HEADER IMMUNE SYSTEM 05-MAY-04 1T5W TITLE HLA-DR1 IN COMPLEX WITH A SYNTHETIC PEPTIDE (AAYSDQATPLLLSPR) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN; 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, E; COMPND 10 FRAGMENT: EXTRACELLULAR DOMAIN; COMPND 11 SYNONYM: MHC CLASS I ANTIGEN DRB1*1, DR-1, DR1; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 15-MER PEPTIDE FRAGMENT OF REGULATORY PROTEIN MIG1; COMPND 15 CHAIN: C, F; COMPND 16 FRAGMENT: SYNTHETIC PEPTIDE; COMPND 17 SYNONYM: REGULATORY PROTEIN CAT4; COMPND 18 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: HLA-DRA; SOURCE 6 EXPRESSION_SYSTEM: DROSOPHILA MELANOGASTER; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FRUIT FLY; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7227; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: S2; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PRMAHA-3; 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: DROSOPHILA MELANOGASTER; SOURCE 18 EXPRESSION_SYSTEM_COMMON: FRUIT FLY; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 7227; SOURCE 20 EXPRESSION_SYSTEM_CELL_LINE: S2; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PRMHA-3; SOURCE 23 MOL_ID: 3; SOURCE 24 SYNTHETIC: YES; SOURCE 25 OTHER_DETAILS: SYNTHETIC PEPTIDE DESINGED TO STUDY THE P10 SIDE SOURCE 26 CHAIN SPECIFICITY OF HLA-DR1 KEYWDS MHC CLASS II; NAJOR HISTOCOMPATIBILITY COMPLEX PROTEIN; HLA-DR1; KEYWDS 2 ANTIGEN; PEPTIDE, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR Z.ZAVALA-RUIZ,I.STRUG,M.W.ANDERSON,J.GORSKI,L.J.STERN REVDAT 4 23-AUG-23 1T5W 1 SEQADV REVDAT 3 24-FEB-09 1T5W 1 VERSN REVDAT 2 01-FEB-05 1T5W 1 JRNL REMARK REVDAT 1 17-AUG-04 1T5W 0 JRNL AUTH Z.ZAVALA-RUIZ,I.STRUG,M.W.ANDERSON,J.GORSKI,L.J.STERN JRNL TITL A POLYMORPHIC POCKET AT THE P10 POSITION CONTRIBUTES TO JRNL TITL 2 PEPTIDE BINDING SPECIFICITY IN CLASS II MHC PROTEINS JRNL REF CHEM.BIOL. V. 11 1395 2004 JRNL REFN ISSN 1074-5521 JRNL PMID 15489166 JRNL DOI 10.1016/J.CHEMBIOL.2004.08.007 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.90 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) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 44322 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) : 0.231 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 3143 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE : 0.3440 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 532 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6259 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 148 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -10.81000 REMARK 3 B22 (A**2) : 20.61000 REMARK 3 B33 (A**2) : -9.80000 REMARK 3 B12 (A**2) : 0.00000 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) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.31 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) : 0.36 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.39 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.810 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 1T5W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1000022351. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 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) : 1.1000 REMARK 200 MONOCHROMATOR : CYLINDRICAL PLATINUM-COATED REMARK 200 SILICON MIRROR REMARK 200 OPTICS : CYLINDRICAL PLATINUM-COATED REMARK 200 SILICON MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADSC REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44505 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 23.