PDB Short entry for 5AC2 HEADER OXIDOREDUCTASE 11-AUG-15 5AC2 TITLE HUMAN ALDEHYDE DEHYDROGENASE 1A1 WITH DUOCARMYCIN ANALOG COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINAL DEHYDROGENASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RALDH 1, RALDH1, ALDH-E1, ALHDII, ALDEHYDE DEHYDROGENASE COMPND 5 FAMILY 1 MEMBER A1, ALDEHYDE DEHYDROGENASE CYTOSOLIC, ALDEHYDE COMPND 6 DEHYDROGENASE 1A1; COMPND 7 EC: 1.2.1.36; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE, OXIDATION-REDUCTION PROCESS, ALDEHYDE DEHYDROGENASE KEYWDS 2 ACTIVITY EXPDTA X-RAY DIFFRACTION AUTHOR M.F.KOCH,S.HARTEIS,I.D.BLANK,G.PESTEL,L.F.TIETZE,C.OCHSENFELD, AUTHOR 2 S.SCHNEIDER,S.A.SIEBER REVDAT 4 10-JAN-24 5AC2 1 COMPND REMARK HETNAM LINK REVDAT 3 18-NOV-15 5AC2 1 JRNL REVDAT 2 30-SEP-15 5AC2 1 JRNL REVDAT 1 26-AUG-15 5AC2 0 JRNL AUTH M.F.KOCH,S.HARTEIS,I.D.BLANK,G.PESTEL,L.F.TIETZE, JRNL AUTH 2 C.OCHSENFELD,S.SCHNEIDER,S.A.SIEBER JRNL TITL STRUCTURAL, BIOCHEMICAL, AND COMPUTATIONAL STUDIES REVEAL JRNL TITL 2 THE MECHANISM OF SELECTIVE ALDEHYDE DEHYDROGENASE 1A1 JRNL TITL 3 INHIBITION BY CYTOTOXIC DUOCARMYCIN ANALOGUES. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 54 13550 2015 JRNL REFN ISSN 1433-7851 JRNL PMID 26373694 JRNL DOI 10.1002/ANIE.201505749 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 41466 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2182 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.89 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2925 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.3440 REMARK 3 BIN FREE R VALUE SET COUNT : 153 REMARK 3 BIN FREE R VALUE : 0.3770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3816 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 69 REMARK 3 SOLVENT ATOMS : 167 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.83000 REMARK 3 B22 (A**2) : -0.83000 REMARK 3 B33 (A**2) : 1.66000 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): 0.151 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.148 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.130 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.591 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3999 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3808 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5431 ; 1.900 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8798 ; 0.865 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 501 ; 6.734 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 168 ;37.965 ;24.821 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 677 ;15.481 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;20.223 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 598 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4523 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 889 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1989 ; 2.445 ; 2.893 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1988 ; 2.445 ; 2.893 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2490 ; 3.080 ; 4.327 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2010 ; 3.096 ; 3.229 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES WITH TLS ADDED REMARK 4 REMARK 4 5AC2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1290064665. 