HEADER HYDROLASE 20-JUN-08 2VWD TITLE NIPAH VIRUS ATTACHMENT GLYCOPROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMAGGLUTININ-NEURAMINIDASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RECEPTOR-BINDING DOMAIN, RESIDUES 183-602; COMPND 5 SYNONYM: NIV-G; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NIPAH VIRUS; SOURCE 3 ORGANISM_TAXID: 121791; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 EXPRESSION_SYSTEM_CELL_LINE: HEK293T; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PHLSEC; SOURCE 8 OTHER_DETAILS: SYNTHETICALLY OPTIMIZED CDNA (GENEART) KEYWDS HYDROLASE, TRANSMEMBRANE, VIRAL ATTACHMENT, ENVELOPE PROTEIN, KEYWDS 2 PARAMYXOVIRUS, SIGNAL-ANCHOR, HEMAGGLUTININ, NIV, HEV, NIPAH, HEV-G, KEYWDS 3 VIRUS, NIV-G, HENDRA, VIRION, MEMBRANE, HENIPAVIRUS, GLYCOPROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.A.BOWDEN,M.CRISPIN,D.J.HARVEY,A.R.ARICESCU,J.M.GRIMES,E.Y.JONES, AUTHOR 2 D.I.STUART REVDAT 8 23-OCT-24 2VWD 1 REMARK REVDAT 7 13-DEC-23 2VWD 1 HETSYN REVDAT 6 29-JUL-20 2VWD 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE REVDAT 5 28-FEB-18 2VWD 1 SOURCE REVDAT 4 13-JUL-11 2VWD 1 VERSN REVDAT 3 24-FEB-09 2VWD 1 VERSN REVDAT 2 25-NOV-08 2VWD 1 JRNL REVDAT 1 07-OCT-08 2VWD 0 JRNL AUTH T.A.BOWDEN,M.CRISPIN,D.J.HARVEY,A.R.ARICESCU,J.M.GRIMES, JRNL AUTH 2 E.Y.JONES,D.I.STUART JRNL TITL CRYSTAL STRUCTURE AND CARBOHYDRATE ANALYSIS OF NIPAH VIRUS JRNL TITL 2 ATTACHMENT GLYCOPROTEIN: A TEMPLATE FOR ANTIVIRAL AND JRNL TITL 3 VACCINE DESIGN. JRNL REF J.VIROL. V. 82 11628 2008 JRNL REFN ISSN 0022-538X JRNL PMID 18815311 JRNL DOI 10.1128/JVI.01344-08 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.94 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 43463 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2323 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3152 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1870 REMARK 3 BIN FREE R VALUE SET COUNT : 167 REMARK 3 BIN FREE R VALUE : 0.2350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6510 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 190 REMARK 3 SOLVENT ATOMS : 578 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.39000 REMARK 3 B22 (A**2) : 0.86000 REMARK 3 B33 (A**2) : -1.21000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.08000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.281 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.207 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.131 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.410 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6878 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4682 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9367 ; 1.209 