HEADER OXIDOREDUCTASE 22-JUN-00 1E3S TITLE RAT BRAIN 3-HYDROXYACYL-COA DEHYDROGENASE BINARY COMPLEX WITH NADH COMPND MOL_ID: 1; COMPND 2 MOLECULE: SHORT CHAIN 3-HYDROXYACYL-COA DEHYDROGENASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: HADH II; COMPND 5 EC: 1.1.1.35; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 ORGAN: BRAIN; SOURCE 6 ORGANELLE: MITOCHONRIA; SOURCE 7 CELLULAR_LOCATION: CYTOPLASM; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 11 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS OXIDOREDUCTASE, DEHYDROGENASE, BETA-OXIDATION OF FATTY ACIDS, KEYWDS 2 STEROIDS, AMYLOID BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.J.POWELL,J.A.READ,M.J.BANFIELD,R.L.BRADY REVDAT 4 13-DEC-23 1E3S 1 REMARK REVDAT 3 08-MAY-19 1E3S 1 REMARK REVDAT 2 24-FEB-09 1E3S 1 VERSN REVDAT 1 25-MAY-01 1E3S 0 JRNL AUTH A.J.POWELL,J.A.READ,M.J.BANFIELD,F.GUNN-MOORE,S.D.YAN, JRNL AUTH 2 J.LUSTBADER,A.R.STERN,D.M.STERN,R.L.BRADY JRNL TITL RECOGNITION OF STRUCTURALLY DIVERSE SUBSTRATES BY TYPE II JRNL TITL 2 3-HYDROXYACYL-COA DEHYDROGENASE (HADH II) AMYLOID-BETA JRNL TITL 3 BINDING ALCOHOL DEHYDROGENASE (ABAD) JRNL REF J.MOL.BIOL. V. 303 311 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 11023795 JRNL DOI 10.1006/JMBI.2000.4139 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 62009 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6937 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 176 REMARK 3 SOLVENT ATOMS : 492 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.40 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.011 ; NULL REMARK 3 ANGLE DISTANCE (A) : 0.030 ; 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: NULL REMARK 4 REMARK 4 1E3S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-JUN-00. REMARK 100 THE DEPOSITION ID IS D_1290004912. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX7.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.488 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62009 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 1.500 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : 0.05900 REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22700 REMARK 200 R SYM FOR SHELL (I) : 0.22700 REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 2HSD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP PROT: 5MG/ML, 0.75 MM REMARK 280 NADH, 50 MM NACL, 10 MM HEPES PH 7.5 WELL: 30% PEG 4000, 0.2 M REMARK 280 LI SO4, 0.1 M TRIS PH 8.5. 