HEADER INHIBITOR 16-JUL-03 1OK0 TITLE CRYSTAL STRUCTURE OF TENDAMISTAT COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-AMYLASE INHIBITOR HOE-467A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TENDAMISTAT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES TENDAE; SOURCE 3 ORGANISM_TAXID: 1932; SOURCE 4 STRAIN: 4158; SOURCE 5 ATCC: 31210 KEYWDS INHIBITOR, ALPHA AMYLASE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR V.KOENIG,L.VERTESY,T.R.SCHNEIDER REVDAT 6 09-OCT-24 1OK0 1 REMARK REVDAT 5 13-DEC-23 1OK0 1 REMARK REVDAT 4 24-JUL-19 1OK0 1 REMARK REVDAT 3 08-MAY-19 1OK0 1 REMARK REVDAT 2 24-FEB-09 1OK0 1 VERSN REVDAT 1 15-JAN-04 1OK0 0 JRNL AUTH V.KOENIG,L.VERTESY,T.R.SCHNEIDER JRNL TITL CRYSTAL STRUCTURE OF THE ALPHA-AMYLASE INHIBITOR TENDAMISTAT JRNL TITL 2 AT 0.93 A JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 59 1737 2003 JRNL REFN ISSN 0907-4449 JRNL PMID 14501112 JRNL DOI 10.1107/S0907444903015828 REMARK 2 REMARK 2 RESOLUTION. 0.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.103 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.103 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.130 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 5 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 2054 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.093 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.092 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.120 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 558 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 159 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 15 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 7433 REMARK 3 NUMBER OF RESTRAINTS : 10184 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 ANGLE DISTANCES (A) : 0.033 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.341 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.082 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.097 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.026 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.033 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.087 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OK0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1290013036. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 1.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.911 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 261064 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.930 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.32600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1HOE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MG OF LYOPHILIZED PROTEIN WERE REMARK 280 DISSOLVED IN 1ML OF DOUBLE-DISTILLED WATER. USING THE HANGING REMARK 280 DROP METHOD WITH DROPS OF 2MUL PROTEIN SOLUTION (20 MG/ML) AND REMARK 280 2MUL RESERVOIR SOLUTION (0.1-0.5 M NACL ADJUSTED TO PH 1.3 WITH REMARK 280 HYDROCHLORIC ACID), YIELDED TUFT-SHAPED AGGLOMERATES OF REMARK 280 ESSENTIALLY ONE-DIMENSIONAL CRYSTALS. STREAK SEEDING {EM VIA} A REMARK 280 CAT WHISKER AFTER TOUCHING THESE AGGLOMERATES GAVE SINGLE REMARK 280 CRYSTALS WITH DIMENSIONS UP TO 0.1 X 0.01 X 0.01MM^3, PH 1.50, REMARK 280 VAPOR DIFFUSION, HANGING DROP 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 12.84000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.47500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.39000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.47500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.84000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.39000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 400 REMARK 400 COMPOUND REMARK 400 MAMMALIAN ALPHA-AMYLASES, BUT DOES NOT INHIBIT PLANT AND REMARK 400 MICROBIAL ALPHA-AMYLASES. KNOWN TO FORM A 1:1 COMPLEX WITH REMARK 400 ALPHA-AMYLASE 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 ASP A 1 CB - CG - OD1 ANGL. DEV. = 9.1 DEGREES REMARK 500 TYR A 15 CB - CG - CD2 ANGL. DEV. = 5.0 DEGREES REMARK 500 TYR A 15 CB - CG - CD1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ASP A 58 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES 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 A2043 DISTANCE = 6.21 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BVN RELATED DB: PDB REMARK 900 PIG PANCREATIC ALPHA-AMYLASE IN COMPLEX WITH THEPROTEINACEOUS REMARK 900 INHIBITOR TENDAMISTAT REMARK 900 RELATED ID: 1HOE RELATED DB: PDB REMARK 900 ALPHA-AMYLASE INHIBITOR HOE-467A REMARK 900 RELATED ID: 2AIT RELATED DB: PDB REMARK 900 TENDAMISTAT REMARK 900 RELATED ID: 3AIT RELATED DB: PDB REMARK 900 TENDAMISTAT (ENERGY MINIMIZED MODEL USING "AMBER" 3.0) (NMR) REMARK 900 RELATED ID: 4AIT RELATED DB: PDB REMARK 900 TENDAMISTAT (ENERGY MINIMIZED MODEL USING "FANTOM") (NMR) REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE CONFLICT IS DESCRIBED IN THE REFERENCES THAT REMARK 999 ACCOMPANY THE SWS ENTRY P01092 DBREF 1OK0 A 1 74 UNP P01092 IAA_STRTE 31 104 SEQADV 1OK0 GLU A 29 UNP P01092 GLN 59 SEE REMARK 999 SEQRES 1 A 74 ASP THR THR VAL SER GLU PRO ALA PRO SER CYS VAL THR SEQRES 2 A 74 LEU TYR GLN SER TRP ARG TYR SER GLN ALA ASP ASN GLY SEQRES 3 A 74 CYS ALA GLU THR VAL THR VAL LYS VAL VAL TYR GLU ASP SEQRES 4 A 74 ASP THR GLU GLY LEU CYS TYR ALA VAL ALA PRO GLY GLN SEQRES 5 A 74 ILE THR THR VAL GLY ASP GLY TYR ILE GLY SER HIS GLY SEQRES 6 A 74 HIS ALA ARG TYR LEU ALA ARG CYS LEU HET GOL A 501 6 HET GOL A 601 6 HET CL A 701 2 HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 CL CL 1- FORMUL 5 HOH *159(H2 O) SHEET 1 AA 3 VAL A 12 GLN A 16 0 SHEET 2 AA 3 TYR A 20 ASN A 25 -1 O GLN A 22 N TYR A 15 SHEET 3 AA 3 ILE A 53 ASP A 58 -1 O THR A 54 N ALA A 23 SHEET 1 AB 3 TYR A 46 VAL A 48 0 SHEET 2 AB 3 VAL A 31 TYR A 37 -1 O VAL A 31 N VAL A 48 SHEET 3 AB 3 ALA A 67 ARG A 72 -1 N ARG A 68 O VAL A 36 SSBOND 1 CYS A 11 CYS A 27 1555 1555 2.05 SSBOND 2 CYS A 45 CYS A 73 1555 1555 2.06 SITE 1 AC1 7 THR A 2 THR A 3 ARG A 19 CYS A 45 SITE 2 AC1 7 GOL A 601 HOH A2156 HOH A2159 SITE 1 AC2 7 GLN A 52 ASP A 58 GLY A 62 SER A 63 SITE 2 AC2 7 HOH A2118 HOH A2131 HOH A2152 SITE 1 AC3 13 SER A 10 CYS A 11 TYR A 20 CYS A 45 SITE 2 AC3 13 CL A 701 HOH A2030 HOH A2102 HOH A2154 SITE 3 AC3 13 HOH A2155 HOH A2156 HOH A2157 HOH A2158 SITE 4 AC3 13 HOH A2159 CRYST1 25.680 40.780 60.950 90.00 90.00 90.00 P 21 21 21 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 0.038941 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024522 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016407 0.00000