HEADER HYDROLASE/HYDROLASE INHIBITOR 21-AUG-02 1MHW TITLE DESIGN OF NON-COVALENT INHIBITORS OF HUMAN CATHEPSIN L. FROM THE 96- TITLE 2 RESIDUE PROREGION TO OPTIMIZED TRIPEPTIDES COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHEPSIN L; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: HEAVY CHAIN (RESIDUES 114-288); COMPND 5 SYNONYM: MAJOR EXCRETED PROTEIN, MEP; COMPND 6 EC: 3.4.22.15; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: CATHEPSIN L; COMPND 10 CHAIN: C, D; COMPND 11 FRAGMENT: LIGHT CHAIN (RESIDUES 292-333); COMPND 12 SYNONYM: MAJOR EXCRETED PROTEIN, MEP; COMPND 13 EC: 3.4.22.15; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: 4-BIPHENYLACETYL-CYS-(D)ARG-TYR-N-(2-PHENYLETHYL) AMIDE; COMPND 17 CHAIN: E, F, G, H; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS CATHEPSIN L, CYSTEINE PROTEASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.CHOWDHURY,J.SIVARAMAN,J.WANG,G.DEVANATHAN,P.LACHANCE,H.QI,R.MENARD, AUTHOR 2 J.LEFEBVRE,Y.KONISHI,M.CYGLER,T.SULEA,E.O.PURISIMA REVDAT 6 11-OCT-17 1MHW 1 REMARK REVDAT 5 19-NOV-14 1MHW 1 HET HETATM HETNAM REVDAT 4 13-JUL-11 1MHW 1 VERSN REVDAT 3 24-FEB-09 1MHW 1 VERSN REVDAT 2 11-FEB-03 1MHW 1 JRNL REVDAT 1 11-DEC-02 1MHW 0 JRNL AUTH S.CHOWDHURY,J.SIVARAMAN,J.WANG,G.DEVANATHAN,P.LACHANCE,H.QI, JRNL AUTH 2 R.MENARD,J.LEFEBVRE,Y.KONISHI,M.CYGLER,T.SULEA,E.O.PURISIMA JRNL TITL DESIGN OF NON-COVALENT INHIBITORS OF HUMAN CATHEPSIN L. FROM JRNL TITL 2 THE 96-RESIDUE PROREGION TO OPTIMIZED TRIPEPTIDES JRNL REF J.MED.CHEM. V. 45 5321 2002 JRNL REFN ISSN 0022-2623 JRNL PMID 12431059 JRNL DOI 10.1021/JM020238T REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 34139 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2391 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3482 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 525 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.266 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : BPA_INH.PAR REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MHW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016922. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IIC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 134326 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04900 REMARK 200 FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.0 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1CJL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8K, NA CITRATE, LISO4, REMARK 280 ISOPROPONAL, PH 4.