HEADER IMMUNE SYSTEM 12-OCT-06 2IPK TITLE CRYSTAL STRUCTURE OF THE MHC CLASS II MOLECULE HLA-DR1 IN COMPLEX WITH TITLE 2 THE FLUOROGENIC PEPTIDE, ACPKXVKQNTLKLAT (X=3-[5-(DIMETHYLAMINO)-1,3- TITLE 3 DIOXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL]-L-ALANINE) AND THE SUPERANTIGEN, TITLE 4 SEC3 VARIANT 3B2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN, RESIDUES 26-207; COMPND 5 SYNONYM: MHC CLASS II ANTIGEN DRA; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-1 BETA CHAIN; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: EXTRACELLULAR DOMAIN, RESIDUES 30-219; COMPND 11 SYNONYM: MHC CLASS I ANTIGEN DRB1*1, DR-1, DR1; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: HA RELATED FLUOROGENIC PEPTIDE, ACPKXVKQNTLKLAT (X=3-[5- COMPND 15 (DIMETHYLAMINO)-1,3-DIOXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL]-L-ALANINE); COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES; COMPND 18 MOL_ID: 4; COMPND 19 MOLECULE: ENTEROTOXIN TYPE C-3; COMPND 20 CHAIN: D; COMPND 21 FRAGMENT: RESIDUES 28-266; COMPND 22 SYNONYM: SEC3; COMPND 23 ENGINEERED: YES; COMPND 24 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HLA-DRA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: T7 POLYMERASE/LAC; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PLM1; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 GENE: HLA-DRB1; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 19 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 21 EXPRESSION_SYSTEM_VECTOR: T7 POLYMERASE/LAC; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PLM1; SOURCE 23 MOL_ID: 3; SOURCE 24 SYNTHETIC: YES; SOURCE 25 ORGANISM_SCIENTIFIC: INFLUENZA A VIRUS; SOURCE 26 ORGANISM_TAXID: 11320; SOURCE 27 OTHER_DETAILS: SYNTHESIZED PEPTIDE; SOURCE 28 MOL_ID: 4; SOURCE 29 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50; SOURCE 30 ORGANISM_TAXID: 158878; SOURCE 31 STRAIN: MU50/ATCC 700699; SOURCE 32 GENE: ENTC3; SOURCE 33 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 34 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 35 EXPRESSION_SYSTEM_STRAIN: HB 2151; SOURCE 36 EXPRESSION_SYSTEM_VECTOR: LAC KEYWDS HLA, DR1, MHC, MAJOR HISTOCOMPATIBILITY COMPLEX, FLUOROGENIC PROBE, KEYWDS 2 SEC3, 4-(N, N-DIMETHYLAMINO)PHTHALIMIDOALANYL, DAPA, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR T.T.NGUYEN,L.J.STERN REVDAT 6 30-AUG-23 2IPK 1 REMARK REVDAT 5 20-OCT-21 2IPK 1 SEQADV LINK REVDAT 4 18-OCT-17 2IPK 1 SOURCE REMARK REVDAT 3 24-FEB-09 2IPK 1 VERSN REVDAT 2 03-APR-07 2IPK 1 JRNL REVDAT 1 13-MAR-07 2IPK 0 JRNL AUTH P.VENKATRAMAN,T.T.NGUYEN,M.SAINLOS,O.BILSEL,S.CHITTA, JRNL AUTH 2 B.IMPERIALI,L.J.STERN JRNL TITL FLUOROGENIC PROBES FOR MONITORING PEPTIDE BINDING TO CLASS JRNL TITL 2 II MHC PROTEINS IN LIVING CELLS. JRNL REF NAT.CHEM.BIOL. V. 3 222 2007 JRNL REFN ISSN 1552-4450 JRNL PMID 17351628 JRNL DOI 10.1038/NCHEMBIO868 REMARK 2 REMARK 2 RESOLUTION. 