HEADER HYDROLASE 29-SEP-09 3K24 TITLE CRYSTAL STRUCTURE OF MATURE APO-CATHEPSIN L C25A MUTANT IN COMPLEX TITLE 2 WITH GLN-LEU-ALA PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHEPSIN L1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: MC25A: UNP RESIDUES 114-333; COMPND 5 SYNONYM: MAJOR EXCRETED PROTEIN, MEP, CATHEPSIN L1 HEAVY CHAIN AND COMPND 6 CATHEPSIN L1 LIGHT CHAIN; COMPND 7 EC: 3.4.22.15; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: H3 PEPTIDE; COMPND 12 CHAIN: C, D; COMPND 13 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: CTSL1, CTSL; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 OTHER_DETAILS: SYNTHETIC PEPTIDE KEYWDS CO-CRYSTAL, SUBSTRATE, PROTEASE, STRUCTURAL GENOMICS, STRUCTURAL KEYWDS 2 GENOMICS CONSORTIUM, SGC, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.A.ADAMS-CIOABA,J.C.KRUPA,J.S.MORT,C.BOUNTRA,J.WEIGELT, AUTHOR 2 C.H.ARROWSMITH,A.M.EDWARDS,A.BOCHKAREV,J.MIN,STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (SGC) REVDAT 6 06-SEP-23 3K24 1 REMARK REVDAT 5 13-OCT-21 3K24 1 SEQADV HETSYN REVDAT 4 29-JUL-20 3K24 1 COMPND REMARK DBREF HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 13-JUL-11 3K24 1 VERSN REVDAT 2 02-MAR-11 3K24 1 JRNL REVDAT 1 23-MAR-10 3K24 0 JRNL AUTH M.A.ADAMS-CIOABA,J.C.KRUPA,C.XU,J.S.MORT,J.MIN JRNL TITL STRUCTURAL BASIS FOR THE RECOGNITION AND CLEAVAGE OF HISTONE JRNL TITL 2 H3 BY CATHEPSIN L. JRNL REF NAT COMMUN V. 2 197 2011 JRNL REFN ESSN 2041-1723 JRNL PMID 21326229 JRNL DOI 10.1038/NCOMMS1204 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 3 NUMBER OF REFLECTIONS : 15283 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) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 823 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 706 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 60.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE SET COUNT : 29 REMARK 3 BIN FREE R VALUE : 0.2310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3436 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 89 REMARK 3 SOLVENT ATOMS : 32 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.69000 REMARK 3 B22 (A**2) : 0.69000 REMARK 3 B33 (A**2) : -1.03000 REMARK 3 B12 (A**2) : 0.34000 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): 0.996 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.338 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.232 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 22.192 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.905 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3620 ; 0.003 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4910 ; 0.545 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 442 ;10.481 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 172 ;39.244 ;25.233 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 556 ;19.799 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;24.256 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 511 ; 0.046 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2802 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2196 ; 1.108 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3488 ; 1.942 