HEADER TOXIN/PEPTIDE INHIBITOR 18-OCT-10 3PA8 TITLE STRUCTURE OF THE C. DIFFICILE TCDB CYSTEINE PROTEASE DOMAIN IN COMPLEX TITLE 2 WITH A PEPTIDE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOXIN B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 544-797; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM DIFFICILE; SOURCE 3 ORGANISM_TAXID: 272563; SOURCE 4 STRAIN: 630; SOURCE 5 GENE: CD0660, TCDB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS CLAN CD CYSTEINE PROTEASE, PROTEASE, TOXIN, TOXIN-PEPTIDE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.J.LUPARDUS,K.C.GARCIA REVDAT 6 16-OCT-24 3PA8 1 REMARK REVDAT 5 06-SEP-23 3PA8 1 REMARK REVDAT 4 14-OCT-20 3PA8 1 REMARK HETSYN LINK REVDAT 3 13-JUL-11 3PA8 1 VERSN REVDAT 2 22-DEC-10 3PA8 1 JRNL REVDAT 1 15-DEC-10 3PA8 0 JRNL AUTH A.W.PURI,P.J.LUPARDUS,E.DEU,V.E.ALBROW,K.C.GARCIA,M.BOGYO, JRNL AUTH 2 A.SHEN JRNL TITL RATIONAL DESIGN OF INHIBITORS AND ACTIVITY-BASED PROBES JRNL TITL 2 TARGETING CLOSTRIDIUM DIFFICILE VIRULENCE FACTOR TCDB. JRNL REF CHEM.BIOL. V. 17 1201 2010 JRNL REFN ISSN 1074-5521 JRNL PMID 21095570 JRNL DOI 10.1016/J.CHEMBIOL.2010.09.011 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 31754 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1692 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2328 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 101 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3886 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 119 REMARK 3 SOLVENT ATOMS : 286 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.22000 REMARK 3 B22 (A**2) : 1.47000 REMARK 3 B33 (A**2) : -0.97000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.60000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.174 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.128 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.154 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4071 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5511 ; 1.304 ; 2.004 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 485 ; 5.523 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 185 ;38.589 ;25.946 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 752 ;13.978 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;15.314 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 615 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2973 ; 0.004 ; 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): 2439 ; 0.560 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3964 ; 1.076 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1632 ; 1.667 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1547 ; 2.719 ; 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 -10 A 9999 REMARK 3 ORIGIN FOR THE GROUP (A): 20.9941 11.3946 23.7716 REMARK 3 T TENSOR REMARK 3 T11: 0.0578 T22: 0.0699 REMARK 3 T33: 0.0441 T12: -0.0432 REMARK 3 T13: 0.0013 T23: 0.0177 REMARK 3 L TENSOR REMARK 3 L11: 1.4985 L22: 1.0178 REMARK 3 L33: 1.7819 L12: -0.2224 REMARK 3 L13: 0.3725 L23: -0.2677 REMARK 3 S TENSOR REMARK 