HEADER HYDROLASE/HYDROLASE INHIBITOR 02-MAR-93 1BLL TITLE X-RAY CRYSTALLOGRAPHIC DETERMINATION OF THE STRUCTURE OF BOVINE LENS TITLE 2 LEUCINE AMINOPEPTIDASE COMPLEXED WITH AMASTATIN: FORMULATION OF A TITLE 3 CATALYTIC MECHANISM FEATURING A GEM-DIOLATE TRANSITION STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUCINE AMINOPEPTIDASE; COMPND 3 CHAIN: E; COMPND 4 EC: 3.4.11.1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: AMASTATIN; COMPND 8 CHAIN: I; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 TISSUE: LENS; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: STREPTOMYCES SP. ME98-M3 KEYWDS ALPHA-AMINOACYLPEPTIDE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.KIM,W.N.LIPSCOMB REVDAT 8 30-OCT-24 1BLL 1 REMARK REVDAT 7 15-NOV-23 1BLL 1 REMARK SEQADV LINK ATOM REVDAT 6 13-JUL-11 1BLL 1 VERSN REVDAT 5 25-AUG-09 1BLL 1 SOURCE REVDAT 4 24-FEB-09 1BLL 1 VERSN REVDAT 3 15-JAN-95 1BLL 1 SEQRES REVDAT 2 31-JUL-94 1BLL 1 SEQRES REVDAT 1 31-JAN-94 1BLL 0 JRNL AUTH H.KIM,W.N.LIPSCOMB JRNL TITL X-RAY CRYSTALLOGRAPHIC DETERMINATION OF THE STRUCTURE OF JRNL TITL 2 BOVINE LENS LEUCINE AMINOPEPTIDASE COMPLEXED WITH AMASTATIN: JRNL TITL 3 FORMULATION OF A CATALYTIC MECHANISM FEATURING A GEM-DIOLATE JRNL TITL 4 TRANSITION STATE. JRNL REF BIOCHEMISTRY V. 32 8465 1993 JRNL REFN ISSN 0006-2960 JRNL PMID 8357796 JRNL DOI 10.1021/BI00084A011 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.K.BURLEY,P.R.DAVID,R.M.SWEET,A.TAYLOR,W.N.LIPSCOMB REMARK 1 TITL STRUCTURE DETERMINATION AND REFINEMENT OF BOVINE LENS REMARK 1 TITL 2 LEUCINE AMINOPEPTIDASE AND ITS COMPLEX WITH BESTATIN REMARK 1 REF J.MOL.BIOL. V. 224 113 1992 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.K.BURLEY,P.R.DAVID,W.N.LIPSCOMB REMARK 1 TITL LEUCINE AMINOPEPTIDASE: BESTATIN INHIBITION AND A MODEL FOR REMARK 1 TITL 2 ENZYME-CATALYZED PEPTIDE HYDROLYSIS REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 88 6916 1991 REMARK 1 REFN ISSN 0027-8424 REMARK 1 REFERENCE 3 REMARK 1 AUTH S.K.BURLEY,P.R.DAVID,A.TAYLOR,W.N.LIPSCOMB REMARK 1 TITL MOLECULAR STRUCTURE OF LEUCINE AMINOPEPTIDASE AT 2.7 REMARK 1 TITL 2 ANGSTROMS RESOLUTION REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 87 6878 1990 REMARK 1 REFN ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3704 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 132 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 3.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BLL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171892. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 60.95000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 60.95000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 60.95000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 60.95000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 60.95000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 60.95000 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: DODECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 30630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 87610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -568.