HEADER HYDROLASE 19-NOV-23 8V15 TITLE HUMAN SIRT3 BOUND TO P53-AMC PEPTIDE, CARBA-NAD, AND HONOKIOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: GLN-PRO-LYS-FDL; COMPND 7 CHAIN: B, D; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: RESIDUES 317-320 OF ACETYLATED P53 -- QPK(KAC) -- COMPND 10 LINKED TO 7-AMINO-4-METHYLCOUMARIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SIRT3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS ACTIVATOR, COMPLEX, DEACYLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.CHAKRABARTI,A.GHOSH,X.GUAN,A.UPADHYAY,R.K.DUMPATI,S.MUNSHI,S.ROY, AUTHOR 2 S.CHALL,A.RAHNAMOUN,C.REVERDY,G.ERRASTI,T.DELACROIX REVDAT 1 06-DEC-23 8V15 0 JRNL AUTH R.CHAKRABARTI,A.GHOSH,X.GUAN,A.UPADHYAY,R.K.DUMPATI, JRNL AUTH 2 S.MUNSHI,S.ROY,S.CHALL,A.RAHNAMOUN,C.REVERDY,G.ERRASTI, JRNL AUTH 3 T.DELACROIX JRNL TITL COMPUTATIONALLY DRIVEN DISCOVERY AND CHARACTERIZATION OF JRNL TITL 2 SIRT3 ACTIVATING COMPOUNDS THAT FULLY RECOVER CATALYTIC JRNL TITL 3 ACTIVITY UNDER NAD+ DEPLETION JRNL REF BIORXIV 2023 JRNL REFN ISSN 2692-8205 JRNL DOI 10.1101/2023.11.09.566481 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0419 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) : 44.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 20550 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.303 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1038 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) : 1310 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4286 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 110 REMARK 3 SOLVENT ATOMS : 31 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.43000 REMARK 3 B22 (A**2) : -0.15000 REMARK 3 B33 (A**2) : -0.29000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.12000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.608 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.348 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.301 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.322 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.891 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4529 ; 0.016 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 4301 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6194 ; 2.914 ; 1.844 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9891 ; 0.957 ; 1.731 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 547 ; 9.779 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 43 ;22.072 ; 5.349 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 685 ;18.943 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 707 ; 0.131 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5235 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1017 ; 0.002 ; 0.020 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): 2194 ; 9.938 ; 5.495 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2191 ; 9.939 ; 5.494 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2730 ;12.832 ; 9.832 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2729 ;12.833 ; 9.831 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2335 ;11.318 ; 6.287 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2336 ;11.316 ; 6.288 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3462 ;15.754 ;11.275 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5350 ;18.661 ;60.340 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5348 ;18.663 ;60.350 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 8V15 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1000279200. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21620 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 44.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 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) : 2.44 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SIRT3 (118-399) (10.3 MG/ML) WAS REMARK 280 CRYSTALLIZED IN COMPLEX WITH FDL (QPKKAC-7-AMINO-4- REMARK 280 METHYLCOUMARIN) PEPTIDE (3 MM) AND HONOKIOL (1 MM) IN 25% PEG REMARK 280 3350, 0.2 M LI2SO4 (OR 0.2 M NACL), AND 0.1M HEPES, PH 7.5 AS REMARK 280 RESERVOIR. FOLLOWING FORMATION OF THE TERNARY COMPLEX, CRYSTALS REMARK 280 WERE SOAKED WITH CARBA-NAD (10 MM)., VAPOR DIFFUSION, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 79.71600 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 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: 2070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 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: 2200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 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 SER A 118 REMARK 465 ASP A 119 REMARK 465 LYS A 120 REMARK 465 SER A 159 REMARK 465 PRO A 160 REMARK 465 GLY A 161 REMARK 465 LEU A 394 REMARK 465 ASP A 395 REMARK 465 GLY A 396 REMARK 465 PRO A 397 REMARK 465 ASP A 398 REMARK 465 LYS A 399 REMARK 465 SER C 118 REMARK 465 ASP C 119 REMARK 465 LYS C 120 REMARK 465 GLY C 121 REMARK 465 TYR C 171 REMARK 465 LEU C 394 REMARK 465 ASP C 395 REMARK 465 GLY C 396 REMARK 465 PRO C 397 REMARK 465 ASP C 398 REMARK 465 LYS C 399 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 LYS A 122 CG CD CE NZ REMARK 470 ARG A 158 CG CD NE CZ NH1 NH2 REMARK 470 SER A 162 OG REMARK 470 SER A 166 OG REMARK 470 ASN A 167 CG OD1 ND2 REMARK 470 GLN A 169 CG CD OE1 NE2 REMARK 470 LYS A 190 CG CD CE NZ REMARK 470 ARG A 261 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 1 CG CD OE1 NE2 REMARK 470 LYS C 122 CG CD CE NZ REMARK 470 ARG C 135 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 190 CG CD CE NZ REMARK 470 ARG C 261 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 325 CG CD OE1 OE2 REMARK 470 GLN D 1 CG CD OE1 NE2 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 O TYR A 165 N LEU A 168 2.03 REMARK 500 OG SER A 321 OE1 GLU A 323 2.10 REMARK 500 OAY FDL D 4 O3D CNA C 403 2.15 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 A 201 CD PRO A 201 N 0.107 REMARK 500 PRO C 160 CD PRO C 160 N 0.161 REMARK 500 SER C 372 CA SER C 372 CB -0.110 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 133 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 139 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 GLU A 177 CB - CA - C ANGL. DEV. = 13.7 DEGREES REMARK 500 LEU A 213 CB - CG - CD1 ANGL. DEV. = 11.1 DEGREES REMARK 500 ARG A 214 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 214 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 279 CD - NE - CZ ANGL. DEV. = 8.5 DEGREES REMARK 500 LEU A 322 CB - CG - CD1 ANGL. DEV. = -10.9 DEGREES REMARK 500 ASP A 346 CB - CA - C ANGL. DEV. = -14.3 DEGREES REMARK 500 ARG A 356 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 356 NE - CZ - NH2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG A 358 CB - CA - C ANGL. DEV. = 12.1 DEGREES REMARK 500 ARG A 358 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 358 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 LEU A 363 CB - CG - CD1 ANGL. DEV. = -10.6 DEGREES REMARK 500 ARG A 389 CD - NE - CZ ANGL. DEV. = 9.7 DEGREES REMARK 500 ARG A 389 NE - CZ - NH1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ARG A 389 NE - CZ - NH2 ANGL. DEV. = -9.1 DEGREES REMARK 500 ARG C 139 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 PHE C 157 N - CA - CB ANGL. DEV. = -12.8 DEGREES REMARK 500 GLU C 177 CB - CA - C ANGL. DEV. = 12.4 DEGREES REMARK 500 GLU C 198 CB - CA - C ANGL. DEV. = 14.7 DEGREES REMARK 500 MET C 273 CG - SD - CE ANGL. DEV. = 10.6 DEGREES REMARK 500 MET C 311 CG - SD - CE ANGL. DEV. = 9.9 DEGREES REMARK 500 GLU C 325 CB - CA - C ANGL. DEV. = 13.4 DEGREES REMARK 500 THR C 331 CA - CB - OG1 ANGL. DEV. = -18.5 DEGREES REMARK 500 ARG C 335 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG C 340 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG C 356 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG C 356 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG C 358 CD - NE - CZ ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG C 358 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG C 358 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG C 389 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 THR C 391 CA - CB - OG1 ANGL. DEV. = -20.4 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 134 33.59 -88.94 REMARK 500 ARG A 135 49.43 -0.25 REMARK 500 SER A 166 -47.44 -22.05 REMARK 500 ASP A 172 112.70 52.46 REMARK 500 GLN A 260 -7.60 74.60 REMARK 500 THR A 284 -7.25 84.88 REMARK 500 ASP A 290 36.68 -75.97 REMARK 500 LEU A 304 -6.91 -56.83 REMARK 500 ASN A 344 154.00 171.46 REMARK 500 VAL A 348 -54.10 18.96 REMARK 500 HIS A 354 58.62 -149.83 REMARK 500 ALA C 134 11.87 -67.31 REMARK 500 ARG C 135 27.29 31.51 REMARK 500 ASP C 156 -168.80 -113.78 REMARK 500 PHE C 157 -90.50 -141.52 REMARK 500 ARG C 158 81.08 -37.02 REMARK 500 SER C 162 177.59 -40.19 REMARK 500 LEU C 164 -54.05 -25.92 REMARK 500 SER C 166 -49.30 -29.37 REMARK 500 TYR C 175 135.31 170.30 REMARK 500 ASN C 188 94.66 -162.95 REMARK 500 ASN C 203 -81.60 -76.72 REMARK 500 ASP C 267 -8.26 -59.53 REMARK 500 THR C 284 9.80 44.65 REMARK 500 ASP C 290 44.18 -81.15 REMARK 500 VAL C 324 123.04 -176.06 REMARK 500 HIS C 354 59.53 -145.34 REMARK 500 PRO D 2 -177.30 -64.29 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 ASP A 172 LEU A 173 140.35 REMARK 500 ASP C 156 PHE C 157 -142.41 REMARK 500 PHE C 157 ARG C 158 131.43 REMARK 500 GLY C 163 LEU C 164 135.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 133 0.14 SIDE CHAIN REMARK 500 ARG A 135 0.10 SIDE CHAIN REMARK 500 ARG A 279 0.14 SIDE CHAIN REMARK 500 ARG A 345 0.08 SIDE CHAIN REMARK 500 ARG A 356 0.11 SIDE CHAIN REMARK 500 ARG A 358 0.15 SIDE CHAIN REMARK 500 ARG A 389 0.13 SIDE CHAIN REMARK 500 ARG C 133 0.21 SIDE CHAIN REMARK 500 ARG C 276 0.12 SIDE CHAIN 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 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 256 SG REMARK 620 2 CYS A 259 SG 103.8 REMARK 620 3 CYS A 280 SG 102.1 96.7 REMARK 620 4 CYS A 283 SG 98.2 132.9 118.