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11283 ; 0.839 ; 3.006 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 818 ; 6.334 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 299 ;33.138 ;24.415 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1114 ;13.018 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;15.875 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1055 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7645 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1328 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1057 ; 0.175 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4941 ; 0.184 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3226 ; 0.171 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 3599 ; 0.093 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 475 ; 0.135 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 33 ; 0.147 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 61 ; 0.159 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 16 ; 0.132 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 5358 ; 0.642 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6743 ; 0.705 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3246 ; 0.988 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2624 ; 1.611 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 4 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 187 A 204 4 REMARK 3 1 B 187 B 204 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 243 ; 0.39 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 243 ; 0.13 ; 2.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 216 A 236 4 REMARK 3 1 B 216 B 236 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 A (A): 286 ; 0.26 ; 0.50 REMARK 3 MEDIUM THERMAL 2 A (A**2): 286 ; 0.28 ; 2.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 3 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 245 A 578 4 REMARK 3 1 B 245 B 578 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 3 A (A): 4512 ; 0.31 ; 0.50 REMARK 3 MEDIUM THERMAL 3 A (A**2): 4512 ; 0.35 ; 2.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 4 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 591 A 602 4 REMARK 3 1 B 591 B 602 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 4 A (A): 166 ; 0.08 ; 0.50 REMARK 3 MEDIUM THERMAL 4 A (A**2): 166 ; 0.15 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 188 A 602 REMARK 3 ORIGIN FOR THE GROUP (A): -25.7910 -17.3380 -24.1080 REMARK 3 T TENSOR REMARK 3 T11: -0.1331 T22: -0.1480 REMARK 3 T33: -0.1327 T12: 0.0204 REMARK 3 T13: -0.0034 T23: 0.0077 REMARK 3 L TENSOR REMARK 3 L11: 1.3770 L22: 1.1127 REMARK 3 L33: 3.0402 L12: -0.1513 REMARK 3 L13: -0.8424 L23: 0.6978 REMARK 3 S TENSOR REMARK 3 