PDB Short entry for 3DP3 HEADER LYASE 07-JUL-08 3DP3 TITLE CRYSTAL STRUCTURE OF (3R)-HYDROXYACYL-ACYL CARRIER PROTEIN DEHYDRATASE TITLE 2 (FABZ) FROM HELICOBACTER PYLORI IN COMPLEX WITH COMPOUND 3Q COMPND MOL_ID: 1; COMPND 2 MOLECULE: (3R)-HYDROXYMYRISTOYL-ACYL CARRIER PROTEIN DEHYDRATASE; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 EC: 4.2.1.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_COMMON: CAMPYLOBACTER PYLORI; SOURCE 4 ORGANISM_TAXID: 210; SOURCE 5 STRAIN: SS1; SOURCE 6 GENE: FABZ; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS FABZ COMPLEX, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR L.ZHANG,L.HE,X.LIU,H.LIU,X.SHEN,H.JIANG REVDAT 4 01-NOV-23 3DP3 1 REMARK REVDAT 3 30-JUN-09 3DP3 1 REMARK REVDAT 2 26-MAY-09 3DP3 1 COMPND REVDAT 1 05-MAY-09 3DP3 0 JRNL AUTH L.HE,L.ZHANG,X.LIU,X.LI,M.ZHENG,H.LI,K.YU,K.CHEN,X.SHEN, JRNL AUTH 2 H.JIANG,H.LIU JRNL TITL DISCOVERING POTENT INHIBITORS AGAINST THE JRNL TITL 2 BETA-HYDROXYACYL-ACYL CARRIER PROTEIN DEHYDRATASE (FABZ) OF JRNL TITL 3 HELICOBACTER PYLORI: STRUCTURE-BASED DESIGN, SYNTHESIS, JRNL TITL 4 BIOASSAY, AND CRYSTAL STRUCTURE DETERMINATION. JRNL REF J.MED.CHEM. V. 52 2465 2009 JRNL REFN ISSN 0022-2623 JRNL PMID 19309082 JRNL DOI 10.1021/JM8015602 REMARK 2 REMARK 2 RESOLUTION. 2.30 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 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) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 61984 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) : 0.203 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3098 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 : 7274 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 110 REMARK 3 SOLVENT ATOMS : 401 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.03300 REMARK 3 B22 (A**2) : 4.91800 REMARK 3 B33 (A**2) : -3.88500 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) : 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) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL 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) : 1.017 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.608 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.880 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.784 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 39.97 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : CIS_PEPTIDE.PARAM REMARK 3 PARAMETER FILE 5 : BEN-22.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3DP3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048313. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.8 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) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : D*TREK, SCALA 3.2.