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 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43648 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 109.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 26.00 REMARK 200 R MERGE (I) : 0.18820 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 26.50 REMARK 200 R MERGE FOR SHELL (I) : 2.70000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.200 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: PDB ENTRY 4X4L REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 2 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 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: 22390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 58570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -124.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 0.00000 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 350 BIOMT1 3 -1.000000 0.000000 0.000000 109.12300 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 109.12300 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2014 LIES ON A SPECIAL POSITION. 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 SER A 2 REMARK 465 SER A 3 REMARK 465 SER A 4 REMARK 465 GLY A 5 REMARK 465 THR A 6 REMARK 465 PRO A 7 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 2163 O HOH A 2166 1.96 REMARK 500 O HOH A 2123 O HOH A 2167 2.04 REMARK 500 O HOH A 2164 O HOH A 2165 2.06 REMARK 500 O HOH A 2122 O HOH A 2166 2.09 REMARK 500 OE2 GLU A 349 O HOH A 2123 2.18 REMARK 500 O HOH A 2016 O HOH A 2165 2.18 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 ASP A 8 C LEU A 9 N -0.223 REMARK 500 LEU A 9 C PRO A 10 N -0.279 REMARK 500 LEU A 101 C LEU A 102 N -0.244 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 A 10 C - N - CA ANGL. DEV. = 12.2 DEGREES REMARK 500 PRO A 10 C - N - CD ANGL. DEV. = -15.1 DEGREES REMARK 500 ARG A 78 NE - CZ - NH1 ANGL. DEV. = 3.1 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 THR A 21 14.03 -141.68 REMARK 500 ASN A 121 -61.97 -109.30 REMARK 500 ASN A 121 -64.94 -107.24 REMARK 500 THR A 228 -76.77 -104.22 REMARK 500 SER A 261 -88.03 -89.98 REMARK 500 GLN A 301 43.43 -100.41 REMARK 500 TYR A 380 56.00 -98.31 REMARK 500 LYS A 470 -140.75 59.77 REMARK 500 LEU A 478 -175.58 69.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 LEU A 102 15.64 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 YB A1503 YB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 283 OD1 REMARK 620 2 ASP A 283 OD2 42.