HEADER TRANSFERASE 30-OCT-19 6L71 TITLE SIRTUIN 2 DEMYRISTOYLATION NATIVE INTERMEDIATE I & II MIXTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: REGULATORY PROTEIN SIR2 HOMOLOG 2,SIR2-LIKE PROTEIN 2; COMPND 5 EC: 2.3.1.286; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PRO-ARG-LYS-GLN-LEU-ALA; COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SIRT2, SIR2L, SIR2L2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: K-12; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630 KEYWDS SIRTUIN, MYRISTOYLATION, INTERMEDIATE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.F.CHEN REVDAT 2 22-NOV-23 6L71 1 REMARK REVDAT 1 31-MAR-21 6L71 0 JRNL AUTH L.F.CHEN JRNL TITL SIRTUIN 2 PROTEIN WITH H3K18 MYRISTOYLATED PEPTIDE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.0 REMARK 3 NUMBER OF REFLECTIONS : 15873 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.320 REMARK 3 FREE R VALUE TEST SET COUNT : 844 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 27.9240 - 3.8290 0.99 2948 179 0.1385 0.1801 REMARK 3 2 3.8290 - 3.0404 1.00 2952 181 0.1530 0.2162 REMARK 3 3 3.0404 - 2.6564 0.99 2896 158 0.1921 0.2370 REMARK 3 4 2.6564 - 2.4137 0.91 2696 135 0.2108 0.3108 REMARK 3 5 2.4137 - 2.2407 0.73 2155 112 0.2164 0.2943 REMARK 3 6 2.2407 - 2.1090 0.47 1382 79 0.2129 0.3238 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 2608 REMARK 3 ANGLE : 1.216 3526 REMARK 3 CHIRALITY : 0.053 383 REMARK 3 PLANARITY : 0.005 434 REMARK 3 DIHEDRAL : 20.012 1586 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6L71 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1300014306. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97930 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18062 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.109 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 (%) : 96.7 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 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 : 1.500 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: 4R8M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES, PH 6.5, 6%-20% (W/V) PEG REMARK 280 10000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 39.04750 REMARK 290 SMTRY3 2 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: 2810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 52 REMARK 465 GLY A 298 REMARK 465 MET A 299 REMARK 465 ILE A 300 REMARK 465 MET A 301 REMARK 465 GLY A 302 REMARK 465 LEU A 303 REMARK 465 GLY A 304 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 THR A 89 N CA C O CB OG1 CG2 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 NZ LYS C 9 H132 YDD C 402 0.68 REMARK 500 CE LYS C 9 H132 YDD C 402 1.59 REMARK 500 O HOH A 613 O HOH A 649 1.65 REMARK 500 O HOH C 504 O HOH C 506 1.66 REMARK 500 O HOH A 564 O HOH A 630 1.83 REMARK 500 O HOH A 694 O HOH A 698 1.84 REMARK 500 N SER A 53 O HOH A 501 1.88 REMARK 500 NE2 GLN A 225 O HOH A 502 1.96 REMARK 500 O14 YOY C 401 O HOH C 501 1.96 REMARK 500 O HOH A 501 O HOH A 621 2.03 REMARK 500 NH2 ARG A 347 O HOH A 503 2.05 REMARK 500 NZ LYS C 9 C12 YDD C 402 2.06 REMARK 500 O HOH A 664 O HOH A 695 2.07 REMARK 500 O LEU A 297 O HOH A 504 2.09 REMARK 500 O HOH A 628 O HOH A 641 2.09 REMARK 500 OE1 GLU A 120 OG SER A 122 2.09 REMARK 500 NZ LYS C 9 O9 YOY C 401 2.10 