HEADER OXIDOREDUCTASE/INHIBITOR 03-JUN-13 4L1O TITLE CRYSTAL STRUCTURE OF HUMAN ALDH3A1 WITH INHIBITOR 1-{[4-(1,3- TITLE 2 BENZODIOXOL-5-YLMETHYL)PIPERAZIN-1-YL]METHYL}-1H-INDOLE-2,3-DIONE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALDEHYDE DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ALDHIII, ALDEHYDE DEHYDROGENASE 3, ALDEHYDE DEHYDROGENASE COMPND 5 FAMILY 3 MEMBER A1; COMPND 6 EC: 1.2.1.5; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ALDH3, ALDH3A1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS CATALYZES BENZALDEHYDE, ROSSMANN FOLD, DEHYDROGENASE, NADP+ BINDING, KEYWDS 2 OXIDOREDUCTASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.D.HURLEY,B.PARAJULI REVDAT 4 20-SEP-23 4L1O 1 REMARK REVDAT 3 21-DEC-22 4L1O 1 REMARK SEQADV LINK REVDAT 2 12-NOV-14 4L1O 1 KEYWDS REVDAT 1 16-APR-14 4L1O 0 JRNL AUTH B.PARAJULI,A.KIMBLE-HILL,C.H.CHEN,D.MOCHLY-ROSEN,T.D.HURLEY JRNL TITL DISCOVERY OF INDOLE-2,3-DIONES AS NOVEL CLASS OF INHIBITORS JRNL TITL 2 FOR ALDH ISOZYMES. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 37399 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1990 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2529 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.66 REMARK 3 BIN R VALUE (WORKING SET) : 0.2010 REMARK 3 BIN FREE R VALUE SET COUNT : 129 REMARK 3 BIN FREE R VALUE : 0.2680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7019 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 648 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.88000 REMARK 3 B22 (A**2) : 0.37000 REMARK 3 B33 (A**2) : 0.50000 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): 0.483 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.245 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.158 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.435 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7366 ; 0.005 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 7128 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10011 ; 1.089 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 16468 ; 0.724 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 937 ; 5.494 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 317 ;37.161 ;24.479 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1297 ;12.650 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;10.917 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1116 ; 0.056 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8349 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1613 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 REMARK 4 REMARK 4 4L1O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUN-13. REMARK 100 THE DEPOSITION ID IS D_1000080068. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC CONFOCAL BLUE REMARK 200 OPTICS : OSMIC CONFOCAL BLUE REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37399 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.200 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.14600 REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 16.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.14600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.700 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: PDB ENTRY 3SZA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M POTASSIUM ACETATE, 20% PEG 3350, REMARK 280 (3 MICROLITRES OF 3MG/ML OF ALDH3A1+ 3 MICROLITRES OF MOTHER REMARK 280 LIQUOR), PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 30.62850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 85.11250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.19800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 85.11250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.62850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.19800 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: 9520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 SER A -10 REMARK 465 SER A -9 REMARK 465 GLY A -8 REMARK 465 LEU A -7 REMARK 465 VAL A -6 REMARK 465 PRO A -5 REMARK 465 ARG A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 LYS A 448 REMARK 465 MET A 449 REMARK 465 THR A 450 REMARK 465 GLN A 451 REMARK 465 HIS A 452 REMARK 465 HIS B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 SER B -10 REMARK 465 SER B -9 REMARK 465 GLY B -8 REMARK 465 LEU B -7 REMARK 465 VAL B -6 REMARK 465 PRO B -5 REMARK 465 ARG B -4 REMARK 465 GLY B -3 REMARK 465 SER B -2 REMARK 465 HIS B -1 REMARK 465 MET B 0 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 62 -66.72 -155.31 REMARK 500 LEU A 210 -154.01 -117.92 REMARK 500 ILE A 391 -52.76 71.47 REMARK 500 HIS A 413 128.59 90.50 REMARK 500 GLU B 62 -69.11 -157.33 REMARK 500 LEU B 210 -165.80 -111.70 REMARK 500 ILE B 391 -54.76 71.93 REMARK 500 HIS B 413 137.83 90.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 1VL A 601 REMARK 610 1VL B 601 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 K A 602 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 321 O REMARK 620 2 ASP A 322 O 64.6 REMARK 620 3 HOH A 715 O 54.4 100.5 REMARK 620 4 HOH A 821 O 106.7 80.0 74.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 603 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 439 O REMARK 620 2 TYR A 442 O 82.