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62202 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 93.315 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : 0.10200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : 0.39000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP, CNS REMARK 200 STARTING MODEL: 2GLL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE TRIHYDRATE, 2.0M REMARK 280 SODIUM FORMATE, 20% W/V BENZAMIDINE HCL, PH 3.8, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 277K 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 36.94850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 93.31500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.11300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 93.31500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.94850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.11300 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 GLU A 2 REMARK 465 GLN A 3 REMARK 465 SER A 4 REMARK 465 HIS A 5 REMARK 465 GLN A 6 REMARK 465 ASN A 7 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 GLN B 3 REMARK 465 SER B 4 REMARK 465 HIS B 5 REMARK 465 GLN B 6 REMARK 465 ASN B 7 REMARK 465 LEU B 8 REMARK 465 GLN B 9 REMARK 465 GLU B 159 REMARK 465 MET C 1 REMARK 465 GLU C 2 REMARK 465 GLN C 3 REMARK 465 SER C 4 REMARK 465 HIS C 5 REMARK 465 GLN C 6 REMARK 465 ASN C 7 REMARK 465 LEU C 8 REMARK 465 MET D 1 REMARK 465 GLU D 2 REMARK 465 GLN D 3 REMARK 465 SER D 4 REMARK 465 HIS D 5 REMARK 465 GLN D 6 REMARK 465 ASN D 7 REMARK 465 GLU D 159 REMARK 465 MET E 1 REMARK 465 GLU E 2 REMARK 465 GLN E 3 REMARK 465 SER E 4 REMARK 465 HIS E 5 REMARK 465 GLN E 6 REMARK 465 ASN E 7 REMARK 465 MET F 1 REMARK 465 GLU F 2 REMARK 465 GLN F 3 REMARK 465 SER F 4 REMARK 465 HIS F 5 REMARK 465 GLN F 6 REMARK 465 ASN F 7 REMARK 465 LEU F 8 REMARK 465 GLN F 9 REMARK 465 GLU F 159 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 GLU C 159 O REMARK 470 ARG D 158 O REMARK 470 GLU E 159 O 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 PRO A 26 46.64 -101.86 REMARK 500 GLN A 40 -58.28 -123.84 REMARK 500 ASN A 51 41.81 -69.17 REMARK 500 LYS A 62 74.17 -152.41 REMARK 500 LYS A 127 135.95 -173.35 REMARK 500 PRO B 26 48.63 -106.18 REMARK 500 GLN B 40 -62.72 -126.91 REMARK 500 ASN B 51 36.52 -70.97 REMARK 500 LYS B 62 78.61 -161.82 REMARK 500 SER C 10 -51.66 -120.03 REMARK 500 PRO C 26 40.68 -100.01 REMARK 500 ASN C 51 43.68 -74.70 REMARK 500 LYS C 62 75.28 -152.92 REMARK 500 ALA C 149 149.69 -174.19 REMARK 500 PRO D 26 47.66 -100.47 REMARK 500 GLN D 40 -58.57 -122.43 REMARK 500 ASN D 51 38.29 -70.89 REMARK 500 LYS D 62 81.00 -151.81 REMARK 500 GLU D 157 -166.56 -68.29 REMARK 500 PRO E 26 41.33 -100.41 REMARK 500 GLN E 40 -72.41 -124.52 REMARK 500 ASN E 51 39.28 -68.08 REMARK 500 ASN E 61 -0.42 72.57 REMARK 500 LYS E 106 55.29 35.15 REMARK 500 LYS E 127 134.50 179.20 REMARK 500 LYS E 129 110.45 -160.61 REMARK 500 PRO F 26 41.35 -101.79 REMARK 500 ASN F 39 15.17 57.26 REMARK 500 GLN F 40 -74.02 -123.60 REMARK 500 ASN F 51 40.68 -73.82 REMARK 500 LYS F 62 82.67 -157.41 REMARK 500 LYS F 129 119.46 -171.22 