HEADER GLYCOPROTEIN 16-JAN-03 1OAN TITLE CRYSTAL STRUCTURE OF THE DENGUE 2 VIRUS ENVELOPE PROTEIN CAVEAT 1OAN FUC C 4 HAS WRONG CHIRALITY AT ATOM C1 FUC D 4 HAS WRONG CAVEAT 2 1OAN CHIRALITY AT ATOM C1 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DENGUE VIRUS TYPE 2; SOURCE 3 ORGANISM_TAXID: 11060; SOURCE 4 STRAIN: 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 GLYCOPROTEIN, DENGUE VIRUS, MEMBRANE FUSION, FLAVIVIRUS, FUSION KEYWDS 2 PEPTIDE, LOW-PH CONFORMATIONAL CHANGE EXPDTA X-RAY DIFFRACTION AUTHOR Y.MODIS,S.C.HARRISON REVDAT 6 13-NOV-24 1OAN 1 REMARK REVDAT 5 13-DEC-23 1OAN 1 HETSYN REVDAT 4 29-JUL-20 1OAN 1 CAVEAT COMPND REMARK HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 24-FEB-09 1OAN 1 VERSN REVDAT 2 12-JUN-03 1OAN 1 JRNL REVDAT 1 16-MAY-03 1OAN 0 JRNL AUTH Y.MODIS,S.OGATA,D.CLEMENTS,S.C.HARRISON JRNL TITL A LIGAND-BINDING POCKET IN THE DENGUE VIRUS ENVELOPE JRNL TITL 2 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 VIRUS REMARK 1 TITL 2 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. 2.75 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) : 2.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1691401.100 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 83.2 REMARK 3 NUMBER OF REFLECTIONS : 24851 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) : 0.261 REMARK 3 FREE R VALUE : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1281 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 2.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.92 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 42.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1961 REMARK 3 BIN R VALUE (WORKING SET) : 0.4780 REMARK 3 BIN FREE R VALUE : 0.5400 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 119 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.049 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 : 127 REMARK 3 SOLVENT ATOMS : 45 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 76.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 11.16000 REMARK 3 B22 (A**2) : 11.16000 REMARK 3 B33 (A**2) : -22.31000 REMARK 3 B12 (A**2) : 3.91000 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) : 0.52 REMARK 3 ESD FROM SIGMAA (A) : 0.89 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) : 0.55 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.91 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.040 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) : 3.300 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.530 ; 4.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.870 ; 5.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 8.360 ; 6.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 49.89 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.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 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OAN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JAN-03. REMARK 100 THE DEPOSITION ID IS D_1290011842. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-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 REMARK 200 RADIATION SOURCE : CHESS REMARK 200 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 CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27029 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.750 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 (%) : 90.3 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 48.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.40900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1OAM 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: 11% PEG 8000, 1 M NACL, 0.1 M TRIS/HCL REMARK 280 PH 9.0, 20% GLYCEROL, PH 8.50 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 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 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: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 OE1 GLU B 383 O HOH B 2022 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 2003 O HOH B 2003 6555 1.99 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 92 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 PRO A 132 C - N - CA ANGL. DEV. = 11.0 DEGREES REMARK 500 PRO A 384 CA - N - CD ANGL. DEV. = -9.9 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 ILE A 4 104.88 -57.01 REMARK 500 SER A 16 91.47 -22.93 REMARK 500 SER A 19 49.06 -87.07 REMARK 500 GLU A 26 139.77 -176.43 REMARK 500 LYS A 36 132.81 -34.92 REMARK 500 ASN A 37 49.01 37.93 REMARK 500 ILE A 46 -75.24 -52.27 REMARK 