18 C, PH 8.50, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 ALA A 4 REMARK 465 VAL A 5 REMARK 465 ARG A 6 REMARK 465 LEU A 205 REMARK 465 LEU A 206 REMARK 465 THR A 207 REMARK 465 THR A 208 REMARK 465 LEU A 209 REMARK 465 PRO A 210 REMARK 465 ASP A 211 REMARK 465 LYS A 212 REMARK 465 VAL A 213 REMARK 465 ARG A 214 REMARK 465 ASN A 215 REMARK 465 PHE A 216 REMARK 465 LEU A 217 REMARK 465 ALA A 218 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ALA B 3 REMARK 465 ALA B 4 REMARK 465 VAL B 5 REMARK 465 ARG B 6 REMARK 465 LEU B 205 REMARK 465 LEU B 206 REMARK 465 THR B 207 REMARK 465 THR B 208 REMARK 465 LEU B 209 REMARK 465 PRO B 210 REMARK 465 ASP B 211 REMARK 465 LYS B 212 REMARK 465 VAL B 213 REMARK 465 ARG B 214 REMARK 465 ASN B 215 REMARK 465 PHE B 216 REMARK 465 LEU B 217 REMARK 465 ALA B 218 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 ALA C 3 REMARK 465 ALA C 4 REMARK 465 VAL C 5 REMARK 465 ARG C 6 REMARK 465 LEU C 205 REMARK 465 LEU C 206 REMARK 465 THR C 207 REMARK 465 THR C 208 REMARK 465 LEU C 209 REMARK 465 PRO C 210 REMARK 465 ASP C 211 REMARK 465 LYS C 212 REMARK 465 VAL C 213 REMARK 465 ARG C 214 REMARK 465 ASN C 215 REMARK 465 PHE C 216 REMARK 465 LEU C 217 REMARK 465 ALA C 218 REMARK 465 MET D 1 REMARK 465 ALA D 2 REMARK 465 ALA D 3 REMARK 465 ALA D 4 REMARK 465 VAL D 5 REMARK 465 ARG D 6 REMARK 465 LEU D 205 REMARK 465 LEU D 206 REMARK 465 THR D 207 REMARK 465 THR D 208 REMARK 465 LEU D 209 REMARK 465 PRO D 210 REMARK 465 ASP D 211 REMARK 465 LYS D 212 REMARK 465 VAL D 213 REMARK 465 ARG D 214 REMARK 465 ASN D 215 REMARK 465 PHE D 216 REMARK 465 LEU D 217 REMARK 465 ALA D 218 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 103 CB CG CD OE1 OE2 REMARK 470 LYS A 104 CB CG CD CE NZ REMARK 470 LYS A 105 CG CD CE NZ REMARK 470 ASN A 106 CG OD1 ND2 REMARK 470 GLU A 140 CG CD OE1 OE2 REMARK 470 GLN A 143 CG CD OE1 NE2 REMARK 470 SER A 219 CB OG REMARK 470 GLN A 220 CB CG CD OE1 NE2 REMARK 470 GLU B 103 CG CD OE1 OE2 REMARK 470 LYS B 104 CB CG CD CE NZ REMARK 470 LYS B 105 CB CG CD CE NZ REMARK 470 ASN B 106 CB CG OD1 ND2 REMARK 470 GLN B 143 CG CD OE1 NE2 REMARK 470 SER B 219 CB OG REMARK 470 GLN B 220 CB CG CD OE1 NE2 REMARK 470 LYS C 104 CG CD CE NZ REMARK 470 LYS C 105 CG CD CE NZ REMARK 470 ASN C 106 CB CG OD1 ND2 REMARK 470 GLU C 140 CG CD OE1 OE2 REMARK 470 GLN C 143 CG CD OE1 NE2 REMARK 470 SER C 219 CB OG REMARK 470 GLN C 220 CB CG CD OE1 NE2 REMARK 470 GLU D 103 CG CD OE1 OE2 REMARK 470 LYS D 104 CG CD CE NZ REMARK 470 LYS D 105 CG CD CE NZ REMARK 470 GLN D 143 CG CD OE1 NE2 REMARK 470 SER D 219 CB OG REMARK 470 GLN D 220 CB CG CD OE1 NE2 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 LYS A 79 CD CE NZ REMARK 480 LYS D 9 CD CE NZ 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 LYS A 79 CG LYS A 79 CD -0.312 REMARK 