HEADER HYDROLASE 06-MAY-03 1P7W TITLE CRYSTAL STRUCTURE OF THE COMPLEX OF PROTEINASE K WITH A DESIGNED TITLE 2 HEPTAPEPTIDE INHIBITOR PRO-ALA-PRO-PHE-ALA-SER-ALA AT ATOMIC TITLE 3 RESOLUTION CAVEAT 1P7W CHIRALITY ERRORS AT CA CENTER OF B ALA 5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEINASE K; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRITIRACHIUM ALKALINE PROTEINASE, ENDOPEPTIDASE K; COMPND 5 EC: 3.4.21.64; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: INHIBITOR PEPTIDE; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENGYODONTIUM ALBUM; SOURCE 3 ORGANISM_TAXID: 37998; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES KEYWDS PROTEINASE K, ATOMIC RESOLUTION, INHIBITOR PEPTIDE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.BILGRAMI,M.PERBANDT,V.CHANDRA,S.BANUMATHI,P.KAUR,C.BETZEL,T.P.SINGH REVDAT 4 16-AUG-23 1P7W 1 REMARK SEQADV LINK REVDAT 3 09-MAR-11 1P7W 1 REMARK REVDAT 2 24-FEB-09 1P7W 1 VERSN REVDAT 1 18-MAY-04 1P7W 0 JRNL AUTH S.BILGRAMI,M.PERBANDT,V.CHANDRA,S.BANUMATHI,P.KAUR,C.BETZEL, JRNL AUTH 2 T.P.SINGH JRNL TITL CRYSTAL STRUCTURE OF THE COMPLEX OF PROTEINASE K WITH JRNL TITL 2 HEPTAPEPTIDE INHIBITOR PRO-ALA-PRO-PHE-ALA-SER-ALA AT ATOMIC JRNL TITL 3 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.02 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) : 1.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 119205 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) : 0.129 REMARK 3 R VALUE (WORKING SET) : 0.129 REMARK 3 FREE R VALUE : 0.142 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1192 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) : 1.02 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8138 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1820 REMARK 3 BIN FREE R VALUE SET COUNT : 91 REMARK 3 BIN FREE R VALUE : 0.2140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2077 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 432 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 5.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 7.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.01000 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): 0.022 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.021 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.013 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.235 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.974 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2141 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1821 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2903 ; 1.482 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4233 ; 0.919 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 284 ; 6.716 ; 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): 319 ; 0.218 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2487 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 443 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 554 ; 0.263 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2388 ; 0.276 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1107 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; 0.199 ; 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): 85 ; 0.543 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 131 ; 0.412 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 115 ; 0.409 ; 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): 1427 ; 1.066 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2231 ; 1.704 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 714 ; 2.486 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 672 ; 3.736 ; 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): 2141 ; 1.095 ; 2.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 455 ; 6.967 ; 2.