S11: -0.0219 S12: 0.0373 S13: 0.0131 REMARK 3 S21: 0.0187 S22: -0.0152 S23: 0.0334 REMARK 3 S31: -0.1090 S32: -0.0242 S33: 0.0371 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 188 B 602 REMARK 3 ORIGIN FOR THE GROUP (A): -56.7890 17.4410 -19.9310 REMARK 3 T TENSOR REMARK 3 T11: -0.1096 T22: -0.0847 REMARK 3 T33: -0.1278 T12: -0.0332 REMARK 3 T13: 0.0113 T23: -0.0150 REMARK 3 L TENSOR REMARK 3 L11: 2.1798 L22: 0.9297 REMARK 3 L33: 1.4698 L12: -0.2682 REMARK 3 L13: -0.0510 L23: -0.2479 REMARK 3 S TENSOR REMARK 3 S11: -0.0657 S12: 0.2517 S13: 0.0489 REMARK 3 S21: -0.0949 S22: 0.0379 S23: 0.0683 REMARK 3 S31: 0.0356 S32: -0.1291 S33: 0.0278 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2VWD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1290036625. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-AUG-07 REMARK 200 TEMPERATURE (KELVIN) : 77.2 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : SI(III) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45810 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.87000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2VSM REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (V/V) PEG 6000, 0.1 M MES PH 6.0, REMARK 280 0.1 M LICL AND 0.1 M GAMMA-BUTYLACTONE 18% REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 43.46800 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 183 REMARK 465 LEU A 184 REMARK 465 PRO A 185 REMARK 465 ASN A 186 REMARK 465 TYR A 205 REMARK 465 SER A 241 REMARK 465 ARG A 242 REMARK 465 GLY B 183 REMARK 465 LEU B 184 REMARK 465 PRO B 185 REMARK 465 ASN B 186 REMARK 465 VAL B 209 REMARK 465 VAL B 210 REMARK 465 GLY B 211 REMARK 465 GLN B 212 REMARK 465 SER B 213 REMARK 465 GLY B 214 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 203 -168.17 -103.19 REMARK 500 VAL A 210 85.94 -68.70 REMARK 500 VAL A 244 92.53 -162.56 REMARK 500 ASN A 269 117.99 -164.03 REMARK 500 TYR A 351 79.87 -155.15 REMARK 500 SER A 459 -146.46 -149.34 REMARK 500 SER A 486 -151.16 -138.11 REMARK 500 GLN A 490 -156.60 -114.63 REMARK 500 ASP A 515 102.40 -163.35 REMARK 500 ASN A 534 71.51 65.30 REMARK 500 ALA A 552 -128.23 -134.86 REMARK 500 GLN A 559 -109.60 -133.33 REMARK 500 ASN B 269 117.85 -165.94 REMARK 500 GLU B 289 -7.29 82.48 REMARK 500 TYR B 351 78.97 -157.94 REMARK 500 SER B 459 -134.35 -145.30 REMARK 500 SER B 486 -159.86 -143.01 REMARK 500 GLN B 490 -151.48 -113.17 REMARK 500 ASN B 534 67.62 63.09 REMARK 500 ALA B 552 -133.81 -148.05 REMARK 500 GLN B 559 -108.80 -145.36 REMARK 500 ASP B 585 37.75 -95.76 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 A2084 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH A2120 DISTANCE = 6.12 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 