REMARK 500 REMARK 500 REMARK: NULL 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 160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL C 160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL D 160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL E 160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL F 160 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN A 161 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN A 162 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 4BB A 163 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN B 161 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN B 162 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN C 161 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 4BB C 162 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN E 161 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GLL RELATED DB: PDB REMARK 900 RELATED ID: 3DOY RELATED DB: PDB REMARK 900 RELATED ID: 3DOZ RELATED DB: PDB REMARK 900 RELATED ID: 3DP0 RELATED DB: PDB REMARK 900 RELATED ID: 3DP1 RELATED DB: PDB REMARK 900 RELATED ID: 3DP2 RELATED DB: PDB DBREF 3DP3 A 1 159 UNP Q5G940 Q5G940_HELPY 1 159 DBREF 3DP3 B 1 159 UNP Q5G940 Q5G940_HELPY 1 159 DBREF 3DP3 C 1 159 UNP Q5G940 Q5G940_HELPY 1 159 DBREF 3DP3 D 1 159 UNP Q5G940 Q5G940_HELPY 1 159 DBREF 3DP3 E 1 159 UNP Q5G940 Q5G940_HELPY 1 159 DBREF 3DP3 F 1 159 UNP Q5G940 Q5G940_HELPY 1 159 SEQRES 1 A 159 MET GLU GLN SER HIS GLN ASN LEU GLN SER GLN PHE PHE SEQRES 2 A 159 ILE GLU HIS ILE LEU GLN ILE LEU PRO HIS ARG TYR PRO SEQRES 3 A 159 MET LEU LEU VAL ASP ARG ILE THR GLU LEU GLN ALA ASN SEQRES 4 A 159 GLN LYS ILE VAL ALA TYR LYS ASN ILE THR PHE ASN GLU SEQRES 5 A 159 ASP VAL PHE ASN GLY HIS PHE PRO ASN LYS PRO ILE PHE SEQRES 6 A 159 PRO GLY VAL LEU ILE VAL GLU GLY MET ALA GLN SER GLY SEQRES 7 A 159 GLY PHE LEU ALA PHE THR SER LEU TRP GLY PHE ASP PRO SEQRES 8 A 159 GLU ILE ALA LYS THR LYS ILE VAL TYR PHE MET THR ILE SEQRES 9 A 159 ASP LYS VAL LYS PHE ARG ILE PRO VAL THR PRO GLY ASP SEQRES 10 A 159 ARG LEU GLU TYR HIS LEU GLU VAL LEU LYS HIS LYS GLY SEQRES 11 A 159 MET ILE TRP GLN VAL GLY GLY THR ALA GLN VAL ASP GLY SEQRES 12 A 159 LYS VAL VAL ALA GLU ALA GLU LEU LYS ALA MET ILE ALA SEQRES 13 A 159 GLU ARG GLU SEQRES 1 B 159 MET GLU GLN SER HIS GLN ASN LEU GLN SER GLN PHE PHE SEQRES 2 B 159 ILE GLU HIS ILE LEU GLN ILE LEU PRO HIS ARG TYR PRO SEQRES 3 B 159 MET LEU LEU VAL ASP ARG ILE THR GLU LEU GLN ALA ASN SEQRES 4 B 159 GLN LYS ILE VAL ALA TYR LYS ASN ILE THR PHE ASN GLU SEQRES 5 B 159 ASP VAL PHE ASN GLY HIS PHE PRO ASN LYS PRO ILE PHE SEQRES 6 B 159 PRO GLY VAL LEU ILE VAL GLU GLY MET ALA GLN SER GLY SEQRES 7 B 159 GLY PHE LEU ALA PHE THR SER LEU TRP GLY PHE ASP PRO SEQRES 8 B 159 GLU ILE ALA LYS THR LYS ILE VAL TYR PHE MET THR ILE SEQRES 9 B 159 ASP LYS VAL LYS PHE ARG ILE PRO VAL THR PRO GLY ASP SEQRES 10 B 159 ARG LEU GLU TYR HIS LEU GLU VAL LEU LYS HIS LYS GLY