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 602 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 79 O REMARK 620 2 TRP B 80 O 70.8 REMARK 620 3 ALA B 82 O 93.5 76.0 REMARK 620 4 HOH B 893 O 145.3 78.8 95.0 REMARK 620 5 HOH B 991 O 77.4 98.5 170.6 91.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 603 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS B 439 O REMARK 620 2 TYR B 442 O 91.5 REMARK 620 3 HOH B 829 O 161.3 96.4 REMARK 620 4 HOH B 854 O 111.8 80.2 86.3 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 1VL A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1VL B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 604 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3SZA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ALDH3A1-APO FORM REMARK 900 RELATED ID: 3SZB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN ALDH3A1 MODIFIED WITH THE BETA REMARK 900 ELIMINATION PRODUCT OF ALDI-1; 1-PHENYL-2-PROPEN-1-ONE REMARK 900 RELATED ID: 4L2O RELATED DB: PDB DBREF 4L1O A 0 452 UNP P30838 AL3A1_HUMAN 1 453 DBREF 4L1O B 0 452 UNP P30838 AL3A1_HUMAN 1 453 SEQADV 4L1O HIS A -16 UNP P30838 EXPRESSION TAG SEQADV 4L1O HIS A -15 UNP P30838 EXPRESSION TAG SEQADV 4L1O HIS A -14 UNP P30838 EXPRESSION TAG SEQADV 4L1O HIS A -13 UNP P30838 EXPRESSION TAG SEQADV 4L1O HIS A -12 UNP P30838 EXPRESSION TAG SEQADV 4L1O HIS A -11 UNP P30838 EXPRESSION TAG SEQADV 4L1O SER A -10 UNP P30838 EXPRESSION TAG SEQADV 4L1O SER A -9 UNP P30838 EXPRESSION TAG SEQADV 4L1O GLY A -8 UNP P30838 EXPRESSION TAG SEQADV 4L1O LEU A -7 UNP P30838 EXPRESSION TAG SEQADV 4L1O VAL A -6 UNP P30838 EXPRESSION TAG SEQADV 4L1O PRO A -5 UNP P30838 EXPRESSION TAG SEQADV 4L1O ARG A -4 UNP P30838 EXPRESSION TAG SEQADV 4L1O GLY A -3 UNP P30838 EXPRESSION TAG SEQADV 4L1O SER A -2 UNP P30838 EXPRESSION TAG SEQADV 4L1O HIS A -1 UNP P30838 EXPRESSION TAG SEQADV 4L1O ALA A 133 UNP P30838 SER 134 VARIANT SEQADV 4L1O HIS B -16 UNP P30838 EXPRESSION TAG SEQADV 4L1O HIS B -15 UNP P30838 EXPRESSION TAG SEQADV 4L1O HIS B -14 UNP P30838 EXPRESSION TAG SEQADV 4L1O HIS B -13 UNP P30838 EXPRESSION TAG SEQADV 4L1O HIS B -12 UNP P30838 EXPRESSION TAG SEQADV 4L1O HIS B -11 UNP P30838 EXPRESSION TAG SEQADV 4L1O SER B -10 UNP P30838 EXPRESSION TAG SEQADV 4L1O SER B -9 UNP P30838 EXPRESSION TAG SEQADV 4L1O GLY B -8 UNP P30838 EXPRESSION TAG SEQADV 4L1O LEU B -7 UNP P30838 EXPRESSION TAG SEQADV 4L1O VAL B -6 UNP P30838 EXPRESSION TAG SEQADV 4L1O PRO B -5 UNP P30838 EXPRESSION TAG SEQADV 4L1O ARG B -4 UNP P30838 EXPRESSION TAG SEQADV 4L1O GLY B -3 UNP P30838 EXPRESSION TAG SEQADV 4L1O SER B -2 UNP P30838 EXPRESSION TAG SEQADV 4L1O HIS B -1 UNP P30838 EXPRESSION TAG SEQADV 4L1O ALA B 133 UNP P30838 SER 134 VARIANT SEQRES 