2.30 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 59125 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3005 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE : 0.3130 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 517 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5045 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 419 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.11000 REMARK 3 B22 (A**2) : -1.11000 REMARK 3 B33 (A**2) : 2.21900 REMARK 3 B12 (A**2) : -3.00500 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.28 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.33 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.370 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 : 44.51 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : DRGCNS_1.PAR REMARK 3 PARAMETER FILE 4 : CAPPING.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2IPK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000039857. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : PT-COATED TOROIDAL SI MIRROR FOR REMARK 200 HORIZONTAL AND VERTICAL REMARK 200 FOCUSSING FOLLOWED BY DOUBLE REMARK 200 FLAT SI CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67968 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 33.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : 0.08700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.36800 REMARK 200 R SYM FOR SHELL (I) : 0.36300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1PYW. MODEL OF HLA-DR1 WITH SEC3-3B2 REMARK 200 OMITTING THE PEPTIDE (CHAIN C). REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, ETHYLENE GLYCOL, SODIUM REMARK 280 ACETATE, PH 5.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 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 1.000000 0.000000 0.000000 85.99000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 49.64635 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 40.37633 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 85.99000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 49.64635 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 40.37633 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 85.99000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 49.64635 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.37633 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 99.29270 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 80.75267 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 99.29270 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 80.75267 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 99.29270 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 80.75267 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: TETRAMERIC 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 MET A 0 REMARK 465 ILE A 1 REMARK 465 LYS A 2 REMARK 465 ALA A 