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.31200 REMARK 200 R SYM FOR SHELL (I) : 0.37800 REMARK 200 FOR SHELL : 3.500 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: PDB ENTRY 1AQD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, PH 4.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 103.48800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 103.48800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 48.27700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 56.32300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 48.27700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 56.32300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 103.48800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 48.27700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 56.32300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 103.48800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 48.27700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 56.32300 REMARK 290 SMTRY3 8 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 300 REMARK: TOW MOLECULES IN THE ASYMTERIC UNIT ARE RELATED BY AN REMARK 300 APPROXIMATE 2-FOLD AXIS 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, 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 PRO C 13 REMARK 465 ARG C 14 REMARK 465 LYS D 2 REMARK 465 PRO F 13 REMARK 465 ARG F 14 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 LYS A 2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 PRO B 108 CB CG CD REMARK 480 LEU B 109 CB CG CD1 CD2 REMARK 480 GLN B 110 CB CG CD OE1 NE2 REMARK 480 VAL B 170 CB CG1 CG2 REMARK 480 ARG B 189 CB CG CD NE CZ NH1 NH2 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 O LEU B 8 O TYR B 32 2.08 REMARK 500 O LEU E 8 O TYR E 32 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NE2 GLN A 57 NE2 GLN A 57 4555 1.83 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 B 166 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG B 166 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG E 166 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG E 166 NE - CZ - NH2 ANGL. DEV. = -3.7 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 78 44.09 73.60 REMARK 500 THR A 113 146.62 -172.54 REMARK 500 TYR B 32 -92.10 -68.29 REMARK 500 ASN B 33 -76.59 -92.52 REMARK 500 THR B 90 -71.82 -119.53 REMARK 500 LYS B 105 132.10 66.46 REMARK 500 ASN D 78 42.43 72.99 REMARK 500 THR D 113 146.89 -173.24 REMARK 500 TYR E 32 -93.65 -68.61 REMARK 500 ASN E 33 -75.76 -91.07 REMARK 500 THR E 90 -74.61 -118.71 REMARK 500 LYS E 105 131.66 65.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DLH RELATED DB: PDB REMARK 900 HLA-DR1/HA, SIMILAR TO CURRENT ENTRY BUT WITH A DIFFERENT PEPTIDE REMARK 900 BOUND TO HLA-DR1 REMARK 900 RELATED ID: 1AQD RELATED DB: PDB REMARK 900 HLA-DR1/A2, SIMILAR TO CURRENT ENTRY BUT WITH A DIFFERENT PEPTIDE REMARK 900 BOUND TO HLA-DR1 REMARK 900 RELATED ID: 1T5X RELATED DB: PDB DBREF 1T5W A 2 181 UNP P01903 2DRA_HUMAN 27 206 DBREF 1T5W D 2 181 UNP P01903 2DRA_HUMAN 27 206 DBREF 1T5W B 1 190 UNP P04229 2B11_HUMAN 30 219 DBREF 1T5W E 1 190 UNP P04229 2B11_HUMAN 30 219 DBREF 1T5W C 7 14 UNP P27705 MIG1_YEAST 455 462 DBREF 1T5W F 7 14 UNP P27705 MIG1_YEAST 455 462 SEQADV 1T5W ALA C 0 UNP P27705 INSERTION SEQADV 1T5W ALA C 1 UNP P27705 INSERTION SEQADV 1T5W TYR C 2 UNP P27705 INSERTION SEQADV 1T5W SER C 3 UNP P27705 INSERTION SEQADV 1T5W ASP C 4 UNP P27705 INSERTION SEQADV 1T5W GLN C 5 UNP P27705 INSERTION SEQADV 1T5W ALA C 6 UNP P27705 INSERTION SEQADV 1T5W