10 20 30 40 50 60 70 80 1OKE - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER VIRAL PROTEIN 22-JUL-03 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: MAJOR ENVELOPE PROTEIN E; 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
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DENGUE VIRUS TYPE 2; SOURCE 3 ORGANISM_TAXID: 11060; SOURCE 4 STRAIN: PR159/S1; SOURCE 5 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 7227; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: SCHNEIDER 2; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PMTT
KEYWDS VIRAL PROTEIN, MEMBRANE FUSION, FLAVIVIRUS, FUSION PEPTIDE, VIRAL KEYWDS 2 PROTEIN, LOW-PH CONFORMATIONAL CHANGE, CLASS 2 FUSION PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.MODIS,S.C.HARRISON
REVDAT 3 18-JAN-12 1OKE 1 HEADER KEYWDS JRNL REMARK REVDAT 3 2 HET HETNAM HETSYN FORMUL REVDAT 3 3 LINK SITE HETATM MASTER REVDAT 2 24-FEB-09 1OKE 1 VERSN REVDAT 1 24-JUL-03 1OKE 0
SPRSDE 24-JUL-03 1OKE 1OAM
JRNL AUTH Y.MODIS,S.OGATA,D.CLEMENTS,S.C.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 ISSN 0027-8424 JRNL PMID 12759475 JRNL DOI 10.1073/PNAS.0832193100
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 ENCEPHALITIS REMARK 1 TITL 2 VIRUS AT 2 A RESOLUTION. REMARK 1 REF NATURE V. 375 291 1995 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 7753193 REMARK 1 DOI 10.1038/375291A0
REMARK 2 REMARK 2 RESOLUTION. 2.4 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.4 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.0 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 3441686.19 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) : .263 REMARK 3 FREE R VALUE : .294 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 2130 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : .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) (%) : 70.5 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4887 REMARK 3 BIN R VALUE (WORKING SET) : .416 REMARK 3 BIN FREE R VALUE : .437 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 256 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : .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) : 40.2 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 76.5 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.02 REMARK 3 B22 (A**2) : 6.92 REMARK 3 B33 (A**2) : -16.94 REMARK 3 B12 (A**2) : 4.55 REMARK 3 B13 (A**2) : 0.0 REMARK 3 B23 (A**2) : 0.0 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : .44 REMARK 3 ESD FROM SIGMAA (A) : .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) : .53 REMARK 3 ESD FROM C-V SIGMAA (A) : .63 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : .012 REMARK 3 BOND ANGLES (DEGREES) : 1.7 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.4 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) : 4.37 ; 3.00 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 6.50 ; 4.00 REMARK 3 SIDE-CHAIN BOND (A**2) : 7.39 ; 5.00 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 9.40 ; 6.00 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : .303875 REMARK 3 BSOL : 42.312 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : 0.1188; 200 REMARK 3 GROUP 1 B-FACTOR (A**2) : 14.292; 999 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: NCS GROUP1, RESIDUES 52-131 AND AND REMARK 3 193-279; NCS GROUP 2, RESIDUES 1-51, 132-192, 280-295; NCS REMARK 3 GROUP 3, RESIDUES 296-394