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 25.76100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.72250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.31600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 75.72250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.76100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.31600 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, F, G 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D, E, H 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE 4-BIPHENYLACETYL-CYS-(D)ARG-TYR-N-(2-PHENYLETHYL) AMIDE IS REMARK 400 PEPTIDE-LIKE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: 4-BIPHENYLACETYL-CYS-(D)ARG-TYR-N-(2-PHENYLETHYL) AMIDE REMARK 400 CHAIN: E, F, G, H REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 THR A 175 REMARK 465 ASN C 179 REMARK 465 THR B 175 REMARK 465 ASN D 179 REMARK 465 TYR E 44 REMARK 465 PEA E 45 REMARK 465 TYR F 44 REMARK 465 PEA F 45 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 THR A 110 OG1 CG2 REMARK 470 LYS A 120 CG CD CE NZ REMARK 470 THR B 110 OG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DAR E 43P CD DAR E 43P NE 0.219 REMARK 500 DAR E 43P CZ DAR E 43P NH2 0.128 REMARK 500 DAR E 43P C DAR E 43P O 0.242 REMARK 500 DAR F 43P CD DAR F 43P NE 0.233 REMARK 500 DAR F 43P CZ DAR F 43P NH1 0.140 REMARK 500 DAR F 43P C DAR F 43P O 0.252 REMARK 500 DAR G 43P NE DAR G 43P CZ 0.085 REMARK 500 TYR G 44P CG TYR G 44P CD2 0.097 REMARK 500 TYR G 44P C PEA G 45P N 0.150 REMARK 500 DAR H 43P CD DAR H 43P NE -0.118 REMARK 500 TYR H 44P CG TYR H 44P CD2 0.094 REMARK 500 TYR H 44P C PEA H 45P N 0.147 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 PRO B 90 C - N - CA ANGL. DEV. = 9.8 DEGREES REMARK 500 CYS E 42P N - CA - CB ANGL. DEV. = 14.2 DEGREES REMARK 500 CYS E 42P O - C - N ANGL. DEV. = -11.5 DEGREES REMARK 500 DAR E 43P CB - CA - C ANGL. DEV. = 16.4 DEGREES REMARK 500 DAR E 43P CD - NE - CZ ANGL. DEV. = -11.9 DEGREES REMARK 500 DAR E 43P NH1 - CZ - NH2 ANGL. DEV. = -10.8 DEGREES REMARK 500 DAR E 43P NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 DAR E 43P NE - CZ - NH2 ANGL. DEV. = 5.0 DEGREES REMARK 500 CYS F 42P N - CA - CB ANGL. DEV. = 12.7 DEGREES REMARK 500 CYS F 42P N - CA - C ANGL. DEV. = 16.2 DEGREES REMARK 500 CYS F 42P O - C - N ANGL. DEV. = -10.6 DEGREES REMARK 500 DAR F 43P C - N - CA ANGL. DEV. = 15.3 DEGREES REMARK 500 DAR F 43P CB - CA - C ANGL. DEV. = 15.6 DEGREES REMARK 500 DAR F 43P CD - NE - CZ ANGL. DEV. = -9.8 DEGREES REMARK 500 DAR F 43P NH1 - CZ - NH2 ANGL. DEV. = -11.3 DEGREES REMARK 500 DAR F 43P NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 DAR F 43P NE - CZ - NH2 ANGL. DEV. = 6.5 DEGREES REMARK 500 DAR G 43P NE - CZ - NH2 ANGL. DEV. = 4.1 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 ALA C 202 124.72 -38.06 REMARK 500 ALA C 214 53.31 -147.60 REMARK 500 ALA D 214 53.99 -146.11 REMARK 500 DAR G 43P 24.81 168.13 REMARK 500 DAR H 43P 40.71 168.42 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 BP4 G 41P -10.