HEADER VIRAL PROTEIN 01-OCT-07 2RFU TITLE CRYSTAL STRUCTURE OF INFLUENZA B VIRUS HEMAGGLUTININ IN COMPLEX WITH TITLE 2 LSTC RECEPTOR ANALOG COMPND MOL_ID: 1; COMPND 2 MOLECULE: INFLUENZA B HEMAGGLUTININ (HA); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: INFLUENZA B HEMAGGLUTININ (HA); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: INFLUENZA B VIRUS (STRAIN B/HONG KONG/8/73); SOURCE 3 ORGANISM_TAXID: 11531; SOURCE 4 STRAIN: B/HONGKONG/8/73; SOURCE 5 GENE: HEMAGGLUTININ; SOURCE 6 EXPRESSION_SYSTEM: INFLUENZA B VIRUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 11520; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: INFLUENZA B VIRUS (STRAIN B/HONG KONG/8/73); SOURCE 10 ORGANISM_TAXID: 11531; SOURCE 11 STRAIN: B/HONGKONG/8/73; SOURCE 12 GENE: HEMAGGLUTININ; SOURCE 13 EXPRESSION_SYSTEM: INFLUENZA B VIRUS; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 11520 KEYWDS INFLUENZA, RECEPTOR SPECIFICITY, HUMAN RECEPTOR ANALOG, ENVELOPE KEYWDS 2 PROTEIN, FUSION PROTEIN, HEMAGGLUTININ, MEMBRANE, TRANSMEMBRANE, KEYWDS 3 VIRION, GLYCOPROTEIN, LIPOPROTEIN, PALMITATE, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Q.WANG,X.TIAN,X.CHEN,J.MA REVDAT 6 30-OCT-24 2RFU 1 REMARK REVDAT 5 03-APR-24 2RFU 1 HETSYN REVDAT 4 29-JUL-20 2RFU 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 13-JUL-11 2RFU 1 VERSN REVDAT 2 24-FEB-09 2RFU 1 VERSN REVDAT 1 05-FEB-08 2RFU 0 JRNL AUTH Q.WANG,X.TIAN,X.CHEN,J.MA JRNL TITL STRUCTURAL BASIS FOR RECEPTOR SPECIFICITY OF INFLUENZA B JRNL TITL 2 VIRUS HEMAGGLUTININ. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 16874 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17942670 JRNL DOI 10.1073/PNAS.0708363104 REMARK 2 REMARK 2 RESOLUTION. 2.80 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 3 NUMBER OF REFLECTIONS : 15990 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) : 0.296 REMARK 3 R VALUE (WORKING SET) : 0.295 REMARK 3 FREE R VALUE : 0.311 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1753 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1116 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.4430 REMARK 3 BIN FREE R VALUE SET COUNT : 131 REMARK 3 BIN FREE R VALUE : 0.4530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3864 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 199 REMARK 3 SOLVENT ATOMS : 2 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.59000 REMARK 3 B22 (A**2) : 6.59000 REMARK 3 B33 (A**2) : -9.89000 REMARK 3 B12 (A**2) : 3.30000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.467 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.391 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.930 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.887 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.875 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4159 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2792 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5656 ; 1.519 ; 2.018 