3 S11: -0.0316 S12: -0.1052 S13: 0.0689 REMARK 3 S21: -0.0846 S22: 0.0218 S23: 0.0273 REMARK 3 S31: 0.0218 S32: -0.0850 S33: 0.0098 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 : B -10 B 9999 REMARK 3 ORIGIN FOR THE GROUP (A): 52.0775 18.2508 19.3863 REMARK 3 T TENSOR REMARK 3 T11: 0.0537 T22: 0.0759 REMARK 3 T33: 0.0750 T12: -0.0284 REMARK 3 T13: 0.0060 T23: 0.0622 REMARK 3 L TENSOR REMARK 3 L11: 2.0130 L22: 1.2686 REMARK 3 L33: 2.4315 L12: 0.1009 REMARK 3 L13: 0.6811 L23: -0.3868 REMARK 3 S TENSOR REMARK 3 S11: -0.0741 S12: 0.1965 S13: 0.1763 REMARK 3 S21: -0.0124 S22: -0.0398 S23: -0.0109 REMARK 3 S31: -0.0376 S32: 0.2035 S33: 0.1138 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: NULL REMARK 4 REMARK 4 3PA8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000062151. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33449 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.53400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900 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 3HO6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS HCL PH 8.0, 30% PEG2000 MME, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 64.15500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.74000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 64.15500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.74000 REMARK 290 SMTRY3 4 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 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: 2950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -68.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 339 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 375 LIES ON A SPECIAL POSITION. 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 GLY A 1 REMARK 465 GLU A 2 REMARK 465 ASP A 3 REMARK 465 ASP A 4 REMARK 465 ASN A 5 REMARK 465 LEU A 6 REMARK 465 PRO A 252 REMARK 465 GLU A 253 REMARK 465 LEU A 254 REMARK 465 GLY B 1 REMARK 465 GLU B 2 REMARK 465 ASP B 3 REMARK 465 ASP B 4 REMARK 465 ASN B 5 REMARK 465 LEU B 6 REMARK 465 ASP B 7 REMARK 465 PHE B 8 REMARK 465 SER B 9 REMARK 465 PRO B 252 REMARK 465 GLU B 253 REMARK 465 LEU B 254 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 GLU A 84 CG CD OE1 OE2 REMARK 470 GLU A 114 CG CD OE1 OE2 REMARK 470 ASP B 113 CG OD1 OD2 REMARK 470 GLU B 114 CG CD OE1 OE2 REMARK 470 LYS B 240 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD1 ASN A 79 OH TYR A 199 1565 2.05 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 VAL A 14 122.57 -33.01 REMARK 500 ASP A 71 17.74 58.14 REMARK 500 TYR A 199 -154.36 -126.28 REMARK 500 TYR B 91 18.94 58.85 REMARK 500 TYR B 199 -150.02 -130.62 REMARK 500 ASP B 213 -162.71 -75.50 REMARK 500 LYS B 232 171.14 176.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE STARTING PEPTIDE INHIBITOR IS ACE-GLY-SER-LEU ACYL-OXY-METHYL- REMARK 600 KETONE. UPON REACTION IT FORMS COVALENT BOND THROUGH CAC ATOM OF REMARK 600 THE 621 INHIBITOR TO CYS 155 OF THE PROTEIN 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 255 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 IHP A 257 O23 REMARK 620 2 IHP A 257 O32 91.3 REMARK 620 3 HOH A 260 O 105.2 90.9 REMARK 620 4 IHP B 256 O33 172.8 89.1 82.0 REMARK 620 5 IHP B 256 O32 83.8 162.1 106.9 93.6 REMARK 620 6 HOH B 258 O 93.6 81.0 159.8 79.3 82.