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 YB A1508 YB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TXE A1504 O1N REMARK 620 2 TXE A1504 O2P 80.2 REMARK 620 3 HOH A2089 O 83.6 80.5 REMARK 620 4 HOH A2091 O 174.9 95.7 98.9 REMARK 620 5 HOH A2122 O 67.8 120.2 139.1 112.2 REMARK 620 6 HOH A2123 O 80.0 158.8 89.7 104.4 57.9 REMARK 620 7 HOH A2163 O 114.5 78.3 149.0 61.3 71.8 117.2 REMARK 620 8 HOH A2166 O 109.8 118.7 157.6 69.4 43.4 75.6 41.6 REMARK 620 9 HOH A2167 O 123.3 156.3 103.1 60.6 72.3 44.5 88.1 54.6 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 YB A1507 YB REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2016 O REMARK 620 2 HOH A2017 O 72.8 REMARK 620 3 HOH A2018 O 92.7 93.8 REMARK 620 4 HOH A2124 O 109.1 73.5 149.4 REMARK 620 5 HOH A2130 O 151.6 87.9 67.5 83.9 REMARK 620 6 HOH A2164 O 121.0 166.2 85.0 100.7 79.0 REMARK 620 7 HOH A2165 O 49.6 55.8 135.0 59.7 133.2 132.5 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K9P A 1502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YB A 1503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TXE A 1504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YB A 1507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YB A 1508 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ABM RELATED DB: PDB REMARK 900 SHEEP ALDEHYDE DEHYDROGENASE 1A1 REMARK 900 RELATED ID: 5AC0 RELATED DB: PDB REMARK 900 OVIS ARIES ALDEHYDE DEHYDROGENASE 1A1 IN COMPLEX WITH A DUOCARMYCIN REMARK 900 ANALOG REMARK 900 RELATED ID: 5AC1 RELATED DB: PDB REMARK 900 SHEEP ALDEHYDE DEHYDROGENASE 1A1 WITH DUOCARMYCIN ANALOG INHIBITOR DBREF 5AC2 A 1 501 UNP P00352 AL1A1_HUMAN 1 501 SEQRES 1 A 501 MET SER SER SER GLY THR PRO ASP LEU PRO VAL LEU LEU SEQRES 2 A 501 THR ASP LEU LYS ILE GLN TYR THR LYS ILE PHE ILE ASN SEQRES 3 A 501 ASN GLU TRP HIS ASP SER VAL SER GLY LYS LYS PHE PRO SEQRES 4 A 501 VAL PHE ASN PRO ALA THR GLU GLU GLU LEU CYS GLN VAL SEQRES 5 A 501 GLU GLU GLY ASP LYS GLU ASP VAL ASP LYS ALA VAL LYS SEQRES 6 A 501 ALA ALA ARG GLN ALA PHE GLN ILE GLY SER PRO TRP ARG SEQRES 7 A 501 THR MET ASP ALA SER GLU ARG GLY ARG LEU LEU TYR LYS SEQRES 8 A 501 LEU ALA ASP LEU ILE GLU ARG ASP ARG LEU LEU LEU ALA SEQRES 9 A 501 THR MET GLU SER MET ASN GLY GLY LYS LEU TYR SER ASN SEQRES 10 A 501 ALA TYR LEU ASN ASP LEU ALA GLY CYS ILE LYS THR LEU SEQRES 11 A 501 ARG TYR CYS ALA GLY TRP ALA ASP LYS ILE GLN GLY ARG SEQRES 12 A 501 THR ILE PRO ILE ASP GLY ASN PHE PHE THR TYR THR ARG SEQRES 13 A 501 HIS GLU PRO ILE GLY VAL CYS GLY GLN ILE ILE PRO TRP SEQRES 14 A 501 ASN PHE PRO LEU VAL MET LEU ILE TRP LYS ILE GLY PRO SEQRES 15 A 501 ALA LEU SER CYS GLY ASN THR VAL VAL VAL LYS PRO ALA SEQRES 16 A 501 GLU GLN THR PRO LEU THR ALA LEU HIS VAL ALA SER LEU SEQRES 17 A 501 ILE LYS GLU ALA GLY PHE PRO PRO GLY VAL VAL ASN ILE SEQRES 18 A 501 VAL PRO GLY TYR GLY PRO THR ALA GLY ALA ALA ILE SER SEQRES 19 A 