SEQRES 11 B 159 MET ILE TRP GLN VAL GLY GLY THR ALA GLN VAL ASP GLY SEQRES 12 B 159 LYS VAL VAL ALA GLU ALA GLU LEU LYS ALA MET ILE ALA SEQRES 13 B 159 GLU ARG GLU SEQRES 1 C 159 MET GLU GLN SER HIS GLN ASN LEU GLN SER GLN PHE PHE SEQRES 2 C 159 ILE GLU HIS ILE LEU GLN ILE LEU PRO HIS ARG TYR PRO SEQRES 3 C 159 MET LEU LEU VAL ASP ARG ILE THR GLU LEU GLN ALA ASN SEQRES 4 C 159 GLN LYS ILE VAL ALA TYR LYS ASN ILE THR PHE ASN GLU SEQRES 5 C 159 ASP VAL PHE ASN GLY HIS PHE PRO ASN LYS PRO ILE PHE SEQRES 6 C 159 PRO GLY VAL LEU ILE VAL GLU GLY MET ALA GLN SER GLY SEQRES 7 C 159 GLY PHE LEU ALA PHE THR SER LEU TRP GLY PHE ASP PRO SEQRES 8 C 159 GLU ILE ALA LYS THR LYS ILE VAL TYR PHE MET THR ILE SEQRES 9 C 159 ASP LYS VAL LYS PHE ARG ILE PRO VAL THR PRO GLY ASP SEQRES 10 C 159 ARG LEU GLU TYR HIS LEU GLU VAL LEU LYS HIS LYS GLY SEQRES 11 C 159 MET ILE TRP GLN VAL GLY GLY THR ALA GLN VAL ASP GLY SEQRES 12 C 159 LYS VAL VAL ALA GLU ALA GLU LEU LYS ALA MET ILE ALA SEQRES 13 C 159 GLU ARG GLU SEQRES 1 D 159 MET GLU GLN SER HIS GLN ASN LEU GLN SER GLN PHE PHE SEQRES 2 D 159 ILE GLU HIS ILE LEU GLN ILE LEU PRO HIS ARG TYR PRO SEQRES 3 D 159 MET LEU LEU VAL ASP ARG ILE THR GLU LEU GLN ALA ASN SEQRES 4 D 159 GLN LYS ILE VAL ALA TYR LYS ASN ILE THR PHE ASN GLU SEQRES 5 D 159 ASP VAL PHE ASN GLY HIS PHE PRO ASN LYS PRO ILE PHE SEQRES 6 D 159 PRO GLY VAL LEU ILE VAL GLU GLY MET ALA GLN SER GLY SEQRES 7 D 159 GLY PHE LEU ALA PHE THR SER LEU TRP GLY PHE ASP PRO SEQRES 8 D 159 GLU ILE ALA LYS THR LYS ILE VAL TYR PHE MET THR ILE SEQRES 9 D 159 ASP LYS VAL LYS PHE ARG ILE PRO VAL THR PRO GLY ASP SEQRES 10 D 159 ARG LEU GLU TYR HIS LEU GLU VAL LEU LYS HIS LYS GLY SEQRES 11 D 159 MET ILE TRP GLN VAL GLY GLY THR ALA GLN VAL ASP GLY SEQRES 12 D 159 LYS VAL VAL ALA GLU ALA GLU LEU LYS ALA MET ILE ALA SEQRES 13 D 159 GLU ARG GLU SEQRES 1 E 159 MET GLU GLN SER HIS GLN ASN LEU GLN SER GLN PHE PHE SEQRES 2 E 159 ILE GLU HIS ILE LEU GLN ILE LEU PRO HIS ARG TYR PRO SEQRES 3 E 159 MET LEU LEU VAL ASP ARG ILE THR GLU LEU GLN ALA ASN SEQRES 4 E 159 GLN LYS ILE VAL ALA TYR LYS ASN ILE THR PHE ASN GLU SEQRES 5 E 159 ASP VAL PHE ASN GLY HIS PHE PRO ASN LYS PRO ILE PHE SEQRES 6 E 159 PRO GLY VAL LEU ILE VAL GLU GLY MET ALA GLN SER GLY SEQRES 7 E 159 GLY PHE LEU ALA PHE THR SER LEU TRP GLY PHE ASP PRO SEQRES 8 E 159 GLU ILE ALA LYS THR LYS ILE VAL TYR PHE MET THR ILE SEQRES 9 E 159 ASP LYS VAL LYS PHE ARG ILE PRO VAL THR PRO GLY ASP SEQRES 10 E 159 ARG LEU GLU TYR HIS LEU GLU VAL LEU LYS HIS LYS GLY SEQRES 11 E 159 MET ILE TRP GLN VAL GLY GLY THR ALA GLN VAL ASP GLY SEQRES 12 E 159 LYS VAL VAL ALA GLU ALA GLU LEU LYS ALA MET ILE ALA SEQRES 13 E 159 GLU ARG GLU SEQRES 1 F 159 MET GLU GLN SER HIS GLN ASN LEU GLN SER GLN PHE PHE SEQRES 2 F 159 ILE GLU HIS ILE LEU GLN ILE LEU PRO HIS ARG TYR PRO SEQRES 3 F 159 MET LEU LEU VAL ASP ARG ILE THR GLU LEU GLN ALA ASN SEQRES 4 F 159 GLN LYS ILE VAL ALA TYR LYS ASN ILE