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 256 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 IHP A 257 O24 REMARK 620 2 IHP A 257 O45 109.7 REMARK 620 3 IHP A 257 O15 86.4 49.8 REMARK 620 4 HOH A 262 O 117.2 88.0 59.9 REMARK 620 5 HOH A 274 O 120.6 108.3 151.9 108.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 255 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 IHP B 256 O46 REMARK 620 2 IHP B 256 O15 62.0 REMARK 620 3 HOH B 259 O 121.4 63.1 REMARK 620 4 HOH B 305 O 85.4 113.2 135.3 REMARK 620 5 HOH B 308 O 120.4 147.5 96.3 99.1 REMARK 620 N 1 2 3 4 REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: N-ACETYLGLYCYL-N-[(3S)-1-HYDROXY-5-METHYL-2- REMARK 630 OXOHEXAN-3-YL]-L-SERINAMIDE 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 630 621 A 300 REMARK 630 621 B 300 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: ACE GLY SER LEX 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 621 B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 621 A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 255 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 256 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 255 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IHP B 256 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IHP A 257 DBREF 3PA8 A 1 254 UNP Q189K3 Q189K3_CLOD6 544 797 DBREF 3PA8 B 1 254 UNP Q189K3 Q189K3_CLOD6 544 797 SEQRES 1 A 254 GLY GLU ASP ASP ASN LEU ASP PHE SER GLN ASN ILE VAL SEQRES 2 A 254 VAL ASP LYS GLU TYR LEU LEU GLU LYS ILE SER SER LEU SEQRES 3 A 254 ALA ARG SER SER GLU ARG GLY TYR ILE HIS TYR ILE VAL SEQRES 4 A 254 GLN LEU GLN GLY ASP LYS ILE SER TYR GLU ALA ALA CYS SEQRES 5 A 254 ASN LEU PHE ALA LYS THR PRO TYR ASP SER VAL LEU PHE SEQRES 6 A 254 GLN LYS ASN ILE GLU ASP SER GLU ILE ALA TYR TYR TYR SEQRES 7 A 254 ASN PRO GLY ASP GLY GLU ILE GLN GLU ILE ASP LYS TYR SEQRES 8 A 254 LYS ILE PRO SER ILE ILE SER ASP ARG PRO LYS ILE LYS SEQRES 9 A 254 LEU THR PHE ILE GLY HIS GLY LYS ASP GLU PHE ASN THR SEQRES 10 A 254 ASP ILE PHE ALA GLY PHE ASP VAL ASP SER LEU SER THR SEQRES 11 A 254 GLU ILE GLU ALA ALA ILE ASP LEU ALA LYS GLU ASP ILE SEQRES 12 A 254 SER PRO LYS SER ILE GLU ILE ASN LEU LEU GLY CYS ASN SEQRES 13 A 254 MET PHE SER TYR SER ILE ASN VAL GLU GLU THR TYR PRO SEQRES 14 A 254 GLY LYS LEU LEU LEU LYS VAL LYS ASP LYS ILE SER GLU SEQRES 15 A 254 LEU MET PRO SER ILE SER GLN ASP SER ILE ILE VAL SER SEQRES 16 A 254 ALA ASN GLN TYR GLU VAL ARG ILE ASN SER GLU GLY ARG SEQRES 17 A 254 ARG GLU LEU LEU ASP HIS SER GLY GLU TRP ILE ASN LYS SEQRES 18 A 254 GLU GLU SER ILE ILE LYS ASP ILE SER SER LYS GLU TYR SEQRES 19 A 254 ILE SER PHE ASN PRO LYS GLU ASN LYS ILE THR VAL LYS SEQRES 20 A 254 SER LYS ASN LEU PRO GLU LEU SEQRES 1 B 254 GLY GLU ASP ASP ASN LEU ASP PHE SER GLN ASN ILE