HEADER IMMUNE SYSTEM 02-DEC-13 3WN4 TITLE CRYSTAL STRUCTURE OF HUMAN TLR8 IN COMPLEX WITH DS-877 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOLL-LIKE RECEPTOR 8; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TLR8, UNQ249/PRO286; SOURCE 6 EXPRESSION_SYSTEM: DROSOPHILA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7215; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: S2 KEYWDS LEUCINE RICH REPEAT, RNA, GLYCOSYLATION, INNATE IMMUNITY, RNA KEYWDS 2 RECOGNITION, SSRNAR, STRUCTURE-BASED LIGAND DESIGN, TLR8-SPECIFIC KEYWDS 3 AGONIST, VACCINE ADJUVANTS, ANTIVIRAL-ANTITUMOR DRUG BINDING, IMMUNE KEYWDS 4 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR H.TANJI,U.OHTO,T.SHIMIZU REVDAT 3 24-AUG-22 3WN4 1 JRNL HETSYN REVDAT 2 29-JUL-20 3WN4 1 COMPND REMARK SEQADV HETNAM REVDAT 2 2 1 LINK SITE ATOM REVDAT 1 19-FEB-14 3WN4 0 JRNL AUTH H.P.KOKATLA,D.SIL,H.TANJI,U.OHTO,S.S.MALLADI,L.M.FOX, JRNL AUTH 2 T.SHIMIZU,S.A.DAVID JRNL TITL STRUCTURE-BASED DESIGN OF NOVEL HUMAN TOLL-LIKE RECEPTOR 8 JRNL TITL 2 AGONISTS. JRNL REF CHEMMEDCHEM V. 9 719 2014 JRNL REFN ESSN 1860-7187 JRNL PMID 24474703 JRNL DOI 10.1002/CMDC.201300573 REMARK 2 REMARK 2 RESOLUTION. 1.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 80153 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4237 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) : 1.81 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5481 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.22 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE SET COUNT : 255 REMARK 3 BIN FREE R VALUE : 0.3070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6013 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 283 REMARK 3 SOLVENT ATOMS : 472 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.112 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.112 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.086 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.883 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6447 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6117 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8765 ; 2.048 ; 2.023 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14008 ; 0.966 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 743 ; 6.829 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 298 ;38.676 ;24.899 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1091 ;14.677 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;17.384 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1045 ; 0.131 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7063 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1456 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2984 ; 2.413 ; 2.600 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2983 ; 2.405 ; 2.598 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3723 ; 3.116 ; 3.879 