THR PHE ASN GLU SEQRES 5 F 159 ASP VAL PHE ASN GLY HIS PHE PRO ASN LYS PRO ILE PHE SEQRES 6 F 159 PRO GLY VAL LEU ILE VAL GLU GLY MET ALA GLN SER GLY SEQRES 7 F 159 GLY PHE LEU ALA PHE THR SER LEU TRP GLY PHE ASP PRO SEQRES 8 F 159 GLU ILE ALA LYS THR LYS ILE VAL TYR PHE MET THR ILE SEQRES 9 F 159 ASP LYS VAL LYS PHE ARG ILE PRO VAL THR PRO GLY ASP SEQRES 10 F 159 ARG LEU GLU TYR HIS LEU GLU VAL LEU LYS HIS LYS GLY SEQRES 11 F 159 MET ILE TRP GLN VAL GLY GLY THR ALA GLN VAL ASP GLY SEQRES 12 F 159 LYS VAL VAL ALA GLU ALA GLU LEU LYS ALA MET ILE ALA SEQRES 13 F 159 GLU ARG GLU HET CL A 160 1 HET BEN A 161 9 HET BEN A 162 9 HET 4BB A 163 25 HET CL B 160 1 HET BEN B 161 9 HET BEN B 162 9 HET CL C 160 1 HET BEN C 161 9 HET 4BB C 162 25 HET CL D 160 1 HET CL E 160 1 HET BEN E 161 9 HET CL F 160 1 HETNAM CL CHLORIDE ION HETNAM BEN BENZAMIDINE HETNAM 4BB 4-TERT-BUTYL-N'-[(1E)-(3,5-DIBROMO-2,4- HETNAM 2 4BB DIHYDROXYPHENYL)METHYLIDENE]BENZOHYDRAZIDE FORMUL 7 CL 6(CL 1-) FORMUL 8 BEN 6(C7 H8 N2) FORMUL 10 4BB 2(C18 H18 BR2 N2 O3) FORMUL 21 HOH *401(H2 O) HELIX 1 1 ILE A 14 LEU A 21 1 8 HELIX 2 2 ASP A 53 HIS A 58 1 6 HELIX 3 3 PRO A 66 GLY A 88 1 23 HELIX 4 4 ASP A 90 LYS A 95 1 6 HELIX 5 5 PHE B 13 LEU B 21 1 9 HELIX 6 6 GLU B 52 GLY B 57 5 6 HELIX 7 7 PRO B 66 GLY B 88 1 23 HELIX 8 8 ASP B 90 LYS B 95 1 6 HELIX 9 9 PHE C 13 LEU C 21 1 9 HELIX 10 10 GLU C 52 GLY C 57 5 6 HELIX 11 11 PRO C 66 GLY C 88 1 23 HELIX 12 12 ASP C 90 LYS C 95 1 6 HELIX 13 13 PHE D 13 LEU D 21 1 9 HELIX 14 14 ASP D 53 HIS D 58 1 6 HELIX 15 15 PRO D 66 GLY D 88 1 23 HELIX 16 16 ASP D 90 LYS D 95 1 6 HELIX 17 17 ILE E 14 LEU E 21 1 8 HELIX 18 18 GLU E 52 GLY E 57 5 6 HELIX 19 19 PRO E 66 GLY E 88 1 23 HELIX 20 20 ASP E 90 LYS E 95 1 6 HELIX 21 21 PHE F 13 LEU F 21 1 9 HELIX 22 22 ASP F 53 HIS F 58 1 6 HELIX 23 23 PRO F 66 GLY F 88 1 23 HELIX 24 24 ASP F 90 LYS F 95 1 6 SHEET 1 A13 PHE A 12 PHE A 13 0 SHEET 2 A13 ARG A 32 GLN A 37 -1 O ILE A 33 N PHE A 12 SHEET 3 A13 LYS A 41 ASN A 47 -1 O LYS A 41 N GLN A 37 SHEET 4 A13 ARG A 118 LYS A 129 -1 O TYR A 121 N ALA A 44 SHEET 5 A13 ILE A 132 VAL A 141 -1 O GLN A 140 N GLU A 120 SHEET 6 A13 LYS A 144 GLU A 157 -1 O ALA A 153 N TRP A 133 SHEET 7 A13 LYS A 97 PHE A 109 -1 N TYR A 100 O MET A 154 SHEET 8 A13 LYS B 97 PHE B 109 -1 O MET B 102 N PHE A 109 SHEET 9 A13 LYS B 144 GLU B 157 -1 O ALA B 156 N ILE B 98 SHEET 10 A13 ILE B 132 VAL B 141 -1 N ALA B 139 O VAL B 146 SHEET 11 A13 ARG B 118 LYS B 129 -1 N LYS B 127 O GLN B 134 SHEET 12 A13 LYS B 41 ASN B 47 -1 N ALA B 44 O TYR B 121 SHEET 13 A13 ARG B 32 GLN B 37 -1 N GLN B 37 O LYS B 41 SHEET 1 B12 ARG C 32 GLN C 37 0 SHEET 2 B12 LYS C 41 ASN C 47 -1 O VAL C 43 N GLU C 35 SHEET 3 B12 ARG C 118 LYS C 129 -1 O LEU C 123 N ILE C 42 SHEET 4 B12 ILE C 132 VAL C 141 -1 O GLN C 134 N LEU C 126 SHEET 5 B12 LYS C 144 GLU C 157 -1 O LEU C 151 N VAL C 135 SHEET 6 B12 LYS C 97 PHE C 109 -1 N ASP C 105 O GLU C 150 SHEET 