HEADER GLYCOPROTEIN 16-JAN-03 1OAM OBSLTE 24-JUL-03 1OAM 1OKE TITLE CRYSTAL STRUCTURE OF THE DENGUE 2 VIRUS ENVELOPE PROTEIN IN TITLE 2 COMPLEX WITH N-OCTYL-BETA-D-GLUCOSIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENVELOPE GLYCOPROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SOLUBLE ECTODOMAIN, RESIDUES 281-674; COMPND 5 SYNONYM: DENGUE VIRUS TYPE 2 MAJOR ENVELOPE PROTEIN E; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: DISULFIDE LINKS BETWEEN RESIDUES 3 AND 30, COMPND 8 60 AND 121, 74 AND 105, 92 AND 116, 185 AND 285, 302 AND COMPND 9 333 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DENGUE VIRUS TYPE 2; SOURCE 3 STRAIN: STRAIN PR159/S1; SOURCE 4 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 5 EXPRESSION_SYSTEM_CELL_LINE: SCHNEIDER 2; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PMTT KEYWDS DENGUE VIRUS, MEMBRANE FUSION, FLAVIVIRUS, FUSION PEPTIDE, KEYWDS 2 LOW-PH CONFORMATIONAL CHANGE, GLYCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.MODIS,S.C.HARRISON REVDAT 2 12-JUN-03 1OAM 1 JRNL REVDAT 1 16-MAY-03 1OAM 0 JRNL AUTH Y.MODIS,S.OGATA,D.CLEMENTS,S.HARRISON JRNL TITL A LIGAND-BINDING POCKET IN THE DENGUE VIRUS JRNL TITL 2 ENVELOPE GLYCOPROTEIN JRNL REF PROC.NATL.ACAD.SCI.USA V. 100 6986 2003 JRNL REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.A.REY,F.X.HEINZ,C.MANDL,C.KUNZ,S.C.HARRISON REMARK 1 TITL THE ENVELOPE GLYCOPROTEIN FROM TICK-BORNE REMARK 1 TITL 2 ENCEPHALITIS VIRUS AT 2 ARESOLUTION REMARK 1 REF NATURE V. 375 291 1995 REMARK 1 REFN ASTM NATUAS UK ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.00 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) (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 42218 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) : 0.263 REMARK 3 FREE R VALUE : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2130 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4887 REMARK 3 BIN R VALUE (WORKING SET) : 0.4160 REMARK 3 BIN FREE R VALUE : 0.4370 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 256 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6124 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 166 REMARK 3 SOLVENT ATOMS : 136 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 76.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.02000 REMARK 3 B22 (A**2) : 6.92000 REMARK 3 B33 (A**2) : -16.94000 REMARK 3 B12 (A**2) : 4.55000 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) : 0.44 REMARK 3 ESD FROM SIGMAA (A) : 0.57 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) : 0.53 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.63 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.70 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.09 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 4.370 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 6.500 ; 4.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 7.390 ; 5.