ALA F 0 UNP P27705 INSERTION SEQADV 1T5W ALA F 1 UNP P27705 INSERTION SEQADV 1T5W TYR F 2 UNP P27705 INSERTION SEQADV 1T5W SER F 3 UNP P27705 INSERTION SEQADV 1T5W ASP F 4 UNP P27705 INSERTION SEQADV 1T5W GLN F 5 UNP P27705 INSERTION SEQADV 1T5W ALA F 6 UNP P27705 INSERTION SEQRES 1 A 180 LYS GLU GLU HIS VAL ILE ILE GLN ALA GLU PHE TYR LEU SEQRES 2 A 180 ASN PRO ASP GLN SER GLY GLU PHE MET PHE ASP PHE ASP SEQRES 3 A 180 GLY ASP GLU ILE PHE HIS VAL ASP MET ALA LYS LYS GLU SEQRES 4 A 180 THR VAL TRP ARG LEU GLU GLU PHE GLY ARG PHE ALA SER SEQRES 5 A 180 PHE GLU ALA GLN GLY ALA LEU ALA ASN ILE ALA VAL ASP SEQRES 6 A 180 LYS ALA ASN LEU GLU ILE MET THR LYS ARG SER ASN TYR SEQRES 7 A 180 THR PRO ILE THR ASN VAL PRO PRO GLU VAL THR VAL LEU SEQRES 8 A 180 THR ASN SER PRO VAL GLU LEU ARG GLU PRO ASN VAL LEU SEQRES 9 A 180 ILE CYS PHE ILE ASP LYS PHE THR PRO PRO VAL VAL ASN SEQRES 10 A 180 VAL THR TRP LEU ARG ASN GLY LYS PRO VAL THR THR GLY SEQRES 11 A 180 VAL SER GLU THR VAL PHE LEU PRO ARG GLU ASP HIS LEU SEQRES 12 A 180 PHE ARG LYS PHE HIS TYR LEU PRO PHE LEU PRO SER THR SEQRES 13 A 180 GLU ASP VAL TYR ASP CYS ARG VAL GLU HIS TRP GLY LEU SEQRES 14 A 180 ASP GLU PRO LEU LEU LYS HIS TRP GLU PHE ASP 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 15 ALA ALA TYR SER ASP GLN ALA THR PRO LEU LEU LEU SER SEQRES 2 C 15 PRO ARG SEQRES 1 D 180 LYS GLU GLU HIS VAL ILE ILE GLN ALA GLU PHE TYR LEU SEQRES 2 D 180 ASN PRO ASP GLN SER GLY GLU PHE MET PHE ASP PHE ASP SEQRES 3 D 180 GLY ASP GLU ILE PHE HIS VAL ASP MET ALA LYS LYS GLU SEQRES 4 D 180 THR VAL TRP ARG LEU GLU GLU PHE GLY ARG PHE ALA SER SEQRES 5 D 180 PHE GLU ALA GLN GLY ALA LEU ALA ASN ILE ALA VAL ASP SEQRES 6 D 180 LYS ALA ASN LEU GLU ILE MET THR LYS ARG SER ASN TYR SEQRES 7 D 180 THR PRO ILE THR ASN VAL PRO PRO GLU VAL THR VAL LEU SEQRES 8 D 180 THR ASN SER PRO VAL GLU LEU ARG GLU PRO ASN VAL LEU SEQRES 9 D 180 ILE CYS PHE ILE ASP LYS PHE THR PRO PRO VAL VAL ASN SEQRES 10 D 180 VAL THR TRP LEU ARG ASN GLY LYS PRO VAL THR THR GLY SEQRES 11 D 180 VAL SER GLU THR VAL PHE LEU PRO ARG GLU ASP HIS LEU SEQRES 12 D 180 PHE ARG LYS PHE HIS TYR LEU PRO PHE LEU PRO SER THR SEQRES 13 D 180 GLU ASP VAL TYR ASP CYS ARG VAL GLU HIS TRP GLY LEU SEQRES 14 D 180 ASP GLU PRO LEU LEU LYS HIS TRP GLU PHE ASP SEQRES 1 E 190 GLY ASP THR ARG PRO ARG PHE LEU TRP GLN LEU LYS PHE SEQRES 2 E 190 GLU CYS HIS PHE PHE ASN GLY THR GLU ARG VAL ARG LEU SEQRES 3 E 190 LEU GLU ARG CYS ILE TYR ASN GLN GLU GLU SER VAL ARG SEQRES 4 E 190 PHE ASP SER ASP VAL GLY GLU TYR ARG ALA VAL THR GLU SEQRES 5 E 190 LEU GLY ARG PRO ASP ALA GLU TYR TRP ASN SER GLN LYS SEQRES 6 E 190 ASP LEU LEU GLU GLN ARG ARG ALA ALA VAL ASP THR TYR SEQRES 7 E 190 CYS ARG HIS ASN TYR GLY VAL GLY GLU SER PHE THR VAL SEQRES 8 E 190 GLN ARG ARG VAL GLU PRO LYS VAL THR VAL TYR PRO SER SEQRES 9 E 190 LYS THR GLN PRO LEU GLN HIS HIS ASN LEU LEU VAL CYS SEQRES 10 E 190 SER VAL SER GLY PHE TYR PRO GLY SER ILE GLU VAL ARG SEQRES 11 E 190 TRP PHE ARG ASN GLY GLN GLU GLU LYS ALA GLY VAL VAL SEQRES 12 E 190 SER THR GLY LEU ILE GLN ASN GLY ASP TRP THR PHE GLN SEQRES 13 E 190 THR LEU VAL MET LEU GLU THR VAL PRO ARG SER GLY GLU SEQRES 14 E 190 VAL TYR THR CYS GLN VAL GLU HIS PRO SER VAL THR SER SEQRES 15 E 190 PRO LEU THR VAL GLU TRP ARG ALA SEQRES 1 F 15 ALA ALA TYR SER ASP GLN ALA THR PRO LEU LEU LEU SER SEQRES 2 F 15 PRO ARG FORMUL 7 HOH *148(H2 O) HELIX 1 1 LEU A 45 PHE A 51 5 7 HELIX 2 2 GLU A 55 SER A 77 1 23 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 LEU D 45 PHE D 51 5 7 HELIX 8 8 GLU D 55 