PDB Short entry for 3MAT HEADER HYDROLASE/HYDROLASE INHIBITOR 29-MAR-99 3MAT TITLE E.COLI METHIONINE AMINOPEPTIDASE TRANSITION-STATE INHIBITOR COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHIONINE AMINOPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.11.18; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: BESTATIN-BASED INHIBITOR (3R)-AMINO-(2S)-HYDROXYHEPTANOYL- COMPND 9 L-ALA-L-LEU-L-VAL-L-PHE-OME; COMPND 10 CHAIN: I; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: SYNTHETIC SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET28B; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES KEYWDS ALPHA-AMINOACYLPEPTIDE, TRANSITION-STATE ANALOG, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR W.T.LOWTHER,A.M.ORVILLE,D.T.MADDEN,S.LIM,D.H.RICH,B.W.MATTHEWS REVDAT 9 06-SEP-23 3MAT 1 REMARK LINK REVDAT 8 20-NOV-19 3MAT 1 JRNL SEQADV LINK REVDAT 7 14-MAR-18 3MAT 1 SEQADV REVDAT 6 13-JUL-11 3MAT 1 VERSN REVDAT 5 24-FEB-09 3MAT 1 VERSN REVDAT 4 01-APR-03 3MAT 1 JRNL REVDAT 3 24-AUG-00 3MAT 1 COMPND MODRES REVDAT 2 23-JUN-00 3MAT 1 COMPND REMARK SEQRES DBREF REVDAT 2 2 1 SEQADV REVDAT 1 18-JUN-99 3MAT 0 JRNL AUTH W.T.LOWTHER,A.M.ORVILLE,D.T.MADDEN,S.LIM,D.H.RICH, JRNL AUTH 2 B.W.MATTHEWS JRNL TITL ESCHERICHIA COLI METHIONINE AMINOPEPTIDASE: IMPLICATIONS OF JRNL TITL 2 CRYSTALLOGRAPHIC ANALYSES OF THE NATIVE, MUTANT, AND JRNL TITL 3 INHIBITED ENZYMES FOR THE MECHANISM OF CATALYSIS. JRNL REF BIOCHEMISTRY V. 38 7678 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10387007 JRNL DOI 10.1021/BI990684R REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.T.LOWTHER,D.A.MCMILLEN,A.M.ORVILLE,B.W.MATTHEWS REMARK 1 TITL THE ANTI-ANGIOGENIC AGENT FUMAGILLIN COVALENTLY MODIFIES A REMARK 1 TITL 2 CONSERVED ACTIVE-SITE HISTIDINE IN THE ESCHERICHIA COLI REMARK 1 TITL 3 METHIONINE AMINOPEPTIDASE. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 95 12153 1998 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 9770455 REMARK 1 DOI 10.1073/PNAS.95.21.12153 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.L.RODERICK,B.W.MATTHEWS REMARK 1 TITL STRUCTURE OF THE COBALT-DEPENDENT METHIONINE AMINOPEPTIDASE REMARK 1 TITL 2 FROM ESCHERICHIA COLI: A NEW TYPE OF PROTEOLYTIC ENZYME. REMARK 1 REF BIOCHEMISTRY V. 32 3907 1993 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 8471602 REMARK 1 DOI 10.1021/BI00066A009 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT 5F PRERELEASE REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 13762 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : NULL 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 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.1560 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 13762 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2031 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 91 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 17.400 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.013 ; 0.800 ; 2068 REMARK 3 BOND ANGLES (DEGREES) : 2.300 ; 1.300 ; 2792 REMARK 3 TORSION ANGLES (DEGREES) : 17.400; 0.000 ; 1242 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.008 ; 2.000 ; 53 REMARK 3 GENERAL PLANES (A) : 0.013 ; 5.000 ; 298 