N-ACETYL-D-GLUCOSAMINE (NAG): N-ACETYLGLUCOSAMINE LINKAGES REMARK 600 OBSERVED IN ASN306 ASN378 ASN417 ASN481 ASN529 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VSM RELATED DB: PDB REMARK 900 NIPAH VIRUS ATTACHMENT GLYCOPROTEIN IN COMPLEX WITH HUMAN CELL REMARK 900 SURFACE RECEPTOR EPHRINB2 DBREF 2VWD A 183 602 UNP Q9IH62 HN_NIPAV 183 602 DBREF 2VWD B 183 602 UNP Q9IH62 HN_NIPAV 183 602 SEQRES 1 A 420 GLY LEU PRO ASN ASN ILE CYS LEU GLN LYS THR SER ASN SEQRES 2 A 420 GLN ILE LEU LYS PRO LYS LEU ILE SER TYR THR LEU PRO SEQRES 3 A 420 VAL VAL GLY GLN SER GLY THR CYS ILE THR ASP PRO LEU SEQRES 4 A 420 LEU ALA MET ASP GLU GLY TYR PHE ALA TYR SER HIS LEU SEQRES 5 A 420 GLU ARG ILE GLY SER CYS SER ARG GLY VAL SER LYS GLN SEQRES 6 A 420 ARG ILE ILE GLY VAL GLY GLU VAL LEU ASP ARG GLY ASP SEQRES 7 A 420 GLU VAL PRO SER LEU PHE MET THR ASN VAL TRP THR PRO SEQRES 8 A 420 PRO ASN PRO ASN THR VAL TYR HIS CYS SER ALA VAL TYR SEQRES 9 A 420 ASN ASN GLU PHE TYR TYR VAL LEU CYS ALA VAL SER THR SEQRES 10 A 420 VAL GLY ASP PRO ILE LEU ASN SER THR TYR TRP SER GLY SEQRES 11 A 420 SER LEU MET MET THR ARG LEU ALA VAL LYS PRO LYS SER SEQRES 12 A 420 ASN GLY GLY GLY TYR ASN GLN HIS GLN LEU ALA LEU ARG SEQRES 13 A 420 SER ILE GLU LYS GLY ARG TYR ASP LYS VAL MET PRO TYR SEQRES 14 A 420 GLY PRO SER GLY ILE LYS GLN GLY ASP THR LEU TYR PHE SEQRES 15 A 420 PRO ALA VAL GLY PHE LEU VAL ARG THR GLU PHE LYS TYR SEQRES 16 A 420 ASN ASP SER ASN CYS PRO ILE THR LYS CYS GLN TYR SER SEQRES 17 A 420 LYS PRO GLU ASN CYS ARG LEU SER MET GLY ILE ARG PRO SEQRES 18 A 420 ASN SER HIS TYR ILE LEU ARG SER GLY LEU LEU LYS TYR SEQRES 19 A 420 ASN LEU SER ASP GLY GLU ASN PRO LYS VAL VAL PHE ILE SEQRES 20 A 420 GLU ILE SER ASP GLN ARG LEU SER ILE GLY SER PRO SER SEQRES 21 A 420 LYS ILE TYR ASP SER LEU GLY GLN PRO VAL PHE TYR GLN SEQRES 22 A 420 ALA SER PHE SER TRP ASP THR MET ILE LYS PHE GLY ASP SEQRES 23 A 420 VAL LEU THR VAL ASN PRO LEU VAL VAL ASN TRP ARG ASN SEQRES 24 A 420 ASN THR VAL ILE SER ARG PRO GLY GLN SER GLN CYS PRO SEQRES 25 A 420 ARG PHE ASN THR CYS PRO GLU ILE CYS TRP GLU GLY VAL SEQRES 26 A 420 TYR ASN ASP ALA PHE LEU ILE ASP ARG ILE ASN TRP ILE SEQRES 27 A 420 SER ALA GLY VAL PHE LEU ASP SER ASN GLN THR ALA GLU SEQRES 28 A 420 ASN PRO VAL PHE THR VAL PHE LYS ASP ASN GLU ILE LEU SEQRES 29 A 420 TYR ARG ALA GLN LEU ALA SER GLU ASP THR ASN ALA GLN SEQRES 30 A 420 LYS THR ILE THR ASN CYS PHE LEU LEU LYS ASN LYS ILE SEQRES 31 A 420 TRP CYS ILE SER LEU VAL GLU ILE TYR ASP THR GLY ASP SEQRES 32 A 420 ASN VAL ILE ARG PRO LYS LEU PHE ALA VAL LYS ILE PRO SEQRES 33 A 420 GLU GLN CYS THR SEQRES 1 B 420 GLY LEU PRO ASN ASN ILE CYS LEU GLN LYS THR SER ASN SEQRES 2 B 420 GLN ILE LEU LYS PRO LYS LEU ILE SER TYR THR LEU PRO