HEADER TRANSFERASE 10-MAR-10 3AFO TITLE CRYSTAL STRUCTURE OF YEAST NADH KINASE COMPLEXED WITH NADH COMPND MOL_ID: 1; COMPND 2 MOLECULE: NADH KINASE POS5; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 27-414; COMPND 5 EC: 2.7.1.86; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: POS5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTABLUE(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28B KEYWDS ALPHA/BETA+BETA SANDWICH, ATP-BINDING, KINASE, MITOCHONDRION, NAD, KEYWDS 2 NADP, NUCLEOTIDE-BINDING, TRANSFERASE, TRANSIT PEPTIDE EXPDTA X-RAY DIFFRACTION AUTHOR T.ANDO,K.OHASHI,A.OCHIAI,H.MIYAGI,S.KAWAI,B.MIKAMI,K.MURATA REVDAT 2 01-NOV-23 3AFO 1 REMARK REVDAT 1 16-MAR-11 3AFO 0 JRNL AUTH T.ANDO,K.OHASHI,A.OCHIAI,H.MIYAGI,S.KAWAI,B.MIKAMI,K.MURATA JRNL TITL THE STRUCTURAL FACTOR CONFERRING NADH KINASE ACTIVITY ON JRNL TITL 2 YEAST MITOCHONDRIAL POS5 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0088 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 (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 50821 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2702 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) : 3709 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 199 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5462 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 120 REMARK 3 SOLVENT ATOMS : 478 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.66000 REMARK 3 B22 (A**2) : 0.97000 REMARK 3 B33 (A**2) : -0.31000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.200 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.175 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.121 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.275 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5981 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8183 ; 1.187 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 750 ; 5.905 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 248 ;37.027 ;24.355 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1017 ;14.442 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;15.756 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 943 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4495 ; 0.005 ; 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): 3670 ; 0.659 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6043 ; 1.208 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2311 ; 1.419 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2140 ; 2.409 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3AFO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000029194. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-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 : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 MONOCHROMETER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59896 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.39900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.920 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: PDB ENTRY 2AN1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% 2-METHYL-2,4-PENTANEDIOL, 5% PEG REMARK 280 4000, 100MM IMIDAZOLE-HCL, 5MM NADH, PH 8.