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6807 ; 2.658 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 509 ; 7.784 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 156 ;40.401 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 675 ;20.975 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;21.418 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 670 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4442 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 722 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1142 ; 0.245 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3063 ; 0.242 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2010 ; 0.189 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2254 ; 0.105 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 154 ; 0.192 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.011 ; 0.200 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): 39 ; 0.235 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 77 ; 0.236 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.179 ; 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): 3244 ; 1.364 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1044 ; 0.124 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4078 ; 1.631 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1852 ; 1.974 ; 6.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1578 ; 3.041 ; 8.000 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 2RFU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000044807. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : BENT GE(111) MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19705 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.29700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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: UNLIGANDED INFLUENZA B VIRUS HEMAGGLUTININ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM PIPES, 2.5 M AMMONIUM SULFATE, REMARK 280 PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 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 REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 0.00000 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 0.00000 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 0.00000 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 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 44650 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 98.36900 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 49.18450 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 85.19005 REMARK 350 BIOMT3 3 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 GLU A 343 REMARK 465 ARG A 344 REMARK 465 LEU B 170 REMARK 465 ASN B 171 REMARK 465 ILE B 172 REMARK 465 THR B 173 REMARK 465 ALA B 174 REMARK 465 ALA B 175 REMARK 465 SER B 176 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 O4 NAG F 1 O5 NAG F 2 2.07 REMARK 500 OE1 GLN A 268 N2 NAG D 1 2.13 REMARK 500 OG SER A 240 O9 