HEADER HYDROLASE/HYDROLASE INHIBITOR 22-DEC-10 3Q43 TITLE X-RAY CRYSTAL STRUCTURE OF PFA-M1 BOUND TO BESTATIN DERIVATIVE 15 COMPND MOL_ID: 1; COMPND 2 MOLECULE: M1 FAMILY AMINOPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 195-1085; COMPND 5 SYNONYM: PFA-M1; COMPND 6 EC: 3.4.11.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM FCB1/COLUMBIA; SOURCE 3 ORGANISM_TAXID: 186763; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PTRC-2B KEYWDS M1 AMINOPEPTIDASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.MCGOWAN,D.C.GREENBAUM REVDAT 3 13-SEP-23 3Q43 1 REMARK SEQADV LINK REVDAT 2 30-MAR-11 3Q43 1 JRNL REVDAT 1 16-MAR-11 3Q43 0 JRNL AUTH G.VELMOUROUGANE,M.B.HARBUT,S.DALAL,S.MCGOWAN,C.A.OELLIG, JRNL AUTH 2 N.MEINHARDT,J.C.WHISSTOCK,M.KLEMBA,D.C.GREENBAUM JRNL TITL SYNTHESIS OF NEW (-)-BESTATIN-BASED INHIBITOR LIBRARIES JRNL TITL 2 REVEALS A NOVEL BINDING MODE IN THE S1 POCKET OF THE JRNL TITL 3 ESSENTIAL MALARIA M1 METALLOAMINOPEPTIDASE. JRNL REF J.MED.CHEM. V. 54 1655 2011 JRNL REFN ISSN 0022-2623 JRNL PMID 21366301 JRNL DOI 10.1021/JM101227T REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0063 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.07 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 86687 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4578 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6298 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE SET COUNT : 283 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7195 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 930 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05000 REMARK 3 B22 (A**2) : -0.75000 REMARK 3 B33 (A**2) : 0.70000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.119 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.117 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.075 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.247 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7443 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10082 ; 1.531 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 900 ; 6.811 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 356 ;36.369 ;24.860 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1314 ;13.321 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;18.117 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1117 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5604 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 4464 ; 0.880 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7250 ; 1.557 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2979 ; 2.752 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2826 ; 4.409 ; 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 196 A 393 REMARK 3 RESIDUE RANGE : A 394 A 650 REMARK 3 RESIDUE RANGE : A 651 A 