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, I 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 -0.500000 -0.866025 0.000000 130.30000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 65.15000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 112.84311 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 65.15000 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 112.84311 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 60.95000 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 130.30000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 60.95000 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 60.95000 REMARK 400 REMARK 400 COMPOUND REMARK 400 THE AMASTATIN INHIBITOR, (2S,3R)3-AMINO-2-HYDROXYL-5-METHYL, - REMARK 400 HEXANOYL-L-VAL-L-VAL-L-ASP, IS PRESENTED IN THIS ENTRY AS CHAIN I REMARK 400 REMARK 400 THE AMASTATIN IS PEPTIDE-LIKE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: AMASTATIN REMARK 400 CHAIN: I REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 ACE E 0 REMARK 465 LYS E 13 REMARK 465 GLU E 14 REMARK 465 GLU E 15 REMARK 465 ASP E 485 REMARK 465 SER E 486 REMARK 465 ALA E 487 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 HIS E 58 NE2 HIS E 58 CD2 -0.069 REMARK 500 HIS E 83 NE2 HIS E 83 CD2 -0.075 REMARK 500 HIS E 146 NE2 HIS E 146 CD2 -0.070 REMARK 500 HIS E 233 NE2 HIS E 233 CD2 -0.071 REMARK 500 HIS E 347 NE2 HIS E 347 CD2 -0.074 REMARK 500 SER E 370 CA SER E 370 CB 0.118 REMARK 500 HIS E 405 NE2 HIS E 405 CD2 -0.080 REMARK 500 HIS E 447 NE2 HIS E 447 CD2 -0.077 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 E 11 N - CA - C ANGL. DEV. = 20.4 DEGREES REMARK 500 ARG E 36 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG E 36 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 TRP E 82 CD1 - CG - CD2 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG E 98 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG E 98 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 GLU E 109 CA - CB - CG ANGL. DEV. = -14.5 DEGREES REMARK 500 ARG E 137 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 GLU E 152 CA - CB - CG ANGL. DEV. = 13.8 DEGREES REMARK 500 TRP E 154 CD1 - CG - CD2 ANGL. DEV. = 7.2 DEGREES REMARK 500 TRP E 154 CG - CD1 - NE1 ANGL. DEV. = -6.1 DEGREES REMARK 500 TRP E 154 CE2 - CD2 - CG ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG E 156 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG E 168 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG E 168 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG E 169 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 TRP E 207 CD1 - CG - CD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 TRP E 207 CE2 - CD2 - CG ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG E 271 NE - CZ - NH1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ARG E 271 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 LEU E 302 CA - CB - CG ANGL. DEV. = 17.7 DEGREES REMARK 500 ARG E 321 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG E 321 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG E 336 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG E 336 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ILE E 338 CA - CB - CG1 ANGL. DEV. = -12.9 DEGREES REMARK 500 GLY E 369 O - C - N ANGL. DEV. = 10.9 DEGREES REMARK 500 SER E 370 CA - CB - OG ANGL. DEV. = 24.9 DEGREES REMARK 500 TRP E 381 CD1 - CG - CD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 TRP E 381 CB - CG - CD1 ANGL. DEV. = -8.1 DEGREES REMARK 500 TRP E 381 CE2 - CD2 - CG ANGL. DEV. = -5.9 DEGREES REMARK 500 TRP E 381 CG - CD2 - CE3 ANGL. DEV. = 5.7 DEGREES REMARK 500 TRP E 383 CD1 - CG - CD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 TRP E 383 CB - CG - CD1 ANGL. DEV. = -8.6 DEGREES REMARK 500 TRP E 383 CE2 - CD2 - CG ANGL. DEV. = -6.0 DEGREES REMARK 500 TRP E 383 CG - CD2 - CE3 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG E 396 CB - CG - CD ANGL. DEV. = -16.2 DEGREES REMARK 500 VAL E 397 N - CA - CB ANGL. DEV. = -14.4 DEGREES REMARK 500 TRP E 398 CD1 - CG - CD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 TRP E 398 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES REMARK 500 TYR E 424 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 TRP E 445 CD1 - CG - CD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 TRP E 445 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES REMARK 500 TRP E 445 CG - CD2 - CE3 ANGL. DEV. = 5.4 DEGREES REMARK 500 ILE E 450 N - CA - CB ANGL. DEV. = -14.9 DEGREES REMARK 500 ILE E 450 CA - CB - CG1 ANGL. DEV. = -13.4 DEGREES REMARK 500 MET E 454 CG - SD - CE ANGL. DEV. = -11.5 DEGREES REMARK 500 TYR E 462 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG E 470 NE - CZ - NH1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG E 470 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 51 ANGLE DEVIATIONS. 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 LYS E 2 -167.92 -116.73 REMARK 500 LYS E 11 146.22 -34.74 REMARK 500 ASP E 16 -38.42 -166.10 REMARK 500 ASP E 115 79.73 -152.37 REMARK 500 GLU E 129 -46.47 -131.13 REMARK 500 TYR E 130 84.52 80.00 REMARK 500 SER E 195 142.47 -179.92 REMARK 500 PRO E 293 46.31 -81.62 REMARK 500 LYS E 310 12.34 -140.42 REMARK 500 ALA E 333 61.20 -115.91 REMARK 500 ALA E 367 -75.06 -75.56 REMARK 500 SER E 370 -48.35 114.50 REMARK 500 LEU E 402 51.30 -114.85 REMARK 500 GLN E 414 -75.32 -58.55 REMARK 500 LYS E 457 -74.45 -122.40 REMARK 500 PRO E 471 55.60 -104.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR E 9 0.07 SIDE CHAIN REMARK 500 TYR E 128 0.07 SIDE CHAIN REMARK 500 TYR E 130 0.07 SIDE CHAIN REMARK 500 PHE E 254 0.08 SIDE CHAIN REMARK 500 PHE E 349 0.08 SIDE CHAIN REMARK 500 PHE E 480 0.10 SIDE CHAIN 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 L2O I 2 -16.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE AMASTATIN INHIBITOR, (2S,3R)3-AMINO-2-HYDROXYL-5-METHYL REMARK 600 -HEXANOYL-L-VAL-L-VAL-L-ASP, IS PRESENTED IN THIS ENTRY AS REMARK 600 CHAIN *I*. THE HET GROUP FOR IS A CARBOXYL LINKAGE INSERTED REMARK 600 BETWEEN THE CARBOXY TERMINUS OF LEU I 1 AND THE AMINO REMARK 600 TERMINUS OF VAL I 2. 