500 PRO A 261 CD PRO A 261 N 0.086 REMARK 500 PRO B 261 CD PRO B 261 N 0.094 REMARK 500 PRO D 261 CD PRO D 261 N 0.092 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 LYS A 79 CB - CG - CD ANGL. DEV. = 33.7 DEGREES REMARK 500 ARG A 84 CD - NE - CZ ANGL. DEV. = 44.4 DEGREES REMARK 500 ARG A 84 NH1 - CZ - NH2 ANGL. DEV. = -6.7 DEGREES REMARK 500 ARG A 84 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 84 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 130 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 142 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 GLU A 160 OE1 - CD - OE2 ANGL. DEV. = -11.0 DEGREES REMARK 500 ARG A 258 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 84 CD - NE - CZ ANGL. DEV. = 45.0 DEGREES REMARK 500 ARG B 84 NE - CZ - NH2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG B 130 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 GLU B 160 OE1 - CD - OE2 ANGL. DEV. = -28.6 DEGREES REMARK 500 GLU B 160 CG - CD - OE1 ANGL. DEV. = 14.9 DEGREES REMARK 500 GLU B 160 CG - CD - OE2 ANGL. DEV. = 13.8 DEGREES REMARK 500 ARG B 192 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG C 29 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG C 84 CD - NE - CZ ANGL. DEV. = 49.6 DEGREES REMARK 500 ARG C 130 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP C 142 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 GLU C 160 OE1 - CD - OE2 ANGL. DEV. = -9.2 DEGREES REMARK 500 ASP C 229 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG D 84 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG D 84 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG D 116 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG D 130 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 GLU D 160 OE1 - CD - OE2 ANGL. DEV. = -9.4 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 GLU A 103 -86.95 -48.64 REMARK 500 ASP A 142 -168.93 -74.22 REMARK 500 ALA A 154 -127.67 -93.80 REMARK 500 ASP A 254 14.94 -151.25 REMARK 500 LYS B 104 -43.66 -28.91 REMARK 500 ASP B 142 -165.24 -74.17 REMARK 500 ALA B 154 -123.08 -100.43 REMARK 500 SER B 155 155.67 178.21 REMARK 500 PHE B 223 132.75 -170.45 REMARK 500 ASP B 254 12.78 -151.90 REMARK 500 ALA C 154 -125.47 -102.05 REMARK 500 GLN C 220 -77.78 104.68 REMARK 500 PHE C 223 135.39 -170.15 REMARK 500 ASP C 254 16.21 -150.57 REMARK 500 ASP D 142 -165.03 -72.12 REMARK 500 ALA D 154 -121.87 -96.43 REMARK 500 SER D 155 158.66 178.70 REMARK 500 PHE D 223 132.68 -170.36 REMARK 500 ASP D 254 15.94 -152.96 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 A2013 DISTANCE = 5.83 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD D 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HSD RELATED DB: PDB REMARK 900 ALPHA, 20 BETA-HYDROXYSTEROID DEHYDROGENASE (HOLO FORM) REMARK 900 RELATED ID: 1E3W RELATED DB: PDB REMARK 900 RAT BRAIN 3-HYDROXYACYL-COA DEHYDROGENASE BINARY COMPLEX WITH NADH REMARK 900 AND 3-KETO BUTYRATE DBREF 1E3S A 1 1 PDB 1E3S 1E3S 1 1 DBREF 1E3S A 2 261 UNP O70351 HCD2_RAT 1 260 DBREF 1E3S B 1 1 PDB 1E3S 1E3S 1 1 DBREF 1E3S B 2 261 UNP O70351 HCD2_RAT 1 260 DBREF 1E3S C 1 1 PDB 1E3S 1E3S 1 1 DBREF 1E3S C 2 261 UNP O70351 HCD2_RAT 1 260 DBREF 1E3S D 1 1 PDB 1E3S 1E3S 1 1 DBREF 1E3S D 2 261 UNP O70351 HCD2_RAT 1 260 SEQRES 1 A 261 MET ALA ALA ALA VAL ARG SER VAL LYS GLY LEU VAL ALA SEQRES 2 A 261 VAL ILE THR GLY GLY ALA SER GLY LEU GLY LEU SER THR SEQRES 3 A 261 ALA LYS ARG LEU VAL GLY GLN GLY ALA THR ALA VAL LEU SEQRES 4 A 261 LEU ASP VAL PRO ASN SER GLU GLY GLU THR GLU ALA LYS SEQRES 5 A 261 LYS LEU GLY GLY ASN CYS ILE PHE ALA PRO ALA ASN VAL SEQRES 6 A 261 THR SER GLU LYS GLU VAL GLN ALA ALA LEU THR LEU ALA SEQRES 7 A 261 LYS GLU LYS PHE GLY ARG ILE ASP VAL ALA VAL ASN CYS SEQRES 8 A 261 ALA GLY ILE ALA VAL ALA ILE LYS THR TYR HIS GLU LYS SEQRES 9 A 261 LYS ASN GLN VAL HIS THR LEU GLU ASP PHE GLN ARG VAL SEQRES 10 A 261 ILE ASN VAL ASN LEU ILE GLY THR PHE ASN VAL ILE ARG SEQRES 11 A 261 LEU VAL ALA GLY VAL MET GLY GLN ASN GLU PRO ASP GLN SEQRES 12 A 261 GLY GLY GLN ARG GLY VAL ILE ILE ASN THR ALA SER VAL SEQRES 13 A 261 ALA ALA PHE GLU GLY GLN VAL GLY GLN ALA ALA TYR SER SEQRES 14 A 261 ALA SER LYS GLY GLY ILE VAL GLY MET THR LEU PRO ILE SEQRES 15 A 261 ALA ARG ASP LEU ALA PRO ILE GLY ILE ARG VAL VAL THR SEQRES 16 A 261 ILE ALA PRO GLY LEU PHE ALA THR PRO LEU LEU THR THR SEQRES 17 A 261 LEU PRO ASP LYS VAL ARG ASN PHE LEU ALA SER GLN VAL SEQRES 18 A 261 PRO PHE PRO SER ARG LEU GLY ASP PRO ALA GLU TYR ALA SEQRES 19 A 261 HIS LEU VAL GLN MET VAL ILE GLU ASN PRO PHE LEU ASN SEQRES 20 A 261 GLY GLU VAL ILE ARG LEU ASP GLY ALA ILE ARG MET GLN SEQRES 21 A 261 PRO SEQRES 1 B 261 MET ALA ALA ALA VAL ARG SER VAL LYS GLY LEU VAL ALA SEQRES 2 B 261 VAL ILE THR GLY GLY ALA SER GLY LEU GLY LEU SER THR SEQRES 3 B 261 ALA LYS ARG LEU VAL GLY GLN GLY ALA THR ALA VAL LEU SEQRES 4 B 261 LEU ASP VAL PRO ASN SER GLU GLY GLU THR GLU ALA LYS SEQRES 5 B 261 LYS LEU GLY GLY ASN CYS ILE PHE ALA PRO ALA ASN VAL SEQRES 6 B 261 THR SER GLU LYS GLU VAL GLN ALA ALA LEU THR LEU ALA SEQRES 7 B 261 LYS GLU LYS PHE GLY ARG ILE ASP VAL ALA VAL ASN CYS SEQRES 8 B 261 ALA GLY ILE ALA VAL ALA ILE LYS THR TYR HIS GLU LYS SEQRES 9 B 261 LYS ASN GLN VAL HIS THR LEU GLU ASP PHE GLN ARG VAL SEQRES 10 B 261 ILE ASN VAL ASN LEU