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1424 ; 3.284 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1422 ; 5.124 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : B A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 0 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1696 ; 0.25 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1696 ; 1.38 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 220 REMARK 3 RESIDUE RANGE : B 221 B 226 REMARK 3 RESIDUE RANGE : B 227 B 246 REMARK 3 ORIGIN FOR THE GROUP (A): 5.4940 0.4009 -18.8503 REMARK 3 T TENSOR REMARK 3 T11: 0.1383 T22: 0.1640 REMARK 3 T33: 0.0251 T12: 0.0020 REMARK 3 T13: 0.0067 T23: -0.0190 REMARK 3 L TENSOR REMARK 3 L11: 1.6329 L22: 1.7951 REMARK 3 L33: 1.8279 L12: 0.4266 REMARK 3 L13: -0.1507 L23: -0.1665 REMARK 3 S TENSOR REMARK 3 S11: 0.0395 S12: -0.1525 S13: 0.0208 REMARK 3 S21: 0.1546 S22: -0.0293 S23: -0.0886 REMARK 3 S31: 0.2494 S32: -0.1406 S33: -0.0102 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 220 REMARK 3 RESIDUE RANGE : A 221 A 221 REMARK 3 RESIDUE RANGE : A 222 A 233 REMARK 3 ORIGIN FOR THE GROUP (A): 3.9897 -27.1625 -9.2215 REMARK 3 T TENSOR REMARK 3 T11: 0.1162 T22: 0.3143 REMARK 3 T33: 0.2271 T12: 0.0181 REMARK 3 T13: -0.0941 T23: 0.1069 REMARK 3 L TENSOR REMARK 3 L11: 1.1016 L22: 3.6201 REMARK 3 L33: 3.1488 L12: 1.3432 REMARK 3 L13: 0.4098 L23: 0.8002 REMARK 3 S TENSOR REMARK 3 S11: 0.2505 S12: -0.0244 S13: -0.2042 REMARK 3 S21: 0.5470 S22: -0.2681 S23: -0.5415 REMARK 3 S31: 0.1667 S32: 0.5846 S33: 0.0176 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 3K24 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055449. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15954 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07400 REMARK 200 FOR THE DATA SET : 31.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 59.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.19800 REMARK 200 FOR SHELL : 6.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3IV2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% ISOPROPANOL, 0.1 M SODIUM ACETATE REMARK 280 TRIHYDRATE PH 4.0, 22% PEG 6000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 137.24533 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 68.62267 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 68.62267 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 137.24533 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 UNIT IS A MONOMERIC COMPLEX OF THE PROTEIN REMARK 300 WITH PEPTIDE. WORD "DIMERIC" IN REMARK 350 IS INCORRECT AS IT IS REMARK 300 ONLY CHAIN COUNT. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, E 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 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 O3 MAN E 3 C1 MAN E 6 2.12 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 GLN A 21 69.83 -100.95 REMARK 500 THR A 110 21.88 -141.11 REMARK 500 THR A 175 64.46 30.13 REMARK 500 GLU A 176 -133.24 160.23 REMARK 500 SER A 177 122.94 129.00 REMARK 500 ASN A 179 101.26 117.05 REMARK 500 ALA A 202 128.03 -39.13 REMARK 500 ARG A 205 63.87 -119.78 REMARK 500 ASN A 207 59.38 39.51 REMARK 500 ALA A 214 55.32 -154.31 REMARK 500 LYS B 147 -37.46 -137.51 REMARK 500 SER B 174 -33.17 -147.44 REMARK 500 THR B 175 -29.30 74.91 REMARK 500 SER B 177 160.25 90.40 REMARK 500 ARG B 205 61.59 -104.04 REMARK 500 ARG B 206 63.10 60.23 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 GLU A 173 SER A 174 -143.50 REMARK 500 GLU A 176 SER A 177 139.69 REMARK 500 ASP A 178 ASN A 179 -74.21 REMARK 500 GLU B 173 SER B 174 -79.