SEQRES 3 B 420 VAL VAL GLY GLN SER GLY THR CYS ILE THR ASP PRO LEU SEQRES 4 B 420 LEU ALA MET ASP GLU GLY TYR PHE ALA TYR SER HIS LEU SEQRES 5 B 420 GLU ARG ILE GLY SER CYS SER ARG GLY VAL SER LYS GLN SEQRES 6 B 420 ARG ILE ILE GLY VAL GLY GLU VAL LEU ASP ARG GLY ASP SEQRES 7 B 420 GLU VAL PRO SER LEU PHE MET THR ASN VAL TRP THR PRO SEQRES 8 B 420 PRO ASN PRO ASN THR VAL TYR HIS CYS SER ALA VAL TYR SEQRES 9 B 420 ASN ASN GLU PHE TYR TYR VAL LEU CYS ALA VAL SER THR SEQRES 10 B 420 VAL GLY ASP PRO ILE LEU ASN SER THR TYR TRP SER GLY SEQRES 11 B 420 SER LEU MET MET THR ARG LEU ALA VAL LYS PRO LYS SER SEQRES 12 B 420 ASN GLY GLY GLY TYR ASN GLN HIS GLN LEU ALA LEU ARG SEQRES 13 B 420 SER ILE GLU LYS GLY ARG TYR ASP LYS VAL MET PRO TYR SEQRES 14 B 420 GLY PRO SER GLY ILE LYS GLN GLY ASP THR LEU TYR PHE SEQRES 15 B 420 PRO ALA VAL GLY PHE LEU VAL ARG THR GLU PHE LYS TYR SEQRES 16 B 420 ASN ASP SER ASN CYS PRO ILE THR LYS CYS GLN TYR SER SEQRES 17 B 420 LYS PRO GLU ASN CYS ARG LEU SER MET GLY ILE ARG PRO SEQRES 18 B 420 ASN SER HIS TYR ILE LEU ARG SER GLY LEU LEU LYS TYR SEQRES 19 B 420 ASN LEU SER ASP GLY GLU ASN PRO LYS VAL VAL PHE ILE SEQRES 20 B 420 GLU ILE SER ASP GLN ARG LEU SER ILE GLY SER PRO SER SEQRES 21 B 420 LYS ILE TYR ASP SER LEU GLY GLN PRO VAL PHE TYR GLN SEQRES 22 B 420 ALA SER PHE SER TRP ASP THR MET ILE LYS PHE GLY ASP SEQRES 23 B 420 VAL LEU THR VAL ASN PRO LEU VAL VAL ASN TRP ARG ASN SEQRES 24 B 420 ASN THR VAL ILE SER ARG PRO GLY GLN SER GLN CYS PRO SEQRES 25 B 420 ARG PHE ASN THR CYS PRO GLU ILE CYS TRP GLU GLY VAL SEQRES 26 B 420 TYR ASN ASP ALA PHE LEU ILE ASP ARG ILE ASN TRP ILE SEQRES 27 B 420 SER ALA GLY VAL PHE LEU ASP SER ASN GLN THR ALA GLU SEQRES 28 B 420 ASN PRO VAL PHE THR VAL PHE LYS ASP ASN GLU ILE LEU SEQRES 29 B 420 TYR ARG ALA GLN LEU ALA SER GLU ASP THR ASN ALA GLN SEQRES 30 B 420 LYS THR ILE THR ASN CYS PHE LEU LEU LYS ASN LYS ILE SEQRES 31 B 420 TRP CYS ILE SER LEU VAL GLU ILE TYR ASP THR GLY ASP SEQRES 32 B 420 ASN VAL ILE ARG PRO LYS LEU PHE ALA VAL LYS ILE PRO SEQRES 33 B 420 GLU GLN CYS THR MODRES 2VWD ASN A 306 ASN GLYCOSYLATION SITE MODRES 2VWD ASN A 378 ASN GLYCOSYLATION SITE MODRES 2VWD ASN A 417 ASN GLYCOSYLATION SITE MODRES 2VWD ASN A 481 ASN GLYCOSYLATION SITE MODRES 2VWD ASN A 529 ASN GLYCOSYLATION SITE MODRES 2VWD ASN B 306 ASN GLYCOSYLATION SITE MODRES 2VWD ASN B 378 ASN GLYCOSYLATION SITE MODRES 2VWD ASN B 417 ASN GLYCOSYLATION SITE MODRES 2VWD ASN B 481 ASN GLYCOSYLATION SITE MODRES 2VWD ASN B 529 ASN GLYCOSYLATION SITE HET GBL A1603 6 HET GBL A1604 6 HET GBL A1605 6 HET GBL A1606 6 HET GBL A1607 6 HET GBL A1608 6 HET NAG A1609 14 HET NAG A1610 14 HET NAG A1611 14 HET NAG A1612 14 HET NAG A1613 14 HET CL B1603 1 HET CL B1604 1 HET