ILE GLY THR PHE ASN VAL ILE ARG SEQRES 11 B 261 LEU VAL ALA GLY VAL MET GLY GLN ASN GLU PRO ASP GLN SEQRES 12 B 261 GLY GLY GLN ARG GLY VAL ILE ILE ASN THR ALA SER VAL SEQRES 13 B 261 ALA ALA PHE GLU GLY GLN VAL GLY GLN ALA ALA TYR SER SEQRES 14 B 261 ALA SER LYS GLY GLY ILE VAL GLY MET THR LEU PRO ILE SEQRES 15 B 261 ALA ARG ASP LEU ALA PRO ILE GLY ILE ARG VAL VAL THR SEQRES 16 B 261 ILE ALA PRO GLY LEU PHE ALA THR PRO LEU LEU THR THR SEQRES 17 B 261 LEU PRO ASP LYS VAL ARG ASN PHE LEU ALA SER GLN VAL SEQRES 18 B 261 PRO PHE PRO SER ARG LEU GLY ASP PRO ALA GLU TYR ALA SEQRES 19 B 261 HIS LEU VAL GLN MET VAL ILE GLU ASN PRO PHE LEU ASN SEQRES 20 B 261 GLY GLU VAL ILE ARG LEU ASP GLY ALA ILE ARG MET GLN SEQRES 21 B 261 PRO SEQRES 1 C 261 MET ALA ALA ALA VAL ARG SER VAL LYS GLY LEU VAL ALA SEQRES 2 C 261 VAL ILE THR GLY GLY ALA SER GLY LEU GLY LEU SER THR SEQRES 3 C 261 ALA LYS ARG LEU VAL GLY GLN GLY ALA THR ALA VAL LEU SEQRES 4 C 261 LEU ASP VAL PRO ASN SER GLU GLY GLU THR GLU ALA LYS SEQRES 5 C 261 LYS LEU GLY GLY ASN CYS ILE PHE ALA PRO ALA ASN VAL SEQRES 6 C 261 THR SER GLU LYS GLU VAL GLN ALA ALA LEU THR LEU ALA SEQRES 7 C 261 LYS GLU LYS PHE GLY ARG ILE ASP VAL ALA VAL ASN CYS SEQRES 8 C 261 ALA GLY ILE ALA VAL ALA ILE LYS THR TYR HIS GLU LYS SEQRES 9 C 261 LYS ASN GLN VAL HIS THR LEU GLU ASP PHE GLN ARG VAL SEQRES 10 C 261 ILE ASN VAL ASN LEU ILE GLY THR PHE ASN VAL ILE ARG SEQRES 11 C 261 LEU VAL ALA GLY VAL MET GLY GLN ASN GLU PRO ASP GLN SEQRES 12 C 261 GLY GLY GLN ARG GLY VAL ILE ILE ASN THR ALA SER VAL SEQRES 13 C 261 ALA ALA PHE GLU GLY GLN VAL GLY GLN ALA ALA TYR SER SEQRES 14 C 261 ALA SER LYS GLY GLY ILE VAL GLY MET THR LEU PRO ILE SEQRES 15 C 261 ALA ARG ASP LEU ALA PRO ILE GLY ILE ARG VAL VAL THR SEQRES 16 C 261 ILE ALA PRO GLY LEU PHE ALA THR PRO LEU LEU THR THR SEQRES 17 C 261 LEU PRO ASP LYS VAL ARG ASN PHE LEU ALA SER GLN VAL SEQRES 18 C 261 PRO PHE PRO SER ARG LEU GLY ASP PRO ALA GLU TYR ALA SEQRES 19 C 261 HIS LEU VAL GLN MET VAL ILE GLU ASN PRO PHE LEU ASN SEQRES 20 C 261 GLY GLU VAL ILE ARG LEU ASP GLY ALA ILE ARG MET GLN SEQRES 21 C 261 PRO SEQRES 1 D 261 MET ALA ALA ALA VAL ARG SER VAL LYS GLY LEU VAL ALA SEQRES 2 D 261 VAL ILE THR GLY GLY ALA SER GLY LEU GLY LEU SER THR SEQRES 3 D 261 ALA LYS ARG LEU VAL GLY GLN GLY ALA THR ALA VAL LEU SEQRES 4 D 261 LEU ASP VAL PRO ASN SER GLU GLY GLU THR GLU ALA LYS SEQRES 5 D 261 LYS LEU GLY GLY ASN CYS ILE PHE ALA PRO ALA ASN VAL SEQRES 6 D 261 THR SER GLU LYS GLU VAL GLN ALA ALA LEU THR LEU ALA SEQRES 7 D 261 LYS GLU LYS PHE GLY ARG ILE ASP VAL ALA VAL ASN CYS SEQRES 8 D 261 ALA GLY ILE ALA VAL ALA ILE LYS THR TYR HIS GLU LYS SEQRES 