PDB Short entry for 3ULA HEADER IMMUNE SYSTEM 10-NOV-11 3ULA TITLE CRYSTAL STRUCTURE OF THE TV3 MUTANT F63W-MD-2-ERITORAN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOLL-LIKE RECEPTOR 4, VARIABLE LYMPHOCYTE RECEPTOR B; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: UNP RESIDUES 27-228, UNP RESIDUES 126-199; COMPND 5 SYNONYM: HTOLL; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: THE FUSION PROTEIN OF TLR4 (UNP RESIDUES 27-228) AND COMPND 9 VLRB (UNP RESIDUES 126-199); COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: LYMPHOCYTE ANTIGEN 96; COMPND 12 CHAIN: B, D; COMPND 13 FRAGMENT: UNP RESIDUES 19-158; COMPND 14 SYNONYM: LY-96, ESOP-1, PROTEIN MD-2; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS, EPTATRETUS BURGERI; SOURCE 3 ORGANISM_COMMON: HUMAN, INSHORE HAGFISH; SOURCE 4 ORGANISM_TAXID: 9606, 7764; SOURCE 5 GENE: TLR4, VLRB; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: LY96, ESOP1, MD2; SOURCE 15 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 16 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS LRR, LPS BINDING, MD-2, EXTRACELLULAR MATRIX, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR H.J.KIM,H.K.CHEONG,Y.H.JEON REVDAT 5 01-NOV-23 3ULA 1 HETSYN REVDAT 4 29-JUL-20 3ULA 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 HETSYN LINK SITE ATOM REVDAT 3 23-AUG-17 3ULA 1 SOURCE REMARK REVDAT 2 09-OCT-13 3ULA 1 REMARK REVDAT 1 04-APR-12 3ULA 0 JRNL AUTH J.HAN,H.J.KIM,S.C.LEE,S.HONG,K.PARK,Y.H.JEON,D.KIM, JRNL AUTH 2 H.K.CHEONG,H.S.KIM JRNL TITL STRUCTURE-BASED RATIONAL DESIGN OF A TOLL-LIKE RECEPTOR 4 JRNL TITL 2 (TLR4) DECOY RECEPTOR WITH HIGH BINDING AFFINITY FOR A JRNL TITL 3 TARGET PROTEIN. JRNL REF PLOS ONE V. 7 30929 2012 JRNL REFN ESSN 1932-6203 JRNL PMID 22363519 JRNL DOI 10.1371/JOURNAL.PONE.0030929 REMARK 2 REMARK 2 RESOLUTION. 3.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 15790 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.306 REMARK 3 FREE R VALUE : 0.341 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 769 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.79 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6650 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 312 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3ULA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000068896. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15854 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 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 <I/SIGMA(I)> 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: 2Z65 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE (PH4.5), 22% W/V REMARK 280 PEG 8000, 0.2M LITHIUM SULFATE, VAPOR DIFFUSION, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 40.10500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.75300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 63.46750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.75300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.10500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 63.46750 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, D, E 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, F 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 25 REMARK 465 SER A 26 REMARK 465 THR A 303 REMARK 465 GLY B 17 REMARK 465 SER B 18 REMARK 465 GLY C 25 REMARK 465 SER C 26 REMARK 465 THR C 303 REMARK 465 GLY D 17 REMARK 465 SER D 18 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 PRO A 145 C - N - CA ANGL. DEV. = 9.1 DEGREES REMARK 500 PRO A 202 C - N - CA ANGL. DEV. = 11.5 DEGREES REMARK 500 PRO B 142 C - N - CA ANGL. DEV. = -13.2 DEGREES REMARK 500 PRO B 142 C - N - CD ANGL. DEV. = 13.5 DEGREES REMARK 500 PRO C 145 C - N - CA ANGL. DEV. = 9.1 DEGREES REMARK 500 PRO C 202 C - N - CA ANGL. DEV. = 11.7 DEGREES REMARK 500 PRO D 142 C - N - CA ANGL. DEV. = -13.8 DEGREES REMARK 500 PRO D 142 C - N - CD ANGL. DEV. = 14.0 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 ASN A 35 16.27 56.50 REMARK 500 ILE A 36 -56.34 -131.70 REMARK 500 CYS A 40 44.37 -85.71 REMARK 500 LEU A 43 30.41 -87.05 REMARK 500 ASN A 44 27.96 43.86 REMARK 500 PRO A 49 -170.99 -57.78 REMARK 500 ASP A 50 2.39 -177.18 REMARK 500 PRO A 53 162.20 -38.49 REMARK 500 THR A 56 136.74 -37.26 REMARK 500 PRO A 65 53.38 -50.17 REMARK 500 ARG A 67 -44.17 39.50 REMARK 500 SER A 71 136.48 -34.56 REMARK 500 SER A 73 -12.41 -44.55 REMARK 500 PHE A 75 -7.87 -47.31 REMARK 500 PRO A 78 -2.98 -56.24 REMARK 500 GLN A 81 -53.34 -122.22 REMARK 500 LEU A 85 39.67 -140.01 REMARK 500 ARG A 87 67.43 31.00 REMARK 500 GLU A 89 16.63 41.10 REMARK 500 ASP A 95 148.78 -34.95 REMARK 500 GLN A 99 -43.51 -18.87 REMARK 500 LEU A 101 58.31 -94.03 REMARK 500 PRO A 113 49.06 -50.37 REMARK 500 GLN A 115 -26.55 -144.84 REMARK 500 LEU A 119 35.62 -73.36 REMARK 500 ALA A 121 -68.83 -28.51 REMARK 500 LEU A 125 48.21 -80.78 REMARK 500 GLN A 129 -57.52 -135.32 REMARK 500 ALA A 133 37.06 -155.88 REMARK 500 