746 REMARK 3 RESIDUE RANGE : A 747 A 1085 REMARK 3 ORIGIN FOR THE GROUP (A): 17.6760 4.1310 10.2170 REMARK 3 T TENSOR REMARK 3 T11: 0.0162 T22: 0.0150 REMARK 3 T33: 0.0120 T12: 0.0008 REMARK 3 T13: 0.0053 T23: 0.0020 REMARK 3 L TENSOR REMARK 3 L11: 0.0775 L22: 0.1968 REMARK 3 L33: 0.0972 L12: -0.0557 REMARK 3 L13: 0.0084 L23: 0.0527 REMARK 3 S TENSOR REMARK 3 S11: -0.0189 S12: 0.0019 S13: 0.0070 REMARK 3 S21: -0.0001 S22: 0.0023 S23: -0.0049 REMARK 3 S31: -0.0026 S32: -0.0022 S33: 0.0166 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 3Q43 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000063168. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SILICON 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 91348 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 55.050 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3EBG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% (VOL/VOL) POLYETHYLENE GLYCOL REMARK 280 8000, 10% (VOL/VOL) GLYCEROL, 0.1 M TRIS (PH 8.5), 0.2M MGCL2, REMARK 280 VAPOR DIFFUSION, HANGING 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 37.88600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.34150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.40700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.34150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.88600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.40700 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 195 REMARK 465 LEU A 1085 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 202 CD CE NZ REMARK 470 LYS A 205 CG CD CE NZ REMARK 470 ASP A 222 CG OD1 OD2 REMARK 470 ARG A 228 CD NE CZ NH1 NH2 REMARK 470 LYS A 252 CD CE NZ REMARK 470 VAL A 264 CG1 CG2 REMARK 470 GLU A 267 CG CD OE1 OE2 REMARK 470 GLU A 299 CD OE1 OE2 REMARK 470 GLU A 348 CG CD OE1 OE2 REMARK 470 GLU A 409 CD OE1 OE2 REMARK 470 LYS A 480 CE NZ REMARK 470 GLU A 572 CG CD OE1 OE2 REMARK 470 GLU A 597 CG CD OE1 OE2 REMARK 470 LYS A 608 CG CD CE NZ REMARK 470 GLU A 663 CG CD OE1 OE2 REMARK 470 GLU A 679 CG CD OE1 OE2 REMARK 470 LYS A 682 CG CD CE NZ REMARK 470 GLU A 683 CG CD OE1 OE2 REMARK 470 GLU A 699 CG CD OE1 OE2 REMARK 470 GLU A 749 CG CD OE1 OE2 REMARK 470 HIS A 815 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 973 CG CD CE NZ REMARK 470 GLU A 977 CD OE1 OE2 REMARK 470 LYS A 980 CD CE NZ REMARK 470 ASP A 989 CG OD1 OD2 REMARK 470 LYS A1019 CD CE NZ REMARK 470 LYS A1030 CE NZ REMARK 470 LYS A1048 CD CE NZ REMARK 470 GLN A1066 CD OE1 NE2 REMARK 470 LYS A1075 CE NZ REMARK 470 LYS A1084 CG CD CE NZ 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 1225 O HOH A 1673 1.99 REMARK 500 O PRO A 558 O HOH A 1225 2.07 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 A1080 NE - CZ - NH2 ANGL. DEV. = -3.2 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 