SIA G 3 2.15 REMARK 500 O GLY A 51 NE2 HIS A 85 2.19 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 ARG A 276 NE - CZ - NH1 ANGL. DEV. = 3.0 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 LYS A 45 -81.33 -54.43 REMARK 500 LEU A 53 -36.62 -32.67 REMARK 500 LEU A 58 -158.08 44.93 REMARK 500 ASN A 59 86.30 -52.61 REMARK 500 PRO A 77 -133.81 -96.47 REMARK 500 CYS A 94 -163.47 60.81 REMARK 500 ASP A 100 8.06 -56.81 REMARK 500 ARG A 112 -37.72 -37.82 REMARK 500 SER A 120 136.82 151.05 REMARK 500 ALA A 121 36.12 -92.00 REMARK 500 ARG A 122 177.56 160.27 REMARK 500 THR A 125 112.02 67.79 REMARK 500 ALA A 127 -36.32 -39.84 REMARK 500 PRO A 131 151.83 -49.60 REMARK 500 VAL A 137 87.64 -67.54 REMARK 500 SER A 142 -3.24 80.43 REMARK 500 PRO A 144 -178.10 -40.09 REMARK 500 ASN A 148 67.66 76.10 REMARK 500 PHE A 153 101.16 10.85 REMARK 500 ASN A 163 76.51 73.89 REMARK 500 PRO A 169 127.68 -35.23 REMARK 500 ILE A 177 -28.73 80.24 REMARK 500 LYS A 180 -150.18 71.20 REMARK 500 ASP A 204 138.64 176.47 REMARK 500 ASP A 234 -153.94 -147.89 REMARK 500 GLU A 235 -79.31 -135.36 REMARK 500 LEU A 237 5.14 81.04 REMARK 500 PRO A 238 56.82 -67.31 REMARK 500 GLN A 261 -97.10 -136.21 REMARK 500 VAL A 264 98.53 -42.86 REMARK 500 GLN A 268 -97.94 -140.70 REMARK 500 LYS A 281 98.24 -62.60 REMARK 500 LEU A 286 109.39 -57.85 REMARK 500 LYS A 296 -114.88 -80.15 REMARK 500 TYR A 297 -30.42 -8.09 REMARK 500 SER A 303 -70.95 -93.84 REMARK 500 LEU B 38 49.89 -84.83 REMARK 500 LYS B 39 -52.78 -149.16 REMARK 500 LEU B 63 87.58 83.21 REMARK 500 GLN B 64 -156.19 -119.08 REMARK 500 HIS B 74 53.46 -116.07 REMARK 500 GLU B 111 -70.64 -25.91 REMARK 500 SER B 163 94.15 -50.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 284 PRO A 285 132.95 REMARK 500 ALA A 338 LYS A 339 145.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAG D 1 REMARK 610 NAG G 1 REMARK 610 NAG A 348 REMARK 630 REMARK 630 MOLECULE TYPE: OLIGOSACCHARIDE GLYCAN COMPONENT REMARK 630 MOLECULE NAME: 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 NAG A 347 REMARK 630 NAG A 348 REMARK 630 NAG B 170 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: NULL REMARK 630 DETAILS: OLIGOSACCHARIDE REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RFT RELATED DB: PDB REMARK 900 2RFT IS THE SAME PROTEIN IN COMPLEX WITH LSTA RECEPTOR ANALOG DBREF 2RFU A 1 344 UNP Q84097 Q84097_9INFB 16 359 DBREF 2RFU B 1 176 UNP Q84097 Q84097_9INFB 360 535 SEQRES 1 A 344 ASP ARG ILE CYS THR GLY ILE THR SER SER ASN SER PRO SEQRES 2 A 344 HIS VAL VAL LYS THR ALA THR GLN GLY GLU VAL ASN VAL SEQRES 3 A 344 THR GLY VAL ILE PRO LEU THR THR THR PRO THR LYS SER SEQRES 4 A 344 HIS PHE ALA ASN LEU LYS GLY THR GLN THR ARG GLY LYS SEQRES 5 A 344 LEU CYS PRO ASN CYS LEU ASN CYS THR ASP LEU ASP VAL SEQRES 6 A 344 ALA LEU GLY ARG PRO LYS CYS MET GLY THR ILE PRO SER SEQRES 7 A 344 ALA LYS ALA SER ILE LEU HIS GLU VAL LYS PRO VAL THR SEQRES 8 A 344 SER GLY CYS PHE PRO ILE MET HIS ASP ARG THR LYS ILE SEQRES 9 A 344 ARG