HEADER HYDROLASE 14-SEP-17 6B09 TITLE CRYSTAL STRUCTURE OF HSNUDT16 IN COMPLEX WITH DIADPR (SOAKED) COMPND MOL_ID: 1; COMPND 2 MOLECULE: U8 SNORNA-DECAPPING ENZYME; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: IDP PHOSPHATASE,IDPASE,INOSINE DIPHOSPHATE PHOSPHATASE, COMPND 5 NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 16,NUDIX MOTIF 16,NUDIX COMPND 6 HYDROLASE 16,U8 SNORNA-BINDING PROTEIN H29K,M7GPPPN-MRNA HYDROLASE; COMPND 7 EC: 3.6.1.62,3.6.1.64; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NUDT16; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON PLUS RIPL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS NUDIX HYDROLASE, DECAPPING ENZYME, DEMODIFICATION OF PARYLATION, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.THIRAWATANANOND,S.B.GABELLI REVDAT 3 13-MAR-24 6B09 1 LINK REVDAT 2 24-APR-19 6B09 1 JRNL REVDAT 1 09-JAN-19 6B09 0 JRNL AUTH P.THIRAWATANANOND,R.L.MCPHERSON,J.MALHI,S.NATHAN, JRNL AUTH 2 M.J.LAMBRECHT,M.BRICHACEK,P.J.HERGENROTHER,A.K.L.LEUNG, JRNL AUTH 3 S.B.GABELLI JRNL TITL STRUCTURAL ANALYSES OF NUDT16-ADP-RIBOSE COMPLEXES DIRECT JRNL TITL 2 RATIONAL DESIGN OF MUTANTS WITH IMPROVED PROCESSING OF JRNL TITL 3 POLY(ADP-RIBOSYL)ATED PROTEINS. JRNL REF SCI REP V. 9 5940 2019 JRNL REFN ESSN 2045-2322 JRNL PMID 30976021 JRNL DOI 10.1038/S41598-019-39491-W REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 5564 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) : 0.257 REMARK 3 R VALUE (WORKING SET) : 0.256 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 283 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2740 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 131 REMARK 3 SOLVENT ATOMS : 3 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.21000 REMARK 3 B22 (A**2) : -2.15000 REMARK 3 B33 (A**2) : 5.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.58000 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): 0.674 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.445 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 26.612 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6B09 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1000230093. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ DW REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5417 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6140 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 200 DATA REDUNDANCY : 2.200 REMARK 200 R MERGE (I) : 0.16700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.59200 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, CHES, PH 9.5, VAPOR REMARK 280 DIFFUSION, 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 56.69750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.53150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 56.69750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.53150 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: 