SER D 77 1 23 HELIX 9 9 THR E 51 LEU E 53 5 3 HELIX 10 10 GLY E 54 ASN E 62 1 9 HELIX 11 11 GLN E 64 TYR E 78 1 15 HELIX 12 12 TYR E 78 GLU E 87 1 10 HELIX 13 13 SER E 88 THR E 90 5 3 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 LEU A 14 O SER A 19 SHEET 5 A 8 PHE B 7 PHE B 18 -1 O CYS B 15 N ILE A 7 SHEET 6 A 8 ARG B 23 ILE B 31 -1 O LEU B 27 N GLU B 14 SHEET 7 A 8 GLU B 36 ASP B 41 -1 O PHE B 40 N GLU B 28 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 HIS A 149 N CYS A 107 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 HIS A 149 N CYS A 107 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 TYR A 161 GLU A 166 -1 O GLU A 166 N ASN A 118 SHEET 4 D 4 LEU A 174 TRP A 178 -1 O TRP A 178 N TYR A 161 SHEET 1 E 4 LYS B 98 SER B 104 0 SHEET 2 E 4 ASN B 113 PHE B 122 -1 O LEU B 114 N SER B 104 SHEET 3 E 4 PHE B 155 THR B 163 -1 O THR B 163 N ASN B 113 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 SER B 104 0 SHEET 2 F 4 ASN B 113 PHE B 122 -1 O LEU B 114 N SER B 104 SHEET 3 F 4 PHE B 155 THR B 163 -1 O THR B 163 N ASN B 113 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 TRP B 188 N TYR B 171 SHEET 1 H 8 GLU D 40 TRP D 43 0 SHEET 2 H 8 ASP D 29 ASP D 35 -1 N HIS D 33 O VAL D 42 SHEET 3 H 8 SER D 19 PHE D 26 -1 N PHE D 26 O ASP D 29 SHEET 4 H 8 HIS D 5 ASN D 15 -1 N LEU D 14 O SER D 19 SHEET 5 H 8 PHE E 7 PHE E 18 -1 O CYS E 15 N ILE D 7 SHEET 6 H 8 ARG E 23 ILE E 31 -1 O ARG E 25 N HIS E 16 SHEET 7 H 8 GLU E 36 ASP E 41 -1 O PHE E 40 N GLU E 28 SHEET 8 H 8 TYR E 47 ALA E 49 -1 O ARG E 48 N ARG E 39 SHEET 1 I 4 GLU D 88 THR D 93 0 SHEET 2 I 4 ASN D 103 PHE D 112 -1 O ILE D 106 N LEU D 92 SHEET 3 I 4 PHE D 145 PHE D 153 -1 O HIS D 149 N CYS D 107 SHEET 4 I 4 SER D 133 GLU D 134 -1 N SER D 133 O TYR D 150 SHEET 1 J 4 GLU D 88 THR D 93 0 SHEET 2 J 4 ASN D 103 PHE D 112 -1 O ILE D 106 N LEU D 92 SHEET 3 J 4 PHE D 145 PHE D 153 -1 O HIS D 149 N CYS D 107 SHEET 4 J 4 LEU D 138 PRO D 139 -1 N LEU D 138 O ARG D 146 SHEET 1 K 4 LYS D 126 VAL D 128 0 SHEET 2 K 4 ASN D 118 ARG D 123 -1 N ARG D 123 O LYS D 126 SHEET 3 K 4 TYR D 161 GLU D 166 -1 O ARG D 164 N THR D 120 SHEET 4 K 4 LEU D 174 TRP D 178 -1 O TRP D 178 N TYR D 161 SHEET 1 L 4 LYS E 98 SER E 104 0 SHEET 2 L 4 ASN E 113 PHE E 122 -1 O LEU E 114 N SER E 104 SHEET 3 L 4 PHE E 155 THR E 163 -1 O THR E 163 N ASN E 113 SHEET 4 L 4 VAL E 142 SER E 144 -1 N VAL E 143 O MET E 160 SHEET 1 M 4 LYS E 98 SER E 104 0 SHEET 2 M 4 ASN E 113 PHE E 122 -1 O LEU E 114 N SER E 104 SHEET 3 M 4 PHE E 155 THR E 163 -1 O THR E 163 N ASN E 113 SHEET 4 M 4 ILE E 148 GLN E 149 -1 N ILE E 148 O GLN E 156 SHEET 1 N 4 GLN E 136 GLU E 138 0 SHEET 2 N 4 GLU E 128 ARG E 133 -1 N ARG E 133 O GLN E 136 SHEET 3 N 4 VAL E 170 GLU E 176 -1 O GLN E 174 N ARG E 130 SHEET 4 N 4 LEU E 184 ARG E 189 -1 O TRP E 188 N TYR E 171 SSBOND 1 CYS A 107 CYS A 163 1555 1555 2.04 SSBOND 2 CYS B 15 CYS B 79 1555 1555 2.06 SSBOND 3 CYS B 117 CYS B 173 1555 1555 2.03 SSBOND 4 CYS D 107 CYS D 163 1555 1555 2.04 SSBOND 5 CYS E 15 CYS E 79 1555 1555 2.04 SSBOND 6 CYS E 117 CYS E 173 1555 1555 2.03 CISPEP 1 ASN A 15 PRO A 16 0 0.34 CISPEP 2 THR A 113 PRO A 114 0 0.00 CISPEP 3 TYR B 123 PRO B 124 0 0.60 CISPEP 4 ASN D 15 PRO D 16 0 0.22 CISPEP 5 THR D 113 PRO D 114 0 -0.14 CISPEP 6 TYR E 123 PRO E 124 0 0.80 CRYST1 96.554 112.646 206.976 90.00 90.00 90.00 C 2 2 21 16 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 0.010357 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008877 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004831 0.00000