182 REMARK 465 MET D 0 REMARK 465 ASP D 99 REMARK 465 ASN D 100 REMARK 465 VAL D 101 REMARK 465 GLY D 102 REMARK 465 LYS D 103 REMARK 465 VAL D 104 REMARK 465 THR D 105 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 B 165 C - N - CA ANGL. DEV. = 9.6 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 GLU A 4 -53.00 -131.32 REMARK 500 SER A 95 152.90 176.93 REMARK 500 SER A 156 145.15 -174.83 REMARK 500 ASN B 33 -102.09 52.48 REMARK 500 THR B 90 -72.72 -126.84 REMARK 500 HIS B 111 21.50 45.96 REMARK 500 SER B 167 135.37 -34.70 REMARK 500 TYR D 32 155.09 179.11 REMARK 500 LYS D 57 -88.15 -65.28 REMARK 500 PHE D 95 155.03 174.19 REMARK 500 SER D 178 -152.45 -148.87 REMARK 500 ASN D 238 -87.69 -123.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JWU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF THE MHC CLASS II MOLECULE HLA- REMARK 900 DR1 (HA PEPTIDE 306-318) WITH THE SUPERANTIGEN SEC3 VARIANT 3B1 REMARK 900 RELATED ID: 1DLH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HUMAN CLASS II MHC PROTEIN HLA-DR1 REMARK 900 COMPLEXED WITH AN INFLUENZA VIRUS PEPTIDE (HA PEPTIDE) DBREF 2IPK A 1 182 UNP P01903 2DRA_HUMAN 26 207 DBREF 2IPK B 1 190 UNP P04229 2B11_HUMAN 30 219 DBREF 2IPK D 1 239 UNP P0A0L3 ENTC3_STAAM 28 266 DBREF 2IPK C 305 318 PDB 2IPK 2IPK 305 318 SEQADV 2IPK MET A 0 UNP P01903 CLONING ARTIFACT SEQADV 2IPK MET D 0 UNP P0A0L3 CLONING ARTIFACT SEQADV 2IPK SER D 43 UNP P0A0L3 LYS 70 ENGINEERED MUTATION SEQADV 2IPK PHE D 45 UNP P0A0L3 LEU 72 ENGINEERED MUTATION SEQADV 2IPK LYS D 46 UNP P0A0L3 ALA 73 ENGINEERED MUTATION SEQADV 2IPK TRP D 47 UNP P0A0L3 HIS 74 ENGINEERED MUTATION SEQRES 1 A 183 MET ILE LYS GLU GLU HIS VAL ILE ILE GLN ALA GLU PHE SEQRES 2 A 183 TYR LEU ASN PRO ASP GLN SER GLY GLU PHE MET PHE ASP SEQRES 3 A 183 PHE ASP GLY ASP GLU ILE PHE HIS VAL ASP MET ALA LYS SEQRES 4 A 183 LYS GLU THR VAL TRP ARG LEU GLU GLU PHE GLY ARG PHE SEQRES 5 A 183 ALA SER PHE GLU ALA GLN GLY ALA LEU ALA ASN ILE ALA SEQRES 6 A 183 VAL ASP LYS ALA ASN LEU GLU ILE MET THR LYS ARG SER SEQRES 7 A 183 ASN TYR THR PRO ILE THR ASN VAL PRO PRO GLU VAL THR SEQRES 8 A 183 VAL LEU THR ASN SER PRO VAL GLU LEU ARG GLU PRO ASN SEQRES 9 A 183 VAL LEU ILE CYS PHE ILE ASP LYS PHE THR PRO PRO VAL SEQRES 10 A 183 VAL ASN VAL THR TRP LEU ARG ASN GLY LYS PRO VAL THR SEQRES 11 A 183 THR GLY VAL SER GLU THR VAL PHE LEU PRO ARG GLU ASP SEQRES 12 A 183 HIS LEU PHE ARG LYS PHE HIS TYR LEU PRO PHE LEU PRO SEQRES 13 A 183 SER THR GLU ASP VAL TYR ASP CYS ARG VAL GLU HIS TRP SEQRES 14 A 183 GLY LEU ASP GLU PRO LEU LEU LYS HIS TRP GLU PHE ASP SEQRES 15 A 183 ALA SEQRES 1 B 190 GLY ASP THR ARG PRO ARG PHE LEU TRP GLN LEU LYS PHE SEQRES 2 B 190 GLU CYS HIS PHE PHE ASN GLY THR GLU ARG VAL ARG LEU SEQRES 3 B 190 LEU GLU ARG CYS ILE TYR ASN GLN GLU GLU SER VAL ARG SEQRES 4 B 190 PHE ASP SER ASP VAL GLY GLU TYR ARG ALA VAL THR GLU SEQRES 5 B 190 LEU GLY ARG