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3724 ; 3.120 ; 3.881 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3463 ; 3.788 ; 3.101 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3463 ; 3.787 ; 3.101 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5043 ; 5.717 ; 4.484 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7339 ; 7.071 ;22.120 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7168 ; 7.031 ;21.861 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 : 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 3WN4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000096543. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 4.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81803 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 97.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12300 REMARK 200 FOR THE DATA SET : 23.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% (W/V) PEG 3350, 0.1M SODIUM REMARK 280 CITRATE PH 4.4, 0.3M POTASSIUM FORMATE, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 69.18050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.76400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 69.18050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 51.76400 REMARK 290 SMTRY3 4 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: DIMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 ARG A 23 REMARK 465 SER A 24 REMARK 465 PRO A 25 REMARK 465 TRP A 26 REMARK 465 GLU A 27 REMARK 465 GLU A 28 REMARK 465 ASN A 29 REMARK 465 PHE A 30 REMARK 465 SER A 31 REMARK 465 GLN A 41 REMARK 465 ASN A 42 REMARK 465 VAL A 100 REMARK 465 GLN A 101 REMARK 465 HIS A 102 REMARK 465 GLN A 103 REMARK 465 ASN A 104 REMARK 465 GLY A 105 REMARK 465 ASN A 106 REMARK 465 PRO A 107 REMARK 465 GLY A 108 REMARK 465 ILE A 109 REMARK 465 GLN A 110 REMARK 465 SER A 111 REMARK 465 ASN A 112 REMARK 465 VAL A 434 REMARK 465 LYS A 435 REMARK 465 ASP A 436 REMARK 465 THR A 437 REMARK 465 ARG A 438 REMARK 465 GLN A 439 REMARK 465 SER A 440 REMARK 465 TYR A 441 REMARK 465 ALA A 442 REMARK 465 ASN A 443 REMARK 465 SER A 444 REMARK 465 SER A 445 REMARK 465 SER A 446 REMARK 465 PHE A 447 REMARK 465 GLN A 448 REMARK 465 ARG A 449 REMARK 465 HIS A 450 REMARK 465 ILE A 451 REMARK 465 ARG A 452 REMARK 465 LYS A 453 REMARK 465 ARG A 454 REMARK 465 ARG A 455 REMARK 465 SER A 456 REMARK 465 THR A 457 REMARK 465 ASP A 458 REMARK 465 LEU A 819 REMARK 465 THR A 820 REMARK 465 THR A 821 REMARK 465 CYS A 822 REMARK 465 VAL A 823 REMARK 465 SER A 824 REMARK 465 ASP A 825 REMARK 465 VAL A 826 REMARK 465 THR A 827 REMARK 465 GLU A 828 REMARK 465 PHE A 829 REMARK 465 LEU A 830 REMARK 465 VAL A 831 REMARK 465 PRO A 832 REMARK 465 ARG A 833 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PHE A 678 CG CD1 CD2 CE1 CE2 CZ 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 THR A 287 CB THR A 287 CG2 -0.238 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 