VAL SEQRES 2 B 254 VAL ASP LYS GLU TYR LEU LEU GLU LYS ILE SER SER LEU SEQRES 3 B 254 ALA ARG SER SER GLU ARG GLY TYR ILE HIS TYR ILE VAL SEQRES 4 B 254 GLN LEU GLN GLY ASP LYS ILE SER TYR GLU ALA ALA CYS SEQRES 5 B 254 ASN LEU PHE ALA LYS THR PRO TYR ASP SER VAL LEU PHE SEQRES 6 B 254 GLN LYS ASN ILE GLU ASP SER GLU ILE ALA TYR TYR TYR SEQRES 7 B 254 ASN PRO GLY ASP GLY GLU ILE GLN GLU ILE ASP LYS TYR SEQRES 8 B 254 LYS ILE PRO SER ILE ILE SER ASP ARG PRO LYS ILE LYS SEQRES 9 B 254 LEU THR PHE ILE GLY HIS GLY LYS ASP GLU PHE ASN THR SEQRES 10 B 254 ASP ILE PHE ALA GLY PHE ASP VAL ASP SER LEU SER THR SEQRES 11 B 254 GLU ILE GLU ALA ALA ILE ASP LEU ALA LYS GLU ASP ILE SEQRES 12 B 254 SER PRO LYS SER ILE GLU ILE ASN LEU LEU GLY CYS ASN SEQRES 13 B 254 MET PHE SER TYR SER ILE ASN VAL GLU GLU THR TYR PRO SEQRES 14 B 254 GLY LYS LEU LEU LEU LYS VAL LYS ASP LYS ILE SER GLU SEQRES 15 B 254 LEU MET PRO SER ILE SER GLN ASP SER ILE ILE VAL SER SEQRES 16 B 254 ALA ASN GLN TYR GLU VAL ARG ILE ASN SER GLU GLY ARG SEQRES 17 B 254 ARG GLU LEU LEU ASP HIS SER GLY GLU TRP ILE ASN LYS SEQRES 18 B 254 GLU GLU SER ILE ILE LYS ASP ILE SER SER LYS GLU TYR SEQRES 19 B 254 ILE SER PHE ASN PRO LYS GLU ASN LYS ILE THR VAL LYS SEQRES 20 B 254 SER LYS ASN LEU PRO GLU LEU HET 621 A 300 22 HET CA A 255 1 HET NA A 256 1 HET IHP A 257 36 HET 621 B 300 22 HET NA B 255 1 HET IHP B 256 36 HETNAM 621 N-ACETYLGLYCYL-N-[(3S)-1-HYDROXY-5-METHYL-2-OXOHEXAN-3- HETNAM 2 621 YL]-L-SERINAMIDE HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM IHP INOSITOL HEXAKISPHOSPHATE HETSYN IHP MYO-INOSITOL HEXAKISPHOSPHATE; INOSITOL 1,2,3,4,5,6- HETSYN 2 IHP HEXAKISPHOSPHATE FORMUL 3 621 2(C14 H25 N3 O6) FORMUL 4 CA CA 2+ FORMUL 5 NA 2(NA 1+) FORMUL 6 IHP 2(C6 H18 O24 P6) FORMUL 10 HOH *286(H2 O) HELIX 1 1 ASP A 15 ALA A 27 1 13 HELIX 2 2 ASP A 44 THR A 58 1 15 HELIX 3 3 VAL A 125 LYS A 140 1 16 HELIX 4 4 ASN A 163 GLU A 166 5 4 HELIX 5 5 THR A 167 MET A 184 1 18 HELIX 6 6 SER A 188 ASP A 190 5 3 HELIX 7 7 ASN A 220 LYS A 227 1 8 HELIX 8 8 ASP B 15 ALA B 27 1 13 HELIX 9 9 ASP B 44 THR B 58 1 15 HELIX 10 10 VAL B 125 LYS B 140 1 16 HELIX 11 11 ASN B 163 GLU B 166 5 4 HELIX 12 12 THR B 167 MET B 184 1 18 HELIX 13 13 SER B 188 ASP B 190 5 3 HELIX 14 14 ASN B 220 LYS B 227 1 8 SHEET 1 A 9 GLU A 84 ASP A 89 0 SHEET 2 A 9 ILE A 74 ASN A 79 -1 N ALA A 75 O ILE A 88 SHEET 3 A 9 SER A 62 GLN A 66 -1 N LEU A 64 O TYR A 76 SHEET 4 A 9 ILE A 35 GLN A 40 1 N ILE A 38 O VAL A 63 SHEET 5 A 9 LYS A 102 ILE A 108 1 O LYS A 104 N ILE A 35 SHEET 6 A 9 SER A 147 LEU A 153 1 O GLU A 149 N LEU A 105 SHEET 7 A 9 ILE A 192 ALA A 196 1 O ILE A 193 N ILE A 150 SHEET 8 A 9 GLU A 233 PHE A 237 -1 O GLU A 233 N ALA A 196 SHEET 9 A 9 ILE A 244 SER A 248 -1 O LYS A 247 N TYR A 234 SHEET 1 B 2 ILE A 119 PHE A 120 0 SHEET 2 B 2 PHE A 123 ASP A 124 -1 O PHE A 123 N PHE A 120 SHEET 1 C 3 VAL A 201 ILE A 203 0 SHEET 2 C 3 ARG A 209 LEU A 212 -1 O GLU A 210 N ARG A 202 SHEET 3 C 3 TRP A 218 ILE A 219 -1 O ILE A 219 N LEU A 211 SHEET 1 D 7 SER B 62 GLN B 66 0 SHEET 2 D 7 ILE B 35 GLN