PRO ASP ALA GLU TYR TRP ASN SER GLN LYS SEQRES 6 B 190 ASP LEU LEU GLU GLN ARG ARG ALA ALA VAL ASP THR TYR SEQRES 7 B 190 CYS ARG HIS ASN TYR GLY VAL GLY GLU SER PHE THR VAL SEQRES 8 B 190 GLN ARG ARG VAL GLU PRO LYS VAL THR VAL TYR PRO SER SEQRES 9 B 190 LYS THR GLN PRO LEU GLN HIS HIS ASN LEU LEU VAL CYS SEQRES 10 B 190 SER VAL SER GLY PHE TYR PRO GLY SER ILE GLU VAL ARG SEQRES 11 B 190 TRP PHE ARG ASN GLY GLN GLU GLU LYS ALA GLY VAL VAL SEQRES 12 B 190 SER THR GLY LEU ILE GLN ASN GLY ASP TRP THR PHE GLN SEQRES 13 B 190 THR LEU VAL MET LEU GLU THR VAL PRO ARG SER GLY GLU SEQRES 14 B 190 VAL TYR THR CYS GLN VAL GLU HIS PRO SER VAL THR SER SEQRES 15 B 190 PRO LEU THR VAL GLU TRP ARG ALA SEQRES 1 C 14 ACE PRO LYS 4DP VAL LYS GLN ASN THR LEU LYS LEU ALA SEQRES 2 C 14 THR SEQRES 1 D 240 MET GLU SER GLN PRO ASP PRO MET PRO ASP ASP LEU HIS SEQRES 2 D 240 LYS SER SER GLU PHE THR GLY THR MET GLY ASN MET LYS SEQRES 3 D 240 TYR LEU TYR ASP ASP HIS TYR VAL SER ALA THR LYS VAL SEQRES 4 D 240 LYS SER VAL ASP SER PHE PHE LYS TRP ASP LEU ILE TYR SEQRES 5 D 240 ASN ILE SER ASP LYS LYS LEU LYS ASN TYR ASP LYS VAL SEQRES 6 D 240 LYS THR GLU LEU LEU ASN GLU ASP LEU ALA LYS LYS TYR SEQRES 7 D 240 LYS ASP GLU VAL VAL ASP VAL TYR GLY SER ASN TYR TYR SEQRES 8 D 240 VAL ASN CYS TYR PHE SER SER LYS ASP ASN VAL GLY LYS SEQRES 9 D 240 VAL THR GLY GLY LYS THR CYS MET TYR GLY GLY ILE THR SEQRES 10 D 240 LYS HIS GLU GLY ASN HIS PHE ASP ASN GLY ASN LEU GLN SEQRES 11 D 240 ASN VAL LEU VAL ARG VAL TYR GLU ASN LYS ARG ASN THR SEQRES 12 D 240 ILE SER PHE GLU VAL GLN THR ASP LYS LYS SER VAL THR SEQRES 13 D 240 ALA GLN GLU LEU ASP ILE LYS ALA ARG ASN PHE LEU ILE SEQRES 14 D 240 ASN LYS LYS ASN LEU TYR GLU PHE ASN SER SER PRO TYR SEQRES 15 D 240 GLU THR GLY TYR ILE LYS PHE ILE GLU ASN ASN GLY ASN SEQRES 16 D 240 THR PHE TRP TYR ASP MET MET PRO ALA PRO GLY ASP LYS SEQRES 17 D 240 PHE ASP GLN SER LYS TYR LEU MET MET TYR ASN ASP ASN SEQRES 18 D 240 LYS THR VAL ASP SER LYS SER VAL LYS ILE GLU VAL HIS SEQRES 19 D 240 LEU THR THR LYS ASN GLY MODRES 2IPK 4DP C 308 TRP HET ACE C 305 3 HET 4DP C 308 19 HETNAM ACE ACETYL GROUP HETNAM 4DP 3-[5-(DIMETHYLAMINO)-1,3-DIOXO-1,3-DIHYDRO-2H-ISOINDOL- HETNAM 2 4DP 2-YL]-L-ALANINE HETSYN 4DP 4-(N,N-DIMETHYLAMINO)PHTHALIMIDOALANYL; DAPA FORMUL 3 ACE C2 H4 O FORMUL 3 4DP C13 H15 N3 O4 FORMUL 5 HOH *419(H2 O) HELIX 1 1 GLU A 47 ALA A 52 1 6 HELIX 2 2 ALA A 56 SER A 77 1 22 HELIX 3 3 THR B 51 LEU B 53 5 3 HELIX 4 4 GLY B 54 SER B 63 1 10 HELIX 5 5 GLN B 64 TYR B 78 1 15 HELIX 6 6 TYR B 78 GLU B 87 1 10 HELIX 7 7 SER B 88 THR B 90 5 3 HELIX 8 8 MET D 7 LEU D 11 5 5 HELIX 9 9 LYS D 13 PHE D 17 5 5 HELIX 10 10 MET D 21 TYR D 26 1 6 HELIX 11 11 ASN D 70 ASP D 79 1 10 HELIX 12 12 ALA D 156 ASN D 172 1 17 HELIX 13 13 ASP D 209 MET D 215 1 7 HELIX 14 14 MET D 216 ASN D 220 5 5 SHEET 1 A 8 GLU A 40 TRP A 43 0 SHEET 2 A 8 ASP A 29 ASP A 35 -1 N HIS A 33 O