52 CG - CD - NE ANGL. DEV. = -13.2 DEGREES REMARK 500 ARG A 338 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP A 343 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ASP A 601 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 MET A 675 CG - SD - CE ANGL. DEV. = -13.3 DEGREES REMARK 500 ARG A 689 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ASP A 705 CB - CG - OD1 ANGL. DEV. = 5.9 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 SER A 44 160.91 176.06 REMARK 500 ASN A 73 -157.93 -109.13 REMARK 500 GLN A 84 118.12 -36.11 REMARK 500 ASN A 156 -164.95 -120.15 REMARK 500 PHE A 183 -126.66 52.18 REMARK 500 SER A 214 -35.21 67.79 REMARK 500 LEU A 286 56.20 -93.16 REMARK 500 ASN A 321 -160.58 -111.19 REMARK 500 SER A 329 22.78 -152.65 REMARK 500 VAL A 378 102.71 83.30 REMARK 500 LEU A 396 98.09 -69.05 REMARK 500 ASN A 419 73.99 -169.52 REMARK 500 GLU A 427 62.59 66.80 REMARK 500 ASN A 428 -156.40 -131.51 REMARK 500 ASN A 491 -162.01 -111.78 REMARK 500 ASN A 540 -155.81 -118.51 REMARK 500 ARG A 541 53.02 -141.01 REMARK 500 ASP A 601 -58.03 76.37 REMARK 500 ASN A 618 -165.03 -117.30 REMARK 500 ASN A 674 -153.47 -115.18 REMARK 500 ASN A 698 -158.68 -121.77 REMARK 500 ASN A 746 -149.57 -117.15 REMARK 500 THR A 758 -113.47 -131.13 REMARK 500 LEU A 817 154.02 66.53 REMARK 500 REMARK 500 REMARK: NULL DBREF 3WN4 A 27 827 UNP Q9NR97 TLR8_HUMAN 27 827 SEQADV 3WN4 ARG A 23 UNP Q9NR97 EXPRESSION TAG SEQADV 3WN4 SER A 24 UNP Q9NR97 EXPRESSION TAG SEQADV 3WN4 PRO A 25 UNP Q9NR97 EXPRESSION TAG SEQADV 3WN4 TRP A 26 UNP Q9NR97 EXPRESSION TAG SEQADV 3WN4 GLU A 828 UNP Q9NR97 EXPRESSION TAG SEQADV 3WN4 PHE A 829 UNP Q9NR97 EXPRESSION TAG SEQADV 3WN4 LEU A 830 UNP Q9NR97 EXPRESSION TAG SEQADV 3WN4 VAL A 831 UNP Q9NR97 EXPRESSION TAG SEQADV 3WN4 PRO A 832 UNP Q9NR97 EXPRESSION TAG SEQADV 3WN4 ARG A 833 UNP Q9NR97 EXPRESSION TAG SEQRES 1 A 811 ARG SER PRO TRP GLU GLU ASN PHE SER ARG SER TYR PRO SEQRES 2 A 811 CYS ASP GLU LYS LYS GLN ASN ASP SER VAL ILE ALA GLU SEQRES 3 A 811 CYS SER ASN ARG ARG LEU GLN GLU VAL PRO GLN THR VAL SEQRES 4 A 811 GLY LYS TYR VAL THR GLU LEU ASP LEU SER ASP ASN PHE SEQRES 5 A 811 ILE THR HIS ILE THR ASN GLU SER PHE GLN GLY LEU GLN SEQRES 6 A 811 ASN LEU THR LYS ILE ASN LEU ASN HIS ASN PRO ASN VAL SEQRES 7 A 811 GLN HIS GLN ASN GLY ASN PRO GLY ILE GLN SER ASN GLY SEQRES 8 A 811 LEU ASN ILE THR ASP GLY ALA PHE LEU ASN LEU LYS ASN SEQRES 9 A 811 LEU ARG GLU LEU LEU LEU GLU ASP ASN GLN LEU PRO GLN SEQRES 10 A 811 ILE PRO SER GLY LEU PRO GLU SER LEU THR GLU LEU SER SEQRES 11 A 811 LEU ILE GLN ASN ASN ILE TYR ASN ILE THR LYS GLU GLY SEQRES 12 A 811 ILE SER ARG LEU ILE ASN LEU LYS ASN LEU TYR LEU ALA SEQRES 13 A 811 TRP ASN CYS TYR PHE ASN LYS VAL CYS GLU LYS THR ASN SEQRES 14 A 811 ILE GLU ASP GLY VAL PHE GLU THR LEU THR ASN LEU GLU SEQRES 15 A 811 LEU LEU SER LEU SER PHE ASN SER LEU SER HIS VAL PRO SEQRES 16 A 811 