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2105 ; 2.461 ; 2.000 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1P7W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAY-03. REMARK 100 THE DEPOSITION ID IS D_1000019118. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-00 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE 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 : 119205 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.020 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 15.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 FOR THE DATA SET : 24.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.23400 REMARK 200 FOR SHELL : 5.580 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 1IC6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS HCL, CACL2, NANO3, PH 6.5, REMARK 280 MICROGRAVITY WITH APCF REACTORS, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 50.78150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.91750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.91750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 76.17225 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.91750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.91750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.39075 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.91750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.91750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 76.17225 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.91750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.91750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.39075 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 50.78150 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: 1820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 HB2 ALA B 2 HD3 PRO B 3 1.28 REMARK 500 REMARK 500 REMARK: NULL 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 PRO B 3 C PRO B 3 O 0.121 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 ARG A 188 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 188 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 PRO B 3 N - CD - CG ANGL. DEV. = -10.2 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 39 -147.06 -167.90 REMARK 500 ASP A 207 61.59 60.34 REMARK 500 SER A 216 -169.65 -116.33 REMARK 500 ASN A 270 74.34 -108.32 REMARK 500 ALA B 2 -161.18 80.26 REMARK 500 PRO B 3 -149.67 -107.33 REMARK 500 ALA B 5 102.25 61.24 REMARK 500 SER B 6 64.21 -49.28 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 SER B 6 ALA B 7 -147.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 480 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO A 175 O REMARK 620 2 VAL A 177 O 89.5 REMARK 620 3 ASP A 200 OD1 150.7 112.5 REMARK 620 4 ASP A 200 OD2 157.9 79.5 50.6 REMARK 620 5 HOH A 509 O 95.7 148.5 75.8 84.4 REMARK 620 6 HOH A 510 O 79.1 75.2 123.9 79.5 75.4 REMARK 620 7 HOH A 781 O 75.8 138.7 74.9 124.6 72.3 136.4 REMARK 620 8 HOH A 831 O 91.6 71.4 78.3 102.7 139.1 145.3 70.8 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 481 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 727 O REMARK 620 2 HOH A 776 O 176.4 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 480 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 481 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NO3 A 507 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1P7V RELATED DB: PDB REMARK 900 STRUCTURE OF A COMPLEX FORMED BETWEEN PROTEINASE K AND A DESIGNED REMARK 900 HEPTAPEPTIDE INHIBITOR PRO-ALA-PRO-PHE-ALA-ALA-ALA AT ATOMIC REMARK 900 RESOLUTION DBREF 1P7W A 1 279 UNP P06873 PRTK_TRIAL 106 384 DBREF 1P7W B 1 7 PDB 1P7W 1P7W 1 7 SEQADV 1P7W ASP A 207 UNP P06873 SER 312 CONFLICT SEQRES 1 A 279 ALA ALA GLN THR ASN ALA PRO TRP GLY LEU ALA ARG ILE SEQRES 2 A 279 SER SER THR SER PRO GLY THR SER THR TYR TYR TYR ASP SEQRES 3 A 279 GLU SER ALA GLY GLN GLY SER CYS VAL TYR VAL ILE ASP SEQRES 4 A 279 THR GLY ILE GLU ALA SER HIS PRO GLU PHE GLU GLY ARG SEQRES 