HEADER HYDROLASE/HYDROLASE INHIBITOR 28-MAR-08 2ZKS TITLE STRUCTURAL INSIGHTS INTO THE PROTEOLYTIC MACHINERY OF APOPTOSIS- TITLE 2 INDUCING GRANZYME M COMPND MOL_ID: 1; COMPND 2 MOLECULE: GRANZYME M; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MET-ASE, NATURAL KILLER CELL GRANULAR PROTEASE, HU-MET-1, COMPND 5 MET-1 SERINE PROTEASE; COMPND 6 EC: 3.4.21.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: HGZMM INHIBITOR; COMPND 10 CHAIN: C; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 STRAIN: CTLS, NK CELLS; SOURCE 6 GENE: GZMM, MET1; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET26B-GZMM; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 OTHER_DETAILS: PEPTIDE SYNTHESIS KEYWDS SERINE PROTEASE, GRANZYME, CYTOLYSIS, GLYCOPROTEIN, HYDROLASE, KEYWDS 2 SECRETED, ZYMOGEN, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.F.WU,L.WANG,G.Q.HUA,K.LIU,X.YANG,Y.J.ZHAI,F.SUN,Z.S.FAN REVDAT 5 03-APR-24 2ZKS 1 REMARK SEQADV LINK REVDAT 4 11-OCT-17 2ZKS 1 REMARK REVDAT 3 13-JUL-11 2ZKS 1 VERSN REVDAT 2 07-JUL-09 2ZKS 1 JRNL REVDAT 1 31-MAR-09 2ZKS 0 JRNL AUTH L.WU,L.WANG,G.HUA,K.LIU,X.YANG,Y.ZHAI,M.BARTLAM,F.SUN,Z.FAN JRNL TITL STRUCTURAL BASIS FOR PROTEOLYTIC SPECIFICITY OF THE HUMAN JRNL TITL 2 APOPTOSIS-INDUCING GRANZYME M JRNL REF J.IMMUNOL. V. 183 421 2009 JRNL REFN ISSN 0022-1767 JRNL PMID 19542453 JRNL DOI 10.4049/JIMMUNOL.0803088 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 9978 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) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.293 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 501 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 723 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.3260 REMARK 3 BIN FREE R VALUE SET COUNT : 38 REMARK 3 BIN FREE R VALUE : 0.4080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1783 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 83 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) : 30.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.17000 REMARK 3 B22 (A**2) : -0.17000 REMARK 3 B33 (A**2) : 0.26000 REMARK 3 B12 (A**2) : -0.09000 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): 0.539 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.350 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.256 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 24.538 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.905 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.843 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1842 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2498 ; 1.880 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 232 ; 7.377 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 64 ;32.365 ;21.094 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 309 ;17.656 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;21.018 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 283 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1339 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 922 ; 0.236 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1222 ; 0.320 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 114 ; 0.176 ; 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): 44 ; 0.328 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.275 ; 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): 1199 ; 0.775 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1884 ; 1.348 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 717 ; 2.018 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 614 ; 3.219 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 231 REMARK 3 ORIGIN FOR THE GROUP (A): -21.2686 -13.2913 