1 A 469 HIS HIS HIS HIS HIS HIS SER SER GLY LEU VAL PRO ARG SEQRES 2 A 469 GLY SER HIS MET SER LYS ILE SER GLU ALA VAL LYS ARG SEQRES 3 A 469 ALA ARG ALA ALA PHE SER SER GLY ARG THR ARG PRO LEU SEQRES 4 A 469 GLN PHE ARG ILE GLN GLN LEU GLU ALA LEU GLN ARG LEU SEQRES 5 A 469 ILE GLN GLU GLN GLU GLN GLU LEU VAL GLY ALA LEU ALA SEQRES 6 A 469 ALA ASP LEU HIS LYS ASN GLU TRP ASN ALA TYR TYR GLU SEQRES 7 A 469 GLU VAL VAL TYR VAL LEU GLU GLU ILE GLU TYR MET ILE SEQRES 8 A 469 GLN LYS LEU PRO GLU TRP ALA ALA ASP GLU PRO VAL GLU SEQRES 9 A 469 LYS THR PRO GLN THR GLN GLN ASP GLU LEU TYR ILE HIS SEQRES 10 A 469 SER GLU PRO LEU GLY VAL VAL LEU VAL ILE GLY THR TRP SEQRES 11 A 469 ASN TYR PRO PHE ASN LEU THR ILE GLN PRO MET VAL GLY SEQRES 12 A 469 ALA ILE ALA ALA GLY ASN ALA VAL VAL LEU LYS PRO SER SEQRES 13 A 469 GLU LEU SER GLU ASN MET ALA SER LEU LEU ALA THR ILE SEQRES 14 A 469 ILE PRO GLN TYR LEU ASP LYS ASP LEU TYR PRO VAL ILE SEQRES 15 A 469 ASN GLY GLY VAL PRO GLU THR THR GLU LEU LEU LYS GLU SEQRES 16 A 469 ARG PHE ASP HIS ILE LEU TYR THR GLY SER THR GLY VAL SEQRES 17 A 469 GLY LYS ILE ILE MET THR ALA ALA ALA LYS HIS LEU THR SEQRES 18 A 469 PRO VAL THR LEU GLU LEU GLY GLY LYS SER PRO CYS TYR SEQRES 19 A 469 VAL ASP LYS ASN CYS ASP LEU ASP VAL ALA CYS ARG ARG SEQRES 20 A 469 ILE ALA TRP GLY LYS PHE MET ASN SER GLY GLN THR CYS SEQRES 21 A 469 VAL ALA PRO ASP TYR ILE LEU CYS ASP PRO SER ILE GLN SEQRES 22 A 469 ASN GLN ILE VAL GLU LYS LEU LYS LYS SER LEU LYS GLU SEQRES 23 A 469 PHE TYR GLY GLU ASP ALA LYS LYS SER ARG ASP TYR GLY SEQRES 24 A 469 ARG ILE ILE SER ALA ARG HIS PHE GLN ARG VAL MET GLY SEQRES 25 A 469 LEU ILE GLU GLY GLN LYS VAL ALA TYR GLY GLY THR GLY SEQRES 26 A 469 ASP ALA ALA THR ARG TYR ILE ALA PRO THR ILE LEU THR SEQRES 27 A 469 ASP VAL ASP PRO GLN SER PRO VAL MET GLN GLU GLU ILE SEQRES 28 A 469 PHE GLY PRO VAL LEU PRO ILE VAL CYS VAL ARG SER LEU SEQRES 29 A 469 GLU GLU ALA ILE GLN PHE ILE ASN GLN ARG GLU LYS PRO SEQRES 30 A 469 LEU ALA LEU TYR MET PHE SER SER ASN ASP LYS VAL ILE SEQRES 31 A 469 LYS LYS MET ILE ALA GLU THR SER SER GLY GLY VAL ALA SEQRES 32 A 469 ALA ASN ASP VAL ILE VAL HIS ILE THR LEU HIS SER LEU SEQRES 33 A 469 PRO PHE GLY GLY VAL GLY ASN SER GLY MET GLY SER TYR SEQRES 34 A 469 HIS GLY LYS LYS SER PHE GLU THR PHE SER HIS ARG ARG SEQRES 35 A 469 SER CYS LEU VAL ARG PRO LEU MET ASN ASP GLU GLY LEU SEQRES 36 A 469 LYS VAL ARG TYR PRO PRO SER PRO ALA LYS MET THR GLN SEQRES 37 A 469 HIS SEQRES 1 B 469 HIS HIS HIS HIS HIS HIS SER SER GLY LEU VAL PRO ARG SEQRES 2 B 469 GLY SER HIS MET SER LYS ILE SER GLU ALA VAL LYS ARG SEQRES 3 B 469 ALA ARG ALA ALA PHE SER SER GLY ARG THR ARG PRO LEU SEQRES 