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IV2 RELATED DB: PDB REMARK 900 APO FORM OF PROTEASE DBREF 3K24 A 1 220 UNP P07711 CATL1_HUMAN 114 333 DBREF 3K24 B 1 220 UNP P07711 CATL1_HUMAN 114 333 DBREF 3K24 C 109 111 PDB 3K24 3K24 109 111 DBREF 3K24 D 109 111 PDB 3K24 3K24 109 111 SEQADV 3K24 ALA A 25 UNP P07711 CYS 138 ENGINEERED MUTATION SEQADV 3K24 ALA B 25 UNP P07711 CYS 138 ENGINEERED MUTATION SEQRES 1 A 220 ALA PRO ARG SER VAL ASP TRP ARG GLU LYS GLY TYR VAL SEQRES 2 A 220 THR PRO VAL LYS ASN GLN GLY GLN CYS GLY SER ALA TRP SEQRES 3 A 220 ALA PHE SER ALA THR GLY ALA LEU GLU GLY GLN MET PHE SEQRES 4 A 220 ARG LYS THR GLY ARG LEU ILE SER LEU SER GLU GLN ASN SEQRES 5 A 220 LEU VAL ASP CYS SER GLY PRO GLN GLY ASN GLU GLY CYS SEQRES 6 A 220 ASN GLY GLY LEU MET ASP TYR ALA PHE GLN TYR VAL GLN SEQRES 7 A 220 ASP ASN GLY GLY LEU ASP SER GLU GLU SER TYR PRO TYR SEQRES 8 A 220 GLU ALA THR GLU GLU SER CYS LYS TYR ASN PRO LYS TYR SEQRES 9 A 220 SER VAL ALA ASN ASP THR GLY PHE VAL ASP ILE PRO LYS SEQRES 10 A 220 GLN GLU LYS ALA LEU MET LYS ALA VAL ALA THR VAL GLY SEQRES 11 A 220 PRO ILE SER VAL ALA ILE ASP ALA GLY HIS GLU SER PHE SEQRES 12 A 220 LEU PHE TYR LYS GLU GLY ILE TYR PHE GLU PRO ASP CYS SEQRES 13 A 220 SER SER GLU ASP MET ASP HIS GLY VAL LEU VAL VAL GLY SEQRES 14 A 220 TYR GLY PHE GLU SER THR GLU SER ASP ASN ASN LYS TYR SEQRES 15 A 220 TRP LEU VAL LYS ASN SER TRP GLY GLU GLU TRP GLY MET SEQRES 16 A 220 GLY GLY TYR VAL LYS MET ALA LYS ASP ARG ARG ASN HIS SEQRES 17 A 220 CYS GLY ILE ALA SER ALA ALA SER TYR PRO THR VAL SEQRES 1 B 220 ALA PRO ARG SER VAL ASP TRP ARG GLU LYS GLY TYR VAL SEQRES 2 B 220 THR PRO VAL LYS ASN GLN GLY GLN CYS GLY SER ALA TRP SEQRES 3 B 220 ALA PHE SER ALA THR GLY ALA LEU GLU GLY GLN MET PHE SEQRES 4 B 220 ARG LYS THR GLY ARG LEU ILE SER LEU SER GLU GLN ASN SEQRES 5 B 220 LEU VAL ASP CYS SER GLY PRO GLN GLY ASN GLU GLY CYS SEQRES 6 B 220 ASN GLY GLY LEU MET ASP TYR ALA PHE GLN TYR VAL GLN SEQRES 7 B 220 ASP ASN GLY GLY LEU ASP SER GLU GLU SER TYR PRO TYR SEQRES 8 B 220 GLU ALA THR GLU GLU SER CYS LYS TYR ASN PRO LYS TYR SEQRES 9 B 220 SER VAL ALA ASN ASP THR GLY PHE VAL ASP ILE PRO LYS SEQRES 10 B 220 GLN GLU LYS ALA LEU MET LYS ALA VAL ALA THR VAL GLY SEQRES 11 B 220 PRO ILE SER VAL ALA ILE ASP ALA GLY HIS GLU SER PHE SEQRES 12 B 220 LEU PHE TYR LYS GLU GLY ILE TYR PHE GLU PRO ASP CYS SEQRES 13 B 220 SER SER GLU ASP MET ASP HIS GLY VAL LEU VAL VAL GLY SEQRES 14 B 220 TYR GLY PHE GLU SER THR GLU SER ASP ASN ASN LYS TYR SEQRES 15 B 220 TRP LEU VAL LYS ASN SER TRP GLY GLU GLU TRP GLY MET SEQRES 16 B 220 GLY GLY TYR VAL LYS MET ALA LYS ASP ARG ARG ASN HIS SEQRES 17 B 220 CYS GLY ILE ALA SER ALA ALA SER TYR PRO THR VAL SEQRES 1 C 3 GLN LEU ALA SEQRES 1 D 3 GLN LEU ALA MODRES 3K24 ASN A 108 ASN GLYCOSYLATION SITE MODRES 3K24 ASN B 108 ASN GLYCOSYLATION SITE HET NAG E 1 14 HET NDG