GLU A 274 -41.40 -133.36 REMARK 500 LYS A 311 -113.55 56.31 REMARK 500 VAL A 459 -152.12 -127.19 REMARK 500 GLU A 463 38.71 -86.85 REMARK 500 LEU A 475 -31.09 -131.67 REMARK 500 ASN A 505 -60.49 -101.05 REMARK 500 SER A 549 -75.05 -90.06 REMARK 500 ASN A 613 136.06 -173.06 REMARK 500 ALA A 633 45.52 36.05 REMARK 500 GLN A 707 120.58 -27.15 REMARK 500 PHE A 736 72.49 54.28 REMARK 500 VAL A 986 -53.43 -129.62 REMARK 500 LYS A 988 -130.60 46.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 612 ASN A 613 -101.93 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 ZN A 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 496 NE2 REMARK 620 2 HIS A 500 NE2 98.5 REMARK 620 3 GLU A 519 OE1 105.1 105.6 REMARK 620 4 D66 A1087 O2 105.2 102.5 134.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1086 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 8 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 6 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 7 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D66 A 1087 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3Q44 RELATED DB: PDB DBREF 3Q43 A 195 1085 UNP O96935 AMP1_PLAFQ 195 1085 SEQADV 3Q43 GLN A 213 UNP O96935 ASN 213 ENGINEERED MUTATION SEQADV 3Q43 GLN A 223 UNP O96935 ASN 223 ENGINEERED MUTATION SEQADV 3Q43 PRO A 378 UNP O96935 HIS 378 ENGINEERED MUTATION SEQADV 3Q43 GLN A 501 UNP O96935 ASN 501 ENGINEERED MUTATION SEQADV 3Q43 GLN A 745 UNP O96935 ASN 745 ENGINEERED MUTATION SEQADV 3Q43 GLN A 795 UNP O96935 ASN 795 ENGINEERED MUTATION SEQADV 3Q43 GLN A 1069 UNP O96935 ASN 1069 ENGINEERED MUTATION SEQRES 1 A 891 GLU PRO LYS ILE HIS TYR ARG LYS ASP TYR LYS PRO SER SEQRES 2 A 891 GLY PHE ILE ILE ASN GLN VAL THR LEU ASN ILE ASN ILE SEQRES 3 A 891 HIS ASP GLN GLU THR ILE VAL ARG SER VAL LEU ASP MET SEQRES 4 A 891 ASP ILE SER LYS HIS ASN VAL GLY GLU ASP LEU VAL PHE SEQRES 5 A 891 ASP GLY VAL GLY LEU LYS ILE ASN GLU ILE SER ILE ASN SEQRES 6 A 891 ASN LYS LYS LEU VAL GLU GLY GLU GLU TYR THR TYR ASP SEQRES 7 A 891 ASN GLU PHE LEU THR ILE PHE SER LYS PHE VAL PRO LYS SEQRES 8 A 891 SER LYS PHE ALA PHE SER SER GLU VAL ILE ILE HIS PRO SEQRES 9 A 891 GLU THR ASN TYR ALA LEU THR GLY LEU TYR LYS SER LYS SEQRES 10 A 891 ASN ILE ILE VAL SER GLN CYS GLU ALA THR GLY PHE ARG SEQRES 11 A 891 ARG ILE THR PHE PHE ILE ASP ARG PRO ASP MET MET ALA SEQRES 12 A 891 LYS TYR ASP VAL THR VAL THR ALA ASP LYS GLU LYS TYR SEQRES 13 A 891 PRO VAL LEU LEU SER ASN GLY ASP LYS VAL ASN GLU PHE SEQRES 14 A 891 GLU ILE PRO GLY GLY ARG HIS GLY ALA ARG PHE ASN ASP SEQRES 15 A 891 PRO PRO LEU LYS PRO CYS TYR LEU PHE ALA VAL VAL ALA SEQRES 16 A 891 GLY ASP LEU LYS HIS LEU SER ALA THR TYR ILE THR LYS SEQRES 17 A 891 TYR THR LYS LYS LYS VAL GLU LEU TYR VAL PHE SER GLU SEQRES 18 A 891 GLU LYS TYR VAL SER LYS LEU GLN TRP ALA LEU GLU CYS SEQRES 