PRO LYS LEU PRO SER SER LEU ARG LYS LEU PHE LEU SER SEQRES 17 A 811 ASN THR GLN ILE LYS TYR ILE SER GLU GLU ASP PHE LYS SEQRES 18 A 811 GLY LEU ILE ASN LEU THR LEU LEU ASP LEU SER GLY ASN SEQRES 19 A 811 CYS PRO ARG CYS PHE ASN ALA PRO PHE PRO CYS VAL PRO SEQRES 20 A 811 CYS ASP GLY GLY ALA SER ILE ASN ILE ASP ARG PHE ALA SEQRES 21 A 811 PHE GLN ASN LEU THR GLN LEU ARG TYR LEU ASN LEU SER SEQRES 22 A 811 SER THR SER LEU ARG LYS ILE ASN ALA ALA TRP PHE LYS SEQRES 23 A 811 ASN MET PRO HIS LEU LYS VAL LEU ASP LEU GLU PHE ASN SEQRES 24 A 811 TYR LEU VAL GLY GLU ILE ALA SER GLY ALA PHE LEU THR SEQRES 25 A 811 MET LEU PRO ARG LEU GLU ILE LEU ASP LEU SER PHE ASN SEQRES 26 A 811 TYR ILE LYS GLY SER TYR PRO GLN HIS ILE ASN ILE SER SEQRES 27 A 811 ARG ASN PHE SER LYS LEU LEU SER LEU ARG ALA LEU HIS SEQRES 28 A 811 LEU ARG GLY TYR VAL PHE GLN GLU LEU ARG GLU ASP ASP SEQRES 29 A 811 PHE GLN PRO LEU MET GLN LEU PRO ASN LEU SER THR ILE SEQRES 30 A 811 ASN LEU GLY ILE ASN PHE ILE LYS GLN ILE ASP PHE LYS SEQRES 31 A 811 LEU PHE GLN ASN PHE SER ASN LEU GLU ILE ILE TYR LEU SEQRES 32 A 811 SER GLU ASN ARG ILE SER PRO LEU VAL LYS ASP THR ARG SEQRES 33 A 811 GLN SER TYR ALA ASN SER SER SER PHE GLN ARG HIS ILE SEQRES 34 A 811 ARG LYS ARG ARG SER THR ASP PHE GLU PHE ASP PRO HIS SEQRES 35 A 811 SER ASN PHE TYR HIS PHE THR ARG PRO LEU ILE LYS PRO SEQRES 36 A 811 GLN CYS ALA ALA TYR GLY LYS ALA LEU ASP LEU SER LEU SEQRES 37 A 811 ASN SER ILE PHE PHE ILE GLY PRO ASN GLN PHE GLU ASN SEQRES 38 A 811 LEU PRO ASP ILE ALA CYS LEU ASN LEU SER ALA ASN SER SEQRES 39 A 811 ASN ALA GLN VAL LEU SER GLY THR GLU PHE SER ALA ILE SEQRES 40 A 811 PRO HIS VAL LYS TYR LEU ASP LEU THR ASN ASN ARG LEU SEQRES 41 A 811 ASP PHE ASP ASN ALA SER ALA LEU THR GLU LEU SER ASP SEQRES 42 A 811 LEU GLU VAL LEU ASP LEU SER TYR ASN SER HIS TYR PHE SEQRES 43 A 811 ARG ILE ALA GLY VAL THR HIS HIS LEU GLU PHE ILE GLN SEQRES 44 A 811 ASN PHE THR ASN LEU LYS VAL LEU ASN LEU SER HIS ASN SEQRES 45 A 811 ASN ILE TYR THR LEU THR ASP LYS TYR ASN LEU GLU SER SEQRES 46 A 811 LYS SER LEU VAL GLU LEU VAL PHE SER GLY ASN ARG LEU SEQRES 47 A 811 ASP ILE LEU TRP ASN ASP ASP ASP ASN ARG TYR ILE SER SEQRES 48 A 811 ILE PHE LYS GLY LEU LYS ASN LEU THR ARG LEU ASP LEU SEQRES 49 A 811 SER LEU ASN ARG LEU LYS HIS ILE PRO ASN GLU ALA PHE SEQRES 50 A 811 LEU ASN LEU PRO ALA SER LEU THR GLU LEU HIS ILE ASN SEQRES 51 A 811 ASP ASN MET LEU LYS PHE PHE ASN TRP THR LEU LEU GLN SEQRES 52 A 811 GLN PHE PRO ARG LEU GLU LEU LEU ASP LEU ARG GLY ASN SEQRES 53 A 811 LYS LEU LEU PHE LEU THR ASP SER LEU SER ASP PHE THR SEQRES 54 A 811 SER SER LEU ARG THR LEU LEU LEU SER HIS ASN ARG ILE SEQRES 55 A 811 SER HIS LEU PRO SER GLY PHE LEU SER GLU VAL SER SER SEQRES 56 A 811 LEU LYS HIS LEU ASP LEU SER SER ASN LEU LEU LYS THR SEQRES 57 A 811 ILE ASN LYS SER ALA LEU GLU THR LYS THR THR THR LYS SEQRES 58 A 811 LEU SER MET LEU GLU LEU HIS GLY ASN PRO PHE GLU CYS