PRO A 145 43.69 -52.89 REMARK 500 ASN A 160 -155.91 -124.75 REMARK 500 LEU A 167 123.95 -28.91 REMARK 500 TYR A 170 -17.35 -48.35 REMARK 500 ASN A 173 -6.55 -59.30 REMARK 500 LEU A 174 43.55 -86.80 REMARK 500 THR A 175 22.42 -58.54 REMARK 500 ASN A 176 -5.53 -154.10 REMARK 500 LEU A 182 34.02 -146.44 REMARK 500 ASN A 185 -161.66 -115.88 REMARK 500 CYS A 192 -80.57 -56.60 REMARK 500 THR A 193 -44.66 -25.98 REMARK 500 ASP A 194 -29.35 -35.67 REMARK 500 ARG A 196 -71.90 -30.92 REMARK 500 VAL A 197 -34.50 -34.11 REMARK 500 ASN A 205 50.01 -97.44 REMARK 500 PRO A 214 39.50 -83.89 REMARK 500 ASN A 216 16.27 -146.20 REMARK 500 ARG A 227 78.31 -109.01 REMARK 500 ASN A 236 -141.64 -107.87 REMARK 500 GLN A 237 45.08 -143.41 REMARK 500 REMARK 500 THIS ENTRY HAS 167 RAMACHANDRAN OUTLIERS. 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 A 1205 REMARK 610 NAG C 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UL7 RELATED DB: PDB REMARK 900 RELATED ID: 3UL8 RELATED DB: PDB REMARK 900 RELATED ID: 3UL9 RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 FOR THE CHAIN B/D, THE PROTEIN OF MD2 (UNP RESIDUES 19-158), GLY56 REMARK 999 IS NATURAL VARIANT. FOR THE CHAIN A/C, THE FUSION PROTEIN OF TLR4 REMARK 999 (UNP RESIDUES 27-228) AND VLRB.61 (UNP RESIDUES 126-199). DBREF 3ULA A 27 228 UNP O00206 TLR4_HUMAN 27 228 DBREF 3ULA A 229 302 UNP Q4G1L2 Q4G1L2_EPTBU 126 199 DBREF 3ULA B 19 158 UNP Q9Y6Y9 LY96_HUMAN 19 158 DBREF 3ULA C 27 228 UNP O00206 TLR4_HUMAN 27 228 DBREF 3ULA C 229 302 UNP Q4G1L2 Q4G1L2_EPTBU 126 199 DBREF 3ULA D 19 158 UNP Q9Y6Y9 LY96_HUMAN 19 158 SEQADV 3ULA GLY A 25 UNP O00206 EXPRESSION TAG SEQADV 3ULA SER A 26 UNP O00206 EXPRESSION TAG SEQADV 3ULA TRP A 63 UNP O00206 PHE 63 ENGINEERED MUTATION SEQADV 3ULA THR A 303 UNP Q4G1L2 EXPRESSION TAG SEQADV 3ULA GLY B 17 UNP Q9Y6Y9 EXPRESSION TAG SEQADV 3ULA SER B 18 UNP Q9Y6Y9 EXPRESSION TAG SEQADV 3ULA GLY B 56 UNP Q9Y6Y9 ARG 56 SEE REMARK 999 SEQADV 3ULA GLY C 25 UNP O00206 EXPRESSION TAG SEQADV 3ULA SER C 26 UNP O00206 EXPRESSION TAG SEQADV 3ULA TRP C 63 UNP O00206 PHE 63 ENGINEERED MUTATION SEQADV 3ULA THR C 303 UNP Q4G1L2 EXPRESSION TAG SEQADV 3ULA GLY D 17 UNP Q9Y6Y9 EXPRESSION TAG SEQADV 3ULA SER D 18 UNP Q9Y6Y9 EXPRESSION TAG SEQADV 3ULA GLY D 56 UNP Q9Y6Y9 ARG 56 SEE REMARK 999 SEQRES 1 A 279 GLY SER GLU PRO CYS VAL GLU VAL VAL PRO ASN ILE THR SEQRES 2 A 279 TYR GLN CYS MET GLU LEU ASN PHE TYR LYS ILE PRO ASP SEQRES 3 A 279 ASN LEU PRO PHE SER THR LYS ASN LEU ASP LEU SER