GLN LEU PRO ASN LEU LEU ARG GLY TYR GLU ASN ILE SEQRES 10 A 344 ARG LEU SER ALA ARG ASN VAL THR ASN ALA GLU THR ALA SEQRES 11 A 344 PRO GLY GLY PRO TYR ILE VAL GLY THR SER GLY SER CYS SEQRES 12 A 344 PRO ASN VAL THR ASN GLY ASN GLY PHE PHE ALA THR MET SEQRES 13 A 344 ALA TRP ALA VAL PRO LYS ASN LYS THR ALA THR ASN PRO SEQRES 14 A 344 LEU THR VAL GLU VAL PRO TYR ILE CYS THR LYS GLY GLU SEQRES 15 A 344 ASP GLN ILE THR VAL TRP GLY PHE HIS SER ASP ASP GLU SEQRES 16 A 344 THR GLN MET VAL LYS LEU TYR GLY ASP SER LYS PRO GLN SEQRES 17 A 344 LYS PHE THR SER SER ALA ASN GLY VAL THR THR HIS TYR SEQRES 18 A 344 VAL SER GLN ILE GLY GLY PHE PRO ASN GLN ALA GLU ASP SEQRES 19 A 344 GLU GLY LEU PRO GLN SER GLY ARG ILE VAL VAL ASP TYR SEQRES 20 A 344 MET VAL GLN LYS PRO GLY LYS THR GLY THR ILE ALA TYR SEQRES 21 A 344 GLN ARG GLY VAL LEU LEU PRO GLN LYS VAL TRP CYS ALA SEQRES 22 A 344 SER GLY ARG SER LYS VAL ILE LYS GLY SER LEU PRO LEU SEQRES 23 A 344 ILE GLY GLU ALA ASP CYS LEU HIS GLU LYS TYR GLY GLY SEQRES 24 A 344 LEU ASN LYS SER LYS PRO TYR TYR THR GLY GLU HIS ALA SEQRES 25 A 344 LYS ALA ILE GLY ASN CYS PRO ILE TRP VAL LYS THR PRO SEQRES 26 A 344 LEU LYS LEU ALA ASN GLY THR LYS TYR ARG PRO PRO ALA SEQRES 27 A 344 LYS LEU LEU LYS GLU ARG SEQRES 1 B 176 GLY PHE PHE GLY ALA ILE ALA GLY PHE LEU GLU GLY GLY SEQRES 2 B 176 TRP GLU GLY MET ILE ALA GLY TRP HIS GLY TYR THR SER SEQRES 3 B 176 HIS GLY ALA HIS GLY VAL ALA VAL ALA ALA ASP LEU LYS SEQRES 4 B 176 SER THR GLN GLU ALA ILE ASN LYS ILE THR LYS ASN LEU SEQRES 5 B 176 ASN SER LEU SER GLU LEU GLU VAL LYS ASN LEU GLN ARG SEQRES 6 B 176 LEU SER GLY ALA MET ASP GLU LEU HIS ASN GLU ILE LEU SEQRES 7 B 176 GLU LEU ASP GLU LYS VAL ASP ASP LEU ARG ALA ASP THR SEQRES 8 B 176 ILE SER SER GLN ILE GLU LEU ALA VAL LEU LEU SER ASN SEQRES 9 B 176 GLU GLY ILE ILE ASN SER GLU ASP GLU HIS LEU LEU ALA SEQRES 10 B 176 LEU GLU ARG LYS LEU LYS LYS MET LEU GLY PRO SER ALA SEQRES 11 B 176 VAL ASP ILE GLY ASN GLY CYS PHE GLU THR LYS HIS LYS SEQRES 12 B 176 CYS ASN GLN THR CYS LEU ASP ARG ILE ALA ALA GLY THR SEQRES 13 B 176 PHE ASN ALA GLY GLU PHE SER LEU PRO THR PHE ASP SER SEQRES 14 B 176 LEU ASN ILE THR ALA ALA SER MODRES 2RFU ASN A 25 ASN GLYCOSYLATION SITE MODRES 2RFU ASN A 145 ASN GLYCOSYLATION SITE MODRES 2RFU ASN A 301 ASN GLYCOSYLATION SITE MODRES 2RFU ASN A 330 ASN GLYCOSYLATION SITE MODRES 2RFU ASN B 145 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET NAG E 1 14 HET NAG E 2 14 HET NAG F 1 14 HET NAG F 2 14 HET NAG G 1 14 HET GAL G 2 11 HET SIA G 3 20 HET NAG A 347 14 HET NAG A 348 14 HET NAG B 170 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM SIA N-ACETYL-ALPHA-NEURAMINIC ACID 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 GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN SIA N-ACETYLNEURAMINIC ACID; SIALIC ACID; ALPHA-SIALIC HETSYN 2 SIA ACID; O-SIALIC ACID FORMUL 3 NAG 12(C8 H15 N O6) FORMUL 7 GAL C6 H12 O6 FORMUL 7 SIA C11 H19 N O9 FORMUL 11 HOH *2(H2 O) HELIX 1 1 THR A 61 GLY