GBL B1605 6 HET GBL B1606 6 HET NAG B1607 14 HET NAG B1608 14 HET NAG B1609 14 HET NAG B1610 14 HET NAG B1611 14 HETNAM GBL GAMMA-BUTYROLACTONE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CL CHLORIDE ION HETSYN GBL DIHYDROFURAN-2(3H)-ONE 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 FORMUL 3 GBL 8(C4 H6 O2) FORMUL 9 NAG 10(C8 H15 N O6) FORMUL 14 CL 2(CL 1-) FORMUL 23 HOH *578(H2 O) HELIX 1 1 ASN A 275 ASN A 277 5 3 HELIX 2 2 ASN A 306 TRP A 310 5 5 HELIX 3 3 GLY A 327 TYR A 330 5 4 HELIX 4 4 THR A 373 PHE A 375 5 3 HELIX 5 5 ASN A 378 CYS A 382 5 5 HELIX 6 6 GLU A 393 SER A 398 1 6 HELIX 7 7 SER B 204 LEU B 207 5 4 HELIX 8 8 GLY B 327 TYR B 330 5 4 HELIX 9 9 THR B 373 PHE B 375 5 3 HELIX 10 10 ASN B 378 CYS B 382 5 5 HELIX 11 11 GLU B 393 SER B 398 1 6 SHEET 1 AA 4 LYS A 201 LEU A 202 0 SHEET 2 AA 4 VAL A 587 LYS A 596 -1 O ALA A 594 N LYS A 201 SHEET 3 AA 4 LYS A 571 ASP A 582 -1 O CYS A 574 N VAL A 595 SHEET 4 AA 4 ASN A 557 LEU A 568 -1 O ASN A 557 N TYR A 581 SHEET 1 AB 4 THR A 215 ASP A 225 0 SHEET 2 AB 4 TYR A 228 ILE A 237 -1 O TYR A 228 N ASP A 225 SHEET 3 AB 4 SER A 245 ASP A 257 -1 N LYS A 246 O GLU A 235 SHEET 4 AB 4 PRO A 263 TRP A 271 -1 O SER A 264 N LEU A 256 SHEET 1 AC 4 VAL A 279 ASN A 287 0 SHEET 2 AC 4 PHE A 290 VAL A 297 -1 O PHE A 290 N ASN A 287 SHEET 3 AC 4 LEU A 314 ALA A 320 -1 O MET A 315 N CYS A 295 SHEET 4 AC 4 GLN A 332 LEU A 335 -1 O HIS A 333 N ARG A 318 SHEET 1 AD 5 ILE A 340 GLU A 341 0 SHEET 2 AD 5 VAL A 426 GLU A 430 1 O VAL A 426 N GLU A 341 SHEET 3 AD 5 TYR A 407 ASN A 417 -1 O LEU A 413 N ILE A 429 SHEET 4 AD 5 THR A 361 VAL A 371 -1 O LEU A 362 N TYR A 416 SHEET 5 AD 5 LYS A 347 PRO A 350 -1 O LYS A 347 N PHE A 369 SHEET 1 AE 5 ILE A 340 GLU A 341 0 SHEET 2 AE 5 VAL A 426 GLU A 430 1 O VAL A 426 N GLU A 341 SHEET 3 AE 5 TYR A 407 ASN A 417 -1 O LEU A 413 N ILE A 429 SHEET 4 AE 5 THR A 361 VAL A 371 -1 O LEU A 362 N TYR A 416 SHEET 5 AE 5 ILE A 356 GLN A 358 -1 O ILE A 356 N TYR A 363 SHEET 1 AF 4 SER A 442 SER A 447 0 SHEET 2 AF 4 GLN A 450 GLN A 455 -1 O GLN A 450 N SER A 447 SHEET 3 AF 4 LYS A 465 THR A 471 -1 O LYS A 465 N GLN A 455 SHEET 4 AF 4 VAL A 476 TRP A 479 -1 O VAL A 476 N LEU A 470 SHEET 1 AG 4 ALA A 511 ASP A 515 0 SHEET 2 AG 4 ILE A 520 LEU A 526 -1 O ILE A 520 N ILE A 514 SHEET 3 AG 4 PRO A 535 LYS A 541 -1 O VAL A 536 N PHE A 525 SHEET 4 AG 4 GLU A 544 GLN A 550 -1 O GLU A 544 N LYS A 541 SHEET 1 BA 4 LYS B 201 LEU B 202 0 SHEET 2 BA 4 VAL B 587 LYS B 596 -1 O ALA B 594 N LYS B 201 SHEET 3 BA 4 LYS B 571 ASP B 582 -1 O CYS B 574 N VAL B 595 SHEET 4 BA 4 ALA B 558 LEU B 568 -1 N GLN B 559 O GLU B 579 SHEET 1 BB 4 CYS B 216 ASP B 225 0 SHEET 2 BB 4 TYR B 228 ARG B 236 -1 O TYR B 228 N ASP B 225 SHEET 3 BB 4 SER