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 49.34250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 66.39100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 49.34250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 66.39100 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 54760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 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 BIOMT1 2 -1.000000 0.000000 0.000000 197.37000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 PRO A 53 REMARK 465 PRO A 54 REMARK 465 ASN A 55 REMARK 465 SER A 56 REMARK 465 GLN A 358 REMARK 465 LEU A 359 REMARK 465 PRO A 360 REMARK 465 THR A 361 REMARK 465 THR A 362 REMARK 465 ARG A 363 REMARK 465 LYS A 364 REMARK 465 THR A 365 REMARK 465 GLU A 366 REMARK 465 ASN A 367 REMARK 465 ASP A 368 REMARK 465 PHE A 369 REMARK 465 ASN A 370 REMARK 465 ASN A 371 REMARK 465 SER A 372 REMARK 465 LYS A 373 REMARK 465 LYS A 374 REMARK 465 PRO A 375 REMARK 465 ARG A 409 REMARK 465 GLN A 410 REMARK 465 THR A 411 REMARK 465 ASP A 412 REMARK 465 ASN A 413 REMARK 465 ASP A 414 REMARK 465 LEU B 27 REMARK 465 GLN B 28 REMARK 465 SER B 29 REMARK 465 GLY B 30 REMARK 465 SER B 31 REMARK 465 LYS B 32 REMARK 465 PHE B 33 REMARK 465 LYS B 315 REMARK 465 LEU B 316 REMARK 465 ASN B 317 REMARK 465 GLN B 318 REMARK 465 LYS B 319 REMARK 465 PRO B 320 REMARK 465 VAL B 321 REMARK 465 ASN B 322 REMARK 465 GLY B 350 REMARK 465 THR B 351 REMARK 465 ILE B 352 REMARK 465 TYR B 353 REMARK 465 ILE B 354 REMARK 465 ASP B 355 REMARK 465 GLY B 356 REMARK 465 THR B 357 REMARK 465 GLN B 358 REMARK 465 LEU B 359 REMARK 465 PRO B 360 REMARK 465 THR B 361 REMARK 465 THR B 362 REMARK 465 ARG B 363 REMARK 465 LYS B 364 REMARK 465 THR B 365 REMARK 465 GLU B 366 REMARK 465 ASN B 367 REMARK 465 ASP B 368 REMARK 465 PHE B 369 REMARK 465 ASN B 370 REMARK 465 ASN B 371 REMARK 465 SER B 372 REMARK 465 LYS B 373 REMARK 465 LYS B 374 REMARK 465 PRO B 375 REMARK 465 ARG B 409 REMARK 465 GLN B 410 REMARK 465 THR B 411 REMARK 465 ASP B 412 REMARK 465 ASN B 413 REMARK 465 ASP B 414 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 GLN A 68 -52.31 -132.55 REMARK 500 ASN A 121 16.43 58.78 REMARK 500 THR A 163 -169.94 -119.05 REMARK 500 ASN A 226 -67.49 -97.74 REMARK 500 LEU A 250 -61.23 -93.01 REMARK 500 ALA A 268 -131.10 -103.23 REMARK 500 ASN A 317 114.23 60.96 REMARK 500 LYS A 319 -168.20 -61.46 REMARK 500 ASN A 401 54.02 38.35 REMARK 500 GLN B 68 -46.39 -137.71 REMARK 500 PRO B 123 -7.85 -56.44 REMARK 500 ASN B 226 -65.75 -99.05 REMARK 500 ALA B 268 -129.43 -98.75 REMARK 500 CYS B 291 70.09 44.89 REMARK 500 GLN B 334 -162.81 -107.31 REMARK 500 GLN B 334 -164.39 -107.31 REMARK 500 ASN B 401 55.83 36.