4 B 469 GLN PHE ARG ILE GLN GLN LEU GLU ALA LEU GLN ARG LEU SEQRES 5 B 469 ILE GLN GLU GLN GLU GLN GLU LEU VAL GLY ALA LEU ALA SEQRES 6 B 469 ALA ASP LEU HIS LYS ASN GLU TRP ASN ALA TYR TYR GLU SEQRES 7 B 469 GLU VAL VAL TYR VAL LEU GLU GLU ILE GLU TYR MET ILE SEQRES 8 B 469 GLN LYS LEU PRO GLU TRP ALA ALA ASP GLU PRO VAL GLU SEQRES 9 B 469 LYS THR PRO GLN THR GLN GLN ASP GLU LEU TYR ILE HIS SEQRES 10 B 469 SER GLU PRO LEU GLY VAL VAL LEU VAL ILE GLY THR TRP SEQRES 11 B 469 ASN TYR PRO PHE ASN LEU THR ILE GLN PRO MET VAL GLY SEQRES 12 B 469 ALA ILE ALA ALA GLY ASN ALA VAL VAL LEU LYS PRO SER SEQRES 13 B 469 GLU LEU SER GLU ASN MET ALA SER LEU LEU ALA THR ILE SEQRES 14 B 469 ILE PRO GLN TYR LEU ASP LYS ASP LEU TYR PRO VAL ILE SEQRES 15 B 469 ASN GLY GLY VAL PRO GLU THR THR GLU LEU LEU LYS GLU SEQRES 16 B 469 ARG PHE ASP HIS ILE LEU TYR THR GLY SER THR GLY VAL SEQRES 17 B 469 GLY LYS ILE ILE MET THR ALA ALA ALA LYS HIS LEU THR SEQRES 18 B 469 PRO VAL THR LEU GLU LEU GLY GLY LYS SER PRO CYS TYR SEQRES 19 B 469 VAL ASP LYS ASN CYS ASP LEU ASP VAL ALA CYS ARG ARG SEQRES 20 B 469 ILE ALA TRP GLY LYS PHE MET ASN SER GLY GLN THR CYS SEQRES 21 B 469 VAL ALA PRO ASP TYR ILE LEU CYS ASP PRO SER ILE GLN SEQRES 22 B 469 ASN GLN ILE VAL GLU LYS LEU LYS LYS SER LEU LYS GLU SEQRES 23 B 469 PHE TYR GLY GLU ASP ALA LYS LYS SER ARG ASP TYR GLY SEQRES 24 B 469 ARG ILE ILE SER ALA ARG HIS PHE GLN ARG VAL MET GLY SEQRES 25 B 469 LEU ILE GLU GLY GLN LYS VAL ALA TYR GLY GLY THR GLY SEQRES 26 B 469 ASP ALA ALA THR ARG TYR ILE ALA PRO THR ILE LEU THR SEQRES 27 B 469 ASP VAL ASP PRO GLN SER PRO VAL MET GLN GLU GLU ILE SEQRES 28 B 469 PHE GLY PRO VAL LEU PRO ILE VAL CYS VAL ARG SER LEU SEQRES 29 B 469 GLU GLU ALA ILE GLN PHE ILE ASN GLN ARG GLU LYS PRO SEQRES 30 B 469 LEU ALA LEU TYR MET PHE SER SER ASN ASP LYS VAL ILE SEQRES 31 B 469 LYS LYS MET ILE ALA GLU THR SER SER GLY GLY VAL ALA SEQRES 32 B 469 ALA ASN ASP VAL ILE VAL HIS ILE THR LEU HIS SER LEU SEQRES 33 B 469 PRO PHE GLY GLY VAL GLY ASN SER GLY MET GLY SER TYR SEQRES 34 B 469 HIS GLY LYS LYS SER PHE GLU THR PHE SER HIS ARG ARG SEQRES 35 B 469 SER CYS LEU VAL ARG PRO LEU MET ASN ASP GLU GLY LEU SEQRES 36 B 469 LYS VAL ARG TYR PRO PRO SER PRO ALA LYS MET THR GLN SEQRES 37 B 469 HIS HET 1VL A 601 18 HET K A 602 1 HET K A 603 1 HET ACT A 604 4 HET 1VL B 601 18 HET K B 602 1 HET K B 603 1 HET ACT B 604 4 HETNAM 1VL (3S)-1-{[4-(1,3-BENZODIOXOL-5-YLMETHYL)PIPERAZIN-1- HETNAM 2 1VL YL]METHYL}-3-HYDROXY-1,3-DIHYDRO-2H-INDOL-2-ONE HETNAM K POTASSIUM ION HETNAM ACT ACETATE ION FORMUL 3 1VL 2(C21 H23 N3 O4) FORMUL 4 K 4(K 1+) FORMUL 6 ACT 2(C2 H3 O2 1-) FORMUL 11 HOH *648(H2 O) HELIX 1 1 