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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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