9 D 261 LYS ASN GLN VAL HIS THR LEU GLU ASP PHE GLN ARG VAL SEQRES 10 D 261 ILE ASN VAL ASN LEU ILE GLY THR PHE ASN VAL ILE ARG SEQRES 11 D 261 LEU VAL ALA GLY VAL MET GLY GLN ASN GLU PRO ASP GLN SEQRES 12 D 261 GLY GLY GLN ARG GLY VAL ILE ILE ASN THR ALA SER VAL SEQRES 13 D 261 ALA ALA PHE GLU GLY GLN VAL GLY GLN ALA ALA TYR SER SEQRES 14 D 261 ALA SER LYS GLY GLY ILE VAL GLY MET THR LEU PRO ILE SEQRES 15 D 261 ALA ARG ASP LEU ALA PRO ILE GLY ILE ARG VAL VAL THR SEQRES 16 D 261 ILE ALA PRO GLY LEU PHE ALA THR PRO LEU LEU THR THR SEQRES 17 D 261 LEU PRO ASP LYS VAL ARG ASN PHE LEU ALA SER GLN VAL SEQRES 18 D 261 PRO PHE PRO SER ARG LEU GLY ASP PRO ALA GLU TYR ALA SEQRES 19 D 261 HIS LEU VAL GLN MET VAL ILE GLU ASN PRO PHE LEU ASN SEQRES 20 D 261 GLY GLU VAL ILE ARG LEU ASP GLY ALA ILE ARG MET GLN SEQRES 21 D 261 PRO HET NAD A 301 44 HET NAD B 301 44 HET NAD C 301 44 HET NAD D 301 44 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE FORMUL 5 NAD 4(C21 H27 N7 O14 P2) FORMUL 9 HOH *492(H2 O) HELIX 1 1 SER A 20 GLN A 33 1 14 HELIX 2 2 GLU A 46 LEU A 54 1 9 HELIX 3 3 SER A 67 GLY A 83 1 17 HELIX 4 4 THR A 110 LEU A 122 1 13 HELIX 5 5 LEU A 122 GLN A 138 1 17 HELIX 6 6 SER A 155 PHE A 159 5 5 HELIX 7 7 GLN A 165 ALA A 187 1 23 HELIX 8 8 ASP A 229 ASN A 243 1 15 HELIX 9 9 SER B 20 GLN B 33 1 14 HELIX 10 10 GLU B 46 LEU B 54 1 9 HELIX 11 11 SER B 67 GLY B 83 1 17 HELIX 12 12 GLU B 103 ASN B 106 5 4 HELIX 13 13 THR B 110 LEU B 122 1 13 HELIX 14 14 LEU B 122 GLN B 138 1 17 HELIX 15 15 VAL B 156 GLY B 161 1 6 HELIX 16 16 GLN B 165 ALA B 187 1 23 HELIX 17 17 ASP B 229 ASN B 243 1 15 HELIX 18 18 SER C 20 GLN C 33 1 14 HELIX 19 19 GLU C 46 LEU C 54 1 9 HELIX 20 20 SER C 67 GLY C 83 1 17 HELIX 21 21 THR C 110 LEU C 122 1 13 HELIX 22 22 LEU C 122 GLY C 137 1 16 HELIX 23 23 SER C 155 PHE C 159 5 5 HELIX 24 24 GLN C 165 ALA C 187 1 23 HELIX 25 25 ASP C 229 ASN C 243 1 15 HELIX 26 26 SER D 20 GLN D 33 1 14 HELIX 27 27 GLU D 46 LEU D 54 1 9 HELIX 28 28 SER D 67 GLY D 83 1 17 HELIX 29 29 THR D 110 LEU D 122 1 13 HELIX 30 30 LEU D 122 GLN D 138 1 17 HELIX 31 31 VAL D 156 GLY D 161 1 6 HELIX 32 32 GLN D 165 ALA D 187 1 23 HELIX 33 33 ASP D 229 ASN D 243 1 15 SHEET 1 A 7 VAL A 250 LEU A 253 0 SHEET 2 A 7 ILE A 191 PRO A 198 1 N THR A 195 O ILE A 251 SHEET 3 A 7 GLY A 148 THR A 153 1 N GLY A 148 O ARG A 192 SHEET 4 A 7 VAL A 87 ASN A 90 1 N ALA A 88 O VAL A 149 SHEET 5 A 7 VAL A 12 THR A 16 1 N VAL A 14 O VAL A 87 SHEET 6 A 7 THR A 36 ASP A 41 1 N THR A 36 O ALA A 13 SHEET 7 A 7 CYS A 58 PRO A 62 1 N ILE A 59 O ALA A 37 SHEET 1 B 7 VAL B 250 LEU B 253 0 SHEET 2 B 7 ILE B 191 PRO B 198 1 N THR B 195 O ILE B 251 