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAI A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAI B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 2002 DBREF 3AFO A 27 414 UNP Q06892 POS5_YEAST 27 414 DBREF 3AFO B 27 414 UNP Q06892 POS5_YEAST 27 414 SEQRES 1 A 388 LEU GLN SER GLY SER LYS PHE VAL LYS ILE LYS PRO VAL SEQRES 2 A 388 ASN ASN LEU ARG SER SER SER SER ALA ASP PHE VAL SER SEQRES 3 A 388 PRO PRO ASN SER LYS LEU GLN SER LEU ILE TRP GLN ASN SEQRES 4 A 388 PRO LEU GLN ASN VAL TYR ILE THR LYS LYS PRO TRP THR SEQRES 5 A 388 PRO SER THR ARG GLU ALA MET VAL GLU PHE ILE THR HIS SEQRES 6 A 388 LEU HIS GLU SER TYR PRO GLU VAL ASN VAL ILE VAL GLN SEQRES 7 A 388 PRO ASP VAL ALA GLU GLU ILE SER GLN ASP PHE LYS SER SEQRES 8 A 388 PRO LEU GLU ASN ASP PRO ASN ARG PRO HIS ILE LEU TYR SEQRES 9 A 388 THR GLY PRO GLU GLN ASP ILE VAL ASN ARG THR ASP LEU SEQRES 10 A 388 LEU VAL THR LEU GLY GLY ASP GLY THR ILE LEU HIS GLY SEQRES 11 A 388 VAL SER MET PHE GLY ASN THR GLN VAL PRO PRO VAL LEU SEQRES 12 A 388 ALA PHE ALA LEU GLY THR LEU GLY PHE LEU SER PRO PHE SEQRES 13 A 388 ASP PHE LYS GLU HIS LYS LYS VAL PHE GLN GLU VAL ILE SEQRES 14 A 388 SER SER ARG ALA LYS CYS LEU HIS ARG THR ARG LEU GLU SEQRES 15 A 388 CYS HIS LEU LYS LYS LYS ASP SER ASN SER SER ILE VAL SEQRES 16 A 388 THR HIS ALA MET ASN ASP ILE PHE LEU HIS ARG GLY ASN SEQRES 17 A 388 SER PRO HIS LEU THR ASN LEU ASP ILE PHE ILE ASP GLY SEQRES 18 A 388 GLU PHE LEU THR ARG THR THR ALA ASP GLY VAL ALA LEU SEQRES 19 A 388 ALA THR PRO THR GLY SER THR ALA TYR SER LEU SER ALA SEQRES 20 A 388 GLY GLY SER ILE VAL SER PRO LEU VAL PRO ALA ILE LEU SEQRES 21 A 388 MET THR PRO ILE CYS PRO ARG SER LEU SER PHE ARG PRO SEQRES 22 A 388 LEU ILE LEU PRO HIS SER SER HIS ILE ARG ILE LYS ILE SEQRES 23 A 388 GLY SER LYS LEU ASN GLN LYS PRO VAL ASN SER VAL VAL SEQRES 24 A 388 LYS LEU SER VAL ASP GLY ILE PRO GLN GLN ASP LEU ASP SEQRES 25 A 388 VAL GLY ASP GLU ILE TYR VAL ILE ASN GLU VAL GLY THR SEQRES 26 A 388 ILE TYR ILE ASP GLY THR GLN LEU PRO THR THR ARG LYS SEQRES 27 A 388 THR GLU ASN ASP PHE ASN ASN SER LYS LYS PRO LYS ARG SEQRES 28 A 388 SER GLY ILE TYR CYS VAL ALA LYS THR GLU ASN ASP TRP SEQRES 29 A 388 ILE ARG GLY ILE ASN GLU LEU LEU GLY PHE ASN SER SER SEQRES 30 A 388 PHE ARG LEU THR LYS ARG GLN THR ASP ASN ASP SEQRES 1 B 388 LEU GLN SER GLY SER LYS PHE VAL LYS ILE LYS PRO VAL SEQRES 2 B 388 ASN ASN LEU ARG SER SER SER SER ALA ASP PHE VAL SER SEQRES 3 B 388 PRO PRO ASN SER LYS LEU GLN SER LEU ILE TRP GLN ASN SEQRES 4 B 388 PRO LEU GLN ASN VAL TYR ILE THR LYS LYS PRO TRP THR SEQRES 5 B 388 PRO SER THR ARG GLU ALA MET VAL GLU PHE ILE THR HIS SEQRES 6 B 388 LEU HIS GLU SER TYR PRO GLU VAL ASN VAL ILE VAL GLN SEQRES 7 B 388 PRO ASP VAL ALA GLU GLU ILE SER GLN ASP PHE LYS SER SEQRES 8 B 388 PRO LEU GLU ASN ASP PRO ASN ARG PRO HIS ILE LEU TYR SEQRES 9 B 388 THR GLY PRO GLU GLN ASP ILE VAL ASN ARG THR ASP LEU SEQRES 10 B 388 LEU VAL THR LEU GLY GLY ASP GLY THR ILE LEU HIS GLY SEQRES 11 B 388 VAL SER MET PHE GLY ASN THR GLN VAL PRO PRO VAL LEU SEQRES 12 B 388 ALA PHE ALA LEU GLY THR LEU GLY PHE LEU SER PRO PHE SEQRES 13 B 388 ASP PHE LYS GLU HIS LYS LYS VAL PHE GLN GLU VAL ILE SEQRES 14 B 388 SER SER ARG ALA LYS CYS LEU HIS ARG THR ARG LEU GLU SEQRES 15 B 388 CYS HIS LEU LYS LYS LYS ASP SER ASN SER SER ILE VAL SEQRES 16 B 388 THR HIS ALA MET ASN ASP ILE PHE LEU HIS ARG GLY ASN SEQRES 17 B 388 SER PRO HIS