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAR E 43P REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAR F 43P REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAR G 43P REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAR H 43P REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CJL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN L DBREF 1MHW A 1 175 UNP P07711 CATL_HUMAN 114 288 DBREF 1MHW B 1 175 UNP P07711 CATL_HUMAN 114 288 DBREF 1MHW C 179 220 UNP P07711 CATL_HUMAN 292 333 DBREF 1MHW D 179 220 UNP P07711 CATL_HUMAN 292 333 DBREF 1MHW E 41P 45 PDB 1MHW 1MHW 41 45 DBREF 1MHW F 41P 45 PDB 1MHW 1MHW 41 45 DBREF 1MHW G 41P 45P PDB 1MHW 1MHW 41 45 DBREF 1MHW H 41P 45P PDB 1MHW 1MHW 41 45 SEQADV 1MHW CSD A 25 UNP P07711 CYS 138 MODIFIED RESIDUE SEQADV 1MHW CSD B 25 UNP P07711 CYS 138 MODIFIED RESIDUE SEQRES 1 A 175 ALA PRO ARG SER VAL ASP TRP ARG GLU LYS GLY TYR VAL SEQRES 2 A 175 THR PRO VAL LYS ASN GLN GLY GLN CYS GLY SER CSD TRP SEQRES 3 A 175 ALA PHE SER ALA THR GLY ALA LEU GLU GLY GLN MET PHE SEQRES 4 A 175 ARG LYS THR GLY ARG LEU ILE SER LEU SER GLU GLN ASN SEQRES 5 A 175 LEU VAL ASP CYS SER GLY PRO GLN GLY ASN GLU GLY CYS SEQRES 6 A 175 ASN GLY GLY LEU MET ASP TYR ALA PHE GLN TYR VAL GLN SEQRES 7 A 175 ASP ASN GLY GLY LEU ASP SER GLU GLU SER TYR PRO TYR SEQRES 8 A 175 GLU ALA THR GLU GLU SER CYS LYS TYR ASN PRO LYS TYR SEQRES 9 A 175 SER VAL ALA ASN ASP THR GLY PHE VAL ASP ILE PRO LYS SEQRES 10 A 175 GLN GLU LYS ALA LEU MET LYS ALA VAL ALA THR VAL GLY SEQRES 11 A 175 PRO ILE SER VAL ALA ILE ASP ALA GLY HIS GLU SER PHE SEQRES 12 A 175 LEU PHE TYR LYS GLU GLY ILE TYR PHE GLU PRO ASP CYS SEQRES 13 A 175 SER SER GLU ASP MET ASP HIS GLY VAL LEU VAL VAL GLY SEQRES 14 A 175 TYR GLY PHE GLU SER THR SEQRES 1 C 42 ASN ASN LYS TYR TRP LEU VAL LYS ASN SER TRP GLY GLU SEQRES 2 C 42 GLU TRP GLY MET GLY GLY TYR VAL LYS MET ALA LYS ASP SEQRES 3 C 42 ARG ARG ASN HIS CYS GLY ILE ALA SER ALA ALA SER TYR SEQRES 4 C 42 PRO THR VAL SEQRES 1 B 175 ALA PRO ARG SER VAL ASP TRP ARG GLU LYS GLY TYR VAL SEQRES 2 B 175 THR PRO VAL LYS ASN GLN GLY GLN CYS GLY SER CSD TRP SEQRES 3 B 175 ALA PHE SER ALA THR GLY ALA LEU GLU GLY GLN MET PHE SEQRES 4 B 175 ARG LYS THR GLY ARG LEU ILE SER LEU SER GLU GLN ASN SEQRES 5 B 175 LEU VAL ASP CYS SER GLY PRO GLN GLY ASN GLU GLY CYS SEQRES 6 B 175 ASN GLY GLY LEU MET ASP TYR ALA PHE GLN TYR VAL