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 9.400 ; 6.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 42.31 REMARK 3 REMARK 3 NCS MODEL : RESTRAINTS 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 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : BOG_O18.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 3 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 4 : BOG_O18.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OAM COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY EBI ON 17-JAN-2003. REMARK 100 THE EBI ID CODE IS EBI-11847. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-2002 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 BEAMLINE F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42998 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.28900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: SOLVE, CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,1/3+Z REMARK 290 3555 -X+Y,-X,2/3+Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,2/3-Z REMARK 290 6555 -X,-X+Y,1/3-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 96.20767 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 192.41533 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 192.41533 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 96.20767 REMARK 290 REMARK 290 REMARK: NULL REMARK 295 REMARK 295 NON-CRYSTALLOGRAPHIC SYMMETRY REMARK 295 THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW REMARK 295 DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG ATOMS REMARK 295 IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX REMARK 295 TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD REMARK 295 APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. REMARK 295 CHAIN IDENTIFIERS GIVEN AS "?" REFER TO CHAINS FOR WHICH REMARK 295 ATOMS ARE NOT FOUND IN THIS ENTRY. REMARK 295 REMARK 295 APPLIED TO TRANSFORMED TO REMARK 295 TRANSFORM CHAIN RESIDUES CHAIN RESIDUES RMSD REMARK 295 SSS REMARK 295 M 1 B 1 .. 394 A 1 .. 394 0.307 REMARK 295 REMARK 295 WHERE SSS -> COLUMNS 8-10 OF MTRIX RECORDS REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 APPLY THE FOLLOWING TO CHAINS: A, B, Y, Z 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 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 REMARK 500 O6 NAG B 1395 O HOH Y 84 2.17 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 MET A 96 SD MET A 96 CE -0.081 REMARK 500 MET A 118 SD MET A 118 CE 0.067 REMARK 500 PRO A 143 CB PRO A 143 CG 0.071 REMARK 500 PRO A 187 CB PRO A 187 CG -0.081 REMARK 500 GLU A 383 CB GLU A 383 CG -0.105 REMARK 500 GLU A 383 CG GLU A 383 CD -0.113 REMARK 500 MET B 96 SD MET B 96 CE -0.133 REMARK 500 PRO B 143 CB PRO B 143 CG 0.066 REMARK 500 PRO B 187 CB PRO B 187 CG -0.084 REMARK 500 MET B 201 SD MET B 201 CE -0.100 REMARK 500 PRO B 217 CB PRO B 217 CG 0.065 REMARK 500 MET B 340 SD MET B 340 CE -0.100 REMARK 500 GLU B 383 CG GLU B 383 CD -0.067 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLY A 104 N - CA - C ANGL. DEV. = 13.6 DEGREES REMARK 500 THR A 189 N - CA - C ANGL. DEV. = 15.8 DEGREES REMARK 500 GLY A 190 N - CA - C ANGL. DEV. =-21.5 DEGREES REMARK 500 ILE A 352 N - CA - C ANGL. DEV. =-10.8 DEGREES REMARK 500 ILE A 379 CG1 - CB - CG2 ANGL. DEV. =-10.6 DEGREES REMARK 500 GLU A 383 CA - CB - CG ANGL. DEV. =-18.6 DEGREES REMARK 500 GLU A 383 N - CA - C ANGL. DEV. = 14.0 DEGREES REMARK 500 GLY B 104 N - CA - C ANGL. DEV. = 12.3 DEGREES REMARK 500 ILE B 113 N - CA - C ANGL. DEV. =-11.1 DEGREES REMARK 500 THR B 189 N - CA - C ANGL. DEV. = 16.2 DEGREES REMARK 500 GLY B 190 N - CA - C ANGL. DEV. =-21.9 DEGREES REMARK 500 ILE B 352 N - CA - C ANGL. DEV. =-10.9 DEGREES REMARK 500 ILE B 378 CG1 - CB - CG2 ANGL. DEV. =-12.0 DEGREES REMARK 500 GLU B 383 CA - CB - CG ANGL. DEV. = 12.2 DEGREES REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: PROVIDED BY DEPOSITOR REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 700 DETERMINATION METHOD: PROVIDED BY DEPOSITOR REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 SITE_DESCRIPTION: NAG BINDING SITE FOR CHAIN A REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 SITE_DESCRIPTION: NAG BINDING SITE FOR CHAIN B REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 SITE_DESCRIPTION: AFL BINDING SITE FOR CHAIN B REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 SITE_DESCRIPTION: NAG BINDING SITE FOR CHAIN A REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 SITE_DESCRIPTION: AFL BINDING SITE FOR CHAIN A REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 SITE_DESCRIPTION: BGL BINDING SITE FOR CHAIN B REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 SITE_DESCRIPTION: BGL BINDING SITE FOR CHAIN A REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OAN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DENGUE 2 VIRUS REMARK 900 ENVELOPE PROTEIN IN COMPLEX WITH N-OCTYL- REMARK 900 BETA-D-GLUCOSIDE REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 100-108 FORM THE GLYCINE-RICH, HYDROPHOBIC FUSION REMARK 999 PEPTIDE (ALLISON ET AL., J.VIROL. 75, 4268-75 (2001)) REMARK 999 REMARK 999 RESIDUES 270-279 FORM THE KL-HAIRPIN, WHICH MEDIATES THE REMARK 999 FUSION-ACTIVATING CONFORMATIONAL CHANGE. THE KL HAIRPIN IS REMARK 999 IN THE OPEN CONFORMATION. DBREF 1OAM A 1 394 UNP P12823 POLG_DEN2P 281 674 DBREF 1OAM B 1 394 UNP P12823 POLG_DEN2P 281 674 SEQADV 1OAM GLU A 71 UNP P12823 ASP 351 CONFLICT SEQADV 1OAM ASN A 390 UNP P12823 ASP 670 CONFLICT SEQADV 1OAM GLU B 71 UNP P12823 ASP 351 CONFLICT SEQADV 1OAM ASN B 390 UNP P12823 ASP 670 CONFLICT SEQRES 1 A 394 MET ARG CYS ILE GLY ILE SER ASN ARG ASP PHE VAL GLU SEQRES 2 A 394 GLY VAL SER GLY GLY SER TRP VAL ASP ILE VAL LEU GLU SEQRES 3 A 394 HIS GLY SER CYS VAL THR THR MET ALA LYS ASN LYS PRO SEQRES 4 A 394 THR LEU ASP PHE GLU LEU ILE LYS THR GLU ALA LYS GLN SEQRES 5 A 394 PRO ALA THR LEU ARG LYS TYR CYS ILE GLU ALA LYS LEU SEQRES 6 A 394 THR ASN THR THR