HEADER HYDROLASE 09-SEP-03 1QXY TITLE CRYSTAL STRUCTURE OF S. AUREUS METHIONINE AMINOPEPTIDASE IN COMPLEX TITLE 2 WITH A KETOHETEROCYCLE 618 COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHIONYL AMINOPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.4.11.18; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 STRAIN: AUREUS MU50; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PDS56-RBSII KEYWDS PITA BREAD FOLD, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.DOUANGAMATH,G.E.DALE,A.D'ARCY,C.OEFNER REVDAT 4 14-FEB-24 1QXY 1 REMARK LINK REVDAT 3 24-FEB-09 1QXY 1 VERSN REVDAT 2 07-FEB-06 1QXY 1 REMARK REVDAT 1 16-MAR-04 1QXY 0 JRNL AUTH A.DOUANGAMATH,G.E.DALE,A.D'ARCY,M.ALMSTETTER,R.ECKL, JRNL AUTH 2 A.FRUTOS-HOENER,B.HENKEL,K.ILLGEN,S.NERDINGER,H.SCHULZ, JRNL AUTH 3 A.MACSWEENEY,M.THORMANN,A.TREML,S.PIERAU,S.WADMAN,C.OEFNER JRNL TITL CRYSTAL STRUCTURES OF STAPHYLOCOCCUSAUREUS METHIONINE JRNL TITL 2 AMINOPEPTIDASE COMPLEXED WITH KETO HETEROCYCLE AND JRNL TITL 3 AMINOKETONE INHIBITORS REVEAL THE FORMATION OF A TETRAHEDRAL JRNL TITL 4 INTERMEDIATE. JRNL REF J.MED.CHEM. V. 47 1325 2004 JRNL REFN ISSN 0022-2623 JRNL PMID 14998322 JRNL DOI 10.1021/JM034188J REMARK 2 REMARK 2 RESOLUTION. 1.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 112974 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) : 0.144 REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5957 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) : 1.04 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.07 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8173 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 446 REMARK 3 BIN FREE R VALUE : 0.3170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1904 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 393 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.18000 REMARK 3 B22 (A**2) : -0.32000 REMARK 3 B33 (A**2) : 0.31000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.33000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.024 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.025 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.022 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.802 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1945 ; 0.017 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1760 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2626 ; 1.777 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4130 ; 0.786 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 244 ; 5.877 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 365 ;15.861 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 309 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2120 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 338 ; 0.011 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 487 ; 0.429 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1814 ; 0.214 ; 0.300 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): 289 ; 0.195 ; 0.500 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): 14 ; 0.415 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 34 ; 0.154 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 52 ; 0.249 ; 0.500 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): 1236 ; 1.505 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1993 ; 2.238 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 709 ; 2.843 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 633 ; 4.393 ; 4.500 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): 1945 ; 1.598 ; 2.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 406 ; 4.729 ; 2.