E 2 14 HET MAN E 3 11 HET BMA E 4 11 HET NDG E 5 14 HET MAN E 6 11 HET NAG A 221 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM NDG 2-ACETAMIDO-2-DEOXY-ALPHA-D-GLUCOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE 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 HETSYN NDG N-ACETYL-ALPHA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 NDG ALPHA-D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2- HETSYN 3 NDG ACETAMIDO-2-DEOXY-GLUCOSE; 2-(ACETYLAMINO)-2-DEOXY-A- HETSYN 4 NDG D-GLUCOPYRANOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 5 NAG 2(C8 H15 N O6) FORMUL 5 NDG 2(C8 H15 N O6) FORMUL 5 MAN 2(C6 H12 O6) FORMUL 5 BMA C6 H12 O6 FORMUL 7 HOH *32(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 GLY A 58 GLY A 61 5 4 HELIX 5 5 GLU A 63 GLY A 67 5 5 HELIX 6 6 LEU A 69 GLY A 81 1 13 HELIX 7 7 ASN A 101 LYS A 103 5 3 HELIX 8 8 GLN A 118 GLY A 130 1 13 HELIX 9 9 HIS A 140 PHE A 145 1 6 HELIX 10 10 ASN A 207 ILE A 211 5 5 HELIX 11 11 TRP B 7 GLY B 11 1 5 HELIX 12 12 SER B 24 GLY B 43 1 20 HELIX 13 13 SER B 49 SER B 57 1 9 HELIX 14 14 GLY B 58 GLY B 61 5 4 HELIX 15 15 GLU B 63 GLY B 67 5 5 HELIX 16 16 LEU B 69 GLY B 81 1 13 HELIX 17 17 ASN B 101 LYS B 103 5 3 HELIX 18 18 GLN B 118 VAL B 129 1 12 HELIX 19 19 HIS B 140 PHE B 145 1 6 HELIX 20 20 ASN B 207 ILE B 211 5 5 SHEET 1 A 3 VAL A 5 ASP A 6 0 SHEET 2 A 3 HIS A 163 PHE A 172 -1 O TYR A 170 N VAL A 5 SHEET 3 A 3 ILE A 132 ILE A 136 -1 N VAL A 134 O VAL A 165 SHEET 1 B 5 VAL A 5 ASP A 6 0 SHEET 2 B 5 HIS A 163 PHE A 172 -1 O TYR A 170 N VAL A 5 SHEET 3 B 5 LYS A 181 LYS A 186 -1 O LEU A 184 N GLY A 169 SHEET 4 B 5 TYR A 198 ALA A 202 -1 O VAL A 199 N VAL A 185 SHEET 5 B 5 ILE A 150 TYR A 151 1 N TYR A 151 O LYS A 200 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 A 216 PRO A 218 -1 O TYR A 217 N VAL A 113 SHEET 1 E 3 VAL B 5 ASP B 6 0 SHEET 2 E 3 HIS B 163 PHE B 172 -1 O TYR B 170 N VAL B 5 SHEET 3 E 3 ILE B 132 ILE B 136 -1 N VAL B 134 O VAL B 165 SHEET 1 F 5 VAL B 5 ASP B 6 0 SHEET 2 F 5 HIS B 163 PHE B 172 -1 O TYR B 170 N VAL B 5 SHEET 3 F 5 LYS B 181 LYS B 186 -1 O LYS B 186 N LEU B 166 SHEET 4 F 5 TYR B 198 ALA B 202 -1 O MET B 201 N TRP B 183 SHEET 5 F 5 ILE B 150 TYR B 151 1 N TYR B 151 O LYS B 200 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 GLY B 111 ASP B 114 0 SHEET 2 H 2 SER B 216 THR B 219 -1 O TYR B 217 N VAL B 113 SSBOND 1 CYS A 22 CYS A 65 1555 1555 2.03 SSBOND 2 CYS A 56 CYS A 98 1555 1555 2.04 SSBOND 3 CYS A 156 CYS A 209 1555 1555 2.04 SSBOND 4 CYS B 22 CYS B 65 1555 1555 2.03 SSBOND 5 CYS B 56 CYS B 98 1555 1555 2.04 SSBOND 6 CYS B 156 CYS B 209 1555 1555 2.03 LINK ND2 ASN A 108 C1 NAG A 221 1555 1555 1.44 LINK ND2 ASN B 108 C1 NAG E 1 1555 1555 1.44 LINK O4 NAG E 1 C1 NDG E 2 1555 1555 1.45 LINK O4 NDG E 2 C1 MAN E 3 1555 1555 1.45 LINK O6 MAN E 3 C1 BMA E 4 1555 1555 1.44 LINK O2 MAN E 3 C1 MAN E 6 1555 1555 1.45 LINK O6 BMA E 4 C1 NDG E 5 1555 1555 1.45 CISPEP 1 ASN A 179 ASN A 180 0 5.44 CRYST1 62.697 62.697 205.868 90.00 90.00 120.00 P 32 2 1 12 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 0.015950 0.009209 0.000000 0.00000 SCALE2 0.000000 0.018417 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004857 0.00000