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 4.600 ; 1.000 ; 2068 REMARK 3 NON-BONDED CONTACTS (A) : 0.014 ; 10.000; 14 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : TNT REMARK 3 KSOL : 0.90 REMARK 3 BSOL : 283.1 REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : TNT PROTGEO REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : TNT BCORREL V1.0 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3MAT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-99. REMARK 100 THE DEPOSITION ID IS D_1000000752. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-98 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 6.1 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 : NI FILTER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13762 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 37.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.25500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.900 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: 2MAT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS OF THE CO(II)-SUBSTITUTED REMARK 280 ENZYME WERE GROWN AT ROOM TEMPERATURE BY VAPOR DIFFUSION IN 20- REMARK 280 30 UL SITTING DROPS AFTER MIXING THE PROTEIN, 12 MG/ML SOLUTION REMARK 280 IN STORAGE BUFFER(25 MM HEPES PH 6.8, 25 MM K2SO4, 100 MM NACL, REMARK 280 1 MM COCL2, 15 MM METHIONINE),CONTAINING 48.8 MM N-OCTANOYL REMARK 280 SUCROSE, 1:1 WITH WELL SOLUTIONS (24-26% PEG4000, 0.1M HEPES REMARK 280 PH7.0-7.2,FRESH 2 MM COCL2). CRYSTALS WERE OBTAINED OF THE REMARK 280 INHIBITOR COMPLEX BY INCUBATING THE PROTEIN AS ABOVE AT ROOM REMARK 280 TEMPERATURE FOR 5 MIN WITH A 20-FOLD MOLAR EXCESS OF THE REMARK 280 INHIBITOR DISSOLVED IN DMSO. THE FINAL INHIBITOR:ENZYME RATIO REMARK 280 WAS 10:1 (1% DMSO) AFTER MIXING THE PREFORMED COMPLEX WITH WELL REMARK 280 SOLUTION (0.1M MES PH 6.1, REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 32.57750 REMARK 290 SMTRY3 2 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 1350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 VAL I 4 REMARK 465 0A9 I 5 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 13 CE NZ REMARK 470 LYS A 86 CG CD CE NZ REMARK 470 LYS A 89 CD CE NZ REMARK 470 LYS A 117 CG CD CE NZ REMARK 470 ILE A 120 CD1 REMARK 470 ILE A 144 CD1 REMARK 470 LYS A 155 CD CE NZ REMARK 470 ARG A 189 CD NE CZ NH1 NH2 REMARK 470 LYS A 196 CD CE NZ REMARK 470 ARG A 215 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 226 CG CD CE NZ REMARK 470 ARG A 228 CD NE CZ NH1 NH2 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 GLU A 23 CD GLU A 23 OE2 0.070 REMARK 500 GLU A 75 CD GLU A 75 OE1 0.067 REMARK 500 GLU A 123 CD GLU A 123 OE2 0.068 REMARK 500 GLU A 148 CD GLU A 148 OE2 0.076 REMARK 500 GLU A 160 CD GLU A 160 OE2 0.066 REMARK 500 GLU A 179 CD GLU A 179 OE2 0.071 REMARK 500 GLU A 190 CD GLU A 190 OE1 0.070 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 ARG A 15 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP A 47 CB - CG - OD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 ASP A 83 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 83 CB - CG - OD2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ASP A 90 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP A 97 