3810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 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 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 SER A 17 REMARK 465 GLY A 18 REMARK 465 LEU A 181 REMARK 465 GLN A 182 REMARK 465 SER A 183 REMARK 465 GLY A 184 REMARK 465 SER A 185 REMARK 465 ILE A 186 REMARK 465 SER A 187 REMARK 465 GLY A 188 REMARK 465 LEU A 189 REMARK 465 LYS A 190 REMARK 465 ILE A 191 REMARK 465 PRO A 192 REMARK 465 ALA A 193 REMARK 465 HIS A 194 REMARK 465 HIS A 195 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLY B 3 REMARK 465 GLY B 101 REMARK 465 SER B 102 REMARK 465 GLY B 103 REMARK 465 GLN B 182 REMARK 465 SER B 183 REMARK 465 GLY B 184 REMARK 465 SER B 185 REMARK 465 ILE B 186 REMARK 465 SER B 187 REMARK 465 GLY B 188 REMARK 465 LEU B 189 REMARK 465 LYS B 190 REMARK 465 ILE B 191 REMARK 465 PRO B 192 REMARK 465 ALA B 193 REMARK 465 HIS B 194 REMARK 465 HIS B 195 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 ASP A 63 NH1 ARG A 67 2656 1.91 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 PRO B 40 N - CA - C ANGL. DEV. = 16.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 42 -65.13 63.65 REMARK 500 MET A 47 -164.91 -107.11 REMARK 500 ASP A 63 -164.58 -118.99 REMARK 500 ARG A 92 -33.23 71.82 REMARK 500 LEU A 135 -92.80 -128.99 REMARK 500 ARG A 149 -80.70 81.99 REMARK 500 SER A 166 28.61 -141.45 REMARK 500 ARG B 38 -47.06 -135.11 REMARK 500 PRO B 40 6.87 -50.28 REMARK 500 LEU B 41 -67.60 55.99 REMARK 500 ARG B 42 -75.55 88.84 REMARK 500 ASP B 63 152.15 64.34 REMARK 500 GLN B 65 -34.60 151.99 REMARK 500 ARG B 96 -65.98 -122.99 REMARK 500 LEU B 135 -87.34 -95.89 REMARK 500 TYR B 146 157.97 -44.74 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 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 76 OE1 REMARK 620 2 GLU A 80 OE2 108.3 REMARK 620 3 GLU A 136 OE2 157.8 87.4 REMARK 620 4 C7G A 401 O7 91.8 87.2 72.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 80 OE2 REMARK 620 2 C7G A 401 O5 136.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 31 O REMARK 620 2 PRO B 40 O 97.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 76 OE2 REMARK 620 2 C7G B 401 O9 95.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 76 OE1 REMARK 620 2 GLU B 80 OE2 81.4 REMARK 620 3 ASP B 132 OD2 121.8 92.1 REMARK 620 4 C7G B 401 O7 81.3 71.1 149.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C7G A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue C7G B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5WJI RELATED DB: PDB REMARK 900 RELATED ID: 5W6Z RELATED DB: PDB REMARK 900 RELATED ID: 5W6X RELATED DB: PDB REMARK 900 RELATED ID: 5VY2 RELATED DB: PDB DBREF 6B09 A 1 195 UNP Q96DE0 NUD16_HUMAN 1 195 DBREF 6B09 B 1 195 UNP Q96DE0 NUD16_HUMAN 1 195 SEQADV 6B09 VAL A 22 UNP Q96DE0 ALA 22 ENGINEERED MUTATION SEQADV 6B09 VAL B 22 UNP Q96DE0 ALA 22 ENGINEERED MUTATION SEQRES 1 A 195 MET ALA GLY ALA ARG ARG LEU GLU LEU GLY GLU