LEU THR ASN LEU ASP ILE PHE ILE ASP GLY SEQRES 18 B 388 GLU PHE LEU THR ARG THR THR ALA ASP GLY VAL ALA LEU SEQRES 19 B 388 ALA THR PRO THR GLY SER THR ALA TYR SER LEU SER ALA SEQRES 20 B 388 GLY GLY SER ILE VAL SER PRO LEU VAL PRO ALA ILE LEU SEQRES 21 B 388 MET THR PRO ILE CYS PRO ARG SER LEU SER PHE ARG PRO SEQRES 22 B 388 LEU ILE LEU PRO HIS SER SER HIS ILE ARG ILE LYS ILE SEQRES 23 B 388 GLY SER LYS LEU ASN GLN LYS PRO VAL ASN SER VAL VAL SEQRES 24 B 388 LYS LEU SER VAL ASP GLY ILE PRO GLN GLN ASP LEU ASP SEQRES 25 B 388 VAL GLY ASP GLU ILE TYR VAL ILE ASN GLU VAL GLY THR SEQRES 26 B 388 ILE TYR ILE ASP GLY THR GLN LEU PRO THR THR ARG LYS SEQRES 27 B 388 THR GLU ASN ASP PHE ASN ASN SER LYS LYS PRO LYS ARG SEQRES 28 B 388 SER GLY ILE TYR CYS VAL ALA LYS THR GLU ASN ASP TRP SEQRES 29 B 388 ILE ARG GLY ILE ASN GLU LEU LEU GLY PHE ASN SER SER SEQRES 30 B 388 PHE ARG LEU THR LYS ARG GLN THR ASP ASN ASP HET NAI A1001 44 HET MPD A2001 8 HET MPD A2002 8 HET NAI B1001 44 HET MPD B2001 8 HET MPD B2002 8 HETNAM NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETSYN NAI NADH FORMUL 3 NAI 2(C21 H29 N7 O14 P2) FORMUL 4 MPD 4(C6 H14 O2) FORMUL 9 HOH *478(H2 O) HELIX 1 1 ASN A 40 LEU A 42 5 3 HELIX 2 2 THR A 78 TYR A 96 1 19 HELIX 3 3 GLN A 104 GLN A 113 1 10 HELIX 4 4 PRO A 118 ASP A 122 5 5 HELIX 5 5 PRO A 133 THR A 141 1 9 HELIX 6 6 GLY A 149 MET A 159 1 11 HELIX 7 7 GLU A 186 SER A 196 1 11 HELIX 8 8 PRO A 263 THR A 267 5 5 HELIX 9 9 ALA A 268 ALA A 273 1 6 HELIX 10 10 ASN A 388 LEU A 397 1 10 HELIX 11 11 ASN B 40 LEU B 42 5 3 HELIX 12 12 THR B 78 TYR B 96 1 19 HELIX 13 13 GLN B 104 SER B 112 1 9 HELIX 14 14 GLN B 113 PHE B 115 5 3 HELIX 15 15 PRO B 118 ASP B 122 5 5 HELIX 16 16 PRO B 133 THR B 141 1 9 HELIX 17 17 GLY B 149 PHE B 160 1 12 HELIX 18 18 GLU B 186 SER B 196 1 11 HELIX 19 19 PRO B 263 THR B 267 5 5 HELIX 20 20 ALA B 268 ALA B 273 1 6 HELIX 21 21 ASN B 388 LEU B 397 1 10 SHEET 1 A 2 VAL A 34 PRO A 38 0 SHEET 2 A 2 HIS A 127 THR A 131 1 O HIS A 127 N LYS A 35 SHEET 1 B 4 ASP A 49 VAL A 51 0 SHEET 2 B 4 GLN A 59 ILE A 62 -1 O ILE A 62 N ASP A 49 SHEET 3 B 4 LYS A 200 ARG A 204 -1 O CYS A 201 N GLN A 59 SHEET 4 B 4 ILE A 380 VAL A 383 -1 O ILE A 380 N ARG A 204 SHEET 1 C 5 ASN A 100 ILE A 102 0 SHEET 2 C 5 ASN A 69 LYS A 74 1 N VAL A 70 O ASN A 100 SHEET 3 C 5 LEU A 143 GLY A 148 1 O VAL A 145 N TYR A 71 SHEET 4 C 5 VAL A 168 ALA A 172 1 O LEU A 169 N LEU A 144 SHEET 5 C 5 PHE A 182 ASP A 183 1 O PHE A 182 N ALA A 172 SHEET 1 D 9 ILE A 220 ALA A 224 0 SHEET 2 D 9 LEU A 207 LYS A 212 -1 N LEU A 211 O ILE A 220 SHEET 3 D 9 GLU A 342 ASN A 347 -1 O ILE A 346 N GLU A 208 SHEET 4 D 9 ILE A 308 ILE A 312 -1 N ILE A 308 O VAL A 345 SHEET 5 D 9 THR A 239 ILE A 245 -1 N PHE A 244 O ARG A 309 SHEET 6 D 9 GLU A 248 ALA A 261 -1 O LEU A 250 N ILE A 243 SHEET 7 D 9 ASP A 227 HIS A 231 -1 N ILE A 228 O LEU A 260 SHEET 8 D 9 VAL A 325 VAL A 329 -1 O LYS A 326 N HIS A 231 SHEET 9 D 9 ILE A 332 LEU A 337 -1 O LEU A 337 N VAL A 325 SHEET 1 E 9 ILE A 220 ALA A 224 0 SHEET 2 E 9 LEU A 207 LYS A 212 -1 N LEU A 211 O ILE A 220 SHEET 3 E 9 GLU A 342 ASN A 347 -1 