SER A 1 SER A 16 1 16 HELIX 2 2 PRO A 21 GLN A 39 1 19 HELIX 3 3 GLN A 39 HIS A 52 1 14 HELIX 4 4 ASN A 54 GLU A 61 1 8 HELIX 5 5 GLU A 62 ALA A 82 1 21 HELIX 6 6 THR A 89 GLN A 93 5 5 HELIX 7 7 PHE A 117 ALA A 130 1 14 HELIX 8 8 SER A 142 LEU A 157 1 16 HELIX 9 9 GLY A 168 LEU A 176 1 9 HELIX 10 10 SER A 188 LYS A 201 1 14 HELIX 11 11 ASP A 223 MET A 237 1 15 HELIX 12 12 ASN A 238 GLN A 241 5 4 HELIX 13 13 ILE A 255 GLY A 272 1 18 HELIX 14 14 ASP A 274 SER A 278 5 5 HELIX 15 15 SER A 286 GLU A 298 1 13 HELIX 16 16 SER A 327 GLN A 331 5 5 HELIX 17 17 SER A 346 ARG A 357 1 12 HELIX 18 18 ASN A 369 THR A 380 1 12 HELIX 19 19 ILE A 391 LEU A 396 5 6 HELIX 20 20 VAL A 404 ASN A 406 5 3 HELIX 21 21 GLY A 414 PHE A 421 1 8 HELIX 22 22 LEU A 438 TYR A 442 5 5 HELIX 23 23 LYS B 2 SER B 16 1 15 HELIX 24 24 PRO B 21 GLN B 39 1 19 HELIX 25 25 GLN B 39 HIS B 52 1 14 HELIX 26 26 ASN B 54 GLU B 61 1 8 HELIX 27 27 GLU B 62 ALA B 82 1 21 HELIX 28 28 THR B 89 GLN B 93 5 5 HELIX 29 29 PHE B 117 ALA B 130 1 14 HELIX 30 30 SER B 142 LEU B 157 1 16 HELIX 31 31 GLY B 168 LEU B 176 1 9 HELIX 32 32 SER B 188 LYS B 201 1 14 HELIX 33 33 ASP B 223 MET B 237 1 15 HELIX 34 34 ASN B 238 GLN B 241 5 4 HELIX 35 35 ASP B 252 SER B 254 5 3 HELIX 36 36 ILE B 255 GLY B 272 1 18 HELIX 37 37 ASP B 274 SER B 278 5 5 HELIX 38 38 SER B 286 GLU B 298 1 13 HELIX 39 39 SER B 327 GLN B 331 5 5 HELIX 40 40 SER B 346 ARG B 357 1 12 HELIX 41 41 ASN B 369 THR B 380 1 12 HELIX 42 42 ILE B 391 THR B 395 5 5 HELIX 43 43 VAL B 404 ASN B 406 5 3 HELIX 44 44 GLY B 414 PHE B 421 1 8 HELIX 45 45 ASP B 435 TYR B 442 5 8 SHEET 1 A10 GLU A 84 PRO A 85 0 SHEET 2 A10 GLU A 96 PRO A 103 -1 O ILE A 99 N GLU A 84 SHEET 3 A10 SER A 422 VAL A 429 -1 O HIS A 423 N GLU A 102 SHEET 4 A10 GLY B 384 ALA B 387 1 O ALA B 387 N LEU A 428 SHEET 5 A10 ALA B 362 PHE B 366 1 N LEU B 363 O ALA B 386 SHEET 6 A10 PRO B 215 VAL B 218 1 N TYR B 217 O PHE B 366 SHEET 7 A10 TYR B 248 CYS B 251 1 O LEU B 250 N VAL B 218 SHEET 8 A10 VAL B 338 CYS B 343 1 O VAL B 342 N ILE B 249 SHEET 9 A10 THR B 318 THR B 321 1 N THR B 318 O LEU B 339 SHEET 10 A10 LYS B 301 TYR B 304 -1 N ALA B 303 O ILE B 319 SHEET 1 B 5 ALA A 133 LYS A 137 0 SHEET 2 B 5 VAL A 106 ILE A 110 1 N VAL A 107 O ALA A 133 SHEET 3 B 5 HIS A 182 THR A 186 1 O LEU A 184 N ILE A 110 SHEET 4 B 5 VAL A 206 GLU A 209 1 O THR A 207 N ILE A 183 SHEET 5 B 5 GLY A 408 MET A 409 -1 O MET A 409 N LEU A 208 SHEET 1 C10 LYS A 301 TYR A 304 0 SHEET 2 C10 THR A 318 THR A 321 -1 O ILE A 319 N ALA A 303 SHEET 3 C10 VAL A 338 CYS A 343 1 O LEU A 339 N THR A 318 SHEET 4 C10 TYR A 248 CYS A 251 1 N ILE A 249 O VAL A 342 SHEET 5 C10 PRO A 215 VAL A 218 1 N VAL