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 ZN E 489 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS E 250 NZ REMARK 620 2 ASP E 255 OD2 167.9 REMARK 620 3 ASP E 273 OD2 73.0 95.3 REMARK 620 4 GLU E 334 OE2 93.6 84.4 94.5 REMARK 620 5 L2O I 2 N 91.2 91.1 87.6 175.1 REMARK 620 6 L2O I 2 O1 125.6 66.4 154.9 100.2 76.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN E 488 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP E 255 OD2 REMARK 620 2 ASP E 332 OD1 95.9 REMARK 620 3 ASP E 332 O 158.3 87.0 REMARK 620 4 GLU E 334 OE1 95.2 122.8 101.3 REMARK 620 5 L2O I 2 O1 68.5 122.5 91.8 113.7 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN E 488 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN E 489 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN I OF AMASTATIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE AMINO ACID SEQUENCE USED IN THIS STRUCTURE REMARK 999 DETERMINATION IS TAKEN FROM WALLNER ET AL. (1993) REMARK 999 BIOCHEMISTRY 32, 9296-9301. DBREF 1BLL E 1 487 UNP P00727 AMPL_BOVIN 1 487 DBREF 1BLL I 2 5 PDB 1BLL 1BLL 2 5 SEQADV 1BLL ACE E 0 UNP P00727 ACETYLATION SEQADV 1BLL PRO E 45 UNP P00727 SER 45 CONFLICT SEQRES 1 E 488 ACE THR LYS GLY LEU VAL LEU GLY ILE TYR SER LYS GLU SEQRES 2 E 488 LYS GLU GLU ASP GLU PRO GLN PHE THR SER ALA GLY GLU SEQRES 3 E 488 ASN PHE ASN LYS LEU VAL SER GLY LYS LEU ARG GLU ILE SEQRES 4 E 488 LEU ASN ILE SER GLY PRO PRO LEU LYS ALA GLY LYS THR SEQRES 5 E 488 ARG THR PHE TYR GLY LEU HIS GLU ASP PHE PRO SER VAL SEQRES 6 E 488 VAL VAL VAL GLY LEU GLY LYS LYS THR ALA GLY ILE ASP SEQRES 7 E 488 GLU GLN GLU ASN TRP HIS GLU GLY LYS GLU ASN ILE ARG SEQRES 8 E 488 ALA ALA VAL ALA ALA GLY CYS ARG GLN ILE GLN ASP LEU SEQRES 9 E 488 GLU ILE PRO SER VAL GLU VAL ASP PRO CYS GLY ASP ALA SEQRES 10 E 488 GLN ALA ALA ALA GLU GLY ALA VAL LEU GLY LEU TYR GLU SEQRES 11 E 488 TYR ASP ASP LEU LYS GLN LYS ARG LYS VAL VAL VAL SER SEQRES 12 E 488 ALA LYS LEU HIS GLY SER GLU ASP GLN GLU ALA TRP GLN SEQRES 13 E 488 ARG GLY VAL LEU PHE ALA SER GLY GLN ASN LEU ALA ARG SEQRES 14 E 488 ARG LEU MET GLU THR PRO ALA ASN GLU MET THR PRO THR SEQRES 15 E 488 LYS PHE ALA GLU ILE VAL GLU GLU ASN LEU LYS SER ALA SEQRES 16 E 488 SER ILE LYS THR ASP VAL PHE ILE ARG PRO LYS SER TRP SEQRES 17 E 488 ILE GLU GLU GLN GLU MET GLY SER PHE LEU SER VAL ALA SEQRES 18 E 488 LYS GLY SER GLU GLU PRO PRO VAL PHE LEU GLU ILE HIS SEQRES 19 E 488 TYR LYS GLY SER PRO ASN ALA SER GLU PRO PRO LEU VAL SEQRES 20 E 488 PHE VAL GLY LYS GLY ILE THR PHE ASP SER GLY GLY ILE SEQRES 21 E 488 SER ILE LYS ALA ALA ALA ASN MET ASP LEU MET ARG ALA SEQRES 22 E 488 ASP MET GLY GLY ALA ALA THR ILE CYS SER ALA ILE VAL SEQRES 23 E 488 SER ALA ALA LYS LEU ASP LEU PRO ILE ASN ILE VAL GLY SEQRES 24 E 488 LEU ALA PRO LEU CYS GLU ASN MET PRO SER GLY LYS ALA SEQRES 25 E 488 ASN LYS PRO GLY ASP VAL VAL ARG ALA ARG ASN GLY LYS SEQRES 26 E 488 THR ILE GLN VAL ASP ASN THR ASP ALA GLU GLY ARG LEU SEQRES 27 E 488 ILE LEU ALA ASP ALA LEU CYS TYR ALA HIS THR PHE ASN SEQRES 28 E 488 PRO LYS VAL ILE ILE ASN ALA ALA THR LEU THR GLY ALA SEQRES 29 E 488 MET ASP ILE ALA LEU GLY SER GLY ALA