19 A 891 LEU LYS LYS SER MET ALA PHE ASP GLU ASP TYR PHE GLY SEQRES 20 A 891 LEU GLU TYR ASP LEU SER ARG LEU ASN LEU VAL ALA VAL SEQRES 21 A 891 SER ASP PHE ASN VAL GLY ALA MET GLU ASN LYS GLY LEU SEQRES 22 A 891 ASN ILE PHE ASN ALA ASN SER LEU LEU ALA SER LYS LYS SEQRES 23 A 891 ASN SER ILE ASP PHE SER TYR ALA ARG ILE LEU THR VAL SEQRES 24 A 891 VAL GLY HIS GLU TYR PHE HIS GLN TYR THR GLY ASN ARG SEQRES 25 A 891 VAL THR LEU ARG ASP TRP PHE GLN LEU THR LEU LYS GLU SEQRES 26 A 891 GLY LEU THR VAL HIS ARG GLU ASN LEU PHE SER GLU GLU SEQRES 27 A 891 MET THR LYS THR VAL THR THR ARG LEU SER HIS VAL ASP SEQRES 28 A 891 LEU LEU ARG SER VAL GLN PHE LEU GLU ASP SER SER PRO SEQRES 29 A 891 LEU SER HIS PRO ILE ARG PRO GLU SER TYR VAL SER MET SEQRES 30 A 891 GLU ASN PHE TYR THR THR THR VAL TYR ASP LYS GLY SER SEQRES 31 A 891 GLU VAL MET ARG MET TYR LEU THR ILE LEU GLY GLU GLU SEQRES 32 A 891 TYR TYR LYS LYS GLY PHE ASP ILE TYR ILE LYS LYS ASN SEQRES 33 A 891 ASP GLY ASN THR ALA THR CYS GLU ASP PHE ASN TYR ALA SEQRES 34 A 891 MET GLU GLN ALA TYR LYS MET LYS LYS ALA ASP ASN SER SEQRES 35 A 891 ALA ASN LEU ASN GLN TYR LEU LEU TRP PHE SER GLN SER SEQRES 36 A 891 GLY THR PRO HIS VAL SER PHE LYS TYR ASN TYR ASP ALA SEQRES 37 A 891 GLU LYS LYS GLN TYR SER ILE HIS VAL ASN GLN TYR THR SEQRES 38 A 891 LYS PRO ASP GLU ASN GLN LYS GLU LYS LYS PRO LEU PHE SEQRES 39 A 891 ILE PRO ILE SER VAL GLY LEU ILE ASN PRO GLU ASN GLY SEQRES 40 A 891 LYS GLU MET ILE SER GLN THR THR LEU GLU LEU THR LYS SEQRES 41 A 891 GLU SER ASP THR PHE VAL PHE ASN ASN ILE ALA VAL LYS SEQRES 42 A 891 PRO ILE PRO SER LEU PHE ARG GLY PHE SER ALA PRO VAL SEQRES 43 A 891 TYR ILE GLU ASP GLN LEU THR ASP GLU GLU ARG ILE LEU SEQRES 44 A 891 LEU LEU LYS TYR ASP SER ASP ALA PHE VAL ARG TYR ASN SEQRES 45 A 891 SER CYS THR ASN ILE TYR MET LYS GLN ILE LEU MET ASN SEQRES 46 A 891 TYR ASN GLU PHE LEU LYS ALA LYS ASN GLU LYS LEU GLU SEQRES 47 A 891 SER PHE GLN LEU THR PRO VAL ASN ALA GLN PHE ILE ASP SEQRES 48 A 891 ALA ILE LYS TYR LEU LEU GLU ASP PRO HIS ALA ASP ALA SEQRES 49 A 891 GLY PHE LYS SER TYR ILE VAL SER LEU PRO GLN ASP ARG SEQRES 50 A 891 TYR ILE ILE ASN PHE VAL SER ASN LEU ASP THR ASP VAL SEQRES 51 A 891 LEU ALA ASP THR LYS GLU TYR ILE TYR LYS GLN ILE GLY SEQRES 52 A 891 ASP LYS LEU ASN ASP VAL TYR TYR LYS MET PHE LYS SER SEQRES 53 A 891 LEU GLU ALA LYS ALA ASP ASP LEU THR TYR PHE ASN ASP SEQRES 54 A 891 GLU SER HIS VAL ASP PHE ASP GLN MET ASN MET ARG THR SEQRES 55 A 891 LEU ARG ASN THR LEU LEU SER LEU LEU SER LYS ALA GLN SEQRES 56 A 891 TYR PRO ASN ILE LEU ASN GLU ILE ILE GLU HIS SER LYS SEQRES 57 A 891 SER PRO TYR PRO SER ASN TRP LEU THR SER LEU SER VAL SEQRES 58 A 891 SER ALA TYR PHE ASP LYS TYR PHE GLU LEU TYR ASP LYS SEQRES 59 A 891 THR TYR LYS LEU SER LYS ASP ASP GLU LEU LEU LEU GLN SEQRES 60 A 891 GLU TRP LEU LYS