REMARK 500 O HOH A 512 O HOH A 657 2.14 REMARK 500 O HOH C 507 O HOH C 508 2.16 REMARK 500 N GLY A 306 O HOH A 505 2.19 REMARK 500 ND1 HIS A 202 OD2 ASP A 223 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 611 O HOH A 643 2445 1.97 REMARK 500 O HOH A 522 O HOH A 621 2555 2.05 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 CYS A 200 CB CYS A 200 SG 0.182 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 CYS A 200 CA - CB - SG ANGL. DEV. = 24.7 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 SER A 100 -64.91 88.41 REMARK 500 ASN A 106 31.93 -141.98 REMARK 500 HIS A 111 16.00 55.39 REMARK 500 PRO A 113 -86.71 -44.02 REMARK 500 ALA A 198 -14.74 -47.12 REMARK 500 SER A 199 -85.62 -77.80 REMARK 500 ARG A 201 15.22 50.84 REMARK 500 ASP A 231 40.20 -74.27 REMARK 500 ARG A 316 -1.09 -143.19 REMARK 500 LEU C 11 -141.03 -93.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 707 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A 708 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A 709 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH A 710 DISTANCE = 6.46 ANGSTROMS REMARK 525 HOH A 711 DISTANCE = 6.49 ANGSTROMS REMARK 525 HOH A 712 DISTANCE = 7.02 ANGSTROMS REMARK 525 HOH A 713 DISTANCE = 7.09 ANGSTROMS REMARK 525 HOH A 714 DISTANCE = 8.24 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 YDD AND YOY ARE IN ALTERNATE CONFIRMATIONS OF EACH OTHER. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NCA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue YOY C 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue YDD C 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6L66 RELATED DB: PDB REMARK 900 SIRTUIN 2 PROTEIN WITH H3K18 MYRISTOYLATED PEPTIDE AND INTACT NAD REMARK 900 MOLECULE DBREF 6L71 A 52 355 UNP Q8IXJ6 SIR2_HUMAN 52 355 DBREF 6L71 C 7 12 PDB 6L71 6L71 7 12 SEQRES 1 A 304 GLY SER GLN LYS GLU ARG LEU LEU ASP GLU LEU THR LEU SEQRES 2 A 304 GLU GLY VAL ALA ARG TYR MET GLN SER GLU ARG CYS ARG SEQRES 3 A 304 ARG VAL ILE CYS LEU VAL GLY ALA GLY ILE SER THR SER SEQRES 4 A 304 ALA GLY ILE PRO ASP PHE ARG SER PRO SER THR GLY LEU SEQRES 5 A 304 TYR ASP ASN LEU GLU LYS TYR HIS LEU PRO TYR PRO GLU SEQRES 6 A 304 ALA ILE PHE GLU ILE SER TYR PHE LYS LYS HIS PRO GLU SEQRES 7 A 304 PRO PHE PHE ALA LEU ALA LYS GLU LEU TYR PRO GLY GLN SEQRES 8 A 304 PHE LYS PRO THR ILE CYS HIS TYR PHE MET ARG LEU LEU SEQRES 9 A 304 LYS ASP LYS GLY LEU LEU LEU ARG CYS TYR THR GLN ASN SEQRES 10 A 304 ILE ASP THR LEU GLU ARG ILE ALA GLY LEU GLU GLN GLU SEQRES 11 A 304 ASP LEU VAL GLU ALA HIS GLY THR PHE TYR THR SER HIS SEQRES 12 A 304 CYS VAL SER ALA SER CYS ARG HIS GLU TYR PRO LEU SER SEQRES 13 A 304 TRP MET LYS GLU LYS ILE PHE SER GLU VAL THR PRO LYS SEQRES 14 A 304 CYS GLU ASP CYS GLN SER LEU VAL LYS PRO ASP ILE VAL SEQRES 15 A 304 PHE PHE GLY GLU SER LEU PRO ALA ARG PHE PHE SER CYS SEQRES 16 A 304 MET GLN SER ASP PHE LEU LYS VAL ASP LEU LEU LEU VAL SEQRES 17 A 304 MET GLY THR SER LEU GLN VAL GLN PRO PHE ALA SER LEU SEQRES 18 A 304 ILE SER LYS ALA PRO LEU SER THR PRO ARG LEU LEU ILE SEQRES 19 A 304 ASN LYS GLU LYS ALA GLY GLN SER ASP PRO PHE LEU GLY SEQRES 20 A 304 MET ILE MET GLY LEU GLY GLY GLY MET ASP PHE ASP SER SEQRES 21 A 304 LYS LYS ALA TYR ARG ASP VAL ALA TRP LEU GLY GLU CYS SEQRES 22 A 304 ASP GLN GLY CYS LEU ALA