THR GLY VAL PHE SEQRES 30 E 488 THR ASN SER SER TRP LEU TRP ASN LYS LEU PHE GLU ALA SEQRES 31 E 488 SER ILE GLU THR GLY ASP ARG VAL TRP ARG MET PRO LEU SEQRES 32 E 488 PHE GLU HIS TYR THR ARG GLN VAL ILE ASP CYS GLN LEU SEQRES 33 E 488 ALA ASP VAL ASN ASN ILE GLY LYS TYR ARG SER ALA GLY SEQRES 34 E 488 ALA CYS THR ALA ALA ALA PHE LEU LYS GLU PHE VAL THR SEQRES 35 E 488 HIS PRO LYS TRP ALA HIS LEU ASP ILE ALA GLY VAL MET SEQRES 36 E 488 THR ASN LYS ASP GLU VAL PRO TYR LEU ARG LYS GLY MET SEQRES 37 E 488 ALA GLY ARG PRO THR ARG THR LEU ILE GLU PHE LEU PHE SEQRES 38 E 488 ARG PHE SER GLN ASP SER ALA SEQRES 1 I 4 L2O VAL VAL ASP HET L2O I 2 10 HET ZN E 488 1 HET ZN E 489 1 HETNAM L2O (2S,3R)-3-AMINO-2-HYDROXY-5-METHYLHEXANOIC ACID HETNAM ZN ZINC ION FORMUL 2 L2O C7 H15 N O3 FORMUL 3 ZN 2(ZN 2+) FORMUL 5 HOH *132(H2 O) HELIX 1 A SER E 22 LEU E 30 1 9 HELIX 2 B LYS E 34 ASN E 40 1 7 HELIX 3 C GLU E 84 ASP E 102 1 19 HELIX 4 D ALA E 116 GLY E 126 1 11 HELIX 5 E GLN E 151 GLU E 172 1 22 HELIX 6 F PRO E 180 ALA E 194 1 15 HELIX 7 G LYS E 205 GLU E 210 1 6 HELIX 8 H GLY E 214 ALA E 220 1 7 HELIX 9 I GLY E 275 ALA E 288 1 14 HELIX 10 J GLU E 334 THR E 348 1 15 HELIX 11 K ALA E 363 ALA E 367 1 5 HELIX 12 L SER E 380 GLU E 392 1 13 HELIX 13 M HIS E 405 GLN E 409 1 5 HELIX 14 N GLY E 428 LEU E 436 1 9 HELIX 15 O THR E 472 PHE E 482 1 11 SHEET 1 1 5 GLY E 3 ILE E 8 0 SHEET 2 1 5 GLY E 49 GLY E 56 -1 SHEET 3 1 5 PRO E 62 LEU E 69 -1 SHEET 4 1 5 PRO E 106 ASP E 111 1 SHEET 5 1 5 SER E 142 HIS E 146 1 SHEET 1 2 8 LYS E 197 ARG E 203 0 SHEET 2 2 8 VAL E 228 LYS E 235 -1 SHEET 3 2 8 PRO E 244 SER E 256 -1 SHEET 4 2 8 ASN E 295 ASN E 305 1 SHEET 5 2 8 LYS E 352 ALA E 358 1 SHEET 6 2 8 THR E 373 PHE E 376 -1 SHEET 7 2 8 ARG E 396 MET E 400 1 SHEET 8 2 8 LYS E 444 ILE E 450 -1 SHEET 1 3 3 GLY E 315 ALA E 320 0 SHEET 2 3 3 GLY E 323 VAL E 328 -1 SHEET 3 3 3 ASP E 417 ASN E 420 1 LINK C L2O I 2 N VAL I 3 1555 1555 1.35 LINK NZ LYS E 250 ZN ZN E 489 1555 1555 2.31 LINK OD2 ASP E 255 ZN ZN E 488 1555 1555 2.23 LINK OD2 ASP E 255 ZN ZN E 489 1555 1555 2.24 LINK OD2 ASP E 273 ZN ZN E 489 1555 1555 2.19 LINK OD1 ASP E 332 ZN ZN E 488 1555 1555 2.19 LINK O ASP E 332 ZN ZN E 488 1555 1555 2.38 LINK OE1 GLU E 334 ZN ZN E 488 1555 1555 2.19 LINK OE2 GLU E 334 ZN ZN E 489 1555 1555 2.20 LINK ZN ZN E 488 O1 L2O I 2 1555 1555 2.07 LINK ZN ZN E 489 N L2O I 2 1555 1555 2.10 LINK ZN ZN E 489 O1 L2O I 2 1555 1555 2.18 CISPEP 1 ARG E 470 PRO E 471 0 -2.46 SITE 1 AC1 5 ASP E 255 ASP E 332 GLU E 334 ZN E 489 SITE 2 AC1 5 L2O I 2 SITE 1 AC2 6 LYS E 250 ASP E 255 ASP E 273 GLU E 334 SITE 2 AC2 6 ZN E 488 L2O I 2 SITE 1 AC3 18 LYS E 250 ASP E 255 LYS E 262 MET E 270 SITE 2 AC3 18 ASP E 273 ASP E 332 GLU E 334 ARG E 336 SITE 3 AC3 18 THR E 359 LEU E 360 GLY E 362 ALA E 363 SITE 4 AC3 18 ILE E 366 ARG E 425 GLY E 428 ZN E 488 SITE 5 AC3 18 ZN E 489 HOH E 594 CRYST1 130.300 130.300 121.900 90.00 90.00 120.00 P 63 2 2 12 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 0.007675 0.004431 0.000000 0.00000 SCALE2 0.000000 0.008862 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008203 0.00000