GLN SEQRES 7 B 175 ASP ASN GLY GLY LEU ASP SER GLU GLU SER TYR PRO TYR SEQRES 8 B 175 GLU ALA THR GLU GLU SER CYS LYS TYR ASN PRO LYS TYR SEQRES 9 B 175 SER VAL ALA ASN ASP THR GLY PHE VAL ASP ILE PRO LYS SEQRES 10 B 175 GLN GLU LYS ALA LEU MET LYS ALA VAL ALA THR VAL GLY SEQRES 11 B 175 PRO ILE SER VAL ALA ILE ASP ALA GLY HIS GLU SER PHE SEQRES 12 B 175 LEU PHE TYR LYS GLU GLY ILE TYR PHE GLU PRO ASP CYS SEQRES 13 B 175 SER SER GLU ASP MET ASP HIS GLY VAL LEU VAL VAL GLY SEQRES 14 B 175 TYR GLY PHE GLU SER THR SEQRES 1 D 42 ASN ASN LYS TYR TRP LEU VAL LYS ASN SER TRP GLY GLU SEQRES 2 D 42 GLU TRP GLY MET GLY GLY TYR VAL LYS MET ALA LYS ASP SEQRES 3 D 42 ARG ARG ASN HIS CYS GLY ILE ALA SER ALA ALA SER TYR SEQRES 4 D 42 PRO THR VAL SEQRES 1 E 5 BP4 CYS DAR TYR PEA SEQRES 1 F 5 BP4 CYS DAR TYR PEA SEQRES 1 G 5 BP4 CYS DAR TYR PEA SEQRES 1 H 5 BP4 CYS DAR TYR PEA MODRES 1MHW CSD A 25 CYS 3-SULFINOALANINE MODRES 1MHW CSD B 25 CYS 3-SULFINOALANINE HET CSD A 25 8 HET CSD B 25 8 HET BP4 E 41P 15 HET DAR E 43P 11 HET BP4 F 41P 15 HET DAR F 43P 11 HET BP4 G 41P 15 HET DAR G 43P 11 HET PEA G 45P 9 HET BP4 H 41P 15 HET DAR H 43P 11 HET PEA H 45P 9 HETNAM CSD 3-SULFINOALANINE HETNAM BP4 BIPHENYL-4-YLACETIC ACID HETNAM DAR D-ARGININE HETNAM PEA 2-PHENYLETHYLAMINE HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE FORMUL 1 CSD 2(C3 H7 N O4 S) FORMUL 5 BP4 4(C14 H12 O2) FORMUL 5 DAR 4(C6 H15 N4 O2 1+) FORMUL 7 PEA 2(C8 H12 N 1+) FORMUL 9 HOH *525(H2 O) HELIX 1 1 ARG A 8 GLY A 11 5 4 HELIX 2 2 SER A 24 GLY A 43 1 20 HELIX 3 3 SER A 49 SER A 57 1 9 HELIX 4 4 GLU A 63 GLY A 67 5 5 HELIX 5 5 LEU A 69 GLY A 81 1 13 HELIX 6 6 ASN A 101 LYS A 103 5 3 HELIX 7 7 GLN A 118 VAL A 129 1 12 HELIX 8 8 HIS A 140 PHE A 145 1 6 HELIX 9 9 ASN C 207 ILE C 211 5 5 HELIX 10 10 ARG B 8 GLY B 11 5 4 HELIX 11 11 SER B 24 GLY B 43 1 20 HELIX 12 12 SER B 49 SER B 57 1 9 HELIX 13 13 GLY B 58 GLY B 61 5 4 HELIX 14 14 GLU B 63 GLY B 67 5 5 HELIX 15 15 LEU B 69 GLY B 81 1 13 HELIX 16 16 ASN B 101 LYS B 103 5 3 HELIX 17 17 GLN B 118 GLY B 130 1 13 HELIX 18 18 HIS B 140 PHE B 145 1 6 HELIX 19 19 ASN D 207 ILE D 211 5 5 SHEET 1 A 5 ILE A 150 TYR A 151 0 SHEET 2 A 5 TYR C 198 ALA C 202 1 O LYS C 200 N TYR A 151 SHEET 3 A 5 LYS C 181 LYS C 186 -1 N TRP C 183 O MET C 201 SHEET 4 A 5 HIS A 163 PHE A 172 -1 N LEU A 166 O LYS C 186 SHEET 5 A 5 VAL A 5 ASP A 6 -1 N VAL A 5 O TYR A 170 SHEET 1 B 5 ILE A 150 TYR A 151 0 SHEET 2 B 5 TYR C 198 ALA C 202 1 O LYS C 200 N TYR A 151 SHEET 3 B 5 LYS C 181 LYS C 186 -1 N TRP C 183 O MET C 201 SHEET 4 B 5 HIS A 163 PHE A 172 -1 N LEU A 166 O LYS C 186 SHEET 5 B 5 ILE A 132 ILE A 136 -1 N VAL A 134 O VAL A 