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 256 SG REMARK 620 2 CYS C 259 SG 104.7 REMARK 620 3 CYS C 280 SG 112.3 100.8 REMARK 620 4 CYS C 283 SG 92.4 127.5 118.1 REMARK 620 N 1 2 3 DBREF 8V15 A 118 399 UNP Q9NTG7 SIR3_HUMAN 118 399 DBREF 8V15 B 1 4 PDB 8V15 8V15 1 4 DBREF 8V15 C 118 399 UNP Q9NTG7 SIR3_HUMAN 118 399 DBREF 8V15 D 1 4 PDB 8V15 8V15 1 4 SEQRES 1 A 282 SER ASP LYS GLY LYS LEU SER LEU GLN ASP VAL ALA GLU SEQRES 2 A 282 LEU ILE ARG ALA ARG ALA CYS GLN ARG VAL VAL VAL MET SEQRES 3 A 282 VAL GLY ALA GLY ILE SER THR PRO SER GLY ILE PRO ASP SEQRES 4 A 282 PHE ARG SER PRO GLY SER GLY LEU TYR SER ASN LEU GLN SEQRES 5 A 282 GLN TYR ASP LEU PRO TYR PRO GLU ALA ILE PHE GLU LEU SEQRES 6 A 282 PRO PHE PHE PHE HIS ASN PRO LYS PRO PHE PHE THR LEU SEQRES 7 A 282 ALA LYS GLU LEU TYR PRO GLY ASN TYR LYS PRO ASN VAL SEQRES 8 A 282 THR HIS TYR PHE LEU ARG LEU LEU HIS ASP LYS GLY LEU SEQRES 9 A 282 LEU LEU ARG LEU TYR THR GLN ASN ILE ASP GLY LEU GLU SEQRES 10 A 282 ARG VAL SER GLY ILE PRO ALA SER LYS LEU VAL GLU ALA SEQRES 11 A 282 HIS GLY THR PHE ALA SER ALA THR CYS THR VAL CYS GLN SEQRES 12 A 282 ARG PRO PHE PRO GLY GLU ASP ILE ARG ALA ASP VAL MET SEQRES 13 A 282 ALA ASP ARG VAL PRO ARG CYS PRO VAL CYS THR GLY VAL SEQRES 14 A 282 VAL LYS PRO ASP ILE VAL PHE PHE GLY GLU PRO LEU PRO SEQRES 15 A 282 GLN ARG PHE LEU LEU HIS VAL VAL ASP PHE PRO MET ALA SEQRES 16 A 282 ASP LEU LEU LEU ILE LEU GLY THR SER LEU GLU VAL GLU SEQRES 17 A 282 PRO PHE ALA SER LEU THR GLU ALA VAL ARG SER SER VAL SEQRES 18 A 282 PRO ARG LEU LEU ILE ASN ARG ASP LEU VAL GLY PRO LEU SEQRES 19 A 282 ALA TRP HIS PRO ARG SER ARG ASP VAL ALA GLN LEU GLY SEQRES 20 A 282 ASP VAL VAL HIS GLY VAL GLU SER LEU VAL GLU LEU LEU SEQRES 21 A 282 GLY TRP THR GLU GLU MET ARG ASP LEU VAL GLN ARG GLU SEQRES 22 A 282 THR GLY LYS LEU ASP GLY PRO ASP LYS SEQRES 1 B 4 GLN PRO LYS FDL SEQRES 1 C 282 SER ASP LYS GLY LYS LEU SER LEU GLN ASP VAL ALA GLU SEQRES 2 C 282 LEU ILE ARG ALA ARG ALA CYS GLN ARG VAL VAL VAL MET SEQRES 3 C 282 VAL GLY ALA GLY ILE SER THR PRO SER GLY ILE PRO ASP SEQRES 4 C 282 PHE ARG SER PRO GLY SER GLY LEU TYR SER ASN LEU GLN SEQRES 5 C 282 GLN TYR ASP LEU PRO TYR PRO GLU ALA ILE PHE GLU LEU SEQRES 6 C 282 PRO PHE PHE PHE HIS ASN PRO LYS PRO PHE PHE THR LEU SEQRES 7 C 282 ALA LYS GLU LEU TYR PRO GLY ASN TYR LYS PRO ASN VAL SEQRES 8 C 282 THR HIS TYR PHE LEU ARG LEU LEU HIS ASP LYS GLY LEU SEQRES 9 C 282 LEU LEU ARG LEU TYR THR GLN ASN ILE ASP GLY LEU GLU SEQRES 10 C 282 ARG VAL SER GLY ILE PRO ALA SER LYS LEU VAL GLU ALA SEQRES 11 C 282 HIS GLY THR PHE ALA SER ALA THR CYS THR VAL CYS GLN SEQRES 12 C 282 ARG PRO PHE PRO GLY GLU ASP ILE ARG ALA ASP VAL MET SEQRES 13 C 282 ALA ASP ARG VAL PRO ARG CYS PRO VAL CYS THR GLY VAL SEQRES 14 C 282 VAL LYS PRO ASP ILE VAL PHE PHE GLY GLU PRO LEU PRO SEQRES 15 C 282 GLN ARG PHE LEU LEU HIS VAL VAL ASP PHE PRO MET ALA SEQRES 16 C 282 ASP LEU LEU LEU ILE LEU GLY THR SER LEU GLU VAL GLU SEQRES 17 C 282 PRO PHE ALA SER LEU THR GLU ALA VAL ARG SER SER VAL SEQRES 18 C 282 PRO ARG LEU LEU ILE ASN ARG ASP LEU VAL GLY PRO LEU SEQRES 19 C 282 ALA TRP HIS PRO ARG SER ARG ASP VAL ALA GLN LEU GLY SEQRES 20 C 282 ASP VAL VAL HIS GLY VAL GLU SER LEU VAL GLU LEU LEU SEQRES 21 C 282 GLY TRP THR GLU GLU MET ARG ASP LEU VAL GLN ARG GLU SEQRES 22 C 282 THR GLY LYS LEU ASP GLY PRO ASP LYS SEQRES 1 D 4 GLN PRO LYS FDL HET FDL B 4 25 HET FDL D 4 25 HET ZN A 401 1 HET CNA A 402 44 HET