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 97 CB - CG - OD2 ANGL. DEV. = -7.1 DEGREES REMARK 500 PRO A 118 C - N - CD ANGL. DEV. = -13.4 DEGREES REMARK 500 ARG A 124 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ASP A 219 CB - CG - OD1 ANGL. DEV. = 7.8 DEGREES REMARK 500 ASP A 219 CB - CG - OD2 ANGL. DEV. = -9.1 DEGREES REMARK 500 ASP A 227 CB - CG - OD2 ANGL. DEV. = -7.4 DEGREES REMARK 500 ASP A 242 CB - CG - OD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 253 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP A 253 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ASP A 254 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 254 CB - CG - OD2 ANGL. DEV. = -6.8 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 ASN A 74 -107.63 42.27 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 NA A 501 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 74 O REMARK 620 2 VAL A 76 O 76.9 REMARK 620 3 SER A 231 O 72.6 106.8 REMARK 620 4 HOH A 521 O 143.9 90.2 79.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 402 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 97 OD1 REMARK 620 2 ASP A 97 OD2 54.4 REMARK 620 3 ASP A 108 OD1 103.6 155.5 REMARK 620 4 GLU A 235 OE1 98.3 101.8 91.3 REMARK 620 5 AHH I 1 N 90.3 75.8 95.5 167.5 REMARK 620 6 AHH I 1 O1 144.3 90.1 111.8 85.0 82.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A 401 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 108 OD2 REMARK 620 2 HIS A 171 NE2 96.9 REMARK 620 3 GLU A 204 OE2 162.4 83.0 REMARK 620 4 GLU A 235 OE2 86.7 115.4 77.6 REMARK 620 5 AHH I 1 O1 91.1 152.7 97.0 91.0 REMARK 620 6 AHH I 1 O2 111.4 75.7 85.7 158.2 77.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ACT REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: DINUCLEAR METAL CENTER REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN I OF BESTATIN-BASED REMARK 800 INHIBITOR (3R)-AMINO-(2S)-HYDROXYHEPTANOYL-L-ALA-L-LEU-L-VAL-L- REMARK 800 PHE-OME REMARK 999 REMARK 999 SEQUENCE REMARK 999 GLN 175, SITE-DIRECTED MUTANT REMARK 999 THE PROTEIN WAS TREATED WITH THROMBIN THAT LEFT PART REMARK 999 OF THE CLEAVAGE SITE RECOGNITION SEQUENCE ON REMARK 999 IN THE INHIBITOR SEQUENCE (AHH ALA LEU VAL PHE) PHE REMARK 999 IS METHYL ESTER OF PHE (COOCH3). ONLY THE FIRST REMARK 999 THREE RESIDUES WERE MODELED REMARK 999 RESIDUE LEU265 WAS INSERTED DUE TO HIS TAG DBREF 3MAT A 1 264 UNP P07906 AMPM_ECOLI 1 264 DBREF 3MAT I 1 5 PDB 3MAT 3MAT 1 5 SEQADV 3MAT GLN A 175 UNP P07906 ARG 175 ENGINEERED MUTATION SEQADV 3MAT LEU A 265 UNP P07906 INSERTION SEQRES 1 A 265 MET ALA ILE SER ILE LYS THR PRO GLU ASP ILE GLU LYS SEQRES 2 A 265 MET ARG VAL ALA GLY ARG LEU ALA ALA GLU VAL LEU GLU SEQRES 3 A 265 MET ILE GLU PRO TYR VAL LYS PRO GLY VAL SER THR GLY SEQRES 4 A 265 GLU LEU ASP ARG ILE CYS ASN ASP TYR ILE VAL ASN GLU SEQRES 5 A 265 GLN HIS ALA VAL SER ALA CYS LEU GLY TYR HIS GLY TYR SEQRES 6 A 265 PRO LYS SER VAL CYS ILE SER ILE ASN GLU VAL VAL CYS SEQRES 7 A 265 HIS GLY ILE PRO ASP ASP ALA LYS LEU LEU LYS ASP GLY SEQRES 8 A 265 ASP ILE VAL ASN ILE ASP VAL THR VAL ILE LYS ASP GLY SEQRES 9 A 265 PHE HIS GLY ASP THR SER LYS MET PHE ILE VAL GLY LYS SEQRES 10 A 265 PRO THR ILE MET GLY GLU ARG LEU CYS ARG ILE THR GLN SEQRES 11 A 265 GLU SER LEU