LEU ALA GLU LEU LEU GLY TRP SEQRES 23 A 304 LYS LYS GLU LEU GLU ASP LEU VAL ARG ARG GLU HIS ALA SEQRES 24 A 304 SER ILE ASP ALA GLN SEQRES 1 C 6 PRO ARG LYS GLN LEU ALA HET NCA A 401 9 HET YOY C 401 49 HET YDD C 402 101 HETNAM NCA NICOTINAMIDE HETNAM YOY [[(2S,3AS,5S,6R,6AS)-2-DODECYL-6-OXIDANYL-3A,5,6,6A- HETNAM 2 YOY TETRAHYDROFURO[2,3-D][1,3]DIOXOL-5-YL]METHOXY- HETNAM 3 YOY OXIDANYL-PHOSPHORYL] [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9- HETNAM 4 YOY YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL HYDROGEN HETNAM 5 YOY PHOSPHATE HETNAM YDD [[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4- HETNAM 2 YDD BIS(OXIDANYL)OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] HETNAM 3 YDD [(2R,3S,4R,5S)-3,4-BIS(OXIDANYL)-5-TETRADECOXY-OXOLAN- HETNAM 4 YDD 2-YL]METHYL HYDROGEN PHOSPHATE FORMUL 3 NCA C6 H6 N2 O FORMUL 4 YOY C28 H47 N5 O14 P2 FORMUL 5 YDD C29 H51 N5 O14 P2 FORMUL 6 HOH *223(H2 O) HELIX 1 AA1 THR A 63 GLN A 72 1 10 HELIX 2 AA2 ALA A 85 GLY A 92 5 8 HELIX 3 AA3 GLY A 102 ASN A 106 5 5 HELIX 4 AA4 LEU A 107 HIS A 111 5 5 HELIX 5 AA5 TYR A 114 PHE A 119 5 6 HELIX 6 AA6 GLU A 120 HIS A 127 1 8 HELIX 7 AA7 PRO A 128 TYR A 139 1 12 HELIX 8 AA8 THR A 146 LYS A 158 1 13 HELIX 9 AA9 THR A 171 ALA A 176 1 6 HELIX 10 AB1 LEU A 206 SER A 215 1 10 HELIX 11 AB2 PRO A 240 PHE A 251 1 12 HELIX 12 AB3 PRO A 268 LYS A 275 5 8 HELIX 13 AB4 GLU A 323 GLY A 336 1 14 HELIX 14 AB5 TRP A 337 ALA A 354 1 18 SHEET 1 AA1 6 LEU A 183 GLU A 185 0 SHEET 2 AA1 6 LEU A 161 THR A 166 1 N CYS A 164 O VAL A 184 SHEET 3 AA1 6 VAL A 79 VAL A 83 1 N CYS A 81 O TYR A 165 SHEET 4 AA1 6 LEU A 256 MET A 260 1 O LEU A 258 N ILE A 80 SHEET 5 AA1 6 ARG A 282 ASN A 286 1 O LEU A 283 N VAL A 259 SHEET 6 AA1 6 ASP A 317 LEU A 321 1 O TRP A 320 N LEU A 284 SHEET 1 AA2 3 GLU A 203 PRO A 205 0 SHEET 2 AA2 3 GLY A 188 CYS A 195 -1 N SER A 193 O TYR A 204 SHEET 3 AA2 3 VAL A 228 ILE A 232 -1 O ASP A 231 N THR A 192 SSBOND 1 CYS A 195 CYS A 200 1555 1555 2.05 SSBOND 2 CYS A 200 CYS A 221 1555 1555 2.07 SSBOND 3 CYS A 200 CYS A 224 1555 1555 2.08 LINK NZ LYS C 9 C11BYOY C 401 1555 1555 1.43 LINK NZ LYS C 9 C13AYDD C 402 1555 1555 1.43 CISPEP 1 GLN A 267 PRO A 268 0 -2.88 SITE 1 AC1 11 ALA A 85 ILE A 93 PRO A 94 PHE A 96 SITE 2 AC1 11 ASN A 168 ILE A 169 ASP A 170 HOH A 542 SITE 3 AC1 11 YOY C 401 YDD C 402 HOH C 501 SITE 1 AC2 28 GLY A 84 ALA A 85 GLY A 86 THR A 89 SITE 2 AC2 28 ASP A 95 PHE A 96 ARG A 97 PRO A 140 SITE 3 AC2 28 GLN A 167 ILE A 169 HIS A 187 PHE A 190 SITE 4 AC2 28 VAL A 233 PHE A 235 GLY A 261 THR A 262 SITE 5 AC2 28 SER A 263 ASN A 286 LYS A 287 GLU A 288 SITE 6 AC2 28 GLY A 322 GLU A 323 CYS A 324 NCA A 401 SITE 7 AC2 28 LYS C 9 YDD C 402 HOH C 501 HOH C 502 SITE 1 AC3 26 GLY A 84 ALA A 85 GLY A 86 THR A 89 SITE 2 AC3 26 ASP A 95 PHE A 96 ARG A 97 PHE A 119 SITE 3 AC3 26 GLN A 167 HIS A 187 VAL A 233 PHE A 235 SITE 4 AC3 26 GLY A 261 THR A 262 SER A 263 ASN A 286 SITE 5 AC3 26 LYS A 287 GLU A 288 GLY A 322 GLU A 323 SITE 6 AC3 26 CYS A 324 NCA A 401 LYS C 9 YOY C 401 SITE 7 AC3 26 HOH C 501 HOH C 502 CRYST1 37.601 78.095 56.347 90.00 97.64 90.00 P 1 21 1 2 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 0.026595 0.000000 0.003566 0.00000 SCALE2 0.000000 0.012805 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017906 0.00000