ZN C 401 1 HET Y4T C 402 20 HET CNA C 403 44 HETNAM FDL N~6~-ACETYL-N-(4-METHYL-2-OXO-2H-CHROMEN-7-YL)-L- HETNAM 2 FDL LYSINAMIDE HETNAM ZN ZINC ION HETNAM CNA CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM Y4T (1P)-3',5-DI(PROP-2-EN-1-YL)[1,1'-BIPHENYL]-2,4'-DIOL HETSYN Y4T HONOKIOL FORMUL 2 FDL 2(C18 H23 N3 O4) FORMUL 5 ZN 2(ZN 2+) FORMUL 6 CNA 2(C22 H30 N7 O13 P2 1+) FORMUL 8 Y4T C18 H18 O2 FORMUL 10 HOH *31(H2 O) HELIX 1 AA1 SER A 124 ALA A 134 1 11 HELIX 2 AA2 ALA A 146 GLY A 153 5 8 HELIX 3 AA3 GLY A 163 LEU A 168 5 6 HELIX 4 AA4 TYR A 175 PHE A 180 5 6 HELIX 5 AA5 GLU A 181 ASN A 188 1 8 HELIX 6 AA6 PRO A 189 TYR A 200 1 12 HELIX 7 AA7 ASN A 207 LYS A 219 1 13 HELIX 8 AA8 GLY A 232 SER A 237 1 6 HELIX 9 AA9 PRO A 240 SER A 242 5 3 HELIX 10 AB1 ILE A 268 ALA A 274 1 7 HELIX 11 AB2 PRO A 299 LEU A 303 5 5 HELIX 12 AB3 LEU A 304 ALA A 312 1 9 HELIX 13 AB4 PHE A 327 ALA A 333 5 7 HELIX 14 AB5 GLY A 349 HIS A 354 1 6 HELIX 15 AB6 ASP A 365 GLY A 378 1 14 HELIX 16 AB7 TRP A 379 GLY A 392 1 14 HELIX 17 AB8 SER C 124 ALA C 134 1 11 HELIX 18 AB9 ALA C 146 GLY C 153 5 8 HELIX 19 AC1 LEU C 164 GLN C 169 1 6 HELIX 20 AC2 TYR C 175 PHE C 180 5 6 HELIX 21 AC3 GLU C 181 ASN C 188 1 8 HELIX 22 AC4 PRO C 189 LEU C 199 1 11 HELIX 23 AC5 ASN C 207 LYS C 219 1 13 HELIX 24 AC6 GLY C 232 SER C 237 1 6 HELIX 25 AC7 PRO C 240 SER C 242 5 3 HELIX 26 AC8 ILE C 268 ALA C 274 1 7 HELIX 27 AC9 PRO C 299 LEU C 303 5 5 HELIX 28 AD1 LEU C 304 ALA C 312 1 9 HELIX 29 AD2 PHE C 327 VAL C 334 5 8 HELIX 30 AD3 GLY C 349 HIS C 354 1 6 HELIX 31 AD4 ASP C 365 GLY C 378 1 14 HELIX 32 AD5 TRP C 379 GLY C 392 1 14 SHEET 1 AA1 6 LEU A 244 GLU A 246 0 SHEET 2 AA1 6 LEU A 222 THR A 227 1 N THR A 227 O VAL A 245 SHEET 3 AA1 6 VAL A 140 VAL A 144 1 N VAL A 142 O TYR A 226 SHEET 4 AA1 6 LEU A 314 LEU A 318 1 O LEU A 314 N VAL A 141 SHEET 5 AA1 6 ARG A 340 ASN A 344 1 O LEU A 341 N LEU A 315 SHEET 6 AA1 6 ASP A 359 LEU A 363 1 O VAL A 360 N ARG A 340 SHEET 1 AA2 3 PRO A 262 PRO A 264 0 SHEET 2 AA2 3 GLY A 249 CYS A 256 -1 N ALA A 254 O PHE A 263 SHEET 3 AA2 3 VAL A 287 ILE A 291 -1 O LYS A 288 N THR A 255 SHEET 1 AA3 6 LEU C 244 GLU C 246 0 SHEET 2 AA3 6 LEU C 222 THR C 227 1 N LEU C 225 O VAL C 245 SHEET 3 AA3 6 VAL C 140 VAL C 144 1 N VAL C 142 O TYR C 226 SHEET 4 AA3 6 LEU C 314 LEU C 318 1 O LEU C 314 N VAL C 141 SHEET 5 AA3 6 ARG C 340 ASN C 344 1 O LEU C 341 N LEU C 315 SHEET 6 AA3 6 VAL C 360 LEU C 363 1 O GLN C 362 N LEU C 342 SHEET 1 AA4 3 PRO C 262 PRO C 264 0 SHEET 2 AA4 3 GLY C 249 CYS C 256 -1 N ALA C 254 O PHE C 263 SHEET 3 AA4 3 VAL C 287 ILE C 291 -1 O ASP C 290 N SER C 253 LINK C LYS B 3 N FDL B 4 1555 1555 1.31 LINK C LYS D 3 N FDL D 4 1555 1555 1.33 LINK SG CYS A 256 ZN ZN A 401 1555 1555 2.58 LINK SG CYS A 259 ZN ZN A 401 1555 1555 2.13 LINK SG CYS A 280 ZN ZN A 401 1555 1555 2.18 LINK SG CYS A 283 ZN ZN A 401 1555 1555 2.41 LINK SG CYS C 256 ZN ZN C 401 1555 1555 2.41 LINK SG CYS C 259 ZN ZN C 401 1555 1555 2.35 LINK SG CYS C 280 ZN ZN C 401 1555 1555 2.00 LINK SG CYS C 283 ZN ZN C 401 1555 1555 2.19 CISPEP 1 GLU A 325 PRO A 326 0 6.55 CISPEP 2 GLU C 325 PRO C 326 0 -3.60 CRYST1 34.683 159.432 53.047 90.00 90.61 90.00 P 1 21 1 4 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 0.028833 0.000000 0.000305 0.00000 SCALE2 0.000000 0.006272 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018852 0.00000