HEADER HYDROLASE 05-JAN-04 1S17 TITLE IDENTIFICATION OF NOVEL POTENT BICYCLIC PEPTIDE DEFORMYLASE INHIBITORS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDE DEFORMYLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PDF, POLYPEPTIDE DEFORMYLASE; COMPND 5 EC: 3.5.1.88; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 GENE: DEF, PA0019; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: GENEHOGS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMH4 KEYWDS PEPTIDE DEFORMYLASE INHIBITOR, RATIONAL DRUG DESIGN, ANTIBIOTIC, KEYWDS 2 PROTEIN-LIGAND COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.MOLTENI,X.HE,J.NABAKKA,K.YANG,A.KREUSCH,P.GORDON,B.BURSULAYA, AUTHOR 2 N.S.RYDER,R.GOLDBERG,Y.HE REVDAT 4 23-AUG-23 1S17 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 1S17 1 VERSN REVDAT 2 24-FEB-09 1S17 1 VERSN REVDAT 1 30-MAR-04 1S17 0 JRNL AUTH V.MOLTENI,X.HE,J.NABAKKA,K.YANG,A.KREUSCH,P.GORDON, JRNL AUTH 2 B.BURSULAYA,I.WARNER,T.SHIN,T.BIORAC,N.S.RYDER,R.GOLDBERG, JRNL AUTH 3 J.DOUGHTY,Y.HE JRNL TITL IDENTIFICATION OF NOVEL POTENT BICYCLIC PEPTIDE DEFORMYLASE JRNL TITL 2 INHIBITORS JRNL REF BIOORG.MED.CHEM.LETT. V. 14 1477 2004 JRNL REFN ISSN 0960-894X JRNL PMID 15006385 JRNL DOI 10.1016/J.BMCL.2004.01.014 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.KREUSCH,G.SPRAGGON,C.C.LEE,H.KLOCK,D.MCMULLAN,K.NG,T.SHIN, REMARK 1 AUTH 2 J.VINCENT,I.WARNER,C.ERICSON,S.A.LESLEY REMARK 1 TITL STRUCTURE ANALYSIS OF PEPTIDE DEFORMYLASES FROM REMARK 1 TITL 2 STREPTOCOCCUS PNEUMONIAE, STAPHYLOCOCCUS AUREUS, THERMOTOGA REMARK 1 TITL 3 MARITIMA AND PSEUDOMONAS AERUGINOSA: SNAPSHOTS OF THE OXYGEN REMARK 1 TITL 4 SENSITIVITY OF PEPTIDE DEFORMYLASE REMARK 1 REF J.MOL.BIOL. V. 330 309 2003 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1016/S0022-2836(03)00596-5 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.68 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 28955 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 SET) : 0.196 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1455 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2120 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 242 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2670 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 208 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.01000 REMARK 3 B22 (A**2) : -1.46000 REMARK 3 B33 (A**2) : -2.55000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.11 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.019 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.330 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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 1S17 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021237. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-SEP-02 REMARK 200 TEMPERATURE (KELVIN) : 108 REMARK 200 PH : 5.9 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : OSMIC MIRRORS REMARK 200 OPTICS : MIRROR 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 : 28955 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 25.680 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 17.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.41500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: PDB ENTRY 1N5N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, MGSO4, PH 5.9, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 34.50450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.43200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.99700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.43200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.50450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.99700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: THE FUNCTIONAL UNIT IS A MONOMER 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 -11 REMARK 465 GLY A -10 REMARK 465 SER A -9 REMARK 465 ASP A -8 REMARK 465 LYS A -7 REMARK 465 ILE A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 168 REMARK 465 MET B -11 REMARK 465 GLY