B 40 1 N ILE B 38 O VAL B 63 SHEET 3 D 7 LYS B 102 ILE B 108 1 O LYS B 104 N ILE B 35 SHEET 4 D 7 SER B 147 LEU B 153 1 O GLU B 149 N LEU B 105 SHEET 5 D 7 ILE B 192 ALA B 196 1 O ILE B 193 N ILE B 150 SHEET 6 D 7 GLU B 233 ASN B 238 -1 O ILE B 235 N VAL B 194 SHEET 7 D 7 LYS B 243 SER B 248 -1 O LYS B 247 N TYR B 234 SHEET 1 E 2 ILE B 74 ASN B 79 0 SHEET 2 E 2 GLU B 84 ASP B 89 -1 O ILE B 88 N ALA B 75 SHEET 1 F 2 ILE B 119 PHE B 120 0 SHEET 2 F 2 PHE B 123 ASP B 124 -1 O PHE B 123 N PHE B 120 SHEET 1 G 3 VAL B 201 ILE B 203 0 SHEET 2 G 3 ARG B 209 LEU B 212 -1 O GLU B 210 N ARG B 202 SHEET 3 G 3 TRP B 218 ILE B 219 -1 O ILE B 219 N LEU B 211 LINK SG CYS A 155 CAC 621 A 300 1555 1555 1.49 LINK SG CYS B 155 CAC 621 B 300 1555 1555 1.51 LINK CA CA A 255 O23 IHP A 257 1555 1555 2.15 LINK CA CA A 255 O32 IHP A 257 1555 1555 2.35 LINK CA CA A 255 O HOH A 260 1555 1555 2.46 LINK CA CA A 255 O33 IHP B 256 1555 1555 2.32 LINK CA CA A 255 O32 IHP B 256 1555 1555 2.39 LINK CA CA A 255 O HOH B 258 1555 1555 2.39 LINK NA NA A 256 O24 IHP A 257 1555 1555 2.77 LINK NA NA A 256 O45 IHP A 257 1555 1555 2.78 LINK NA NA A 256 O15 IHP A 257 1555 1555 3.04 LINK NA NA A 256 O HOH A 262 1555 1555 2.80 LINK NA NA A 256 O HOH A 274 1555 1555 2.72 LINK NA NA B 255 O46 IHP B 256 1555 1555 2.65 LINK NA NA B 255 O15 IHP B 256 1555 1555 3.06 LINK NA NA B 255 O HOH B 259 1555 1555 2.79 LINK NA NA B 255 O HOH B 305 1555 1555 2.94 LINK NA NA B 255 O HOH B 308 1555 1555 2.74 SITE 1 AC1 12 ASP A 71 ILE B 46 GLY B 109 HIS B 110 SITE 2 AC1 12 GLY B 111 CYS B 155 GLU B 200 VAL B 201 SITE 3 AC1 12 ARG B 202 TRP B 218 HOH B 299 HOH B 358 SITE 1 AC2 14 GLU A 17 GLU A 21 ILE A 46 GLY A 109 SITE 2 AC2 14 HIS A 110 GLY A 111 CYS A 155 GLU A 200 SITE 3 AC2 14 VAL A 201 ARG A 202 TRP A 218 HOH A 303 SITE 4 AC2 14 HOH A 314 HOH A 410 SITE 1 AC3 4 IHP A 257 HOH A 260 IHP B 256 HOH B 258 SITE 1 AC4 5 ARG A 208 LYS A 221 IHP A 257 HOH A 262 SITE 2 AC4 5 HOH A 274 SITE 1 AC5 5 ARG B 209 IHP B 256 HOH B 259 HOH B 305 SITE 2 AC5 5 HOH B 308 SITE 1 AC6 29 CA A 255 IHP A 257 HOH A 260 ARG B 28 SITE 2 AC6 29 ARG B 32 TYR B 34 LEU B 54 LYS B 57 SITE 3 AC6 29 LYS B 104 ARG B 208 ARG B 209 LYS B 221 SITE 4 AC6 29 LYS B 232 TYR B 234 LYS B 249 NA B 255 SITE 5 AC6 29 HOH B 258 HOH B 259 HOH B 260 HOH B 265 SITE 6 AC6 29 HOH B 266 HOH B 288 HOH B 305 HOH B 319 SITE 7 AC6 29 HOH B 335 HOH B 349 HOH B 351 HOH B 353 SITE 8 AC6 29 HOH B 356 SITE 1 AC7 29 ARG A 28 ARG A 32 TYR A 34 LEU A 54 SITE 2 AC7 29 LYS A 57 LYS A 104 ARG A 208 ARG A 209 SITE 3 AC7 29 LYS A 221 LYS A 232 TYR A 234 LYS A 249 SITE 4 AC7 29 CA A 255 NA A 256 HOH A 260 HOH A 262 SITE 5 AC7 29 HOH A 270 HOH A 291 HOH A 293 HOH A 295 SITE 6 AC7 29 HOH A 318 HOH A 336 HOH A 345 HOH A 358 SITE 7 AC7 29 HOH A 359 HOH A 412 HOH A 417 IHP B 256 SITE 8 AC7 29 HOH B 258 CRYST1 128.310 45.480 87.230 90.00 103.53 90.00 C 1 2 1 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 0.007794 0.000000 0.001875 0.00000 SCALE2 0.000000 0.021988 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011791 0.00000