7 B12 ILE D 98 PHE D 109 -1 O MET D 102 N PHE C 109 SHEET 8 B12 LYS D 144 ALA D 156 -1 O ALA D 156 N ILE D 98 SHEET 9 B12 ILE D 132 VAL D 141 -1 N VAL D 135 O LEU D 151 SHEET 10 B12 ARG D 118 LYS D 129 -1 N LYS D 127 O GLN D 134 SHEET 11 B12 LYS D 41 ASN D 47 -1 N ALA D 44 O TYR D 121 SHEET 12 B12 ARG D 32 GLN D 37 -1 N GLN D 37 O LYS D 41 SHEET 1 C13 PHE E 12 PHE E 13 0 SHEET 2 C13 ARG E 32 GLN E 37 -1 O ILE E 33 N PHE E 12 SHEET 3 C13 LYS E 41 ASN E 47 -1 O LYS E 41 N GLN E 37 SHEET 4 C13 ARG E 118 LYS E 129 -1 O TYR E 121 N ALA E 44 SHEET 5 C13 ILE E 132 VAL E 141 -1 O GLN E 140 N GLU E 120 SHEET 6 C13 LYS E 144 GLU E 157 -1 O LEU E 151 N VAL E 135 SHEET 7 C13 LYS E 97 PHE E 109 -1 N TYR E 100 O MET E 154 SHEET 8 C13 LYS F 97 PHE F 109 -1 O ILE F 104 N VAL E 107 SHEET 9 C13 LYS F 144 GLU F 157 -1 O MET F 154 N TYR F 100 SHEET 10 C13 ILE F 132 VAL F 141 -1 N VAL F 135 O LEU F 151 SHEET 11 C13 ARG F 118 LYS F 129 -1 N LYS F 127 O GLN F 134 SHEET 12 C13 LYS F 41 ASN F 47 -1 N ALA F 44 O TYR F 121 SHEET 13 C13 ARG F 32 GLN F 37 -1 N THR F 34 O VAL F 43 CISPEP 1 TYR A 25 PRO A 26 0 0.21 CISPEP 2 HIS A 58 PHE A 59 0 -0.83 CISPEP 3 TYR B 25 PRO B 26 0 -0.02 CISPEP 4 HIS B 58 PHE B 59 0 0.18 CISPEP 5 TYR C 25 PRO C 26 0 0.04 CISPEP 6 HIS C 58 PHE C 59 0 -1.00 CISPEP 7 TYR D 25 PRO D 26 0 -0.02 CISPEP 8 HIS D 58 PHE D 59 0 -2.97 CISPEP 9 TYR E 25 PRO E 26 0 0.32 CISPEP 10 HIS E 58 PHE E 59 0 -0.62 CISPEP 11 TYR F 25 PRO F 26 0 -0.03 CISPEP 12 HIS F 58 PHE F 59 0 -0.86 SITE 1 AC1 4 HIS A 58 PRO A 66 GLY A 67 HOH B 166 SITE 1 AC2 4 HOH A 166 HIS B 58 GLY B 67 HOH B 200 SITE 1 AC3 2 GLY C 67 HOH D 162 SITE 1 AC4 4 HOH C 168 HOH C 204 HIS D 58 GLY D 67 SITE 1 AC5 3 HIS E 58 GLY E 67 HOH F 236 SITE 1 AC6 2 HOH E 216 GLY F 67 SITE 1 AC7 5 THR A 138 GLU A 148 GLU E 124 VAL E 125 SITE 2 AC7 5 LEU E 126 SITE 1 AC8 6 MET A 131 MET A 154 ILE A 155 LEU F 86 SITE 2 AC8 6 ASP F 90 ILE F 93 SITE 1 AC9 13 PHE A 59 LYS A 62 ILE A 64 PHE A 109 SITE 2 AC9 13 ARG A 110 ILE A 111 PRO A 112 HOH A 217 SITE 3 AC9 13 HOH A 232 ILE B 98 TYR B 100 PHE B 101 SITE 4 AC9 13 ARG B 158 SITE 1 BC1 6 TRP B 87 GLY B 88 LEU E 86 TRP E 87 SITE 2 BC1 6 GLY E 130 MET E 131 SITE 1 BC2 9 ILE B 20 LEU B 21 PRO B 22 PHE B 83 SITE 2 BC2 9 ALA B 94 LYS B 97 VAL B 99 HOH B 229 SITE 3 BC2 9 HOH B 230 SITE 1 BC3 8 GLN C 9 ALA C 38 THR C 84 SER C 85 SITE 2 BC3 8 LEU C 86 TRP C 87 GLY C 88 GLN D 40 SITE 1 BC4 15 ILE C 20 LEU C 21 PRO C 22 HIS C 23 SITE 2 BC4 15 GLY C 79 ILE C 98 VAL C 99 PHE C 101 SITE 3 BC4 15 ARG C 158 HOH C 222 HOH C 226 PHE D 59 SITE 4 BC4 15 PRO D 60 ILE D 64 HOH D 201 SITE 1 BC5 6 GLN A 40 GLU A 124 VAL A 125 THR E 138 SITE 2 BC5 6 VAL E 145 GLU E 148 CRYST1 73.897 100.226 186.630 90.00 90.00 90.00 P 21 21 21 24 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 0.013532 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009977 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005358 0.00000