TRP SEQRES 4 A 279 ASN PRO LEU ARG HIS LEU GLY SER TYR SER PHE PHE SER SEQRES 5 A 279 PHE PRO GLU LEU GLN VAL LEU ASP LEU SER ARG CYS GLU SEQRES 6 A 279 ILE GLN THR ILE GLU ASP GLY ALA TYR GLN SER LEU SER SEQRES 7 A 279 HIS LEU SER THR LEU ILE LEU THR GLY ASN PRO ILE GLN SEQRES 8 A 279 SER LEU ALA LEU GLY ALA PHE SER GLY LEU SER SER LEU SEQRES 9 A 279 GLN LYS LEU VAL ALA VAL GLU THR ASN LEU ALA SER LEU SEQRES 10 A 279 GLU ASN PHE PRO ILE GLY HIS LEU LYS THR LEU LYS GLU SEQRES 11 A 279 LEU ASN VAL ALA HIS ASN LEU ILE GLN SER PHE LYS LEU SEQRES 12 A 279 PRO GLU TYR PHE SER ASN LEU THR ASN LEU GLU HIS LEU SEQRES 13 A 279 ASP LEU SER SER ASN LYS ILE GLN SER ILE TYR CYS THR SEQRES 14 A 279 ASP LEU ARG VAL LEU HIS GLN MET PRO LEU LEU ASN LEU SEQRES 15 A 279 SER LEU ASP LEU SER LEU ASN PRO MET ASN PHE ILE GLN SEQRES 16 A 279 PRO GLY ALA PHE LYS GLU ILE ARG LEU LYS GLU LEU ALA SEQRES 17 A 279 LEU ASP THR ASN GLN LEU LYS SER VAL PRO ASP GLY ILE SEQRES 18 A 279 PHE ASP ARG LEU THR SER LEU GLN LYS ILE TRP LEU HIS SEQRES 19 A 279 THR ASN PRO TRP ASP CYS SER CYS PRO ARG ILE ASP TYR SEQRES 20 A 279 LEU SER ARG TRP LEU ASN LYS ASN SER GLN LYS GLU GLN SEQRES 21 A 279 GLY SER ALA LYS CYS SER GLY SER GLY LYS PRO VAL ARG SEQRES 22 A 279 SER ILE ILE CYS PRO THR SEQRES 1 B 142 GLY SER GLN LYS GLN TYR TRP VAL CYS ASN SER SER ASP SEQRES 2 B 142 ALA SER ILE SER TYR THR TYR CYS ASP LYS MET GLN TYR SEQRES 3 B 142 PRO ILE SER ILE ASN VAL ASN PRO CYS ILE GLU LEU LYS SEQRES 4 B 142 GLY SER LYS GLY LEU LEU HIS ILE PHE TYR ILE PRO ARG SEQRES 5 B 142 ARG ASP LEU LYS GLN LEU TYR PHE ASN LEU TYR ILE THR SEQRES 6 B 142 VAL ASN THR MET ASN LEU PRO LYS ARG LYS GLU VAL ILE SEQRES 7 B 142 CYS ARG GLY SER ASP ASP ASP TYR SER PHE CYS ARG ALA SEQRES 8 B 142 LEU LYS GLY GLU THR VAL ASN THR THR ILE SER PHE SER SEQRES 9 B 142 PHE LYS GLY ILE LYS PHE SER LYS GLY LYS TYR LYS CYS SEQRES 10 B 142 VAL VAL GLU ALA ILE SER GLY SER PRO GLU GLU MET LEU SEQRES 11 B 142 PHE CYS LEU GLU PHE VAL ILE LEU HIS GLN PRO ASN SEQRES 1 C 279 GLY SER GLU PRO CYS VAL GLU VAL VAL PRO ASN ILE THR SEQRES 2 C 279 TYR GLN CYS MET GLU LEU ASN PHE TYR LYS ILE PRO ASP SEQRES 3 C 279 ASN LEU PRO PHE SER THR LYS ASN LEU ASP LEU SER TRP SEQRES 4 C 279 ASN PRO LEU ARG HIS LEU GLY SER TYR SER PHE PHE SER SEQRES 5 C 279 PHE PRO GLU LEU GLN VAL LEU ASP LEU SER ARG CYS GLU SEQRES 6 C 279 ILE GLN THR ILE GLU ASP GLY ALA TYR GLN SER LEU SER SEQRES 7 C 279 HIS LEU SER THR LEU ILE LEU THR GLY ASN PRO ILE GLN SEQRES 8 C 