SEQRES 59 A 811 THR CYS ASP ILE GLY ASP PHE ARG ARG TRP MET ASP GLU SEQRES 60 A 811 HIS LEU ASN VAL LYS ILE PRO ARG LEU VAL ASP VAL ILE SEQRES 61 A 811 CYS ALA SER PRO GLY ASP GLN ARG GLY LYS SER ILE VAL SEQRES 62 A 811 SER LEU GLU LEU THR THR CYS VAL SER ASP VAL THR GLU SEQRES 63 A 811 PHE LEU VAL PRO ARG MODRES 3WN4 ASN A 546 ASN GLYCOSYLATION SITE MODRES 3WN4 ASN A 88 ASN GLYCOSYLATION SITE MODRES 3WN4 ASN A 416 ASN GLYCOSYLATION SITE MODRES 3WN4 ASN A 395 ASN GLYCOSYLATION SITE MODRES 3WN4 ASN A 115 ASN GLYCOSYLATION SITE MODRES 3WN4 ASN A 582 ASN GLYCOSYLATION SITE MODRES 3WN4 ASN A 680 ASN GLYCOSYLATION SITE MODRES 3WN4 ASN A 640 ASN GLYCOSYLATION SITE MODRES 3WN4 ASN A 511 ASN GLYCOSYLATION SITE MODRES 3WN4 ASN A 293 ASN GLYCOSYLATION SITE MODRES 3WN4 ASN A 247 ASN GLYCOSYLATION SITE MODRES 3WN4 ASN A 590 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET MAN B 4 11 HET MAN B 5 11 HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET NAG D 1 14 HET NAG D 2 14 HET BMA D 3 11 HET D87 A 901 18 HET NAG A 902 14 HET NAG A 903 14 HET NAG A 904 14 HET NAG A 910 14 HET NAG A 911 14 HET NAG A 915 14 HET NAG A 916 14 HET NAG A 920 14 HET NAG A 921 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM D87 2-BUTYLFURO[2,3-C]QUINOLIN-4-AMINE 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 MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 NAG 15(C8 H15 N O6) FORMUL 2 BMA 3(C6 H12 O6) FORMUL 2 MAN 2(C6 H12 O6) FORMUL 5 D87 C15 H16 N2 O FORMUL 15 HOH *472(H2 O) HELIX 1 1 THR A 162 SER A 167 1 6 HELIX 2 2 CYS A 270 ALA A 274 5 5 HELIX 3 3 ASN A 303 LYS A 308 5 6 HELIX 4 4 LEU A 323 GLY A 330 1 8 HELIX 5 5 ALA A 331 LEU A 336 5 6 HELIX 6 6 SER A 360 LEU A 366 5 7 HELIX 7 7 ARG A 383 MET A 391 5 9 HELIX 8 8 PHE A 411 PHE A 417 5 7 HELIX 9 9 LYS A 476 ALA A 481 1 6 HELIX 10 10 ASN A 564 ARG A 569 1 6 HELIX 11 11 LEU A 577 PHE A 583 5 7 HELIX 12 12 ARG A 619 TRP A 624 1 6 HELIX 13 13 PRO A 655 ASN A 661 1 7 HELIX 14 14 ASN A 680 PHE A 687 5 8 HELIX 15 15 SER A 706 PHE A 710 5 5 HELIX 16 16 ASN A 752 GLU A 757 1 6 HELIX 17 17 THR A 777 ASP A 779 5 3 HELIX 18 18 ILE A 780 HIS A 790 1 11 HELIX 19 19 ARG A 797 VAL A 801 5 5 SHEET 1 A28 ASP A 37 LYS A 39 0 SHEET 2 A28 ILE A 46 GLU A 48 -1 O GLU A 48 N ASP A 37 SHEET 3 A28 GLU A 67 ASP A 69 1 O GLU A 67 N ALA A 47 SHEET 4 A28 LYS A 91 ASN A 93 1 O ASN A 93 N LEU A 68 SHEET 5 A28 GLU A 129 LEU A 131 1 O LEU A 131 N ILE A 92 SHEET 6 A28 GLU A 150 SER A 152 1 O GLU A 150 N LEU A 130 SHEET 7 A28 ASN A 174 TYR A 176 1 O ASN A 174 N LEU A 151 SHEET 8 A28 LEU A 205 SER A 207 1 O LEU A 205 N LEU A 175 SHEET 9 A28 LYS A 226 PHE A 228 1 O PHE A 228 N LEU A 206 SHEET 10 A28 LEU A 250 ASP A 252 1 O ASP A 252 N LEU A 227 SHEET 11 A28 TYR A 291 ASN A 293 1 O ASN A 293 N LEU A 251 SHEET 12 A28 VAL A 315 ASP A 317 1 O ASP A 317 N LEU A 292 SHEET 13 A28 ILE A 341 ASP A 343 1 O ILE A 341 N LEU A 316 SHEET 14 A28 ALA A 371 