THR GLU SER ARG CYS PRO THR GLN GLY SEQRES 7 A 394 GLU PRO THR LEU ASN GLU GLU GLN ASP LYS ARG PHE VAL SEQRES 8 A 394 CYS LYS HIS SER MET VAL ASP ARG GLY TRP GLY ASN GLY SEQRES 9 A 394 CYS GLY LEU PHE GLY LYS GLY GLY ILE VAL THR CYS ALA SEQRES 10 A 394 MET PHE THR CYS LYS LYS ASN MET GLU GLY LYS ILE VAL SEQRES 11 A 394 GLN PRO GLU ASN LEU GLU TYR THR VAL VAL ILE THR PRO SEQRES 12 A 394 HIS SER GLY GLU GLU HIS ALA VAL GLY ASN ASP THR GLY SEQRES 13 A 394 LYS HIS GLY LYS GLU VAL LYS ILE THR PRO GLN SER SER SEQRES 14 A 394 ILE THR GLU ALA GLU LEU THR GLY TYR GLY THR VAL THR SEQRES 15 A 394 MET GLU CYS SER PRO ARG THR GLY LEU ASP PHE ASN GLU SEQRES 16 A 394 MET VAL LEU LEU GLN MET LYS ASP LYS ALA TRP LEU VAL SEQRES 17 A 394 HIS ARG GLN TRP PHE LEU ASP LEU PRO LEU PRO TRP LEU SEQRES 18 A 394 PRO GLY ALA ASP THR GLN GLY SER ASN TRP ILE GLN LYS SEQRES 19 A 394 GLU THR LEU VAL THR PHE LYS ASN PRO HIS ALA LYS LYS SEQRES 20 A 394 GLN ASP VAL VAL VAL LEU GLY SER GLN GLU GLY ALA MET SEQRES 21 A 394 HIS THR ALA LEU THR GLY ALA THR GLU ILE GLN MET SER SEQRES 22 A 394 SER GLY ASN LEU LEU PHE THR GLY HIS LEU LYS CYS ARG SEQRES 23 A 394 LEU ARG MET ASP LYS LEU GLN LEU LYS GLY MET SER TYR SEQRES 24 A 394 SER MET CYS THR GLY LYS PHE LYS VAL VAL LYS GLU ILE SEQRES 25 A 394 ALA GLU THR GLN HIS GLY THR ILE VAL ILE ARG VAL GLN SEQRES 26 A 394 TYR GLU GLY ASP GLY SER PRO CYS LYS ILE PRO PHE GLU SEQRES 27 A 394 ILE MET ASP LEU GLU LYS ARG HIS VAL LEU GLY ARG LEU SEQRES 28 A 394 ILE THR VAL ASN PRO ILE VAL THR GLU LYS ASP SER PRO SEQRES 29 A 394 VAL ASN ILE GLU ALA GLU PRO PRO PHE GLY ASP SER TYR SEQRES 30 A 394 ILE ILE ILE GLY VAL GLU PRO GLY GLN LEU LYS LEU ASN SEQRES 31 A 394 TRP PHE LYS LYS SEQRES 1 B 394 MET ARG CYS ILE GLY ILE SER ASN ARG ASP PHE VAL GLU SEQRES 2 B 394 GLY VAL SER GLY GLY SER TRP VAL ASP ILE VAL LEU GLU SEQRES 3 B 394 HIS GLY SER CYS VAL THR THR MET ALA LYS ASN LYS PRO SEQRES 4 B 394 THR LEU ASP PHE GLU LEU ILE LYS THR GLU ALA LYS GLN SEQRES 5 B 394 PRO ALA THR LEU ARG LYS TYR CYS ILE GLU ALA LYS LEU SEQRES 6 B 394 THR ASN THR THR THR GLU SER ARG CYS PRO THR GLN GLY SEQRES 7 B 394 GLU PRO THR LEU ASN GLU GLU GLN ASP LYS ARG PHE VAL SEQRES 8 B 394 CYS LYS HIS SER MET VAL ASP ARG GLY TRP GLY ASN GLY SEQRES 9 B 394 CYS GLY LEU PHE GLY LYS GLY GLY ILE VAL THR CYS ALA SEQRES 10 B 394 MET PHE THR CYS LYS LYS ASN MET GLU GLY LYS ILE VAL SEQRES 11 B 394 GLN PRO GLU ASN LEU GLU TYR THR VAL VAL ILE THR PRO SEQRES 12 B 394 HIS SER GLY GLU GLU HIS ALA VAL GLY ASN ASP THR GLY SEQRES 13 B 394 LYS HIS GLY LYS GLU VAL LYS ILE THR PRO GLN SER SER SEQRES 14 B 394 ILE THR GLU ALA GLU LEU THR GLY TYR GLY THR VAL THR SEQRES 15 B 394 MET GLU CYS SER PRO ARG THR GLY LEU ASP PHE ASN GLU SEQRES 16 B 394 MET VAL LEU LEU GLN MET LYS ASP LYS ALA TRP LEU VAL SEQRES 17 B 394 HIS ARG GLN TRP PHE LEU ASP LEU PRO LEU PRO TRP LEU SEQRES 18 B 394 PRO GLY ALA ASP THR GLN GLY SER ASN TRP ILE GLN LYS SEQRES 19 B 394 GLU THR LEU VAL THR PHE