B -10 REMARK 465 SER B -9 REMARK 465 ASP B -8 REMARK 465 LYS B -7 REMARK 465 ILE B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 GLN B 166 REMARK 465 GLN B 167 REMARK 465 ALA B 168 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 GLN A 167 CG CD OE1 NE2 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 GLU B 84 O HOH B 674 2.09 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 B 13 NE - CZ - NH1 ANGL. DEV. = -3.1 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 ASP A 25 -160.21 -100.63 REMARK 500 PRO B 10 31.21 -92.81 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 NI A 301 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 92 SG REMARK 620 2 HIS A 134 NE2 117.2 REMARK 620 3 HIS A 138 NE2 99.9 104.5 REMARK 620 4 GNR A 501 OAN 84.9 112.8 135.0 REMARK 620 5 GNR A 501 OAP 142.4 97.8 82.9 68.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 302 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 92 SG REMARK 620 2 HIS B 134 NE2 118.9 REMARK 620 3 HIS B 138 NE2 96.2 107.7 REMARK 620 4 GNR B 601 OAP 141.6 96.2 86.5 REMARK 620 5 GNR B 601 NAO 133.1 85.4 114.7 28.3 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 NI A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNR A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNR B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1N5N RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PEPTIDE DEFORMYLASE FROM PSEUDOMONAS AERUGINOSA REMARK 900 RELATED ID: 1IX1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF P. AERUGINOSA PEPTIDE DEFORMYLASE COMPLEXED REMARK 900 WITH ANTIBIOTIC ACTINONIN DBREF 1S17 A 1 168 UNP Q9I7A8 DEF_PSEAE 1 168 DBREF 1S17 B 1 168 UNP Q9I7A8 DEF_PSEAE 1 168 SEQADV 1S17 MET A -11 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 GLY A -10 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 SER A -9 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 ASP A -8 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 LYS A -7 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 ILE A -6 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 HIS A -5 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 HIS A -4 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 HIS A -3 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 HIS A -2 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 HIS A -1 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 HIS A 0 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 GLU A 84 UNP Q9I7A8 ASP 84 CONFLICT SEQADV 1S17 MET B -11 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 GLY B -10 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 SER B -9 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 ASP B -8 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 LYS B -7 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 ILE B -6 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 HIS B -5 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 HIS B -4 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 HIS B -3 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 HIS B -2 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 HIS B -1 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 HIS B 0 UNP Q9I7A8 EXPRESSION TAG SEQADV 1S17 GLU B 84 UNP Q9I7A8 ASP 84 CONFLICT SEQRES 1 A 180 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MET SEQRES 2 A 180 ALA ILE LEU ASN ILE LEU GLU PHE PRO ASP PRO ARG LEU SEQRES 3 A 180 ARG THR ILE ALA LYS PRO VAL GLU VAL VAL ASP ASP ALA SEQRES 4 A 180 VAL ARG GLN LEU ILE ASP ASP MET PHE GLU THR MET TYR SEQRES 5 A 180 GLU ALA PRO GLY ILE GLY LEU ALA ALA THR GLN VAL ASN SEQRES 6 A 180 VAL HIS LYS ARG ILE VAL VAL MET ASP LEU SER GLU ASP SEQRES 7 A 180 LYS SER GLU PRO ARG VAL PHE ILE ASN PRO GLU PHE GLU SEQRES 8 A 180 PRO LEU THR GLU GLU MET ASP GLN TYR GLN GLU GLY CYS SEQRES 9 A 180 LEU SER VAL PRO GLY PHE TYR GLU ASN VAL ASP ARG PRO SEQRES 10 A 180 GLN LYS VAL ARG ILE LYS ALA LEU ASP ARG ASP GLY ASN SEQRES 11 A 180 PRO PHE GLU GLU VAL ALA GLU GLY LEU LEU ALA