE MODRES 2DJF ASN B 252 ASN GLYCOSYLATION SITE HET NAG A 601 14 HET NAG A 602 14 HET NAG A 603 14 HET ACY A 700 4 HET NAG B 604 14 HET CL B 500 1 HET 1ZB B 801 16 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM ACY ACETIC ACID HETNAM CL CHLORIDE ION HETNAM 1ZB N-[(1S)-1-BENZYL-3-DIAZEN-1-IUMYLIDENE-2- HETNAM 2 1ZB OXOPROPYL]GLYCINAMIDE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 4 NAG 4(C8 H15 N O6) FORMUL 7 ACY C2 H4 O2 FORMUL 9 CL CL 1- FORMUL 10 1ZB C12 H14 N4 O2 FORMUL 11 HOH *246(H2 O) HELIX 1 1 THR A 7 LEU A 12 1 6 HELIX 2 2 ASN A 29 MET A 33 5 5 HELIX 3 3 SER B 233 THR B 251 1 19 HELIX 4 4 SER B 260 SER B 268 1 9 HELIX 5 5 GLN B 272 GLY B 276 5 5 HELIX 6 6 PHE B 278 ALA B 283 1 6 HELIX 7 7 GLY B 284 PHE B 290 1 7 HELIX 8 8 GLU B 294 PHE B 298 5 5 HELIX 9 9 ASN B 332 GLY B 344 1 13 HELIX 10 10 TYR B 353 HIS B 358 1 6 HELIX 11 11 ASP C 422 ILE C 426 5 5 SHEET 1 A12 TYR A 75 GLU A 86 0 SHEET 2 A12 LYS A 89 THR A 97 -1 O THR A 91 N LYS A 84 SHEET 3 A12 TRP A 110 LYS A 117 -1 O LYS A 117 N ASN A 95 SHEET 4 A12 TYR A 75 GLU A 86 0 SHEET 5 A12 GLY A 67 LEU A 72 -1 N ILE A 70 O TRP A 77 SHEET 6 A12 SER A 57 ILE A 63 -1 N HIS A 59 O VAL A 71 SHEET 7 A12 THR A 49 ASP A 52 -1 N ALA A 50 O GLY A 58 SHEET 8 A12 GLN A 36 GLN A 45 -1 N TYR A 43 O TYR A 51 SHEET 9 A12 GLY A 13 SER A 24 -1 N TRP A 15 O VAL A 42 SHEET 10 A12 TRP A 110 LYS A 117 -1 O CYS A 112 N GLY A 20 SHEET 11 A12 GLY A 100 ASP A 104 -1 N GLY A 100 O PHE A 113 SHEET 12 A12 TRP A 110 LYS A 117 -1 O PHE A 113 N GLY A 100 SHEET 1 B 3 TRP B 211 ASP B 212 0 SHEET 2 B 3 HIS C 381 THR C 390 -1 O TYR C 388 N TRP B 211 SHEET 3 B 3 MET B 346 PHE B 350 -1 N MET B 346 O LEU C 385 SHEET 1 C 5 TRP B 211 ASP B 212 0 SHEET 2 C 5 HIS C 381 THR C 390 -1 O TYR C 388 N TRP B 211 SHEET 3 C 5 ASP C 397 LYS C 402 -1 O LYS C 402 N LEU C 384 SHEET 4 C 5 TYR C 414 ARG C 418 -1 O PHE C 415 N VAL C 401 SHEET 5 C 5 ILE B 363 TYR B 364 1 N TYR B 364 O ARG C 416 SHEET 1 D 2 SER B 318 TYR B 323 0 SHEET 2 D 2 VAL C 431 PRO C 435 -1 O ALA C 432 N HIS B 322 SSBOND 1 CYS A 6 CYS A 94 1555 1555 2.07 SSBOND 2 CYS A 30 CYS A 112 1555 1555 2.02 SSBOND 3 CYS B 231 CYS B 274 1555 1555 2.09 SSBOND 4 CYS B 267 CYS B 307 1555 1555 2.04 SSBOND 5 CYS B 297 CYS B 313 1555 1555 2.04 LINK ND2 ASN A 5 C1 NAG A 601 1555 1555 1.45 LINK ND2 ASN A 29 C1 NAG A 603 1555 1555 1.46 LINK ND2 ASN A 95 C1 NAG A 602 1555 1555 1.46 LINK SG CYS B 234 C2 1ZB B 801 1555 1555 1.86 LINK ND2 ASN B 252 C1 NAG B 604 1555 1555 1.47 CISPEP 1 LYS A 46 LEU A 47 0 1.19 CRYST1 87.000 89.030 115.570 90.00 90.00 90.00 I 2 2 2 8 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 0.011494 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011232 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008653 0.00000