A 218 O LEU A 250 SHEET 6 C10 ALA A 362 PHE A 366 1 O PHE A 366 N TYR A 217 SHEET 7 C10 GLY A 384 ALA A 387 1 O ALA A 386 N LEU A 363 SHEET 8 C10 SER B 422 VAL B 429 1 O LEU B 428 N ALA A 387 SHEET 9 C10 GLU B 96 PRO B 103 -1 N HIS B 100 O ARG B 425 SHEET 10 C10 GLU B 84 PRO B 85 -1 N GLU B 84 O ILE B 99 SHEET 1 D 2 GLY A 308 ASP A 309 0 SHEET 2 D 2 TYR A 314 ILE A 315 -1 O TYR A 314 N ASP A 309 SHEET 1 E 5 ALA B 133 LYS B 137 0 SHEET 2 E 5 VAL B 106 ILE B 110 1 N VAL B 107 O ALA B 133 SHEET 3 E 5 HIS B 182 THR B 186 1 O LEU B 184 N ILE B 110 SHEET 4 E 5 VAL B 206 GLU B 209 1 O GLU B 209 N TYR B 185 SHEET 5 E 5 GLY B 408 MET B 409 -1 O MET B 409 N LEU B 208 SHEET 1 F 2 GLY B 308 ASP B 309 0 SHEET 2 F 2 TYR B 314 ILE B 315 -1 O TYR B 314 N ASP B 309 LINK SG CYS A 243 C7 1VL A 601 1555 1555 1.83 LINK SG CYS B 243 C7 1VL B 601 1555 1555 1.83 LINK O THR A 321 K K A 602 1555 1555 3.24 LINK O ASP A 322 K K A 602 1555 1555 2.90 LINK O LYS A 439 K K A 603 1555 1555 3.04 LINK O TYR A 442 K K A 603 1555 1555 2.97 LINK K K A 602 O HOH A 715 1555 1555 2.59 LINK K K A 602 O HOH A 821 1555 1555 3.02 LINK O GLU B 79 K K B 602 1555 1555 2.80 LINK O TRP B 80 K K B 602 1555 1555 3.33 LINK O ALA B 82 K K B 602 1555 1555 3.00 LINK O LYS B 439 K K B 603 1555 1555 2.74 LINK O TYR B 442 K K B 603 1555 1555 2.87 LINK K K B 602 O HOH B 893 1555 1555 2.93 LINK K K B 602 O HOH B 991 1555 1555 2.79 LINK K K B 603 O HOH B 829 1555 1555 2.63 LINK K K B 603 O HOH B 854 1555 1555 2.75 CISPEP 1 PRO A 443 PRO A 444 0 1.42 CISPEP 2 PRO B 443 PRO B 444 0 -0.65 SITE 1 AC1 18 GLU A 61 TYR A 65 ASN A 114 TYR A 115 SITE 2 AC1 18 ASN A 118 LEU A 119 GLU A 209 MET A 237 SITE 3 AC1 18 THR A 242 CYS A 243 ILE A 391 ILE A 394 SITE 4 AC1 18 THR A 395 PHE A 401 TYR A 412 HIS A 413 SITE 5 AC1 18 HOH A 888 HOH A1011 SITE 1 AC2 7 LYS A 277 THR A 321 ASP A 322 HOH A 715 SITE 2 AC2 7 HOH A 753 HOH A 805 HOH A 821 SITE 1 AC3 3 LYS A 439 TYR A 442 PRO A 444 SITE 1 AC4 4 ASN A 434 ASP A 435 TYR A 442 ARG B 230 SITE 1 AC5 16 ASN B 114 TYR B 115 ASN B 118 LEU B 119 SITE 2 AC5 16 GLU B 209 MET B 237 THR B 242 CYS B 243 SITE 3 AC5 16 ILE B 391 ILE B 394 THR B 395 PHE B 401 SITE 4 AC5 16 TYR B 412 HIS B 413 HOH B 763 HOH B 944 SITE 1 AC6 5 GLU B 79 TRP B 80 ALA B 82 HOH B 893 SITE 2 AC6 5 HOH B 991 SITE 1 AC7 4 LYS B 439 TYR B 442 HOH B 829 HOH B 854 SITE 1 AC8 5 ARG A 230 HOH A 814 ASN B 434 ASP B 435 SITE 2 AC8 5 TYR B 442 CRYST1 61.257 86.396 170.225 90.00 90.00 90.00 P 21 21 21 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 0.016325 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011575 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005875 0.00000