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1918 ; 3.777 ; 2.000 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 1QXY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-03. REMARK 100 THE DEPOSITION ID IS D_1000020204. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-03 REMARK 200 TEMPERATURE (KELVIN) : 200 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 116762 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.040 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.49100 REMARK 200 FOR SHELL : 2.600 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, BIS-TRIS, AMMONIUM ACETATE, REMARK 280 PH 5.5, MICROBATCH, TEMPERATURE 294K 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 38.34500 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: MONOMERIC 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 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 GLU A 252 REMARK 465 GLU A 253 REMARK 465 GLU A 254 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 3387 O HOH A 3388 2.04 REMARK 500 O LYS A 136 O HOH A 3227 2.07 REMARK 500 O HOH A 3127 O HOH A 3296 2.07 REMARK 500 NZ LYS A 138 O HOH A 3275 2.15 REMARK 500 NE2 HIS A 58 O HOH A 3079 2.17 REMARK 500 O HOH A 3388 O HOH A 3389 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 3210 O HOH A 3239 2645 1.96 REMARK 500 OE1 GLU A 113 CG2 THR A 141 2645 2.00 REMARK 500 O HOH A 3354 O HOH A 3364 1556 2.12 REMARK 500 O HOH A 3163 O HOH A 3237 1655 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 VAL A 83 CB VAL A 83 CG2 0.370 REMARK 500 VAL A 83 CB VAL A 83 CG2 0.260 REMARK 500 THR A 141 CB THR A 141 OG1 0.125 REMARK 500 THR A 141 CB THR A 141 CG2 0.950 REMARK 500 THR A 141 CB THR A 141 CG2 0.376 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 ASP A 59 CB - CG - OD1 ANGL. DEV. = 7.8 DEGREES REMARK 500 VAL A 83 CG1 - CB - CG2 ANGL. DEV. = 16.0 DEGREES REMARK 500 VAL A 83 CA - CB - CG1 ANGL. DEV. = 10.1 DEGREES REMARK 500 THR A 141 OG1 - CB - CG2 ANGL. DEV. = 29.3 DEGREES REMARK 500 THR A 141 OG1 - CB - CG2 ANGL. DEV. = -15.6 DEGREES REMARK 500 THR A 141 CA - CB - CG2 ANGL. DEV. = -15.5 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 71 -101.27 58.75 REMARK 500 ASN A 208 -64.71 -159.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 THE ORIGINAL INHIBITOR USED IN THE CRYSTAL WAS REMARK 600 2-AMINO-4-METHYLSULFANYL-1-PYRIDIN-2-YL-BUTAN-1-ONE. REMARK 600 THE M2C COORDINATES IN THIS STRUCTURE ARE THOSE REMARK 600 OF A TRANSITION STATE COMPLEX OF THE INHIBITOR. 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 CO A1002 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 93 OD2 REMARK 620 2 ASP A 93 OD1 58.7 REMARK 620 3 ASP A 104 OD1 100.1 156.5 REMARK 620 4 GLU A 233 OE1 107.8 87.5 90.4 REMARK 620 5 M2C A3001 N10 84.6 99.7 86.9 167.5 REMARK 620 6 M2C A3001 OA 141.8 90.9 112.5 91.8 78.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A1001 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 104 OD2 REMARK 620 2 HIS A 168 NE2 87.4 REMARK 620 3 GLU A 202 OE2 165.2 87.1 REMARK 620 4 GLU A 233 OE2 87.1 119.6 83.6 REMARK 620 5 M2C A3001 OA 99.7 147.4 92.3 92.7 REMARK 620 6 M2C A3001 O8 92.6 86.7 100.9 153.6 61.