SHEET 3 B 7 GLY B 148 THR B 153 1 N GLY B 148 O ARG B 192 SHEET 4 B 7 VAL B 87 ASN B 90 1 N ALA B 88 O VAL B 149 SHEET 5 B 7 VAL B 12 THR B 16 1 N VAL B 14 O VAL B 87 SHEET 6 B 7 THR B 36 ASP B 41 1 N THR B 36 O ALA B 13 SHEET 7 B 7 CYS B 58 PRO B 62 1 N ILE B 59 O ALA B 37 SHEET 1 C 7 VAL C 250 LEU C 253 0 SHEET 2 C 7 ILE C 191 PRO C 198 1 N THR C 195 O ILE C 251 SHEET 3 C 7 GLY C 148 THR C 153 1 N GLY C 148 O ARG C 192 SHEET 4 C 7 VAL C 87 ASN C 90 1 N ALA C 88 O VAL C 149 SHEET 5 C 7 VAL C 12 THR C 16 1 N VAL C 14 O VAL C 87 SHEET 6 C 7 THR C 36 ASP C 41 1 N THR C 36 O ALA C 13 SHEET 7 C 7 CYS C 58 PRO C 62 1 N ILE C 59 O ALA C 37 SHEET 1 D 7 VAL D 250 LEU D 253 0 SHEET 2 D 7 ILE D 191 PRO D 198 1 N THR D 195 O ILE D 251 SHEET 3 D 7 GLY D 148 THR D 153 1 N GLY D 148 O ARG D 192 SHEET 4 D 7 VAL D 87 ASN D 90 1 N ALA D 88 O VAL D 149 SHEET 5 D 7 VAL D 12 THR D 16 1 N VAL D 14 O VAL D 87 SHEET 6 D 7 THR D 36 ASP D 41 1 N THR D 36 O ALA D 13 SHEET 7 D 7 CYS D 58 PRO D 62 1 N ILE D 59 O ALA D 37 CISPEP 1 PHE A 223 PRO A 224 0 -8.11 CISPEP 2 PHE B 223 PRO B 224 0 -6.88 CISPEP 3 PHE C 223 PRO C 224 0 -6.62 CISPEP 4 PHE D 223 PRO D 224 0 -4.22 SITE 1 AC1 23 GLY A 17 SER A 20 GLY A 21 LEU A 22 SITE 2 AC1 23 ASP A 41 ALA A 63 ASN A 64 VAL A 65 SITE 3 AC1 23 CYS A 91 ALA A 92 THR A 153 ALA A 154 SITE 4 AC1 23 TYR A 168 LYS A 172 PRO A 198 GLY A 199 SITE 5 AC1 23 PHE A 201 THR A 203 PRO A 204 HOH A2037 SITE 6 AC1 23 HOH A2107 HOH A2108 HOH A2109 SITE 1 AC2 25 GLY B 17 SER B 20 GLY B 21 LEU B 22 SITE 2 AC2 25 ASP B 41 VAL B 42 ALA B 63 ASN B 64 SITE 3 AC2 25 VAL B 65 CYS B 91 ALA B 92 GLY B 93 SITE 4 AC2 25 THR B 153 ALA B 154 TYR B 168 LYS B 172 SITE 5 AC2 25 PRO B 198 GLY B 199 PHE B 201 THR B 203 SITE 6 AC2 25 PRO B 204 HOH B2127 HOH B2128 HOH B2129 SITE 7 AC2 25 HOH B2130 SITE 1 AC3 24 GLY C 17 SER C 20 GLY C 21 LEU C 22 SITE 2 AC3 24 ASP C 41 ALA C 63 ASN C 64 VAL C 65 SITE 3 AC3 24 CYS C 91 ALA C 92 GLY C 93 THR C 153 SITE 4 AC3 24 ALA C 154 TYR C 168 LYS C 172 PRO C 198 SITE 5 AC3 24 GLY C 199 PHE C 201 THR C 203 PRO C 204 SITE 6 AC3 24 HOH C2047 HOH C2122 HOH C2123 HOH C2124 SITE 1 AC4 24 GLY D 17 SER D 20 GLY D 21 LEU D 22 SITE 2 AC4 24 ASP D 41 ALA D 63 ASN D 64 VAL D 65 SITE 3 AC4 24 CYS D 91 ALA D 92 GLY D 93 THR D 153 SITE 4 AC4 24 ALA D 154 TYR D 168 LYS D 172 GLY D 199 SITE 5 AC4 24 PHE D 201 THR D 203 PRO D 204 HOH D2007 SITE 6 AC4 24 HOH D2126 HOH D2127 HOH D2128 HOH D2129 CRYST1 59.280 68.960 69.550 64.84 72.51 74.98 P 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 0.016869 -0.004526 -0.003897 0.00000 SCALE2 0.000000 0.015014 -0.006111 0.00000 SCALE3 0.000000 0.000000 0.016276 0.00000