501 SER HIS MET ASP ILE ASP LYS VAL ALA PHE THR GLY SER SEQRES 20 A 501 THR GLU VAL GLY LYS LEU ILE LYS GLU ALA ALA GLY LYS SEQRES 21 A 501 SER ASN LEU LYS ARG VAL THR LEU GLU LEU GLY GLY LYS SEQRES 22 A 501 SER PRO CYS ILE VAL LEU ALA ASP ALA ASP LEU ASP ASN SEQRES 23 A 501 ALA VAL GLU PHE ALA HIS HIS GLY VAL PHE TYR HIS GLN SEQRES 24 A 501 GLY GLN CYS CYS ILE ALA ALA SER ARG ILE PHE VAL GLU SEQRES 25 A 501 GLU SER ILE TYR ASP GLU PHE VAL ARG ARG SER VAL GLU SEQRES 26 A 501 ARG ALA LYS LYS TYR ILE LEU GLY ASN PRO LEU THR PRO SEQRES 27 A 501 GLY VAL THR GLN GLY PRO GLN ILE ASP LYS GLU GLN TYR SEQRES 28 A 501 ASP LYS ILE LEU ASP LEU ILE GLU SER GLY LYS LYS GLU SEQRES 29 A 501 GLY ALA LYS LEU GLU CYS GLY GLY GLY PRO TRP GLY ASN SEQRES 30 A 501 LYS GLY TYR PHE VAL GLN PRO THR VAL PHE SER ASN VAL SEQRES 31 A 501 THR ASP GLU MET ARG ILE ALA LYS GLU GLU ILE PHE GLY SEQRES 32 A 501 PRO VAL GLN GLN ILE MET LYS PHE LYS SER LEU ASP ASP SEQRES 33 A 501 VAL ILE LYS ARG ALA ASN ASN THR PHE TYR GLY LEU SER SEQRES 34 A 501 ALA GLY VAL PHE THR LYS ASP ILE ASP LYS ALA ILE THR SEQRES 35 A 501 ILE SER SER ALA LEU GLN ALA GLY THR VAL TRP VAL ASN SEQRES 36 A 501 CYS TYR GLY VAL VAL SER ALA GLN CYS PRO PHE GLY GLY SEQRES 37 A 501 PHE LYS MET SER GLY ASN GLY ARG GLU LEU GLY GLU TYR SEQRES 38 A 501 GLY PHE HIS GLU TYR THR GLU VAL LYS THR VAL THR VAL SEQRES 39 A 501 LYS ILE SER GLN LYS ASN SER HET K9P A1502 22 HET YB A1503 1 HET TXE A1504 44 HET YB A1507 1 HET YB A1508 1 HETNAM K9P 1-[(1S)-1-METHYL-5-OXIDANYL-1,2-DIHYDROBENZO[E]INDOL-3- HETNAM 2 K9P YL]HEXAN-1-ONE HETNAM YB YTTERBIUM (III) ION HETNAM TXE [[(2R,3S,4R,5R)-5-[(3R)-3-AMINOCARBONYL-3,4-DIHYDRO-2H- HETNAM 2 TXE PYRIDIN-1-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHOXY- HETNAM 3 TXE OXIDANIDYL-PH OSPHORYL] [(2R,3S,4R,5R)-5-(6- HETNAM 4 TXE AMINOPURIN-9-YL)-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL HETNAM 5 TXE PHOSPHATE HETSYN TXE 1,2,3,4-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE FORMUL 2 K9P C19 H23 N O2 FORMUL 3 YB 3(YB 3+) FORMUL 4 TXE C21 H31 N7 O14 P2 FORMUL 7 HOH *167(H2 O) HELIX 1 1 ASP A 56 PHE A 71 1 16 HELIX 2 2 SER A 75 MET A 80 1 6 HELIX 3 3 ASP A 81 ASP A 99 1 19 HELIX 4 4 ASP A 99 GLY A 112 1 14 HELIX 5 5 LEU A 114 ASN A 121 1 8 HELIX 6 6 ASN A 121 ALA A 137 1 17 HELIX 7 7 ASP A 138 ILE A 140 5 3 HELIX 8 8 PHE A 171 CYS A 186 1 16 HELIX 9 9 PRO A 199 GLY A 213 1 15 HELIX 10 10 THR A 228 HIS A 236 1 9 HELIX 11 11 SER A 247 SER A 261 1 15 HELIX 12 12 ASP A 283 GLN A 301 1 19 HELIX 13 13 GLU A 313 LYS A 328 1 16 HELIX 14 14 ASP A 347 GLU A 364 1 18 HELIX 15 15 MET A 394 GLU A 399 1 6 HELIX 16 16 SER A 413 ASN A 423 1 11 HELIX 17 17 ASP A 436 LEU A 447 1 12 HELIX 18 18 PHE A 469 MET A 471 5 3 HELIX 19 19 LEU A 478 HIS A 484 1 7 SHEET 1 AA 2 ILE A 23 ILE A 25 0 SHEET 2 AA 2 GLU A 28 HIS A 30 -1 O GLU A 28 N ILE A 25 SHEET 1 AB 2 LYS A 37 PHE A 41 0 SHEET 2 