HIS A 373 1 O HIS A 373 N LEU A 342 SHEET 15 A28 THR A 398 ASN A 400 1 O THR A 398 N LEU A 372 SHEET 16 A28 ILE A 422 TYR A 424 1 O TYR A 424 N ILE A 399 SHEET 17 A28 ALA A 485 ASP A 487 1 O ASP A 487 N ILE A 423 SHEET 18 A28 CYS A 509 ASN A 511 1 O CYS A 509 N LEU A 486 SHEET 19 A28 TYR A 534 ASP A 536 1 O ASP A 536 N LEU A 510 SHEET 20 A28 VAL A 558 ASP A 560 1 O VAL A 558 N LEU A 535 SHEET 21 A28 VAL A 588 ASN A 590 1 O VAL A 588 N LEU A 559 SHEET 22 A28 GLU A 612 VAL A 614 1 O GLU A 612 N LEU A 589 SHEET 23 A28 ARG A 643 ASP A 645 1 O ARG A 643 N LEU A 613 SHEET 24 A28 GLU A 668 HIS A 670 1 O HIS A 670 N LEU A 644 SHEET 25 A28 LEU A 692 ASP A 694 1 O ASP A 694 N LEU A 669 SHEET 26 A28 THR A 716 LEU A 718 1 O LEU A 718 N LEU A 693 SHEET 27 A28 HIS A 740 ASP A 742 1 O HIS A 740 N LEU A 717 SHEET 28 A28 MET A 766 GLU A 768 1 O MET A 766 N LEU A 741 SHEET 1 B 2 HIS A 77 ILE A 78 0 SHEET 2 B 2 ASN A 115 ILE A 116 1 O ASN A 115 N ILE A 78 SHEET 1 C 2 ASN A 160 ILE A 161 0 SHEET 2 C 2 ASN A 191 ILE A 192 1 O ASN A 191 N ILE A 161 SHEET 1 D 2 TYR A 236 ILE A 237 0 SHEET 2 D 2 ASN A 277 ILE A 278 1 O ASN A 277 N ILE A 237 SHEET 1 E 2 GLU A 381 LEU A 382 0 SHEET 2 E 2 GLN A 408 ILE A 409 1 O GLN A 408 N LEU A 382 SHEET 1 F 2 PHE A 774 GLU A 775 0 SHEET 2 F 2 CYS A 803 SER A 805 1 O ALA A 804 N PHE A 774 SSBOND 1 CYS A 36 CYS A 49 1555 1555 2.11 SSBOND 2 CYS A 181 CYS A 187 1555 1555 2.13 SSBOND 3 CYS A 257 CYS A 270 1555 1555 2.10 SSBOND 4 CYS A 260 CYS A 267 1555 1555 2.14 SSBOND 5 CYS A 479 CYS A 509 1555 1555 2.02 SSBOND 6 CYS A 776 CYS A 803 1555 1555 2.00 LINK ND2 ASN A 88 C1 NAG A 902 1555 1555 1.45 LINK ND2 ASN A 115 C1 NAG A 903 1555 1555 1.46 LINK ND2 ASN A 247 C1 NAG A 904 1555 1555 1.50 LINK ND2 ASN A 293 C1 NAG B 1 1555 1555 1.49 LINK ND2 ASN A 395 C1 NAG A 910 1555 1555 1.46 LINK ND2 ASN A 416 C1 NAG A 911 1555 1555 1.45 LINK ND2 ASN A 511 C1 NAG C 1 1555 1555 1.47 LINK ND2 ASN A 546 C1 NAG A 915 1555 1555 1.44 LINK ND2 ASN A 582 C1 NAG A 916 1555 1555 1.46 LINK ND2 ASN A 590 C1 NAG D 1 1555 1555 1.50 LINK ND2 ASN A 640 C1 NAG A 920 1555 1555 1.47 LINK ND2 ASN A 680 C1 NAG A 921 1555 1555 1.47 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.40 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.43 LINK O3 BMA B 3 C1 MAN B 4 1555 1555 1.44 LINK O6 BMA B 3 C2 MAN B 5 1555 1555 1.44 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.40 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.45 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.42 LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.44 CISPEP 1 TYR A 34 PRO A 35 0 -0.06 CISPEP 2 ASN A 97 PRO A 98 0 -1.69 CISPEP 3 SER A 805 PRO A 806 0 -5.89 CRYST1 138.361 103.528 70.724 90.00 106.74 90.00 C 1 2 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 0.007227 0.000000 0.002173 0.00000 SCALE2 0.000000 0.009659 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014765 0.00000