ALA LEU SEQRES 2 A 195 ALA LEU GLY SER GLY TRP ARG HIS VAL CYS HIS ALA LEU SEQRES 3 A 195 LEU TYR ALA PRO ASP PRO GLY MET LEU PHE GLY ARG ILE SEQRES 4 A 195 PRO LEU ARG TYR ALA ILE LEU MET GLN MET ARG PHE ASP SEQRES 5 A 195 GLY ARG LEU GLY PHE PRO GLY GLY PHE VAL ASP THR GLN SEQRES 6 A 195 ASP ARG SER LEU GLU ASP GLY LEU ASN ARG GLU LEU ARG SEQRES 7 A 195 GLU GLU LEU GLY GLU ALA ALA ALA ALA PHE ARG VAL GLU SEQRES 8 A 195 ARG THR ASP TYR ARG SER SER HIS VAL GLY SER GLY PRO SEQRES 9 A 195 ARG VAL VAL ALA HIS PHE TYR ALA LYS ARG LEU THR LEU SEQRES 10 A 195 GLU GLU LEU LEU ALA VAL GLU ALA GLY ALA THR ARG ALA SEQRES 11 A 195 LYS ASP HIS GLY LEU GLU VAL LEU GLY LEU VAL ARG VAL SEQRES 12 A 195 PRO LEU TYR THR LEU ARG ASP GLY VAL GLY GLY LEU PRO SEQRES 13 A 195 THR PHE LEU GLU ASN SER PHE ILE GLY SER ALA ARG GLU SEQRES 14 A 195 GLN LEU LEU GLU ALA LEU GLN ASP LEU GLY LEU LEU GLN SEQRES 15 A 195 SER GLY SER ILE SER GLY LEU LYS ILE PRO ALA HIS HIS SEQRES 1 B 195 MET ALA GLY ALA ARG ARG LEU GLU LEU GLY GLU ALA LEU SEQRES 2 B 195 ALA LEU GLY SER GLY TRP ARG HIS VAL CYS HIS ALA LEU SEQRES 3 B 195 LEU TYR ALA PRO ASP PRO GLY MET LEU PHE GLY ARG ILE SEQRES 4 B 195 PRO LEU ARG TYR ALA ILE LEU MET GLN MET ARG PHE ASP SEQRES 5 B 195 GLY ARG LEU GLY PHE PRO GLY GLY PHE VAL ASP THR GLN SEQRES 6 B 195 ASP ARG SER LEU GLU ASP GLY LEU ASN ARG GLU LEU ARG SEQRES 7 B 195 GLU GLU LEU GLY GLU ALA ALA ALA ALA PHE ARG VAL GLU SEQRES 8 B 195 ARG THR ASP TYR ARG SER SER HIS VAL GLY SER GLY PRO SEQRES 9 B 195 ARG VAL VAL ALA HIS PHE TYR ALA LYS ARG LEU THR LEU SEQRES 10 B 195 GLU GLU LEU LEU ALA VAL GLU ALA GLY ALA THR ARG ALA SEQRES 11 B 195 LYS ASP HIS GLY LEU GLU VAL LEU GLY LEU VAL ARG VAL SEQRES 12 B 195 PRO LEU TYR THR LEU ARG ASP GLY VAL GLY GLY LEU PRO SEQRES 13 B 195 THR PHE LEU GLU ASN SER PHE ILE GLY SER ALA ARG GLU SEQRES 14 B 195 GLN LEU LEU GLU ALA LEU GLN ASP LEU GLY LEU LEU GLN SEQRES 15 B 195 SER GLY SER ILE SER GLY LEU LYS ILE PRO ALA HIS HIS HET C7G A 401 62 HET MG A 402 1 HET MG A 403 1 HET CL A 404 1 HET NA A 405 1 HET C7G B 401 62 HET MG B 402 1 HET MG B 403 1 HET NA B 404 1 HETNAM C7G [(2~{R},3~{S},4~{S},5~{S})-5-(6-AMINOPURIN-9-YL)-4- HETNAM 2 C7G [(2~{S},3~{S},4~{S},5~{S})-5-[[[[(2~{R},3~{R},4~{S}, HETNAM 3 C7G 5~{S})-5-(6-AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN- HETNAM 4 C7G 2-YL]METHOXY-OXIDANYL-PHOSPHORYL]OXY-OXIDANYL- HETNAM 5 C7G PHOSPHORYL]OXYMETHYL]-3,4-BIS(OXIDANYL)OXOLAN-2- HETNAM 6 C7G YL]OXY-3-OXIDANYL-OXOLAN-2-YL]METHYL PHOSPHONO HETNAM 7 C7G HYDROGEN PHOSPHATE HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETSYN C7G DIADPR FORMUL 3 C7G 2(C25 H36 N10 O23 P4) FORMUL 4 MG 4(MG 2+) FORMUL 6 CL CL 1- FORMUL 7 NA 2(NA 1+) FORMUL 12 HOH *3(H2 O) HELIX 1 AA1 GLU A 8 ALA A 14 1 7 HELIX 2 AA2 SER A 68 GLY A 82 1 15 HELIX 3 AA3 ALA A 84 PHE A 88 5 5 HELIX 4 AA4 THR A 116 GLY A 126 1 11 HELIX 5 AA5 GLY A 154 LEU A 159 1 6 HELIX 6 AA6 SER A 166 LEU A 178 1 13 