B 245 ASP B 257 -1 N LYS B 246 O GLU B 235 SHEET 4 BB 4 PRO B 263 TRP B 271 -1 O SER B 264 N LEU B 256 SHEET 1 BC 4 VAL B 279 ASN B 287 0 SHEET 2 BC 4 PHE B 290 VAL B 297 -1 O PHE B 290 N ASN B 287 SHEET 3 BC 4 LEU B 314 ALA B 320 -1 O MET B 315 N CYS B 295 SHEET 4 BC 4 GLN B 332 LEU B 335 -1 O HIS B 333 N ARG B 318 SHEET 1 BD 5 ILE B 340 GLU B 341 0 SHEET 2 BD 5 VAL B 426 GLU B 430 1 O VAL B 426 N GLU B 341 SHEET 3 BD 5 TYR B 407 ASN B 417 -1 O LEU B 413 N ILE B 429 SHEET 4 BD 5 THR B 361 VAL B 371 -1 O LEU B 362 N TYR B 416 SHEET 5 BD 5 LYS B 347 PRO B 350 -1 O LYS B 347 N PHE B 369 SHEET 1 BE 5 ILE B 340 GLU B 341 0 SHEET 2 BE 5 VAL B 426 GLU B 430 1 O VAL B 426 N GLU B 341 SHEET 3 BE 5 TYR B 407 ASN B 417 -1 O LEU B 413 N ILE B 429 SHEET 4 BE 5 THR B 361 VAL B 371 -1 O LEU B 362 N TYR B 416 SHEET 5 BE 5 ILE B 356 GLN B 358 -1 O ILE B 356 N TYR B 363 SHEET 1 BF 4 SER B 442 SER B 447 0 SHEET 2 BF 4 GLN B 450 GLN B 455 -1 O GLN B 450 N SER B 447 SHEET 3 BF 4 LYS B 465 THR B 471 -1 O LYS B 465 N GLN B 455 SHEET 4 BF 4 VAL B 476 TRP B 479 -1 O VAL B 476 N LEU B 470 SHEET 1 BG 4 ALA B 511 ASP B 515 0 SHEET 2 BG 4 ILE B 520 LEU B 526 -1 O ILE B 520 N ILE B 514 SHEET 3 BG 4 PRO B 535 LYS B 541 -1 O VAL B 536 N PHE B 525 SHEET 4 BG 4 GLU B 544 GLN B 550 -1 O GLU B 544 N LYS B 541 SSBOND 1 CYS A 189 CYS A 601 1555 1555 2.03 SSBOND 2 CYS A 216 CYS A 240 1555 1555 2.03 SSBOND 3 CYS A 282 CYS A 295 1555 1555 2.07 SSBOND 4 CYS A 382 CYS A 395 1555 1555 2.06 SSBOND 5 CYS A 387 CYS A 499 1555 1555 2.05 SSBOND 6 CYS A 493 CYS A 503 1555 1555 2.03 SSBOND 7 CYS A 565 CYS A 574 1555 1555 2.03 SSBOND 8 CYS B 189 CYS B 601 1555 1555 2.04 SSBOND 9 CYS B 216 CYS B 240 1555 1555 2.05 SSBOND 10 CYS B 282 CYS B 295 1555 1555 2.05 SSBOND 11 CYS B 382 CYS B 395 1555 1555 2.08 SSBOND 12 CYS B 387 CYS B 499 1555 1555 2.06 SSBOND 13 CYS B 493 CYS B 503 1555 1555 2.03 SSBOND 14 CYS B 565 CYS B 574 1555 1555 2.05 LINK ND2 ASN A 306 C1 NAG A1613 1555 1555 1.45 LINK ND2 ASN A 378 C1 NAG A1612 1555 1555 1.44 LINK ND2 ASN A 417 C1 NAG A1610 1555 1555 1.44 LINK ND2 ASN A 481 C1 NAG A1609 1555 1555 1.44 LINK ND2 ASN A 529 C1 NAG A1611 1555 1555 1.44 LINK ND2 ASN B 306 C1 NAG B1608 1555 1555 1.45 LINK ND2 ASN B 378 C1 NAG B1607 1555 1555 1.44 LINK ND2 ASN B 417 C1 NAG B1609 1555 1555 1.44 LINK ND2 ASN B 481 C1 NAG B1611 1555 1555 1.45 LINK ND2 ASN B 529 C1 NAG B1610 1555 1555 1.44 CISPEP 1 ASN A 473 PRO A 474 0 -1.53 CISPEP 2 ASN B 473 PRO B 474 0 0.15 CISPEP 3 GLY B 584 ASP B 585 0 6.81 CRYST1 71.633 86.936 82.903 90.00 108.32 90.00 P 1 21 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 0.013960 0.000000 0.004622 0.00000 SCALE2 0.000000 0.011503 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012706 0.00000