279 SER LEU ALA LEU GLY ALA PHE SER GLY LEU SER SER LEU SEQRES 9 C 279 GLN LYS LEU VAL ALA VAL GLU THR ASN LEU ALA SER LEU SEQRES 10 C 279 GLU ASN PHE PRO ILE GLY HIS LEU LYS THR LEU LYS GLU SEQRES 11 C 279 LEU ASN VAL ALA HIS ASN LEU ILE GLN SER PHE LYS LEU SEQRES 12 C 279 PRO GLU TYR PHE SER ASN LEU THR ASN LEU GLU HIS LEU SEQRES 13 C 279 ASP LEU SER SER ASN LYS ILE GLN SER ILE TYR CYS THR SEQRES 14 C 279 ASP LEU ARG VAL LEU HIS GLN MET PRO LEU LEU ASN LEU SEQRES 15 C 279 SER LEU ASP LEU SER LEU ASN PRO MET ASN PHE ILE GLN SEQRES 16 C 279 PRO GLY ALA PHE LYS GLU ILE ARG LEU LYS GLU LEU ALA SEQRES 17 C 279 LEU ASP THR ASN GLN LEU LYS SER VAL PRO ASP GLY ILE SEQRES 18 C 279 PHE ASP ARG LEU THR SER LEU GLN LYS ILE TRP LEU HIS SEQRES 19 C 279 THR ASN PRO TRP ASP CYS SER CYS PRO ARG ILE ASP TYR SEQRES 20 C 279 LEU SER ARG TRP LEU ASN LYS ASN SER GLN LYS GLU GLN SEQRES 21 C 279 GLY SER ALA LYS CYS SER GLY SER GLY LYS PRO VAL ARG SEQRES 22 C 279 SER ILE ILE CYS PRO THR SEQRES 1 D 142 GLY SER GLN LYS GLN TYR TRP VAL CYS ASN SER SER ASP SEQRES 2 D 142 ALA SER ILE SER TYR THR TYR CYS ASP LYS MET GLN TYR SEQRES 3 D 142 PRO ILE SER ILE ASN VAL ASN PRO CYS ILE GLU LEU LYS SEQRES 4 D 142 GLY SER LYS GLY LEU LEU HIS ILE PHE TYR ILE PRO ARG SEQRES 5 D 142 ARG ASP LEU LYS GLN LEU TYR PHE ASN LEU TYR ILE THR SEQRES 6 D 142 VAL ASN THR MET ASN LEU PRO LYS ARG LYS GLU VAL ILE SEQRES 7 D 142 CYS ARG GLY SER ASP ASP ASP TYR SER PHE CYS ARG ALA SEQRES 8 D 142 LEU LYS GLY GLU THR VAL ASN THR THR ILE SER PHE SER SEQRES 9 D 142 PHE LYS GLY ILE LYS PHE SER LYS GLY LYS TYR LYS CYS SEQRES 10 D 142 VAL VAL GLU ALA ILE SER GLY SER PRO GLU GLU MET LEU SEQRES 11 D 142 PHE CYS LEU GLU PHE VAL ILE LEU HIS GLN PRO ASN MODRES 3ULA ASN A 205 ASN GLYCOSYLATION SITE MODRES 3ULA ASN C 205 ASN GLYCOSYLATION SITE MODRES 3ULA ASN A 35 ASN GLYCOSYLATION SITE MODRES 3ULA ASN C 35 ASN GLYCOSYLATION SITE HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET NAG F 1 14 HET NAG F 2 14 HET BMA F 3 11 HET NAG A1201 14 HET NAG A1205 14 HET E55 A1206 89 HET E55 C 401 89 HET NAG C 402 14 HET NAG C 406 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM E55 3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)-3- HETNAM 2 E55 METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC-11- HETNAM 3 E55 ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}-2- HETNAM 4 E55 [(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO-ALPHA-D- HETNAM 5 E55 GLUCOPYRANOSE 