VAL A 42 SHEET 3 A 8 SER A 19 PHE A 26 -1 N PHE A 26 O ASP A 29 SHEET 4 A 8 HIS A 5 ASN A 15 -1 N ALA A 10 O MET A 23 SHEET 5 A 8 PHE B 7 PHE B 18 -1 O PHE B 17 N HIS A 5 SHEET 6 A 8 ARG B 23 TYR B 32 -1 O ARG B 29 N LYS B 12 SHEET 7 A 8 GLU B 35 ASP B 41 -1 O GLU B 35 N TYR B 32 SHEET 8 A 8 TYR B 47 ALA B 49 -1 O ARG B 48 N ARG B 39 SHEET 1 B 4 GLU A 88 THR A 93 0 SHEET 2 B 4 ASN A 103 PHE A 112 -1 O ILE A 106 N LEU A 92 SHEET 3 B 4 PHE A 145 PHE A 153 -1 O LEU A 151 N LEU A 105 SHEET 4 B 4 SER A 133 GLU A 134 -1 N SER A 133 O TYR A 150 SHEET 1 C 4 GLU A 88 THR A 93 0 SHEET 2 C 4 ASN A 103 PHE A 112 -1 O ILE A 106 N LEU A 92 SHEET 3 C 4 PHE A 145 PHE A 153 -1 O LEU A 151 N LEU A 105 SHEET 4 C 4 LEU A 138 PRO A 139 -1 N LEU A 138 O ARG A 146 SHEET 1 D 4 LYS A 126 VAL A 128 0 SHEET 2 D 4 ASN A 118 ARG A 123 -1 N ARG A 123 O LYS A 126 SHEET 3 D 4 VAL A 160 GLU A 166 -1 O ARG A 164 N THR A 120 SHEET 4 D 4 LEU A 174 GLU A 179 -1 O TRP A 178 N TYR A 161 SHEET 1 E 4 LYS B 98 PRO B 103 0 SHEET 2 E 4 ASN B 113 PHE B 122 -1 O SER B 120 N LYS B 98 SHEET 3 E 4 PHE B 155 THR B 163 -1 O LEU B 161 N LEU B 115 SHEET 4 E 4 VAL B 142 SER B 144 -1 N VAL B 143 O MET B 160 SHEET 1 F 4 LYS B 98 PRO B 103 0 SHEET 2 F 4 ASN B 113 PHE B 122 -1 O SER B 120 N LYS B 98 SHEET 3 F 4 PHE B 155 THR B 163 -1 O LEU B 161 N LEU B 115 SHEET 4 F 4 ILE B 148 GLN B 149 -1 N ILE B 148 O GLN B 156 SHEET 1 G 4 GLN B 136 GLU B 137 0 SHEET 2 G 4 GLU B 128 ARG B 133 -1 N ARG B 133 O GLN B 136 SHEET 3 G 4 VAL B 170 GLU B 176 -1 O GLN B 174 N ARG B 130 SHEET 4 G 4 LEU B 184 ARG B 189 -1 O LEU B 184 N VAL B 175 SHEET 1 H 3 VAL D 33 VAL D 38 0 SHEET 2 H 3 VAL D 82 GLY D 86 -1 O VAL D 82 N VAL D 38 SHEET 3 H 3 ILE D 115 LYS D 117 -1 O THR D 116 N ASP D 83 SHEET 1 I 3 ASP D 48 ASN D 52 0 SHEET 2 I 3 LYS D 63 GLU D 67 -1 O THR D 66 N LEU D 49 SHEET 3 I 3 LYS D 108 TYR D 112 1 O MET D 111 N GLU D 67 SHEET 1 J 5 ARG D 140 THR D 149 0 SHEET 2 J 5 GLN D 129 GLU D 137 -1 N VAL D 133 O PHE D 145 SHEET 3 J 5 LYS D 229 THR D 235 1 O LEU D 234 N TYR D 136 SHEET 4 J 5 THR D 183 ILE D 189 -1 N LYS D 187 O GLU D 231 SHEET 5 J 5 THR D 195 ASP D 199 -1 O PHE D 196 N PHE D 188 SHEET 1 K 2 SER D 153 THR D 155 0 SHEET 2 K 2 THR D 222 ASP D 224 -1 O VAL D 223 N VAL D 154 SSBOND 1 CYS A 107 CYS A 163 1555 1555 2.05 SSBOND 2 CYS B 15 CYS B 79 1555 1555 2.07 SSBOND 3 CYS B 117 CYS B 173 1555 1555 2.03 SSBOND 4 CYS D 93 CYS D 110 1555 1555 2.03 LINK C ACE C 305 N PRO C 306 1555 1555 1.34 LINK C LYS C 307 N 4DP C 308 1555 1555 1.35 LINK C 4DP C 308 N VAL C 309 1555 1555 1.33 CISPEP 1 ASN A 15 PRO A 16 0 0.26 CISPEP 2 THR A 113 PRO A 114 0 0.04 CISPEP 3 TYR B 123 PRO B 124 0 0.24 CRYST1 171.980 171.980 121.129 90.00 90.00 120.00 H 3 9 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 0.005815 0.003357 0.000000 0.00000 SCALE2 0.000000 0.006714 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008256 0.00000