PDB Short entry for 1ORF HEADER HYDROLASE/HYDROLASE INHIBITOR 12-MAR-03 1ORF TITLE THE OLIGOMERIC STRUCTURE OF HUMAN GRANZYME A REVEALS THE MOLECULAR TITLE 2 DETERMINANTS OF SUBSTRATE SPECIFICITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: GRANZYME A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOTOXIC T-LYMPHOCYTE PROTEINASE 1, HANUKKAH FACTOR, H COMPND 5 FACTOR, HF, GRANZYME 1, CTL TRYPTASE, FRAGMENTIN 1; COMPND 6 EC: 3.4.21.78; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GZMA; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: X33; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPICZALPHAA KEYWDS HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.K.BELL,D.H.GOETZ,S.MAHRUS,J.L.HARRIS,R.J.FLETTERICK,C.S.CRAIK REVDAT 6 13-MAR-24 1ORF 1 COMPND SOURCE REVDAT 5 16-AUG-23 1ORF 1 REMARK REVDAT 4 27-OCT-21 1ORF 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 1ORF 1 VERSN REVDAT 2 24-FEB-09 1ORF 1 VERSN REVDAT 1 01-JUL-03 1ORF 0 JRNL AUTH J.K.BELL,D.H.GOETZ,S.MAHRUS,J.L.HARRIS,R.J.FLETTERICK, JRNL AUTH 2 C.S.CRAIK JRNL TITL THE OLIGOMERIC STRUCTURE OF HUMAN GRANZYME A IS A JRNL TITL 2 DETERMINANT OF ITS EXTENDED SUBSTRATE SPECIFICITY. JRNL REF NAT.STRUCT.BIOL. V. 10 527 2003 JRNL REFN ISSN 1072-8368 JRNL PMID 12819769 JRNL DOI 10.1038/NSB944 REMARK 2 REMARK 2 RESOLUTION. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 12664 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 660 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 873 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE SET COUNT : 46 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1774 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 128 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.98000 REMARK 3 B22 (A**2) : 2.91000 REMARK 3 B33 (A**2) : -0.93000 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): 0.295 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.223 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.158 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.903 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1856 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2514 ; 1.543 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 234 ; 6.345 ; 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): 282 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1372 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 832 ; 0.207 ; 0.200 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): 142 ; 0.137 ; 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): 21 ; 0.400 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.141 ; 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): 1164 ; 0.713 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1882 ; 1.390 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 691 ; 2.039 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 629 ; 3.433 ; 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 : BABINET MODEL WITH 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: NULL REMARK 4 REMARK 4 1ORF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018592. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12664 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 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 <I/SIGMA(I)> 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: EPMR REMARK 200 STARTING MODEL: 1DST REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS PH 8.5, PEG 4000, LITHIUM REMARK 280 SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 19.77750 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 19.77750 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 57.51700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 72.51100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 57.51700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 72.51100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 19.77750 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 57.51700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 72.51100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 19.77750 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 57.51700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 72.51100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DIMER GENERATED BY THE TWO REMARK 300 FOLD AXIS: -X, Y, 1/2-Z 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: 1600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 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 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 19.77750 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 245 REMARK 465 VAL A 246 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 ARG A 37 CD NE CZ NH1 NH2 REMARK 470 LYS A 38 CD CE NZ REMARK 470 ARG A 170B CG CD NE CZ NH1 NH2 REMARK 470 LYS A 233A CD CE NZ REMARK 470 LYS A 243 CG CD CE NZ 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 