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 E55 E5564; ERITORAN FORMUL 5 NAG 8(C8 H15 N O6) FORMUL 5 BMA 2(C6 H12 O6) FORMUL 9 E55 2(C66 H126 N2 O19 P2) HELIX 1 1 SER A 140 PHE A 144 5 5 HELIX 2 2 PRO A 168 LEU A 174 5 7 HELIX 3 3 CYS A 192 MET A 201 5 10 HELIX 4 4 ILE A 269 ASN A 279 1 11 HELIX 5 5 PRO A 295 ILE A 299 5 5 HELIX 6 6 TYR B 102 ALA B 107 5 6 HELIX 7 7 SER C 140 PHE C 144 5 5 HELIX 8 8 PRO C 168 LEU C 174 5 7 HELIX 9 9 CYS C 192 MET C 201 5 10 HELIX 10 10 ILE C 269 ASN C 279 1 11 HELIX 11 11 PRO C 295 ILE C 299 5 5 HELIX 12 12 TYR D 102 ALA D 107 5 6 SHEET 1 A 5 GLU A 31 VAL A 33 0 SHEET 2 A 5 THR A 37 GLN A 39 -1 O THR A 37 N VAL A 32 SHEET 3 A 5 ASN A 58 ASP A 60 1 O ASP A 60 N TYR A 38 SHEET 4 A 5 VAL A 82 ASP A 84 1 O VAL A 82 N LEU A 59 SHEET 5 A 5 THR A 106 ILE A 108 1 O ILE A 108 N LEU A 83 SHEET 1 B 2 HIS A 68 LEU A 69 0 SHEET 2 B 2 THR A 92 ILE A 93 1 O THR A 92 N LEU A 69 SHEET 1 C 7 LYS A 130 VAL A 132 0 SHEET 2 C 7 GLU A 154 ASN A 156 1 O GLU A 154 N LEU A 131 SHEET 3 C 7 HIS A 179 ASP A 181 1 O HIS A 179 N LEU A 155 SHEET 4 C 7 SER A 207 ASP A 209 1 O SER A 207 N LEU A 180 SHEET 5 C 7 GLU A 230 ALA A 232 1 O GLU A 230 N LEU A 208 SHEET 6 C 7 LYS A 254 TRP A 256 1 O LYS A 254 N LEU A 231 SHEET 7 C 7 GLU A 283 GLN A 284 1 O GLN A 284 N ILE A 255 SHEET 1 D 2 SER A 189 ILE A 190 0 SHEET 2 D 2 PHE A 217 ILE A 218 1 O PHE A 217 N ILE A 190 SHEET 1 E 6 TYR B 22 SER B 27 0 SHEET 2 E 6 ALA B 30 THR B 35 -1 O ILE B 32 N CYS B 25 SHEET 3 E 6 GLU B 150 LEU B 154 -1 O VAL B 152 N SER B 33 SHEET 4 E 6 TYR B 131 SER B 139 -1 N CYS B 133 O PHE B 151 SHEET 5 E 6 TYR B 75 THR B 81 -1 N TYR B 75 O ILE B 138 SHEET 6 E 6 ARG B 90 VAL B 93 -1 O ARG B 90 N LEU B 78 SHEET 1 F 5 TYR B 22 SER B 27 0 SHEET 2 F 5 ALA B 30 THR B 35 -1 O ILE B 32 N CYS B 25 SHEET 3 F 5 GLU B 150 LEU B 154 -1 O VAL B 152 N SER B 33 SHEET 4 F 5 TYR B 131 SER B 139 -1 N CYS B 133 O PHE B 151 SHEET 5 F 5 GLU B 144 PHE B 147 -1 O LEU B 146 N ALA B 137 SHEET 1 G 3 SER B 45 ASN B 49 0 SHEET 2 G 3 SER B 57 TYR B 65 -1 O LEU B 60 N ASN B 49 SHEET 3 G 3 VAL B 113 PHE B 121 -1 O PHE B 119 N GLY B 59 SHEET 1 H 5 GLU C 31 VAL C 33 0 SHEET 2 H 5 THR C 37 GLN C 39 -1 O THR C 37 N VAL C 32 SHEET 3 H 5 ASN C 58 ASP C 60 1 O ASP C 60 N TYR C 38 SHEET 4 H 5 VAL C 82 ASP C 84 1 O VAL C 82 N LEU C 59 SHEET 5 H 5 THR C 106 ILE C 108 1 O ILE C 108 N LEU C 83 SHEET 1 I 2 HIS C 68 LEU C 69 0 SHEET 2 I 2 THR C 92 ILE C 93 1 O THR C 92 N LEU C 69 SHEET 1 J 7 LYS C 130 VAL C 132 0 SHEET 2 