HEADER ASPARTIC PROTEASE 13-JUL-98 2FMB TITLE EIAV PROTEASE COMPLEXED WITH AN INHIBITOR LP-130 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EQUINE INFECTIOUS ANEMIA VIRUS PROTEASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EIAV PR, RETROPEPSIN; COMPND 5 EC: 3.4.23.16; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EQUINE INFECTIOUS ANEMIA VIRUS; SOURCE 3 ORGANISM_TAXID: 11665; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: PV KEYWDS ASPARTIC PROTEASE, RETROPEPSIN, RETROVIRUS, EIAV, HORSE EXPDTA X-RAY DIFFRACTION AUTHOR J.KERVINEN,J.LUBKOWSKI,A.ZDANOV,A.WLODAWER,A.GUSTCHINA REVDAT 6 09-AUG-23 2FMB 1 REMARK REVDAT 5 03-NOV-21 2FMB 1 REMARK SEQADV REVDAT 4 29-NOV-17 2FMB 1 HELIX REVDAT 3 13-JUL-11 2FMB 1 VERSN REVDAT 2 24-FEB-09 2FMB 1 VERSN REVDAT 1 13-JAN-99 2FMB 0 JRNL AUTH J.KERVINEN,J.LUBKOWSKI,A.ZDANOV,D.BHATT,B.M.DUNN,K.Y.HUI, JRNL AUTH 2 D.J.POWELL,J.KAY,A.WLODAWER,A.GUSTCHINA JRNL TITL TOWARD A UNIVERSAL INHIBITOR OF RETROVIRAL PROTEASES: JRNL TITL 2 COMPARATIVE ANALYSIS OF THE INTERACTIONS OF LP-130 COMPLEXED JRNL TITL 3 WITH PROTEASES FROM HIV-1, FIV, AND EIAV. JRNL REF PROTEIN SCI. V. 7 2314 1998 JRNL REFN ISSN 0961-8368 JRNL PMID 9827997 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROFFT REMARK 3 AUTHORS : KONNERT,HENDRICKSON,FINZEL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 8460 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 791 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.013 ; 0.017 REMARK 3 ANGLE DISTANCE (A) : 0.045 ; 0.044 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.044 ; 0.059 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.018 ; 0.022 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.177 ; 0.180 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.207 ; 0.500 REMARK 3 MULTIPLE TORSION (A) : 0.450 ; 0.500 REMARK 3 H-BOND (X...Y) (A) : 0.382 ; 0.500 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 3.400 ; 3.500 REMARK 3 STAGGERED (DEGREES) : 19.100; 14.000 REMARK 3 TRANSVERSE (DEGREES) : 32.400; 12.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.916 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.567 ; 3.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.720 ; 4.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.328 ; 7.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FMB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000178097. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-SEP-96 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 4.6 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 : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MACSCIENCE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8666 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04900 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) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: RIGID BODY REFINEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1FMB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 21.32500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.68000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 21.32500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.68000 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 300 REMARK: THIS FILE CONTAINS ONLY A MONOMER, WHILE THE ACTIVE ENZYME REMARK 300 IS A DIMER. IN ORDER TO CREATE A DIMERIC MOLECULE, REMARK 300 CRYSTALLOGRAPHIC COORDINATES NEED TO BE TRANSFORMED TO REMARK 300 (-X), Y, (-Z). THE TWO ORIENTATIONS OF THE INHIBITOR REMARK 300 CREATED IN THAT MANNER OVERLAP, WITH COMPLETE SUPERPOSITION REMARK 300 AT THE PERIPHERY AND SOME DEVIATION IN THE CENTER. REMARK 300 REMARK 300 RESIDUES 56 - 58 HAVE BEEN MODELED WITH TWO ORIENTATIONS REMARK 300 OF THEIR MAIN CHAINS, SINCE THEY FORM ALTERNATE HYDROGEN REMARK 300 BONDS, DUE TO THE SAME DISORDER PHENOMENON. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 6500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 301 LIES ON A SPECIAL POSITION. 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 ARG A 46 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 70 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 VAL A 56 O HOH A 351 2.03 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 TYR A 3 CB - CG - CD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 TYR A 3 CG - CD2 - CE2 ANGL. DEV. = -4.9 DEGREES REMARK 500 GLU A 6 OE1 - CD - OE2 ANGL. DEV. = 7.4 DEGREES REMARK 500 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 8 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ASP A 29 CB - CG - OD1 ANGL. DEV. = 7.3 DEGREES REMARK 500 LEU A 33 CA - CB - CG ANGL. DEV. = 16.7 DEGREES REMARK 500 ASN A 59 O - C - N ANGL. DEV. = 10.5 DEGREES REMARK 500 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ASP A 93 OD1 - CG - OD2 ANGL. DEV. = -12.8 DEGREES REMARK 500 ASP A 93 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 93 CB - CG - OD2 ANGL. DEV. = 6.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 KI VALUE OF LP-130 FOR EIAV PR IS 2 NM REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LP1 A 201 DBREF 2FMB A 1 104 UNP P32542 POL_EIAVC 28 131 SEQADV 2FMB GLY A 54 UNP P32542 ILE 81 ENGINEERED MUTATION SEQRES 1 A 104 VAL THR TYR ASN LEU GLU LYS ARG PRO THR THR ILE VAL SEQRES 2 A 104 LEU ILE ASN ASP THR PRO LEU ASN VAL LEU LEU ASP THR SEQRES 3 A 104 GLY ALA ASP THR SER VAL LEU THR THR ALA HIS TYR ASN SEQRES 4 A 104 ARG LEU LYS TYR ARG GLY ARG LYS TYR GLN GLY THR GLY SEQRES 5 A 104 ILE GLY GLY VAL GLY GLY ASN VAL GLU THR PHE SER THR SEQRES 6 A 104 PRO VAL THR ILE LYS LYS LYS GLY ARG HIS ILE LYS THR SEQRES 7 A 104 ARG MET LEU VAL ALA ASP ILE PRO VAL THR ILE LEU GLY SEQRES 8 A 104 ARG ASP ILE LEU GLN ASP LEU GLY ALA LYS LEU VAL LEU HET LP1 A 201 73 HETNAM LP1 4-[2-(2-ACETYLAMINO-3-NAPHTALEN-1-YL-PROPIONYLAMINO)-4- HETNAM 2 LP1 METHYL-PENTANOYLAMINO]-3-HYDROXY-6-METHYL-HEPTANOIC HETNAM 3 LP1 ACID [1-(1-CARBAMOYL-2-NAPHTHALEN-1-YL- HETNAM 4 LP1 ETHYLCARBAMOYL)-PROPYL]-AMIDE FORMUL 2 LP1 C45 H58 N6 O7 FORMUL 3 HOH *100(H2 O) HELIX 1 1 THR A 35 ARG A 40 1 6 HELIX 2 2 ARG A 92 LEU A 98 1 7 SHEET 1 A 2 THR A 10 ILE A 15 0 SHEET 2 A 2 THR A 18 LEU A 23 -1 N VAL A 22 O THR A 11 SHEET 1 B 4 VAL A 32 THR A 34 0 SHEET 2 B 4 ARG A 74 ALA A 83 1 N LEU A 81 O LEU A 33 SHEET 3 B 4 PHE A 63 LYS A 71 -1 N LYS A 71 O ARG A 74 SHEET 4 B 4 LYS A 47 GLN A 49 -1 N TYR A 48 O SER A 64 SHEET 1 C 2 ILE A 53 GLY A 55 0 SHEET 2 C 2 GLY A 58 VAL A 60 -1 N VAL A 60 O ILE A 53 SITE 1 AC1 16 VAL A 1 THR A 2 ARG A 8 LEU A 23 SITE 2 AC1 16 ASP A 25 GLY A 27 ALA A 28 ASP A 29 SITE 3 AC1 16 ILE A 53 GLY A 54 GLY A 55 PRO A 86 SITE 4 AC1 16 ILE A 89 HOH A 301 HOH A 321 HOH A 322 CRYST1 42.650 45.360 56.760 90.00 110.36 90.00 C 1 2 1 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 0.023447 0.000000 0.008701 0.00000 SCALE2 0.000000 0.022046 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018792 0.00000