OG SER A 195 O2 0G6 A 1 2.19 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 50 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 LEU A 60 CA - CB - CG ANGL. DEV. = 16.1 DEGREES REMARK 500 ASP A 129 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 170A CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 LEU A 185 CA - CB - CG ANGL. DEV. = 21.2 DEGREES REMARK 500 ASP A 221B CB - CG - OD2 ANGL. DEV. = 6.3 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 36 -151.48 -153.83 REMARK 500 ASN A 61 -168.77 -114.82 REMARK 500 HIS A 71 -59.57 -120.11 REMARK 500 ASN A 115 -151.23 -156.37 REMARK 500 ARG A 143 133.75 -39.93 REMARK 500 SER A 148 -172.39 -173.53 REMARK 500 ALA A 149 -158.38 53.83 REMARK 500 SER A 150 -159.94 -128.40 REMARK 500 ASP A 170A 159.37 -37.19 REMARK 500 HIS A 171 -120.90 -127.58 REMARK 500 ILE A 242 -77.11 -64.78 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 HIS A 171 10.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE INHIBITOR IS COVALENTLY CONNECTED TO ACTIVE_SITE REMARK 600 RESIDUES: REMARK 600 1) VIA A HEMIKETAL GROUP TO OG SER A 195, REMARK 600 2) VIA A METHYLENE GROUP TO NE2 HIS A 57. REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL] REMARK 630 AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 0G6 A 1 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO AR7 0QE REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 0G6 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 247 DBREF 1ORF A 16 246 UNP P12544 GRAA_HUMAN 29 262 SEQADV 1ORF GLU A 157 UNP P12544 ASN 170 ENGINEERED MUTATION SEQRES 1 A 234 ILE ILE GLY GLY ASN GLU VAL THR PRO HIS SER ARG PRO SEQRES 2 A 234 TYR MET VAL LEU LEU SER LEU ASP ARG LYS THR ILE CYS SEQRES 3 A 234 ALA GLY ALA LEU ILE ALA LYS ASP TRP VAL LEU THR ALA SEQRES 4 A 234 ALA HIS CYS ASN LEU ASN LYS ARG SER GLN VAL ILE LEU SEQRES 5 A 234 GLY ALA HIS SER ILE THR ARG GLU GLU PRO THR LYS GLN SEQRES 6 A 234 ILE MET LEU VAL LYS LYS GLU PHE PRO TYR PRO CYS TYR SEQRES 7 A 234 ASP PRO ALA THR ARG GLU GLY ASP LEU LYS LEU LEU GLN SEQRES 8 A 234 LEU THR GLU LYS ALA LYS ILE ASN LYS TYR VAL THR ILE SEQRES 9 A 234 LEU HIS LEU PRO LYS LYS GLY ASP ASP VAL LYS PRO GLY SEQRES 10 A 234 THR MET CYS GLN VAL ALA GLY TRP GLY ARG THR HIS ASN SEQRES 11 A 234 SER ALA SER TRP SER ASP THR LEU ARG GLU VAL GLU ILE SEQRES 12 A 234 THR ILE ILE ASP ARG LYS VAL CYS ASN ASP ARG ASN HIS SEQRES 13 A 234 TYR ASN PHE ASN PRO VAL ILE GLY MET ASN MET VAL CYS SEQRES 14 A 234 ALA GLY SER LEU ARG GLY GLY ARG ASP SER CYS ASN GLY SEQRES 15 A 234 ASP SER GLY SER PRO LEU LEU CYS GLU GLY VAL PHE ARG SEQRES 16 A 234 GLY VAL THR SER PHE GLY LEU GLU ASN LYS CYS GLY ASP SEQRES 17 A 234 PRO ARG GLY PRO GLY VAL TYR ILE LEU LEU SER LYS LYS SEQRES 18 A 234 HIS LEU ASN TRP ILE ILE MET THR ILE LYS GLY ALA VAL HET 0G6 A 1 30 HET SO4 A 247 5 HETNAM 0G6 D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO) HETNAM 2 0G6 METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L- HETNAM 3 0G6 PROLINAMIDE HETNAM SO4 SULFATE ION HETSYN 0G6 PPACK FORMUL 2 0G6 C21 H34 CL N6 O3 1+ FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *128(H2 O) HELIX 1 1 ASP A 164 ASN A 169 1 6 HELIX 2 2 SER A 232 LYS A 243 1 13 SHEET 1 A 8 ASN A 20 GLU A 21 0 SHEET 2 A 8 ARG A 156 ILE A 163 -1 O GLU A 157 N ASN A 20 SHEET 3 A 8 MET A 180 GLY A 184A-1 O GLY A 184A N THR A 161 SHEET 4 A 8 GLY A 226 LEU A 230 -1 O TYR A 228 N VAL A 181 SHEET 5 A 8 VAL A 208 PHE A 215 -1 N PHE A 215 O VAL A 227 SHEET 6 A 8 PRO A 198 CYS A 201 -1 N LEU A 199 O ARG A 210 SHEET 7 A 8 MET A 135 GLY A 140 -1 N GLN A 137 O LEU A 200 SHEET 8 A 8 ARG A 156 ILE A 163 -1 O ILE A 160 N CYS A 136 SHEET 1 B 7 GLN A 81 MET A 83 0 SHEET 2 B 7 GLN A 64 LEU A 68 -1 N VAL A 66 O MET A 83 SHEET 3 B 7 MET A 30 SER A 34 -1 N LEU A 32 O ILE A 67 SHEET 4 B 7 ILE A 40 ALA A 48 -1 O CYS A 42 N LEU A 33 SHEET 5 B 7 TRP A 51 THR A 54 -1 O LEU A 53 N ALA A 45 SHEET 6 B 7 LYS A 104 LEU A 108 -1 O LEU A 106 N VAL A 52 SHEET 7 B 7 VAL A 85 PRO A 90 -1 N LYS A 87 O GLN A 107 SSBOND 1 CYS A 42 CYS A 58 1555 1555 2.05 SSBOND 2 CYS A 93 CYS A 93 1555 3555 2.21 SSBOND 3 CYS A 136 CYS A 201 1555 1555 2.05 SSBOND 4 CYS A 168 CYS A 182 1555 1555 2.02 SSBOND 5 CYS A 191 CYS A 220 1555 1555 2.04 LINK C3 0G6 A 1 NE2 HIS A 57 1555 1555 1.54 LINK C2 0G6 A 1 OG SER A 195 1555 1555 1.38 CISPEP 1 ASN A 175A PRO A 175B 0 -10.40 SITE 1 AC1 16 HIS A 57 ASP A 189 SER A 190 CYS A 191 SITE 2 AC1 16 GLY A 193 SER A 195 SER A 214 PHE A 215 SITE 3 AC1 16 GLY A 216 GLU A 218 GLY A 226 HOH A 272 SITE 4 AC1 16 HOH A 372 HOH A 373 HOH A 374 HOH A 375 SITE 1 AC2 5 SER A 184B LEU A 185 ARG A 186 ARG A 188B SITE 2 AC2 5 HOH A 306 CRYST1 115.034 145.022 39.555 90.00 90.00 90.00 C 2 2 21 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 0.008693 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006896 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025281 0.00000