THR VAL SER ARG SER ASP ARG LYS ASP SEQRES 61 A 891 ILE TYR GLU ILE LEU LYS LYS LEU GLU ASN GLU VAL LEU SEQRES 62 A 891 LYS ASP SER LYS ASN PRO ASN ASP ILE ARG ALA VAL TYR SEQRES 63 A 891 LEU PRO PHE THR ASN ASN LEU ARG ARG PHE HIS ASP ILE SEQRES 64 A 891 SER GLY LYS GLY TYR LYS LEU ILE ALA GLU VAL ILE THR SEQRES 65 A 891 LYS THR ASP LYS PHE ASN PRO MET VAL ALA THR GLN LEU SEQRES 66 A 891 CYS GLU PRO PHE LYS LEU TRP ASN LYS LEU ASP THR LYS SEQRES 67 A 891 ARG GLN GLU LEU MET LEU ASN GLU MET ASN THR MET LEU SEQRES 68 A 891 GLN GLU PRO GLN ILE SER ASN ASN LEU LYS GLU TYR LEU SEQRES 69 A 891 LEU ARG LEU THR ASN LYS LEU HET ZN A 1 1 HET MG A1086 1 HET MG A 2 1 HET GOL A 4 6 HET MG A 3 1 HET GOL A 8 6 HET MG A 5 1 HET GOL A 6 6 HET GOL A 7 6 HET D66 A1087 24 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM D66 N-[(2S,3R)-3-AMINO-2-HYDROXY-4-(4-METHOXYPHENYL) HETNAM 2 D66 BUTANOYL]-L-LEUCINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN D66 BESTATIN-DERIVATIVE 7C FORMUL 2 ZN ZN 2+ FORMUL 3 MG 4(MG 2+) FORMUL 5 GOL 4(C3 H8 O3) FORMUL 11 D66 C17 H26 N2 O5 FORMUL 12 HOH *930(H2 O) HELIX 1 1 LYS A 202 TYR A 204 5 3 HELIX 2 2 SER A 280 VAL A 283 5 4 HELIX 3 3 HIS A 297 ASN A 301 5 5 HELIX 4 4 GLY A 322 ILE A 326 5 5 HELIX 5 5 PRO A 381 PHE A 385 5 5 HELIX 6 6 LYS A 417 LYS A 421 5 5 HELIX 7 7 LEU A 422 GLY A 441 1 20 HELIX 8 8 ASN A 473 LEU A 475 5 3 HELIX 9 9 ASP A 484 HIS A 500 1 17 HELIX 10 10 ASP A 511 PHE A 513 5 3 HELIX 11 11 GLN A 514 LYS A 535 1 22 HELIX 12 12 VAL A 537 SER A 556 1 20 HELIX 13 13 SER A 570 TYR A 575 5 6 HELIX 14 14 THR A 576 ASP A 611 1 36 HELIX 15 15 THR A 616 LYS A 632 1 17 HELIX 16 16 ASN A 640 TYR A 642 5 3 HELIX 17 17 LEU A 643 GLN A 648 1 6 HELIX 18 18 THR A 747 ASP A 758 1 12 HELIX 19 19 ASP A 760 GLU A 789 1 30 HELIX 20 20 ASN A 800 GLU A 812 1 13 HELIX 21 21 ASP A 817 VAL A 825 1 9 HELIX 22 22 GLN A 829 ILE A 834 1 6 HELIX 23 23 ASN A 835 VAL A 837 5 3 HELIX 24 24 ASP A 841 LEU A 871 1 31 HELIX 25 25 LEU A 871 ASP A 876 1 6 HELIX 26 26 ASP A 888 ALA A 908 1 21 HELIX 27 27 ASN A 912 SER A 921 1 10 HELIX 28 28 TYR A 925 SER A 936 1 12 HELIX 29 29 ALA A 937 PHE A 939 5 3 HELIX 30 30 LYS A 941 LYS A 954 1 14 HELIX 31 31 ASP A 956 ARG A 969 1 14 HELIX 32 32 ASP A 974 VAL A 986 1 13 HELIX 33 33 ASN A 992 ASN A 1005 1 14 HELIX 34 34 ASN A 1006 HIS A 1011 1 6 HELIX 35 35 GLY A 1015 LYS A 1030 1 16 HELIX 36 36 ASN A 1032 CYS A 1040 1 9 HELIX 37 37 GLU A 1041 LEU A 1049 5 9 HELIX 38 38 ASP A 1050 GLN A 1066 1 17 HELIX 39 39 SER A 1071 THR A 1082 1 12 SHEET 1 A 2 HIS A 199 TYR A 200 0 SHEET 2 A 2 SER A 567 TYR A 568 -1 O TYR A 568 N HIS A 199 SHEET 1 B 8 LYS A 261 LYS A 262 0 SHEET 2 B 8 LYS A 252 ILE A 258 -1 N ILE A 258 O LYS A 261 SHEET 3 B 8 PHE A 288 ILE A 296 -1 O GLU A 293 N ASN A 254 SHEET 4 B 8 THR A 225 ILE A 235 -1 N LEU A 231 O