LYS ASN PRO HIS ALA LYS LYS SEQRES 20 B 394 GLN ASP VAL VAL VAL LEU GLY SER GLN GLU GLY ALA MET SEQRES 21 B 394 HIS THR ALA LEU THR GLY ALA THR GLU ILE GLN MET SER SEQRES 22 B 394 SER GLY ASN LEU LEU PHE THR GLY HIS LEU LYS CYS ARG SEQRES 23 B 394 LEU ARG MET ASP LYS LEU GLN LEU LYS GLY MET SER TYR SEQRES 24 B 394 SER MET CYS THR GLY LYS PHE LYS VAL VAL LYS GLU ILE SEQRES 25 B 394 ALA GLU THR GLN HIS GLY THR ILE VAL ILE ARG VAL GLN SEQRES 26 B 394 TYR GLU GLY ASP GLY SER PRO CYS LYS ILE PRO PHE GLU SEQRES 27 B 394 ILE MET ASP LEU GLU LYS ARG HIS VAL LEU GLY ARG LEU SEQRES 28 B 394 ILE THR VAL ASN PRO ILE VAL THR GLU LYS ASP SER PRO SEQRES 29 B 394 VAL ASN ILE GLU ALA GLU PRO PRO PHE GLY ASP SER TYR SEQRES 30 B 394 ILE ILE ILE GLY VAL GLU PRO GLY GLN LEU LYS LEU ASN SEQRES 31 B 394 TRP PHE LYS LYS MODRES 1OAM ASN A 67 ASN GLYCOSYLATION SITE MODRES 1OAM ASN A 153 ASN GLYCOSYLATION SITE MODRES 1OAM ASN B 67 ASN GLYCOSYLATION SITE MODRES 1OAM ASN B 153 ASN GLYCOSYLATION SITE HET NAG A1395 14 HET NAG A1396 14 HET NAG A1397 14 HET AFL A1398 10 HET BMA A1399 11 HET BGL A1400 20 HET NAG B1395 14 HET NAG B1396 14 HET NAG B1397 14 HET AFL B1398 10 HET BMA B1399 11 HET BGL B1400 20 HETNAM NAG N-ACETYL-D-GLUCOSAMINE HETNAM AFL ALPHA-L-FUCOSE HETNAM BMA BETA-D-MANNOSE HETNAM BGL B-2-OCTYLGLUCOSIDE HETSYN NAG NAG FORMUL 3 NAG 6(C8 H15 N O6) FORMUL 4 AFL 2(C6 H12 O5) FORMUL 4 BMA 2(C6 H12 O6) FORMUL 5 BGL 2(C14 H28 O6) FORMUL 9 HOH *136(H2 O1) HELIX 1 1 ARG A 210 LEU A 216 1 7 HELIX 2 2 GLN A 256 THR A 265 1 10 HELIX 3 3 ARG B 210 LEU B 216 1 7 HELIX 4 4 GLN B 256 THR B 265 1 10 SHEET 1 AA 5 ASN A 8 GLU A 13 0 SHEET 2 AA 5 CYS A 30 ALA A 35 1 O CYS A 30 N ASP A 10 SHEET 3 AA 5 LYS A 38 LYS A 51 -1 O LYS A 38 N ALA A 35 SHEET 4 AA 5 LEU A 135 PRO A 143 -1 O GLU A 136 N GLU A 49 SHEET 5 AA 5 LYS A 160 THR A 165 -1 O LYS A 160 N ILE A 141 SHEET 1 AB 4 TRP A 20 LEU A 25 0 SHEET 2 AB 4 LEU A 283 ARG A 288 -1 O LEU A 283 N LEU A 25 SHEET 3 AB 4 THR A 180 SER A 186 -1 O THR A 182 N ARG A 288 SHEET 4 AB 4 ILE A 170 GLU A 174 -1 O THR A 171 N MET A 183 SHEET 1 AC 4 PHE A 90 ARG A 99 0 SHEET 2 AC 4 GLY A 109 ILE A 129 -1 O GLY A 109 N ARG A 99 SHEET 3 AC 4 ALA A 54 SER A 72 -1 O ALA A 54 N ILE A 129 SHEET 4 AC 4 PRO A 219 PRO A 222 -1 O LEU A 221 N LYS A 58 SHEET 1 AD 5 PHE A 90 ARG A 99 0 SHEET 2 AD 5 GLY A 109 ILE A 129 -1 O GLY A 109 N ARG A 99 SHEET 3 AD 5 MET A 196 MET A 201 -1 O LEU A 198 N LYS A 128 SHEET 4 AD 5 LYS A 204 HIS A 209 -1 O LYS A 204 N MET A 201 SHEET 5 AD 5 THR A 268 GLN A 271 -1 O THR A 268 N LEU A 207 SHEET 1 AE 2 LEU A 237 ASN A 242 0 SHEET 2 AE 2 GLN A 248 LEU A 253 -1 O ASP A 249 N LYS A 241 SHEET 1 AF 7 GLY A 304 GLU A 314 0 SHEET 2 AF 7 THR A 319 TYR A 326 -1 O VAL A 321 N ALA A 313 SHEET 3 AF 7 VAL A 365 GLU A 370 -1 O VAL A 365 N VAL A 324 SHEET 4 AF 7 GLY A 349 ILE A 352 -1 O ARG A 350 N GLU A 370 SHEET 5 AF 7 PRO A 336 MET A 340 -1 O ILE A 339 N LEU A 348 SHEET 6 AF 7 GLY A 374 ILE A 380 -1 O