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A1003 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 175 NE2 REMARK 620 2 M2C A3001 N6 172.0 REMARK 620 3 M2C A3001 O8 98.8 83.5 REMARK 620 4 HOH A3148 O 96.1 88.4 127.8 REMARK 620 5 HOH A3172 O 92.0 80.4 120.2 108.9 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 CO A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE M2C A 3001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QXW RELATED DB: PDB REMARK 900 RELATED ID: 1QXZ RELATED DB: PDB DBREF 1QXY A 1 252 UNP P0A080 AMPM_STAAU 1 252 SEQRES 1 A 252 MET ILE VAL LYS THR GLU GLU GLU LEU GLN ALA LEU LYS SEQRES 2 A 252 GLU ILE GLY TYR ILE CYS ALA LYS VAL ARG ASN THR MET SEQRES 3 A 252 GLN ALA ALA THR LYS PRO GLY ILE THR THR LYS GLU LEU SEQRES 4 A 252 ASP ASN ILE ALA LYS GLU LEU PHE GLU GLU TYR GLY ALA SEQRES 5 A 252 ILE SER ALA PRO ILE HIS ASP GLU ASN PHE PRO GLY GLN SEQRES 6 A 252 THR CYS ILE SER VAL ASN GLU GLU VAL ALA HIS GLY ILE SEQRES 7 A 252 PRO SER LYS ARG VAL ILE ARG GLU GLY ASP LEU VAL ASN SEQRES 8 A 252 ILE ASP VAL SER ALA LEU LYS ASN GLY TYR TYR ALA ASP SEQRES 9 A 252 THR GLY ILE SER PHE VAL VAL GLY GLU SER ASP ASP PRO SEQRES 10 A 252 MET LYS GLN LYS VAL CYS ASP VAL ALA THR MET ALA PHE SEQRES 11 A 252 GLU ASN ALA ILE ALA LYS VAL LYS PRO GLY THR LYS LEU SEQRES 12 A 252 SER ASN ILE GLY LYS ALA VAL HIS ASN THR ALA ARG GLN SEQRES 13 A 252 ASN ASP LEU LYS VAL ILE LYS ASN LEU THR GLY HIS GLY SEQRES 14 A 252 VAL GLY LEU SER LEU HIS GLU ALA PRO ALA HIS VAL LEU SEQRES 15 A 252 ASN TYR PHE ASP PRO LYS ASP LYS THR LEU LEU THR GLU SEQRES 16 A 252 GLY MET VAL LEU ALA ILE GLU PRO PHE ILE SER SER ASN SEQRES 17 A 252 ALA SER PHE VAL THR GLU GLY LYS ASN GLU TRP ALA PHE SEQRES 18 A 252 GLU THR SER ASP LYS SER PHE VAL ALA GLN ILE GLU HIS SEQRES 19 A 252 THR VAL ILE VAL THR LYS ASP GLY PRO ILE LEU THR THR SEQRES 20 A 252 LYS ILE GLU GLU GLU HET CO A1001 1 HET CO A1002 1 HET CO A1003 1 HET ACT A2001 4 HET M2C A3001 15 HETNAM CO COBALT (II) ION HETNAM ACT ACETATE ION HETNAM M2C (2S)-2-AMINO-4-(METHYLSULFANYL)-1-PYRIDIN-2-YLBUTANE-1, HETNAM 2 M2C 1-DIOL FORMUL 2 CO 3(CO 2+) FORMUL 5 ACT C2 H3 O2 1- FORMUL 6 M2C C10 H16 N2 O2 S FORMUL 7 HOH *393(H2 O) HELIX 1 1 THR A 5 THR A 30 1 26 HELIX 2 2 THR A 35 GLY A 51 1 17 HELIX 3 3 ALA A 55 ASN A 61 1 7 HELIX 4 4 PRO A 117 ALA A 135 1 19 HELIX 5 5 LEU A 143 ASN A 157 1 15 LINK OD2 ASP A 93 CO CO A1002 1555 1555 2.04 LINK OD1 ASP A 93 CO CO A1002 1555 1555 2.30 LINK OD2 ASP A 104 CO CO A1001 1555 1555 2.08 LINK OD1 ASP A 104 CO CO A1002 1555 1555 2.02 LINK NE2 HIS A 168 CO CO A1001 1555 1555 2.06 LINK NE2 HIS A 175 CO CO A1003 1555 1555 2.13 LINK OE2 GLU A 202 CO CO A1001 1555 1555 2.17 LINK OE2 GLU A 233 CO CO A1001 1555 1555 2.02 LINK OE1 GLU A 233 CO CO A1002 1555 1555 2.04 LINK CO CO A1001 OA M2C A3001 1555 1555 2.07 LINK CO CO A1001 O8 M2C A3001 1555 1555 2.31 LINK CO CO A1002 N10 M2C A3001 1555 1555 2.12 LINK CO CO A1002 OA M2C A3001 1555 1555 2.04 LINK CO CO A1003 N6 M2C A3001 1555 1555 2.10 LINK CO CO A1003 O8 M2C A3001 1555 1555 1.84 LINK CO CO A1003 O HOH A3148 1555 1555 2.14 LINK CO CO A1003 O HOH A3172 1555 1555 2.38 CISPEP 1 ALA A 177 PRO A 178 0 -2.53 SITE 1 AC1 6 ASP A 104 HIS A 168 GLU A 202 GLU A 233 SITE 2 AC1 6 CO A1002 M2C A3001 SITE 1 AC2 5 ASP A 93 ASP A 104 GLU A 233 CO A1001 SITE 2 AC2 5 M2C A3001 SITE 1 AC3 5 HIS A 168 HIS A 175 M2C A3001 HOH A3148 SITE 2 AC3 5 HOH A3172 SITE 1 AC4 5 HIS A 151 LYS A 160 VAL A 161 SER A 210 SITE 2 AC4 5 HOH A3125 SITE 1 AC5 18 PRO A 56 GLU A 60 ALA A 75 ASP A 93 SITE 2 AC5 18 ASP A 104 HIS A 168 LEU A 174 HIS A 175 SITE 3 AC5 18 GLU A 202 PHE A 204 GLU A 233 CO A1001 SITE 4 AC5 18 CO A1002 CO A1003 HOH A3035 HOH A3148 SITE 5 AC5 18 HOH A3172 HOH A3293 CRYST1 40.970 76.690 41.660 90.00 104.50 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 0.024408 0.000000 0.006312 0.00000 SCALE2 0.000000 0.013040 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024794 0.00000