REMARK 4 REMARK 4 1OKE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JUL-03. REMARK 100 THE PDBE ID CODE IS EBI-13151.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-02 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; Y REMARK 200 RADIATION SOURCE : CHESS; CHESS REMARK 200 BEAMLINE : F-1; A-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91; 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.395 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 11% PEG 8K, 1M NACL, 0.1M TRIS/HCL REMARK 280 PH 9.0, 20% GLYCEROL,0.5% OCTYLGLUCOSIDE
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,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 95.80267 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 191.60533 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 191.60533 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 95.80267 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 29.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 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 O6 NAG B 1395 O HOH B 2084 2.17 REMARK 500 REMARK 500 REMARK: NULL 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),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 383 CG GLU A 383 CD -0.116 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 CYS A 121 CA - CB - SG ANGL. DEV. = -6.7 DEGREES REMARK 500 PRO A 166 C - N - CA ANGL. DEV. = 13.0 DEGREES REMARK 500 GLY A 190 N - CA - C ANGL. DEV. = -22.5 DEGREES REMARK 500 PRO A 243 C - N - CA ANGL. DEV. = 9.1 DEGREES REMARK 500 GLU A 383 CA - CB - CG ANGL. DEV. = -17.7 DEGREES REMARK 500 PRO B 166 C - N - CA ANGL. DEV. = 12.7 DEGREES REMARK 500 GLY B 190 N - CA - C ANGL. DEV. = -22.8 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 GLN A 52 84.72 34.77 REMARK 500 LYS A 88 -2.60 -55.89 REMARK 500 ASN A 134 72.44 -111.00 REMARK 500 LYS A 157 40.91 -94.91 REMARK 500 HIS A 158 -22.81 -141.10 REMARK 500 PRO A 166 -60.18 -17.55 REMARK 500 GLN A 167 60.77 -112.38 REMARK 500 SER A 168 37.99 -143.60 REMARK 500 SER A 169 -162.39 65.61 REMARK 500 THR A 176 118.15 -34.63 REMARK 500 ARG A 188 102.82 -24.61 REMARK 500 THR A 189 171.90 69.55 REMARK 500 LYS A 202 -134.63 61.99 REMARK 500 SER A 229 -16.65 -141.03 REMARK 500 ASN A 230 58.87 -96.09 REMARK 500 SER A 255 133.48 -38.98 REMARK 500 THR A 280 -4.00 -160.90 REMARK 500 MET A 297 12.29 -68.74 REMARK 500 SER A 331 -156.07 50.29 REMARK 500 PRO A 332 99.57 -41.50 REMARK 500 THR A 359 -34.17 -130.03 REMARK 500 LYS A 361 -50.44 -28.57 REMARK 500 GLU A 383 -71.14 -0.43 REMARK 500 PRO A 384 89.31 -59.31 REMARK 500 GLN B 52 84.44 34.37 REMARK 500 LYS B 88 -2.66 -56.49 REMARK 500 SER B 95 -177.58 -173.60 REMARK 500 ASN B 134 73.07 -110.92 REMARK 500 LYS B 157 41.13 -94.38 REMARK 500 HIS B 158 -23.49 -141.16 REMARK 500 PRO B 166 -60.40 -16.78 REMARK 500 GLN B 167 60.76 -112.22 REMARK 500 SER B 168 38.35 -143.94 REMARK 500 SER B 169 -162.59 65.03 REMARK 500 THR B 176 118.83 -36.30 REMARK 500 ARG B 188 100.82 -24.48 REMARK 500 THR B 189 172.01 71.02 REMARK 500 PHE B 193 8.01 -67.15 REMARK 500 LYS B 202 -133.67 63.31 REMARK 500 SER B 229 -14.91 -140.26 REMARK 500 ASN B 230 54.68 -96.38 REMARK 500 THR B 280 -2.20 -163.19 REMARK 500 MET B 297 14.27 -69.01 REMARK 500 SER B 331 -155.78 50.52 REMARK 500 PRO B 332 99.13 -41.81 REMARK 500 LYS B 361 -51.92 -27.43 REMARK 500 GLU B 383 -71.98 7.19 REMARK 500 PRO B 384 89.70 -61.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 THR A 189 21.5 L L OUTSIDE RANGE REMARK 500 GLU A 383 22.9 L L OUTSIDE RANGE REMARK 500 THR B 189 21.5 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL
REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED.
REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED.