17.8701 REMARK 3 T TENSOR REMARK 3 T11: -0.1295 T22: -0.0967 REMARK 3 T33: -0.0870 T12: 0.0242 REMARK 3 T13: 0.0100 T23: 0.0093 REMARK 3 L TENSOR REMARK 3 L11: 1.7491 L22: 4.3848 REMARK 3 L33: 3.6689 L12: -1.5221 REMARK 3 L13: -0.8990 L23: 2.2255 REMARK 3 S TENSOR REMARK 3 S11: 0.0336 S12: -0.0704 S13: 0.0800 REMARK 3 S21: 0.0923 S22: 0.1245 S23: -0.0619 REMARK 3 S31: -0.0585 S32: 0.3025 S33: -0.1581 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 2 C 5 REMARK 3 ORIGIN FOR THE GROUP (A): -28.3112 -23.8417 14.2796 REMARK 3 T TENSOR REMARK 3 T11: -0.0106 T22: 0.1805 REMARK 3 T33: 0.2545 T12: 0.0736 REMARK 3 T13: 0.0507 T23: -0.0095 REMARK 3 L TENSOR REMARK 3 L11: 47.1949 L22: 6.6992 REMARK 3 L33: 39.0259 L12: -7.6319 REMARK 3 L13: 42.8754 L23: -7.5724 REMARK 3 S TENSOR REMARK 3 S11: -0.0020 S12: 0.4777 S13: -1.4530 REMARK 3 S21: -0.1737 S22: 0.3775 S23: 0.3739 REMARK 3 S31: -0.1001 S32: -0.8215 S33: -0.3755 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 2ZKS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000028096. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BSRF REMARK 200 BEAMLINE : 1W2B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : FLAT PANEL REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH FLAT PANEL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9978 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 64.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 2GZC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2M LI2SO4, 0.1M BICINE, REMARK 280 PH8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 37.85233 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 75.70467 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 75.70467 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 37.85233 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 ALA A 232 REMARK 465 LEU A 233 REMARK 465 GLU A 234 REMARK 465 HIS A 235 REMARK 465 HIS A 236 REMARK 465 HIS A 237 REMARK 465 HIS A 238 REMARK 465 HIS A 239 REMARK 465 HIS A 240 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 C 4 CA - C - N ANGL. DEV. = -19.3 DEGREES REMARK 500 PRO C 4 O - C - N ANGL. DEV. = 20.8 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 A 44 53.20 -56.82 REMARK 500 HIS A 57 -58.44 -122.71 REMARK 500 PRO A 62 -77.61 -49.96 REMARK 500 MET A 122 118.73 -162.64 REMARK 500 PHE A 156 -121.03 -101.27 REMARK 500 LYS A 173 -34.93 -24.81 REMARK 500 LYS A 179 129.18 -39.66 REMARK 500 ARG A 192 71.30 52.72 REMARK 500 SER A 199 -52.34 -123.98 REMARK 500 SER A 201 -149.40 -153.84 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 SO4 A 241 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 242 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 243 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 244 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN C OF HGZMM INHIBITOR REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZGC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ACTIVE HUMAN GRANZYME M REMARK 900 RELATED ID: 2ZGH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ACTIVE GRANZYME M BOUND TO ITS CATALYTIC REMARK 900 PRODUCT REMARK 900 RELATED ID: 2ZGJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF D86N-GZMM COMPLEXED WITH ITS OPTIMAL REMARK 900 SYNTHESIZED SUBSTRATE DBREF 2ZKS A 1 232 UNP P51124 GRAM_HUMAN 26 257 DBREF 2ZKS C 1 6 PDB 2ZKS 2ZKS 1 6 SEQADV 2ZKS LEU A 233 UNP P51124 EXPRESSION TAG SEQADV 2ZKS GLU A 234 UNP P51124 EXPRESSION TAG SEQADV 2ZKS HIS A 235 UNP P51124 EXPRESSION TAG SEQADV 2ZKS HIS A 236 UNP P51124 EXPRESSION TAG SEQADV 2ZKS HIS A 237 UNP P51124 EXPRESSION TAG SEQADV 2ZKS HIS A 238 UNP P51124 EXPRESSION TAG SEQADV 2ZKS HIS A 239 UNP P51124 