O ILE A 346 N GLU A 208 SHEET 4 E 9 ILE A 308 ILE A 312 -1 N ILE A 308 O VAL A 345 SHEET 5 E 9 THR A 239 ILE A 245 -1 N PHE A 244 O ARG A 309 SHEET 6 E 9 GLU A 248 ALA A 261 -1 O LEU A 250 N ILE A 243 SHEET 7 E 9 ALA A 284 PRO A 292 -1 O LEU A 286 N ALA A 261 SHEET 8 E 9 LEU A 300 PRO A 303 -1 O LEU A 302 N ILE A 285 SHEET 9 E 9 ILE B 277 VAL B 278 1 O ILE B 277 N ILE A 301 SHEET 1 F 9 ILE A 277 VAL A 278 0 SHEET 2 F 9 LEU B 300 LEU B 302 1 O ILE B 301 N ILE A 277 SHEET 3 F 9 ILE B 285 PRO B 292 -1 N ILE B 285 O LEU B 302 SHEET 4 F 9 GLU B 248 ALA B 261 -1 N ALA B 261 O LEU B 286 SHEET 5 F 9 THR B 239 ILE B 245 -1 N ILE B 243 O LEU B 250 SHEET 6 F 9 ILE B 308 ILE B 312 -1 O ARG B 309 N PHE B 244 SHEET 7 F 9 GLU B 342 ASN B 347 -1 O VAL B 345 N ILE B 308 SHEET 8 F 9 LEU B 207 LYS B 212 -1 N GLU B 208 O ILE B 346 SHEET 9 F 9 ILE B 220 ALA B 224 -1 O THR B 222 N CYS B 209 SHEET 1 G 7 ILE A 277 VAL A 278 0 SHEET 2 G 7 LEU B 300 LEU B 302 1 O ILE B 301 N ILE A 277 SHEET 3 G 7 ILE B 285 PRO B 292 -1 N ILE B 285 O LEU B 302 SHEET 4 G 7 GLU B 248 ALA B 261 -1 N ALA B 261 O LEU B 286 SHEET 5 G 7 ASP B 227 HIS B 231 -1 N ILE B 228 O LEU B 260 SHEET 6 G 7 VAL B 325 VAL B 329 -1 O LYS B 326 N HIS B 231 SHEET 7 G 7 ILE B 332 LEU B 337 -1 O GLN B 334 N LEU B 327 SHEET 1 H 2 LYS B 35 PRO B 38 0 SHEET 2 H 2 ILE B 128 THR B 131 1 O LEU B 129 N LYS B 37 SHEET 1 I 4 ALA B 48 VAL B 51 0 SHEET 2 I 4 GLN B 59 TRP B 63 -1 O ILE B 62 N ASP B 49 SHEET 3 I 4 LYS B 200 ARG B 204 -1 O CYS B 201 N GLN B 59 SHEET 4 I 4 ILE B 380 VAL B 383 -1 O ILE B 380 N ARG B 204 SHEET 1 J 5 ASN B 100 ILE B 102 0 SHEET 2 J 5 ASN B 69 LYS B 74 1 N VAL B 70 O ILE B 102 SHEET 3 J 5 LEU B 143 GLY B 148 1 O VAL B 145 N TYR B 71 SHEET 4 J 5 VAL B 168 ALA B 172 1 O LEU B 169 N LEU B 144 SHEET 5 J 5 PHE B 182 ASP B 183 1 O PHE B 182 N ALA B 172 SITE 1 AC1 27 ASP A 150 GLY A 151 LEU A 154 GLY A 177 SITE 2 AC1 27 PHE A 178 ASN A 226 ASP A 227 THR A 264 SITE 3 AC1 27 THR A 267 ALA A 268 TYR A 269 SER A 272 SITE 4 AC1 27 ASP A 330 GLY A 331 HOH A3033 HOH A3134 SITE 5 AC1 27 HOH A3138 HOH A3141 HOH A3148 HOH A3189 SITE 6 AC1 27 HOH A3240 HOH A3244 LEU B 238 ASP B 256 SITE 7 AC1 27 CYS B 291 ARG B 293 HOH B3170 SITE 1 AC2 6 PHE A 178 LEU A 179 ARG A 204 ASP A 389 SITE 2 AC2 6 GLY A 393 HOH A3233 SITE 1 AC3 4 ALA A 199 LYS A 200 ALA A 384 LYS A 385 SITE 1 AC4 27 LEU A 238 ASP A 256 CYS A 291 ARG A 293 SITE 2 AC4 27 HOH A3018 HOH A3073 HOH A3128 HOH A3172 SITE 3 AC4 27 HOH A3203 HOH A3220 ASP B 150 GLY B 151 SITE 4 AC4 27 LEU B 154 GLY B 177 PHE B 178 ASN B 226 SITE 5 AC4 27 ASP B 227 THR B 264 THR B 267 ALA B 268 SITE 6 AC4 27 TYR B 269 SER B 272 ASP B 330 GLY B 331 SITE 7 AC4 27 HOH B3042 HOH B3165 HOH B3176 SITE 1 AC5 4 ALA B 199 LYS B 200 ALA B 384 LYS B 385 SITE 1 AC6 8 PHE B 178 LEU B 179 PRO B 181 LEU B 202 SITE 2 AC6 8 ARG B 204 ASP B 389 TRP B 390 HOH B3011 CRYST1 98.685 132.782 59.636 90.00 90.00 90.00 P 21 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.010133 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007531 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016768 0.00000