AB 2 GLU A 48 GLU A 53 -1 N LEU A 49 O VAL A 40 SHEET 1 AC 3 THR A 144 ILE A 145 0 SHEET 2 AC 3 PHE A 151 PRO A 159 -1 O THR A 153 N ILE A 145 SHEET 3 AC 3 THR A 487 LYS A 495 -1 O GLU A 488 N GLU A 158 SHEET 1 AD 6 VAL A 219 ILE A 221 0 SHEET 2 AD 6 THR A 189 LYS A 193 1 O VAL A 190 N ASN A 220 SHEET 3 AD 6 VAL A 162 ILE A 166 1 O CYS A 163 N VAL A 191 SHEET 4 AD 6 LYS A 241 THR A 245 1 O LYS A 241 N GLY A 164 SHEET 5 AD 6 ARG A 265 GLU A 269 1 O ARG A 265 N VAL A 242 SHEET 6 AD 6 GLY A 473 ASN A 474 -1 O ASN A 474 N LEU A 268 SHEET 1 AE 7 LYS A 367 CYS A 370 0 SHEET 2 AE 7 THR A 385 SER A 388 -1 O VAL A 386 N GLU A 369 SHEET 3 AE 7 VAL A 405 PHE A 411 1 O GLN A 406 N PHE A 387 SHEET 4 AE 7 ALA A 306 GLU A 312 1 O ILE A 309 N MET A 409 SHEET 5 AE 7 SER A 274 VAL A 278 1 O SER A 274 N ARG A 308 SHEET 6 AE 7 SER A 429 PHE A 433 1 O GLY A 431 N ILE A 277 SHEET 7 AE 7 THR A 451 VAL A 454 1 O THR A 451 N ALA A 430 SHEET 1 AF 2 PRO A 374 TRP A 375 0 SHEET 2 AF 2 PHE A 381 VAL A 382 -1 O PHE A 381 N TRP A 375 LINK SG CYS A 302 C8 K9P A1502 1555 1555 1.82 LINK OD1 ASP A 283 YB YB A1503 1555 1555 3.00 LINK OD2 ASP A 283 YB YB A1503 1555 1555 2.98 LINK O1N TXE A1504 YB YB A1508 1555 1555 2.02 LINK O2P TXE A1504 YB YB A1508 1555 1555 2.57 LINK YB YB A1507 O HOH A2016 1555 1555 2.67 LINK YB YB A1507 O HOH A2017 1555 1555 2.69 LINK YB YB A1507 O HOH A2018 1555 1555 2.08 LINK YB YB A1507 O HOH A2124 1555 1555 2.53 LINK YB YB A1507 O HOH A2130 1555 1555 2.54 LINK YB YB A1507 O HOH A2164 1555 7556 2.68 LINK YB YB A1507 O HOH A2165 1555 1555 2.51 LINK YB YB A1508 O HOH A2089 1555 1555 2.38 LINK YB YB A1508 O HOH A2091 1555 1555 2.35 LINK YB YB A1508 O HOH A2122 1555 1555 2.68 LINK YB YB A1508 O HOH A2123 1555 1555 2.34 LINK YB YB A1508 O HOH A2163 1555 1555 2.43 LINK YB YB A1508 O HOH A2166 1555 1555 2.93 LINK YB YB A1508 O HOH A2167 1555 1555 2.88 SITE 1 AC1 11 PHE A 171 MET A 175 TRP A 178 PHE A 290 SITE 2 AC1 11 HIS A 293 GLY A 294 TYR A 297 CYS A 302 SITE 3 AC1 11 ILE A 304 TYR A 457 GLY A 458 SITE 1 AC2 1 ASP A 283 SITE 1 AC3 29 ILE A 166 ILE A 167 PRO A 168 TRP A 169 SITE 2 AC3 29 ASN A 170 LYS A 193 ALA A 195 GLU A 196 SITE 3 AC3 29 GLY A 226 GLY A 230 ALA A 231 PHE A 244 SITE 4 AC3 29 THR A 245 GLY A 246 SER A 247 VAL A 250 SITE 5 AC3 29 GLU A 269 GLY A 271 CYS A 303 GLU A 349 SITE 6 AC3 29 GLN A 350 LYS A 353 GLU A 400 PHE A 402 SITE 7 AC3 29 YB A1508 HOH A2085 HOH A2089 HOH A2122 SITE 8 AC3 29 HOH A2123 SITE 1 AC4 7 HOH A2016 HOH A2017 HOH A2018 HOH A2124 SITE 2 AC4 7 HOH A2130 HOH A2164 HOH A2165 SITE 1 AC5 8 TXE A1504 HOH A2089 HOH A2091 HOH A2122 SITE 2 AC5 8 HOH A2123 HOH A2163 HOH A2166 HOH A2167 CRYST1 109.123 109.123 83.175 90.00 90.00 90.00 P 4 2 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 0.009164 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009164 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012023 0.00000