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BOG A1400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BOG B1400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR MONO-SACCHARIDE REMARK 800 NAG A1395 BOUND TO ASN A 67 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN A OF SUGAR BOUND TO REMARK 800 ASN A 153 RESIDUES 1396 TO 1399 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR MONO-SACCHARIDE REMARK 800 NAG B1395 BOUND TO ASN B 67 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN B OF SUGAR BOUND TO REMARK 800 ASN B 153 RESIDUES 1396 TO 1399
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1L9K RELATED DB: PDB REMARK 900 DENGUE METHYLTRANSFERASE REMARK 900 RELATED ID: 1OAM 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 900 RELATED ID: 1OAN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DENGUE 2 VIRUS REMARK 900 ENVELOPE PROTEIN REMARK 900 RELATED ID: 1OK8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DENGUE 2 VIRUS REMARK 900 ENVELOPE GLYCOPROTEIN IN THE POSTFUSION REMARK 900 CONFORMATION
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 1OKE A 1 394 UNP P12823 POLG_DEN2P 281 674 DBREF 1OKE B 1 394 UNP P12823 POLG_DEN2P 281 674
SEQADV 1OKE GLU A 71 UNP P12823 ASP 351 CONFLICT SEQADV 1OKE ASN A 390 UNP P12823 ASP 670 CONFLICT SEQADV 1OKE GLU B 71 UNP P12823 ASP 351 CONFLICT SEQADV 1OKE 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
HET NAG A1395 14 HET NAG A1396 14 HET NAG A1397 14 HET FUL A1398 10 HET BMA A1399 11 HET BOG A1400 20 HET NAG B1395 14 HET NAG B1396 14 HET NAG B1397 14 HET FUL B1398 10 HET BMA B1399 11 HET BOG B1400 20
HETNAM NAG N-ACETYL-D-GLUCOSAMINE HETNAM FUL BETA-L-FUCOSE HETNAM BMA BETA-D-MANNOSE HETNAM BOG B-OCTYLGLUCOSIDE
HETSYN FUL 6-DEOXY-BETA-L-GALACTOSE
FORMUL 3 NAG 6(C8 H15 N O6) FORMUL 4 FUL 2(C6 H12 O5) FORMUL 4 BMA 2(C6 H12 O6) FORMUL 5 BOG 2(C14 H28 O6) FORMUL 9 HOH *136(H2 O)
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 1555 1555 2.04 SSBOND 2 CYS A 60 CYS A 121 1555 1555 2.06 SSBOND 3 CYS A 74 CYS A 105 1555 1555 2.04 SSBOND 4 CYS A 92 CYS A 116 1555 1555 2.05 SSBOND 5 CYS A 185 CYS A 285 1555 1555 2.05 SSBOND 6 CYS A 302 CYS A 333 1555 1555 2.05 SSBOND 7 CYS B 3 CYS B 30 1555 1555 2.03 SSBOND 8 CYS B 60 CYS B 121 1555 1555 2.08 SSBOND 9 CYS B 74 CYS B 105 1555 1555 2.07 SSBOND 10 CYS B 92 CYS B 116 1555 1555 2.08 SSBOND 11 CYS B 185 CYS B 285 1555 1555 2.07 SSBOND 12 CYS B 302 CYS B 333 1555 1555 2.06
LINK ND2 ASN A 67 C1 NAG A1395 1555 1555 1.45 LINK ND2 ASN A 153 C1 NAG A1396 1555 1555 1.46 LINK O4 NAG A1396 C1 NAG A1397 1555 1555 1.40 LINK O6 NAG A1396 C1 FUL A1398 1555 1555 1.40 LINK O4 NAG A1397 C1 BMA A1399 1555 1555 1.41 LINK ND2 ASN B 67 C1 NAG B1395 1555 1555 1.45 LINK ND2 ASN B 153 C1 NAG B1396 1555 1555 1.46 LINK O4 NAG B1396 C1 NAG B1397 1555 1555 1.41 LINK O6 NAG B1396 C1 FUL B1398 1555 1555 1.40 LINK O4 NAG B1397 C1 BMA B1399 1555 1555 1.41
SITE 1 AC1 4 GLU A 49 ILE A 270 GLN A 271 LEU A 277 SITE 1 AC2 7 THR B 48 GLU B 49 ALA B 50 PHE B 193 SITE 2 AC2 7 LEU B 207 ILE B 270 GLN B 271 SITE 1 AC3 2 ASN A 67 HOH A2049 SITE 1 AC4 5 GLU A 147 HIS A 149 ASN A 153 LYS A 157 SITE 2 AC4 5 HIS A 158 SITE 1 AC5 4 ASN B 67 HOH B2084 HOH B2085 HOH B2086 SITE 1 AC6 6 GLU B 147 HIS B 149 ASN B 153 LYS B 157 SITE 2 AC6 6 HIS B 158 HOH B2087
CRYST1 81.602 81.602 287.408 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 0.012255 0.007075 0.000000 0.00000
SCALE2 0.000000 0.014150 0.000000 0.00000
SCALE3 0.000000 0.000000 0.003479 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