5 A 279 ALA GLN MET VAL LYS THR TYR TYR TYR SER SER ARG ASP SEQRES 6 A 279 GLY ASN GLY HIS GLY THR HIS CYS ALA GLY THR VAL GLY SEQRES 7 A 279 SER ARG THR TYR GLY VAL ALA LYS LYS THR GLN LEU PHE SEQRES 8 A 279 GLY VAL LYS VAL LEU ASP ASP ASN GLY SER GLY GLN TYR SEQRES 9 A 279 SER THR ILE ILE ALA GLY MET ASP PHE VAL ALA SER ASP SEQRES 10 A 279 LYS ASN ASN ARG ASN CYS PRO LYS GLY VAL VAL ALA SER SEQRES 11 A 279 LEU SER LEU GLY GLY GLY TYR SER SER SER VAL ASN SER SEQRES 12 A 279 ALA ALA ALA ARG LEU GLN SER SER GLY VAL MET VAL ALA SEQRES 13 A 279 VAL ALA ALA GLY ASN ASN ASN ALA ASP ALA ARG ASN TYR SEQRES 14 A 279 SER PRO ALA SER GLU PRO SER VAL CYS THR VAL GLY ALA SEQRES 15 A 279 SER ASP ARG TYR ASP ARG ARG SER SER PHE SER ASN TYR SEQRES 16 A 279 GLY SER VAL LEU ASP ILE PHE GLY PRO GLY THR ASP ILE SEQRES 17 A 279 LEU SER THR TRP ILE GLY GLY SER THR ARG SER ILE SER SEQRES 18 A 279 GLY THR SER MET ALA THR PRO HIS VAL ALA GLY LEU ALA SEQRES 19 A 279 ALA TYR LEU MET THR LEU GLY LYS THR THR ALA ALA SER SEQRES 20 A 279 ALA CYS ARG TYR ILE ALA ASP THR ALA ASN LYS GLY ASP SEQRES 21 A 279 LEU SER ASN ILE PRO PHE GLY THR VAL ASN LEU LEU ALA SEQRES 22 A 279 TYR ASN ASN TYR GLN ALA SEQRES 1 B 7 PRO ALA PRO PHE ALA SER ALA HET CA A 480 1 HET CA A 481 1 HET NO3 A 502 4 HET NO3 A 503 4 HET NO3 A 504 4 HET NO3 A 505 4 HET NO3 A 507 4 HETNAM CA CALCIUM ION HETNAM NO3 NITRATE ION FORMUL 3 CA 2(CA 2+) FORMUL 5 NO3 5(N O3 1-) FORMUL 10 HOH *432(H2 O) HELIX 1 1 PRO A 7 SER A 14 1 8 HELIX 2 2 HIS A 46 GLU A 50 5 5 HELIX 3 3 GLY A 68 SER A 79 1 12 HELIX 4 4 GLN A 103 LYS A 118 1 16 HELIX 5 5 ASN A 119 ARG A 121 5 3 HELIX 6 6 SER A 138 SER A 151 1 14 HELIX 7 7 ASP A 165 ARG A 167 5 3 HELIX 8 8 GLY A 222 LEU A 240 1 19 HELIX 9 9 SER A 247 ALA A 256 1 10 SHEET 1 A 2 ALA A 2 GLN A 3 0 SHEET 2 A 2 TYR A 23 TYR A 24 -1 O TYR A 23 N GLN A 3 SHEET 1 B 7 ALA A 53 THR A 58 0 SHEET 2 B 7 GLN A 89 LYS A 94 1 O LYS A 94 N LYS A 57 SHEET 3 B 7 SER A 33 ASP A 39 1 N VAL A 35 O GLN A 89 SHEET 4 B 7 GLY A 126 LEU A 131 1 O SER A 130 N TYR A 36 SHEET 5 B 7 VAL A 153 ALA A 158 1 O MET A 154 N ALA A 129 SHEET 6 B 7 CYS A 178 SER A 183 1 O VAL A 180 N VAL A 157 SHEET 7 B 7 ILE A 201 PRO A 204 1 O ILE A 201 N GLY A 181 SHEET 1 C 2 GLY A 135 GLY A 136 0 SHEET 2 C 2 TYR A 169 SER A 170 -1 O SER A 170 N GLY A 135 SHEET 1 D 2 ILE A 208 TRP A 212 0 SHEET 2 D 2 SER A 216 ILE A 220 -1 O ILE A 220 N ILE A 208 SHEET 1 E 2 ASN A 257 LYS A 258 0 SHEET 2 E 2 LEU A 271 LEU A 272 -1 O LEU A 272 N ASN A 257 SSBOND 1 CYS A 34 CYS A 123 1555 1555 2.03 SSBOND 2 CYS A 178 CYS A 249 1555 1555 2.03 LINK O PRO A 175 CA CA A 480 1555 1555 2.39 LINK O VAL A 177 CA CA A 480 1555 1555 2.39 LINK OD1 ASP A 200 CA CA A 480 1555 1555 2.67 LINK OD2 ASP A 200 CA CA A 480 1555 1555 2.43 LINK CA CA A 480 O HOH A 509 1555 1555 2.43 LINK CA CA A 480 O HOH A 510 1555 1555 2.42 LINK CA CA A 480 O HOH A 781 1555 1555 2.50 LINK CA CA A 480 O HOH A 831 1555 1555 2.41 LINK CA CA A 481 O HOH A 727 1555 1555 2.85 LINK CA CA A 481 O HOH A 776 1555 1555 3.30 CISPEP 1 SER A 170 PRO A 171 0 0.04 SITE 1 AC1 7 PRO A 175 VAL A 177 ASP A 200 HOH A 509 SITE 2 AC1 7 HOH A 510 HOH A 781 HOH A 831 SITE 1 AC2 4 SER A 17 GLN A 31 GLY A 32 HOH A 727 SITE 1 AC3 5 LYS A 258 GLY A 259 ASN A 270 HOH A 590 SITE 2 AC3 5 HOH A 793 SITE 1 AC4 7 TYR A 60 TYR A 61 LYS A 94 ASP A 97 SITE 2 AC4 7 ASP A 98 HOH A 539 HOH A 635 SITE 1 AC5 7 ARG A 64 ASP A 165 ARG A 167 ASN A 168 SITE 2 AC5 7 GLY A 214 HOH A 637 HOH A 639 SITE 1 AC6 7 TYR A 104 SER A 105 ILE A 108 SER A 140 SITE 2 AC6 7 HOH A 690 HOH A 759 HOH A 837 SITE 1 AC7 7 MET A 55 VAL A 56 LYS A 57 THR A 58 SITE 2 AC7 7 SER A 63 HOH A 730 HOH A 764 CRYST1 67.835 67.835 101.563 90.00 90.00 90.00 P 43 21 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 0.014742 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014742 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009846 0.00000