TYR LEU ALA LEU ARG MET VAL LYS PRO GLY SEQRES 12 A 265 ILE ASN LEU ARG GLU ILE GLY ALA ALA ILE GLN LYS PHE SEQRES 13 A 265 VAL GLU ALA GLU GLY PHE SER VAL VAL ARG GLU TYR CYS SEQRES 14 A 265 GLY HIS GLY ILE GLY GLN GLY PHE HIS GLU GLU PRO GLN SEQRES 15 A 265 VAL LEU HIS TYR ASP SER ARG GLU THR ASN VAL VAL LEU SEQRES 16 A 265 LYS PRO GLY MET THR PHE THR ILE GLU PRO MET VAL ASN SEQRES 17 A 265 ALA GLY LYS LYS GLU ILE ARG THR MET LYS ASP GLY TRP SEQRES 18 A 265 THR VAL LYS THR LYS ASP ARG SER LEU SER ALA GLN TYR SEQRES 19 A 265 GLU HIS THR ILE VAL VAL THR ASP ASN GLY CYS GLU ILE SEQRES 20 A 265 LEU THR LEU ARG LYS ASP ASP THR ILE PRO ALA ILE ILE SEQRES 21 A 265 SER HIS ASP GLU LEU SEQRES 1 I 5 AHH ALA LEU VAL 0A9 HET AHH I 1 10 HET CO A 401 1 HET CO A 402 1 HET NA A 501 1 HETNAM AHH AMINO-HYDROXYHEPTANOIC ACID HETNAM CO COBALT (II) ION HETNAM NA SODIUM ION FORMUL 2 AHH C7 H15 N O3 FORMUL 3 CO 2(CO 2+) FORMUL 5 NA NA 1+ FORMUL 6 HOH *91(H2 O) HELIX 1 A THR A 7 GLU A 29 1 23 HELIX 2 B SER A 37 HIS A 54 1 18 HELIX 3 C ILE A 120 VAL A 140 1 21 HELIX 4 D ASN A 145 GLU A 160 1 16 SHEET 1 1A 5 VAL A 56 ALA A 58 0 SHEET 2 1A 5 ASP A 92 LYS A 102 -1 O ILE A 101 N VAL A 56 SHEET 3 1A 5 HIS A 106 VAL A 115 -1 O THR A 109 N VAL A 98 SHEET 4 1A 5 SER A 231 VAL A 240 -1 N GLU A 235 O SER A 110 SHEET 5 1A 5 MET A 199 ALA A 209 -1 N PHE A 201 O ILE A 238 SHEET 1 1B 6 CYS A 70 ASN A 74 0 SHEET 2 1B 6 ASP A 92 LYS A 102 -1 N ASP A 97 O CYS A 70 SHEET 3 1B 6 HIS A 106 VAL A 115 -1 O THR A 109 N VAL A 98 SHEET 4 1B 6 SER A 231 VAL A 240 -1 N GLU A 235 O SER A 110 SHEET 5 1B 6 GLY A 244 LEU A 248 -1 N GLU A 246 O VAL A 239 SHEET 6 1B 6 ALA A 258 HIS A 262 -1 O ILE A 260 N CYS A 245 LINK C2 AHH I 1 N ALA I 2 1555 1555 1.30 LINK O ASN A 74 NA NA A 501 1555 1555 3.10 LINK O VAL A 76 NA NA A 501 1555 1555 2.70 LINK OD1 ASP A 97 CO CO A 402 1555 1555 2.07 LINK OD2 ASP A 97 CO CO A 402 1555 1555 2.62 LINK OD2 ASP A 108 CO CO A 401 1555 1555 1.92 LINK OD1 ASP A 108 CO CO A 402 1555 1555 2.06 LINK NE2 HIS A 171 CO CO A 401 1555 1555 2.15 LINK OE2 GLU A 204 CO CO A 401 1555 1555 2.46 LINK O SER A 231 NA NA A 501 1555 1555 2.54 LINK OE2 GLU A 235 CO CO A 401 1555 1555 2.17 LINK OE1 GLU A 235 CO CO A 402 1555 1555 2.19 LINK CO CO A 401 O1 AHH I 1 1555 1555 2.07 LINK CO CO A 401 O2 AHH I 1 1555 1555 2.48 LINK CO CO A 402 N AHH I 1 1555 1555 2.35 LINK CO CO A 402 O1 AHH I 1 1555 1555 1.87 LINK NA NA A 501 O HOH A 521 1555 1555 2.79 CISPEP 1 GLU A 180 PRO A 181 0 0.27 SITE 1 ACT 7 ASP A 97 ASP A 108 HIS A 171 GLU A 204 SITE 2 ACT 7 GLU A 235 CO A 401 CO A 402 SITE 1 AC1 6 ASP A 108 HIS A 171 GLU A 204 GLU A 235 SITE 2 AC1 6 CO A 402 AHH I 1 SITE 1 AC2 5 ASP A 97 ASP A 108 GLU A 235 CO A 401 SITE 2 AC2 5 AHH I 1 SITE 1 AC3 5 SER A 72 ASN A 74 VAL A 76 SER A 231 SITE 2 AC3 5 HOH A 521 SITE 1 AC4 16 HIS A 63 HIS A 79 ASP A 97 THR A 99 SITE 2 AC4 16 ASP A 108 TYR A 168 CYS A 169 HIS A 171 SITE 3 AC4 16 PHE A 177 HIS A 178 GLU A 204 GLU A 235 SITE 4 AC4 16 CO A 401 CO A 402 HOH I 7 HOH I 76 CRYST1 39.297 65.155 51.371 90.00 106.12 90.00 P 1 21 1 2 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 0.025447 0.000000 0.007354 0.00000 SCALE2 0.000000 0.015348 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020263 0.00000