165 SHEET 1 C 2 LEU A 83 ASP A 84 0 SHEET 2 C 2 SER A 105 ALA A 107 -1 O VAL A 106 N LEU A 83 SHEET 1 D 2 PHE A 112 ASP A 114 0 SHEET 2 D 2 SER C 216 PRO C 218 -1 O TYR C 217 N VAL A 113 SHEET 1 E 5 ILE B 150 TYR B 151 0 SHEET 2 E 5 TYR D 198 ALA D 202 1 O LYS D 200 N TYR B 151 SHEET 3 E 5 LYS D 181 LYS D 186 -1 N TRP D 183 O MET D 201 SHEET 4 E 5 HIS B 163 PHE B 172 -1 N LEU B 166 O LYS D 186 SHEET 5 E 5 VAL B 5 ASP B 6 -1 N VAL B 5 O TYR B 170 SHEET 1 F 5 ILE B 150 TYR B 151 0 SHEET 2 F 5 TYR D 198 ALA D 202 1 O LYS D 200 N TYR B 151 SHEET 3 F 5 LYS D 181 LYS D 186 -1 N TRP D 183 O MET D 201 SHEET 4 F 5 HIS B 163 PHE B 172 -1 N LEU B 166 O LYS D 186 SHEET 5 F 5 ILE B 132 ILE B 136 -1 N VAL B 134 O VAL B 165 SHEET 1 G 2 LEU B 83 ASP B 84 0 SHEET 2 G 2 SER B 105 ALA B 107 -1 O VAL B 106 N LEU B 83 SHEET 1 H 2 PHE B 112 ASP B 114 0 SHEET 2 H 2 SER D 216 PRO D 218 -1 O TYR D 217 N VAL B 113 SSBOND 1 CYS A 22 CYS A 65 1555 1555 2.34 SSBOND 2 CYS A 56 CYS A 98 1555 1555 2.37 SSBOND 3 CYS A 156 CYS C 209 1555 1555 2.32 SSBOND 4 CYS B 22 CYS B 65 1555 1555 2.30 SSBOND 5 CYS B 56 CYS B 98 1555 1555 2.38 SSBOND 6 CYS B 156 CYS D 209 1555 1555 2.38 SSBOND 7 CYS E 42P CYS H 42P 1555 1555 2.41 SSBOND 8 CYS F 42P CYS G 42P 1555 1555 2.48 LINK C BP4 E 41P N CYS E 42P 1555 1555 1.35 LINK C CYS E 42P N DAR E 43P 1555 1555 1.38 LINK C BP4 F 41P N CYS F 42P 1555 1555 1.37 LINK C CYS F 42P N DAR F 43P 1555 1555 1.40 LINK C BP4 G 41P N CYS G 42P 1555 1555 1.43 LINK C CYS G 42P N DAR G 43P 1555 1555 1.42 LINK C DAR G 43P N TYR G 44P 1555 1555 1.33 LINK C TYR G 44P N PEA G 45P 1555 1555 1.49 LINK C BP4 H 41P N CYS H 42P 1555 1555 1.43 LINK C CYS H 42P N DAR H 43P 1555 1555 1.41 LINK C DAR H 43P N TYR H 44P 1555 1555 1.32 LINK C TYR H 44P N PEA H 45P 1555 1555 1.48 LINK C SER A 24 N CSD A 25 1555 1555 1.33 LINK C CSD A 25 N TRP A 26 1555 1555 1.34 LINK C SER B 24 N CSD B 25 1555 1555 1.33 LINK C CSD B 25 N TRP B 26 1555 1555 1.33 SITE 1 AC1 4 GLN A 21 HOH B 785 CYS E 42P HOH E 497 SITE 1 AC2 5 HOH A 494 HOH A 704 GLN B 21 CYS F 42P SITE 2 AC2 5 HOH F 797 SITE 1 AC3 10 ARG A 8 GLU A 9 GLY A 11 CSD A 25 SITE 2 AC3 10 GLY A 67 GLY A 68 ASP A 162 HOH A 704 SITE 3 AC3 10 CYS G 42P TYR G 44P SITE 1 AC4 14 CSD B 25 TRP B 26 GLY B 67 GLY B 68 SITE 2 AC4 14 GLN B 78 ASP B 79 GLY B 81 MET B 161 SITE 3 AC4 14 ASP B 162 CYS H 42P TYR H 44P PEA H 45P SITE 4 AC4 14 HOH H 458 HOH H 631 CRYST1 51.522 58.632 151.445 90.00 90.00 90.00 P 21 21 21 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 0.019409 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017056 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006603 0.00000