TYR A 377 N MET A 340 SHEET 7 AF 7 LEU A 387 LYS A 393 -1 O LEU A 387 N ILE A 380 SHEET 1 BA 5 ASN B 8 GLU B 13 0 SHEET 2 BA 5 CYS B 30 ALA B 35 1 O CYS B 30 N ASP B 10 SHEET 3 BA 5 LYS B 38 ALA B 50 -1 O LYS B 38 N ALA B 35 SHEET 4 BA 5 LEU B 135 PRO B 143 -1 O GLU B 136 N GLU B 49 SHEET 5 BA 5 LYS B 160 THR B 165 -1 O LYS B 160 N ILE B 141 SHEET 1 BB 4 TRP B 20 LEU B 25 0 SHEET 2 BB 4 LEU B 283 ARG B 288 -1 O LEU B 283 N LEU B 25 SHEET 3 BB 4 THR B 180 SER B 186 -1 O THR B 182 N ARG B 288 SHEET 4 BB 4 ILE B 170 LEU B 175 -1 O THR B 171 N MET B 183 SHEET 1 BC 4 PHE B 90 ARG B 99 0 SHEET 2 BC 4 GLY B 109 ILE B 129 -1 O GLY B 109 N ARG B 99 SHEET 3 BC 4 ALA B 54 SER B 72 -1 O ALA B 54 N ILE B 129 SHEET 4 BC 4 PRO B 219 PRO B 222 -1 O LEU B 221 N LYS B 58 SHEET 1 BD 5 PHE B 90 ARG B 99 0 SHEET 2 BD 5 GLY B 109 ILE B 129 -1 O GLY B 109 N ARG B 99 SHEET 3 BD 5 MET B 196 MET B 201 -1 O LEU B 198 N LYS B 128 SHEET 4 BD 5 LYS B 204 HIS B 209 -1 O LYS B 204 N MET B 201 SHEET 5 BD 5 THR B 268 GLN B 271 -1 O THR B 268 N LEU B 207 SHEET 1 BE 2 LEU B 237 ASN B 242 0 SHEET 2 BE 2 GLN B 248 LEU B 253 -1 O ASP B 249 N LYS B 241 SHEET 1 BF 7 GLY B 304 GLU B 314 0 SHEET 2 BF 7 THR B 319 TYR B 326 -1 O VAL B 321 N ALA B 313 SHEET 3 BF 7 VAL B 365 GLU B 370 -1 O VAL B 365 N VAL B 324 SHEET 4 BF 7 GLY B 349 ILE B 352 -1 O ARG B 350 N GLU B 370 SHEET 5 BF 7 PHE B 337 MET B 340 -1 O ILE B 339 N LEU B 348 SHEET 6 BF 7 GLY B 374 ILE B 380 -1 O TYR B 377 N MET B 340 SHEET 7 BF 7 LEU B 387 LYS B 393 -1 O LEU B 387 N ILE B 380 SSBOND 1 CYS A 3 CYS A 30 SSBOND 2 CYS A 60 CYS A 121 SSBOND 3 CYS A 74 CYS A 105 SSBOND 4 CYS A 92 CYS A 116 SSBOND 5 CYS A 185 CYS A 285 SSBOND 6 CYS A 302 CYS A 333 SSBOND 7 CYS B 3 CYS B 30 SSBOND 8 CYS B 60 CYS B 121 SSBOND 9 CYS B 74 CYS B 105 SSBOND 10 CYS B 92 CYS B 116 SSBOND 11 CYS B 185 CYS B 285 SSBOND 12 CYS B 302 CYS B 333 LINK ND2 ASN A 67 C1 NAG A1395 LINK ND2 ASN A 153 C1 NAG A1396 LINK O4 NAG A1396 C1 NAG A1397 LINK O6 NAG A1396 C1 AFL A1398 LINK O4 NAG A1397 C1 BMA A1399 LINK ND2 ASN B 67 C1 NAG B1395 LINK ND2 ASN B 153 C1 NAG B1396 LINK O4 NAG B1396 C1 NAG B1397 LINK O6 NAG B1396 C1 AFL B1398 LINK O4 NAG B1397 C1 BMA B1399 SITE 1 AC1 4 ASN B 67 HOH Y 84 HOH Y 85 HOH Y 86 SITE 1 AC2 2 ASN A 67 HOH Z 49 SITE 1 AC3 3 HIS B 149 ASN B 153 HIS B 158 SITE 1 AC5 3 GLU B 147 HIS B 149 LYS B 157 SITE 1 AC7 3 HIS A 149 ASN A 153 HIS A 158 SITE 1 AC9 3 GLU A 147 HIS A 149 LYS A 157 SITE 1 BC2 6 THR B 48 ALA B 50 GLN B 200 ILE B 270 SITE 2 BC2 6 GLN B 271 THR B 280 SITE 1 BC3 4 ALA A 50 GLN A 200 ILE A 270 GLN A 271 CRYST1 81.541 81.541 288.623 90.00 90.00 120.00 P 31 2 1 12 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 0.012264 0.007080 0.000000 0.00000 SCALE2 0.000000 0.014161 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003465 0.00000 MTRIX1 1 0.977000 -0.210000 -0.045000 15.37975 1 MTRIX2 1 -0.211000 -0.978000 -0.005000 134.15849 1 MTRIX3 1 -0.043000 0.015000 -0.999000 47.23037 1