EXPRESSION TAG SEQADV 2ZKS HIS A 240 UNP P51124 EXPRESSION TAG SEQRES 1 A 240 ILE ILE GLY GLY ARG GLU VAL ILE PRO HIS SER ARG PRO SEQRES 2 A 240 TYR MET ALA SER LEU GLN ARG ASN GLY SER HIS LEU CYS SEQRES 3 A 240 GLY GLY VAL LEU VAL HIS PRO LYS TRP VAL LEU THR ALA SEQRES 4 A 240 ALA HIS CYS LEU ALA GLN ARG MET ALA GLN LEU ARG LEU SEQRES 5 A 240 VAL LEU GLY LEU HIS THR LEU ASP SER PRO GLY LEU THR SEQRES 6 A 240 PHE HIS ILE LYS ALA ALA ILE GLN HIS PRO ARG TYR LYS SEQRES 7 A 240 PRO VAL PRO ALA LEU GLU ASN ASP LEU ALA LEU LEU GLN SEQRES 8 A 240 LEU ASP GLY LYS VAL LYS PRO SER ARG THR ILE ARG PRO SEQRES 9 A 240 LEU ALA LEU PRO SER LYS ARG GLN VAL VAL ALA ALA GLY SEQRES 10 A 240 THR ARG CYS SER MET ALA GLY TRP GLY LEU THR HIS GLN SEQRES 11 A 240 GLY GLY ARG LEU SER ARG VAL LEU ARG GLU LEU ASP LEU SEQRES 12 A 240 GLN VAL LEU ASP THR ARG MET CYS ASN ASN SER ARG PHE SEQRES 13 A 240 TRP ASN GLY SER LEU SER PRO SER MET VAL CYS LEU ALA SEQRES 14 A 240 ALA ASP SER LYS ASP GLN ALA PRO CYS LYS GLY ASP SER SEQRES 15 A 240 GLY GLY PRO LEU VAL CYS GLY LYS GLY ARG VAL LEU ALA SEQRES 16 A 240 GLY VAL LEU SER PHE SER SER ARG VAL CYS THR ASP ILE SEQRES 17 A 240 PHE LYS PRO PRO VAL ALA THR ALA VAL ALA PRO TYR VAL SEQRES 18 A 240 SER TRP ILE ARG LYS VAL THR GLY ARG SER ALA LEU GLU SEQRES 19 A 240 HIS HIS HIS HIS HIS HIS SEQRES 1 C 6 ACE LYS VAL PRO LEU 0QE HET ACE C 1 3 HET 0QE C 6 1 HET SO4 A 241 5 HET SO4 A 242 5 HET SO4 A 243 5 HET SO4 A 244 5 HETNAM ACE ACETYL GROUP HETNAM 0QE CHLOROMETHANE HETNAM SO4 SULFATE ION HETSYN 0QE CHLORO METHYL GROUP FORMUL 2 ACE C2 H4 O FORMUL 2 0QE C H3 CL FORMUL 3 SO4 4(O4 S 2-) FORMUL 7 HOH *83(H2 O) HELIX 1 1 ALA A 39 ALA A 44 5 6 HELIX 2 2 ARG A 46 ALA A 48 5 3 HELIX 3 3 ASP A 147 ASN A 152 1 6 HELIX 4 4 TYR A 220 GLY A 229 1 10 SHEET 1 A 6 ARG A 5 GLU A 6 0 SHEET 2 A 6 ARG A 139 VAL A 145 -1 O GLU A 140 N ARG A 5 SHEET 3 A 6 ARG A 119 GLY A 124 -1 N CYS A 120 O LEU A 143 SHEET 4 A 6 PRO A 185 CYS A 188 -1 O VAL A 187 N SER A 121 SHEET 5 A 6 VAL A 193 SER A 201 -1 O ALA A 195 N LEU A 186 SHEET 6 A 6 VAL C 3 PRO C 4 -1 O VAL C 3 N SER A 201 SHEET 1 B 6 ARG A 5 GLU A 6 0 SHEET 2 B 6 ARG A 139 VAL A 145 -1 O GLU A 140 N ARG A 5 SHEET 3 B 6 MET A 165 ALA A 169 -1 O ALA A 169 N GLN A 144 SHEET 4 B 6 VAL A 213 ALA A 216 -1 O ALA A 214 N VAL A 166 SHEET 5 B 6 VAL A 193 SER A 201 -1 N VAL A 197 O THR A 215 SHEET 6 B 6 VAL C 3 PRO C 4 -1 O VAL C 3 N SER A 201 SHEET 1 C 7 LEU A 64 PHE A 66 0 SHEET 2 C 7 LEU A 50 LEU A 54 -1 N LEU A 54 O LEU A 64 SHEET 3 C 7 MET A 15 ARG A 20 -1 N GLN A 19 O ARG A 51 SHEET 4 C 7 SER A 23 HIS A 32 -1 O CYS A 26 N LEU A 18 SHEET 5 C 7 TRP A 35 THR A 38 -1 O LEU A 37 N VAL A 29 SHEET 6 C 7 ALA A 88 LEU A 92 -1 O LEU A 90 N VAL A 36 SHEET 7 C 7 ILE A 68 GLN A 73 -1 N ILE A 72 O LEU A 89 SSBOND 1 CYS A 26 CYS A 42 1555 1555 2.08 SSBOND 2 CYS A 120 CYS A 188 1555 1555 2.05 SSBOND 3 CYS A 151 CYS A 167 1555 1555 2.01 SSBOND 4 CYS A 178 CYS A 205 1555 1555 2.05 LINK NE2 HIS A 41 C1 0QE C 6 1555 1555 1.28 LINK C ACE C 1 N LYS C 2 1555 1555 1.34 LINK C LEU C 5 C1 0QE C 6 1555 1555 1.52 CISPEP 1 VAL A 80 PRO A 81 0 0.05 SITE 1 AC1 2 ARG A 51 HIS A 67 SITE 1 AC2 5 THR A 128 SER A 135 ARG A 136 VAL A 137 SITE 2 AC2 5 ARG A 139 SITE 1 AC3 3 LYS A 34 GLN A 91 ARG A 203 SITE 1 AC4 3 GLY A 189 LYS A 190 HOH A 323 SITE 1 AC5 12 HIS A 41 VAL A 80 PRO A 81 LEU A 83 SITE 2 AC5 12 SER A 160 SER A 182 SER A 199 PHE A 200 SITE 3 AC5 12 SER A 201 SER A 202 ARG A 203 HOH A 308 CRYST1 74.671 74.671 113.557 90.00 90.00 120.00 P 31 2 1 6 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 0.013392 0.007732 0.000000 0.00000 SCALE2 0.000000 0.015464 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008806 0.00000