A 68 1 8 HELIX 2 2 MET A 98 ARG A 105 5 8 HELIX 3 3 GLN A 106 GLY A 113 1 8 HELIX 4 4 ASP A 194 TYR A 202 1 9 HELIX 5 5 GLY B 1 ALA B 7 1 7 HELIX 6 6 LYS B 39 LEU B 58 1 20 HELIX 7 7 HIS B 74 GLY B 127 1 54 HELIX 8 8 ASN B 145 GLY B 155 1 11 SHEET 1 A 5 GLY B 31 ALA B 36 0 SHEET 2 A 5 HIS B 22 GLY B 28 -1 N SER B 26 O ALA B 33 SHEET 3 A 5 ARG A 2 ILE A 7 -1 N GLY A 6 O GLY B 23 SHEET 4 A 5 CYS B 137 GLU B 139 -1 O PHE B 138 N ILE A 3 SHEET 5 A 5 VAL B 131 ASP B 132 -1 N VAL B 131 O GLU B 139 SHEET 1 B 2 HIS A 14 LYS A 17 0 SHEET 2 B 2 GLU A 23 VAL A 26 -1 O VAL A 24 N VAL A 16 SHEET 1 C 2 VAL A 29 PRO A 31 0 SHEET 2 C 2 LYS A 327 ALA A 329 -1 O LEU A 328 N ILE A 30 SHEET 1 D 2 ASN A 43 LEU A 44 0 SHEET 2 D 2 GLU A 289 ALA A 290 1 O ALA A 290 N ASN A 43 SHEET 1 E 3 THR A 49 ARG A 50 0 SHEET 2 E 3 ALA A 81 ILE A 83 1 O ILE A 83 N ARG A 50 SHEET 3 E 3 LYS A 278 ILE A 280 1 O LYS A 278 N SER A 82 SHEET 1 F 6 TYR A 114 ARG A 118 0 SHEET 2 F 6 TRP A 271 ARG A 276 -1 O SER A 274 N ASN A 116 SHEET 3 F 6 ASP A 183 SER A 192 -1 N ASP A 183 O ALA A 273 SHEET 4 F 6 VAL A 264 PRO A 267 -1 O LEU A 265 N GLY A 189 SHEET 5 F 6 MET A 156 PRO A 161 -1 N ALA A 157 O LEU A 266 SHEET 6 F 6 TYR A 135 GLY A 138 -1 N ILE A 136 O VAL A 160 SHEET 1 G 4 TYR A 114 ARG A 118 0 SHEET 2 G 4 TRP A 271 ARG A 276 -1 O SER A 274 N ASN A 116 SHEET 3 G 4 ASP A 183 SER A 192 -1 N ASP A 183 O ALA A 273 SHEET 4 G 4 ARG A 242 GLN A 250 -1 O ASP A 246 N TRP A 188 SHEET 1 H 4 LEU A 170 VAL A 172 0 SHEET 2 H 4 GLY A 256 TYR A 260 -1 O TYR A 260 N LEU A 170 SHEET 3 H 4 LYS A 209 ALA A 214 -1 N THR A 211 O ALA A 259 SHEET 4 H 4 VAL A 217 VAL A 222 -1 O TYR A 221 N PHE A 210 SHEET 1 I 3 GLY A 298 LEU A 300 0 SHEET 2 I 3 CYS A 292 HIS A 294 -1 N CYS A 292 O LEU A 300 SHEET 3 I 3 ALA A 314 GLY A 316 -1 O ILE A 315 N LEU A 293 SHEET 1 J 2 TYR A 306 TYR A 307 0 SHEET 2 J 2 ILE A 320 TRP A 321 1 O ILE A 320 N TYR A 307 SSBOND 1 CYS A 4 CYS B 137 1555 1555 2.04 SSBOND 2 CYS A 54 CYS A 57 1555 1555 2.01 SSBOND 3 CYS A 60 CYS A 72 1555 1555 2.02 SSBOND 4 CYS A 94 CYS A 143 1555 1555 2.05 SSBOND 5 CYS A 178 CYS A 272 1555 1555 2.04 SSBOND 6 CYS A 292 CYS A 318 1555 1555 2.04 SSBOND 7 CYS B 144 CYS B 148 1555 1555 2.05 LINK ND2 ASN A 25 C1 NAG C 1 1555 1555 1.45 LINK ND2 ASN A 145 C1 NAG A 347 1555 1555 1.45 LINK ND2 ASN A 301 C1 NAG E 1 1555 1555 1.45 LINK ND2 ASN A 330 C1 NAG F 1 1555 1555 1.45 LINK ND2 ASN B 145 C1 NAG B 170 1555 1555 1.46 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.44 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.45 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.45 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.44 LINK O4 NAG G 1 C1 GAL G 2 1555 1555 1.45 LINK O6 GAL G 2 C2 SIA G 3 1555 1555 1.44 CRYST1 98.369 98.369 135.896 90.00 90.00 120.00 P 3 2 1 6 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 0.010166 0.005869 0.000000 0.00000 SCALE2 0.000000 0.011738 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007359 0.00000