VAL CYS SEQRES 12 A 180 ILE GLN HIS GLU CYS ASP HIS LEU ASN GLY LYS LEU PHE SEQRES 13 A 180 VAL ASP TYR LEU SER THR LEU LYS ARG ASP ARG ILE ARG SEQRES 14 A 180 LYS LYS LEU GLU LYS GLN HIS ARG GLN GLN ALA SEQRES 1 B 180 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS MET SEQRES 2 B 180 ALA ILE LEU ASN ILE LEU GLU PHE PRO ASP PRO ARG LEU SEQRES 3 B 180 ARG THR ILE ALA LYS PRO VAL GLU VAL VAL ASP ASP ALA SEQRES 4 B 180 VAL ARG GLN LEU ILE ASP ASP MET PHE GLU THR MET TYR SEQRES 5 B 180 GLU ALA PRO GLY ILE GLY LEU ALA ALA THR GLN VAL ASN SEQRES 6 B 180 VAL HIS LYS ARG ILE VAL VAL MET ASP LEU SER GLU ASP SEQRES 7 B 180 LYS SER GLU PRO ARG VAL PHE ILE ASN PRO GLU PHE GLU SEQRES 8 B 180 PRO LEU THR GLU GLU MET ASP GLN TYR GLN GLU GLY CYS SEQRES 9 B 180 LEU SER VAL PRO GLY PHE TYR GLU ASN VAL ASP ARG PRO SEQRES 10 B 180 GLN LYS VAL ARG ILE LYS ALA LEU ASP ARG ASP GLY ASN SEQRES 11 B 180 PRO PHE GLU GLU VAL ALA GLU GLY LEU LEU ALA VAL CYS SEQRES 12 B 180 ILE GLN HIS GLU CYS ASP HIS LEU ASN GLY LYS LEU PHE SEQRES 13 B 180 VAL ASP TYR LEU SER THR LEU LYS ARG ASP ARG ILE ARG SEQRES 14 B 180 LYS LYS LEU GLU LYS GLN HIS ARG GLN GLN ALA HET NI A 301 1 HET GNR A 501 16 HET GOL A 401 6 HET NI B 302 1 HET GNR B 601 16 HETNAM NI NICKEL (II) ION HETNAM GNR 2-(3,4-DIHYDRO-3-OXO-2H-BENZO[B][1,4]THIAZIN-2-YL)-N- HETNAM 2 GNR HYDROXYACETAMIDE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NI 2(NI 2+) FORMUL 4 GNR 2(C10 H10 N2 O3 S) FORMUL 5 GOL C3 H8 O3 FORMUL 8 HOH *208(H2 O) HELIX 1 1 ASP A 11 THR A 16 5 6 HELIX 2 2 ASP A 25 ALA A 42 1 18 HELIX 3 3 THR A 50 ASN A 53 5 4 HELIX 4 4 GLY A 126 ASN A 140 1 15 HELIX 5 5 LEU A 143 LEU A 148 5 6 HELIX 6 6 SER A 149 GLN A 167 1 19 HELIX 7 7 ASP B 11 THR B 16 5 6 HELIX 8 8 ASP B 25 ALA B 42 1 18 HELIX 9 9 THR B 50 ASN B 53 5 4 HELIX 10 10 GLY B 126 ASN B 140 1 15 HELIX 11 11 LEU B 143 LEU B 148 5 6 HELIX 12 12 SER B 149 ARG B 165 1 17 SHEET 1 A 5 GLY A 46 ALA A 48 0 SHEET 2 A 5 ILE A 58 ASP A 62 -1 O VAL A 60 N LEU A 47 SHEET 3 A 5 PRO A 70 PRO A 80 -1 O PHE A 73 N VAL A 59 SHEET 4 A 5 LYS A 107 LEU A 113 -1 O ARG A 109 N GLU A 79 SHEET 5 A 5 PRO A 119 GLU A 125 -1 O GLU A 122 N ILE A 110 SHEET 1 B 2 MET A 85 GLU A 90 0 SHEET 2 B 2 GLU A 100 PRO A 105 -1 O GLU A 100 N GLU A 90 SHEET 1 C 5 GLY B 46 ALA B 48 0 SHEET 2 C 5 ILE B 58 ASP B 62 -1 O VAL B 60 N LEU B 47 SHEET 3 C 5 PRO B 70 PRO B 80 -1 O PHE B 73 N VAL B 59 SHEET 4 C 5 LYS B 107 LEU B 113 -1 O ARG B 109 N GLU B 79 SHEET 5 C 5 PRO B 119 GLU B 125 -1 O GLU B 122 N ILE B 110 SHEET 1 D 2 MET B 85 GLU B 90 0 SHEET 2 D 2 GLU B 100 PRO B 105 -1 O GLU B 100 N GLU B 90 LINK SG CYS A 92 NI NI A 301 1555 1555 2.31 LINK NE2 HIS A 134 NI NI A 301 1555 1555 2.02 LINK NE2 HIS A 138 NI NI A 301 1555 1555 2.02 LINK NI NI A 301 OAN GNR A 501 1555 1555 2.61 LINK NI NI A 301 OAP GNR A 501 1555 1555 2.13 LINK SG CYS B 92 NI NI B 302 1555 1555 2.38 LINK NE2 HIS B 134 NI NI B 302 1555 1555 2.01 LINK NE2 HIS B 138 NI NI B 302 1555 1555 2.03 LINK NI NI B 302 OAP GNR B 601 1555 1555 2.08 LINK NI NI B 302 NAO GNR B 601 1555 1555 2.74 CISPEP 1 PHE A 9 PRO A 10 0 0.76 CISPEP 2 ALA A 42 PRO A 43 0 -0.36 CISPEP 3 PHE B 9 PRO B 10 0 0.51 CISPEP 4 ALA B 42 PRO B 43 0 -0.34 SITE 1 AC1 5 GLN A 51 CYS A 92 HIS A 134 HIS A 138 SITE 2 AC1 5 GNR A 501 SITE 1 AC2 5 GLN B 51 CYS B 92 HIS B 134 HIS B 138 SITE 2 AC2 5 GNR B 601 SITE 1 AC3 14 GLY A 44 ILE A 45 GLY A 46 GLN A 51 SITE 2 AC3 14 TYR A 88 GLU A 90 GLY A 91 CYS A 92 SITE 3 AC3 14 LEU A 93 HIS A 134 GLU A 135 HIS A 138 SITE 4 AC3 14 NI A 301 HOH A 584 SITE 1 AC4 13 GLY B 44 ILE B 45 GLY B 46 GLN B 51 SITE 2 AC4 13 TYR B 88 GLU B 90 GLY B 91 CYS B 92 SITE 3 AC4 13 LEU B 93 HIS B 134 GLU B 135 HIS B 138 SITE 4 AC4 13 NI B 302 SITE 1 AC5 6 ARG A 71 VAL A 72 ASP A 114 ARG A 115 SITE 2 AC5 6 PHE A 120 HOH A 503 CRYST1 69.009 73.994 76.864 90.00 90.00 90.00 P 21 21 21 8 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 0.014491 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013515 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013010 0.00000