PHE A 290 SHEET 5 B 8 PHE A 209 ILE A 220 -1 N ASN A 212 O ASP A 232 SHEET 6 B 8 ALA A 337 ASP A 346 1 O THR A 342 N ILE A 218 SHEET 7 B 8 ARG A 369 LYS A 380 -1 O ASP A 376 N TYR A 339 SHEET 8 B 8 ASP A 358 ILE A 365 -1 N PHE A 363 O GLY A 371 SHEET 1 C 3 LEU A 244 ASP A 247 0 SHEET 2 C 3 PHE A 275 ILE A 278 -1 O ILE A 278 N LEU A 244 SHEET 3 C 3 TYR A 269 TYR A 271 -1 N THR A 270 O THR A 277 SHEET 1 D 4 GLY A 306 SER A 310 0 SHEET 2 D 4 ILE A 313 GLN A 317 -1 O ILE A 313 N SER A 310 SHEET 3 D 4 VAL A 387 GLY A 390 -1 O ALA A 389 N ILE A 314 SHEET 4 D 4 VAL A 352 SER A 355 -1 N LEU A 354 O VAL A 388 SHEET 1 E 5 LEU A 392 ILE A 400 0 SHEET 2 E 5 LYS A 407 GLU A 415 -1 O VAL A 408 N TYR A 399 SHEET 3 E 5 ARG A 448 VAL A 454 1 O LEU A 451 N PHE A 413 SHEET 4 E 5 LEU A 467 ASN A 471 1 O PHE A 470 N VAL A 452 SHEET 5 E 5 ALA A 461 MET A 462 -1 N MET A 462 O ILE A 469 SHEET 1 F 2 THR A 508 LEU A 509 0 SHEET 2 F 2 THR A 614 ALA A 615 1 O ALA A 615 N THR A 508 SHEET 1 G 4 SER A 716 PHE A 721 0 SHEET 2 G 4 GLN A 666 TYR A 674 -1 N TYR A 667 O PHE A 721 SHEET 3 G 4 HIS A 653 ASP A 661 -1 N HIS A 653 O TYR A 674 SHEET 4 G 4 TYR A 741 GLU A 743 1 O TYR A 741 N VAL A 654 SHEET 1 H 3 THR A 708 LEU A 712 0 SHEET 2 H 3 ILE A 689 ILE A 696 -1 N ILE A 689 O LEU A 712 SHEET 3 H 3 ILE A 729 LEU A 732 -1 O SER A 731 N GLY A 694 LINK ZN ZN A 1 NE2 HIS A 496 1555 1555 2.03 LINK ZN ZN A 1 NE2 HIS A 500 1555 1555 2.10 LINK ZN ZN A 1 OE1 GLU A 519 1555 1555 1.96 LINK ZN ZN A 1 O2 D66 A1087 1555 1555 1.96 LINK MG MG A 2 O GLY A 250 1555 1555 2.08 LINK MG MG A 3 O HOH A1747 1555 1555 2.38 LINK MG MG A1086 O HOH A1188 1555 1555 2.45 CISPEP 1 GLU A 319 ALA A 320 0 -2.72 SITE 1 AC1 4 HIS A 496 HIS A 500 GLU A 519 D66 A1087 SITE 1 AC2 1 HOH A1188 SITE 1 AC3 1 GLY A 250 SITE 1 AC4 10 HOH A 22 VAL A 459 GLY A 460 ASN A 471 SITE 2 AC4 10 ASN A 473 SER A 474 ARG A 489 ASN A 994 SITE 3 AC4 10 ARG A 997 HOH A1221 SITE 1 AC5 1 HOH A1747 SITE 1 AC6 9 HOH A 120 ASP A 545 TYR A 765 CYS A 768 SITE 2 AC6 9 THR A 769 TYR A 772 TYR A 823 SER A 826 SITE 3 AC6 9 PRO A 828 SITE 1 AC7 1 HIS A 543 SITE 1 AC8 9 HOH A 51 LYS A 479 TYR A 880 VAL A 887 SITE 2 AC8 9 ASP A 888 GLN A 891 ARG A 895 TYR A 925 SITE 3 AC8 9 HOH A1101 SITE 1 AC9 7 HIS A 653 LYS A 676 TYR A 741 ASN A 835 SITE 2 AC9 7 PHE A 836 HOH A1153 HOH A1324 SITE 1 BC1 19 ZN A 1 GLN A 317 GLU A 319 VAL A 459 SITE 2 BC1 19 GLY A 460 ALA A 461 GLU A 463 ARG A 489 SITE 3 BC1 19 THR A 492 HIS A 496 GLU A 497 HIS A 500 SITE 4 BC1 19 LYS A 518 GLU A 519 TYR A 575 TYR A 580 SITE 5 BC1 19 HOH A1173 HOH A1220 HOH A1221 CRYST1 75.772 108.814 118.683 90.00 90.00 90.00 P 21 21 21 4 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 0.013198 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009190 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008426 0.00000