J 7 GLU C 154 ASN C 156 1 O GLU C 154 N LEU C 131 SHEET 3 J 7 HIS C 179 ASP C 181 1 O HIS C 179 N LEU C 155 SHEET 4 J 7 SER C 207 ASP C 209 1 O SER C 207 N LEU C 180 SHEET 5 J 7 GLU C 230 ALA C 232 1 O GLU C 230 N LEU C 208 SHEET 6 J 7 LYS C 254 TRP C 256 1 O LYS C 254 N LEU C 231 SHEET 7 J 7 GLU C 283 GLN C 284 1 O GLN C 284 N ILE C 255 SHEET 1 K 2 SER C 189 ILE C 190 0 SHEET 2 K 2 PHE C 217 ILE C 218 1 O PHE C 217 N ILE C 190 SHEET 1 L 6 TYR D 22 SER D 27 0 SHEET 2 L 6 ALA D 30 THR D 35 -1 O ILE D 32 N CYS D 25 SHEET 3 L 6 GLU D 150 LEU D 154 -1 O VAL D 152 N SER D 33 SHEET 4 L 6 TYR D 131 SER D 139 -1 N CYS D 133 O PHE D 151 SHEET 5 L 6 TYR D 75 THR D 81 -1 N TYR D 75 O ILE D 138 SHEET 6 L 6 ARG D 90 VAL D 93 -1 O ARG D 90 N LEU D 78 SHEET 1 M 5 TYR D 22 SER D 27 0 SHEET 2 M 5 ALA D 30 THR D 35 -1 O ILE D 32 N CYS D 25 SHEET 3 M 5 GLU D 150 LEU D 154 -1 O VAL D 152 N SER D 33 SHEET 4 M 5 TYR D 131 SER D 139 -1 N CYS D 133 O PHE D 151 SHEET 5 M 5 GLU D 144 PHE D 147 -1 O LEU D 146 N ALA D 137 SHEET 1 N 3 SER D 45 ASN D 49 0 SHEET 2 N 3 SER D 57 TYR D 65 -1 O LEU D 60 N ASN D 49 SHEET 3 N 3 VAL D 113 PHE D 121 -1 O PHE D 119 N GLY D 59 SSBOND 1 CYS A 29 CYS A 40 1555 1555 2.05 SSBOND 2 CYS A 264 CYS A 289 1555 1555 2.03 SSBOND 3 CYS A 266 CYS A 301 1555 1555 2.04 SSBOND 4 CYS B 25 CYS B 51 1555 1555 2.06 SSBOND 5 CYS B 37 CYS B 148 1555 1555 2.06 SSBOND 6 CYS B 95 CYS B 105 1555 1555 2.03 SSBOND 7 CYS C 29 CYS C 40 1555 1555 2.06 SSBOND 8 CYS C 264 CYS C 289 1555 1555 2.04 SSBOND 9 CYS C 266 CYS C 301 1555 1555 2.05 SSBOND 10 CYS D 25 CYS D 51 1555 1555 2.06 SSBOND 11 CYS D 37 CYS D 148 1555 1555 2.05 SSBOND 12 CYS D 95 CYS D 105 1555 1555 2.02 LINK ND2 ASN A 35 C1 NAG A1201 1555 1555 1.46 LINK ND2 ASN A 205 C1 NAG E 1 1555 1555 1.45 LINK ND2 ASN C 35 C1 NAG C 402 1555 1555 1.47 LINK ND2 ASN C 205 C1 NAG F 1 1555 1555 1.46 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.40 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.40 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.40 LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.40 CISPEP 1 CYS A 266 PRO A 267 0 0.19 CISPEP 2 ASN B 49 PRO B 50 0 -0.15 CISPEP 3 CYS C 266 PRO C 267 0 0.18 CISPEP 4 ASN D 49 PRO D 50 0 -0.09 CRYST1 80.210 126.935 129.506 90.00 90.00 90.00 P 21 21 21 8 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 0.012467 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007878 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007722 0.00000