HELIX 7 AA7 GLU B 8 ALA B 14 1 7 HELIX 8 AA8 MET B 34 ARG B 38 5 5 HELIX 9 AA9 SER B 68 GLY B 82 1 15 HELIX 10 AB1 GLU B 83 PHE B 88 5 6 HELIX 11 AB2 GLU B 91 THR B 93 5 3 HELIX 12 AB3 THR B 116 ALA B 127 1 12 HELIX 13 AB4 GLY B 153 LEU B 159 1 7 HELIX 14 AB5 SER B 166 LEU B 178 1 13 SHEET 1 AA1 6 ARG A 6 LEU A 7 0 SHEET 2 AA1 6 TYR A 95 GLY A 101 -1 O SER A 98 N LEU A 7 SHEET 3 AA1 6 VAL A 106 ARG A 114 -1 O ALA A 108 N HIS A 99 SHEET 4 AA1 6 ARG A 20 LEU A 35 1 N VAL A 22 O HIS A 109 SHEET 5 AA1 6 ILE A 39 ARG A 50 -1 O ALA A 44 N ALA A 29 SHEET 6 AA1 6 GLY A 59 VAL A 62 0 SHEET 1 AA2 4 LEU A 55 GLY A 56 0 SHEET 2 AA2 4 ILE A 39 ARG A 50 -1 N GLN A 48 O GLY A 56 SHEET 3 AA2 4 ARG A 20 LEU A 35 -1 N ALA A 29 O ALA A 44 SHEET 4 AA2 4 VAL A 137 ARG A 142 0 SHEET 1 AA3 6 ARG B 6 LEU B 7 0 SHEET 2 AA3 6 TYR B 95 HIS B 99 -1 O SER B 98 N LEU B 7 SHEET 3 AA3 6 VAL B 106 ARG B 114 -1 O ALA B 108 N HIS B 99 SHEET 4 AA3 6 ARG B 20 ASP B 31 1 N VAL B 22 O HIS B 109 SHEET 5 AA3 6 ARG B 42 ARG B 50 -1 O ARG B 42 N ASP B 31 SHEET 6 AA3 6 GLY B 59 PHE B 61 0 SHEET 1 AA4 4 LEU B 55 GLY B 56 0 SHEET 2 AA4 4 ARG B 42 ARG B 50 -1 N GLN B 48 O GLY B 56 SHEET 3 AA4 4 ARG B 20 ASP B 31 -1 N ASP B 31 O ARG B 42 SHEET 4 AA4 4 VAL B 137 ARG B 142 0 LINK OE1 GLU A 76 MG MG A 403 1555 1555 2.49 LINK OE2 GLU A 76 NA NA A 405 1555 1555 2.78 LINK OE2 GLU A 80 MG MG A 402 1555 1555 2.52 LINK OE2 GLU A 80 MG MG A 403 1555 1555 2.71 LINK OE2 GLU A 136 MG MG A 403 1555 1555 2.10 LINK O5 C7G A 401 MG MG A 402 1555 1555 2.99 LINK O7 C7G A 401 MG MG A 403 1555 1555 2.59 LINK O ASP B 31 NA NA B 404 1555 1555 2.95 LINK O PRO B 40 NA NA B 404 1555 1555 2.38 LINK OE2 GLU B 76 MG MG B 402 1555 1555 2.35 LINK OE1 GLU B 76 MG MG B 403 1555 1555 2.59 LINK OE2 GLU B 80 MG MG B 403 1555 1555 1.83 LINK OD2 ASP B 132 MG MG B 403 1555 1555 2.78 LINK O9 C7G B 401 MG MG B 402 1555 1555 2.95 LINK O7 C7G B 401 MG MG B 403 1555 1555 2.28 SITE 1 AC1 17 ARG A 20 HIS A 24 ARG A 50 PHE A 51 SITE 2 AC1 17 GLY A 60 PHE A 61 GLU A 76 GLU A 80 SITE 3 AC1 17 GLU A 136 ILE A 164 SER A 166 ALA A 167 SITE 4 AC1 17 GLN A 170 MG A 402 MG A 403 NA A 405 SITE 5 AC1 17 ARG B 38 SITE 1 AC2 4 ARG A 50 GLY A 59 GLU A 80 C7G A 401 SITE 1 AC3 5 GLU A 76 GLU A 80 ASP A 132 GLU A 136 SITE 2 AC3 5 C7G A 401 SITE 1 AC4 3 GLU A 76 GLU A 79 C7G A 401 SITE 1 AC5 19 PHE A 36 ARG A 149 ASP A 150 GLU A 169 SITE 2 AC5 19 HIS B 24 ARG B 50 GLY B 59 GLY B 60 SITE 3 AC5 19 PHE B 61 GLU B 76 GLU B 80 ALA B 108 SITE 4 AC5 19 GLU B 136 ILE B 164 SER B 166 ALA B 167 SITE 5 AC5 19 GLN B 170 MG B 402 MG B 403 SITE 1 AC6 2 GLU B 76 C7G B 401 SITE 1 AC7 5 GLU B 76 GLU B 80 ASP B 132 GLU B 136 SITE 2 AC7 5 C7G B 401 SITE 1 AC8 3 ASP B 31 PRO B 40 ARG B 42 CRYST1 113.395 47.063 75.792 90.00 108.74 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 0.008819 0.000000 0.002992 0.00000 SCALE2 0.000000 0.021248 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013933 0.00000