500 GLN A 52 81.17 -166.51 REMARK 500 THR A 55 85.95 -66.89 REMARK 500 GLU A 62 122.36 -171.58 REMARK 500 ASN A 67 51.54 32.31 REMARK 500 LYS A 88 -17.55 -47.89 REMARK 500 SER A 95 -165.45 -161.10 REMARK 500 GLU A 126 85.51 -174.03 REMARK 500 PRO A 132 -38.16 -35.36 REMARK 500 ASN A 134 55.22 -101.64 REMARK 500 LYS A 157 24.03 -69.38 REMARK 500 GLN A 167 49.95 -97.05 REMARK 500 SER A 168 33.87 -151.70 REMARK 500 SER A 169 -142.64 52.06 REMARK 500 THR A 176 90.77 -27.67 REMARK 500 PRO A 187 -96.71 -38.08 REMARK 500 LYS A 202 -7.54 50.28 REMARK 500 ASP A 203 -64.50 -177.12 REMARK 500 TRP A 206 -163.56 -100.07 REMARK 500 ALA A 224 10.64 -59.37 REMARK 500 SER A 229 -39.35 -143.19 REMARK 500 SER A 255 138.06 -29.93 REMARK 500 LEU A 264 34.19 -98.45 REMARK 500 ILE A 270 91.31 -164.91 REMARK 500 SER A 274 23.28 42.30 REMARK 500 PHE A 279 -162.98 -60.22 REMARK 500 HIS A 282 87.78 -60.68 REMARK 500 LEU A 294 157.58 -42.76 REMARK 500 MET A 297 20.97 -70.12 REMARK 500 GLN A 316 5.10 -62.01 REMARK 500 SER A 331 -168.37 55.45 REMARK 500 PRO A 332 94.01 -33.19 REMARK 500 ARG A 345 -71.36 -101.37 REMARK 500 ASN A 355 74.56 44.98 REMARK 500 LYS A 361 -32.55 -33.73 REMARK 500 GLU A 383 -80.20 6.67 REMARK 500 PRO A 384 80.82 -53.67 REMARK 500 ILE B 4 103.20 -56.75 REMARK 500 SER B 16 95.68 -19.94 REMARK 500 SER B 19 49.17 -86.86 REMARK 500 GLU B 26 140.67 -175.58 REMARK 500 LYS B 36 132.01 -36.47 REMARK 500 ASN B 37 49.30 38.39 REMARK 500 ILE B 46 -75.51 -52.55 REMARK 500 REMARK 500 THIS ENTRY HAS 86 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2006 DISTANCE = 6.12 ANGSTROMS 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 NA A1395 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 85 OE1 REMARK 620 2 HIS A 94 NE2 65.3 REMARK 620 3 HIS A 346 NE2 80.7 86.4 REMARK 620 N 1 2 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OAM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DENGUE 2 VIRUS ENVELOPE PROTEIN IN COMPLEX REMARK 900 WITH N-OCTYL- 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 1OAN A 1 394 UNP P12823 POLG_DEN2P 281 674 DBREF 1OAN B 1 394 UNP P12823 POLG_DEN2P 281 674 SEQADV 1OAN GLU A 71 UNP P12823 ASP 351 CONFLICT SEQADV 1OAN ASN A 390 UNP P12823 ASP 670 CONFLICT SEQADV 1OAN GLU B 71 UNP P12823 ASP 351 CONFLICT SEQADV 1OAN 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 1OAN ASN A 67 ASN GLYCOSYLATION SITE MODRES 1OAN ASN A 153 ASN GLYCOSYLATION SITE MODRES 1OAN ASN B 67 ASN GLYCOSYLATION SITE MODRES 1OAN ASN B 153 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET FUC C 4 10 HET NAG D 1 14 HET NAG D 2 14 HET BMA D 3 11 HET FUC D 4 10 HET NA A1395 1 HET NAG A1396 14 HET NAG B1395 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM NA SODIUM ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 3 NAG 6(C8 H15 N O6) FORMUL 3 BMA 2(C6 H12 O6) FORMUL 3 FUC 2(C6 H12 O5) FORMUL 5 NA NA 1+ FORMUL 8 HOH *45(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 AG 2 GLN A 271 SER A 274 0 SHEET 2 AG 2 GLY A 275 LEU A 278 -1 O ASN A 276 N SER A 273 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 SHEET 1 BG 2 GLN B 271 SER B 274 0 SHEET 2 BG 2 GLY B 275 LEU B 278 -1 O ASN B 276 N SER B 273 SSBOND 1 CYS A 3 CYS A 30 1555 1555 2.04 SSBOND 2 CYS A 60 CYS A 121 1555 1555 2.05 SSBOND 3 CYS A 74 CYS A 105 1555 1555 2.04 SSBOND 4 CYS A 92 CYS A 116 1555 1555 2.04 SSBOND 5 CYS A 185 CYS A 285 1555 1555 2.03 SSBOND 6 CYS A 302 CYS A 333 1555 1555 2.03 SSBOND 7 CYS B 3 CYS B 30 1555 1555 2.02 SSBOND 8 CYS B 60 CYS B 121 1555 1555 2.05 SSBOND 9 CYS B 74 CYS B 105 1555 1555 2.04 SSBOND 10 CYS B 92 CYS B 116 1555 1555 2.04 SSBOND 11 CYS B 185 CYS B 285 1555 1555 2.04 SSBOND 12 CYS B 302 CYS B 333 1555 1555 2.04 LINK ND2 ASN A 67 C1 NAG A1396 1555 1555 1.46 LINK ND2 ASN A 153 C1 NAG C 1 1555 1555 1.45 LINK ND2 ASN B 67 C1 NAG B1395 1555 1555 1.46 LINK ND2 ASN B 153 C1 NAG D 1 1555 1555 1.45 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.40 LINK O6 NAG C 1 C1 FUC C 4 1555 1555 1.40 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.42 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.40 LINK O6 NAG D 1 C1 FUC D 4 1555 1555 1.40 LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.42 LINK OE1 GLU A 85 NA NA A1395 6655 1555 2.09 LINK NE2 HIS A 94 NA NA A1395 6655 1555 2.19 LINK NE2 HIS A 346 NA NA A1395 1555 1555 1.84 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 0.979000 -0.200000 -0.038000 14.47409 1 MTRIX2 1 -0.201000 -0.980000 -0.007000 134.89494 1 MTRIX3 1 -0.036000 0.014000 -0.999000 47.37856 1