HEADER IMMUNE SYSTEM 19-DEC-12 4IHO TITLE CRYSTAL STRUCTURE OF H-2DB Y159F IN COMPLEX WITH CHIMERIC GP100 COMPND MOL_ID: 1; COMPND 2 MOLECULE: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-B ALPHA CHAIN; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: UNP RESIDUES 25-300; COMPND 5 SYNONYM: H-2D(B); COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 10 CHAIN: B, E; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: NONAMERIC PEPTIDE CHIMERIC GP100; COMPND 14 CHAIN: C, F; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: H2-D1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_COMMON: MOUSE; SOURCE 11 ORGANISM_TAXID: 10090; SOURCE 12 GENE: B2M; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 OTHER_DETAILS: SYNTHETIC PEPTIDE KEYWDS MHC, H-2DB, GLYCOPROTEIN, IMMUNE RESPONSE, MHC I, TRANSMEMBRANE, KEYWDS 2 IMMUNOGLOBULIN DOMAIN, DISEASE MUTATION, MELANOMA, IMMUNE SYSTEM, KEYWDS 3 TUMOR ASSOCIATED ANTIGEN, ALTERED PEPTIDE LIGAND, T CELL RECEPTOR EXPDTA X-RAY DIFFRACTION AUTHOR H.UCHTENHAGEN,E.STAHL,A.ACHOUR REVDAT 3 08-NOV-23 4IHO 1 REMARK SEQADV REVDAT 2 11-DEC-13 4IHO 1 JRNL REVDAT 1 11-SEP-13 4IHO 0 JRNL AUTH H.UCHTENHAGEN,E.T.ABUALROUS,E.STAHL,E.B.ALLERBRING, JRNL AUTH 2 M.SLUIJTER,M.ZACHARIAS,T.SANDALOVA,T.VAN HALL,S.SPRINGER, JRNL AUTH 3 P.A.NYGREN,A.ACHOUR JRNL TITL PROLINE SUBSTITUTION INDEPENDENTLY ENHANCES H-2D(B) COMPLEX JRNL TITL 2 STABILIZATION AND TCR RECOGNITION OF MELANOMA-ASSOCIATED JRNL TITL 3 PEPTIDES JRNL REF EUR.J.IMMUNOL. V. 43 3051 2013 JRNL REFN ISSN 0014-2980 JRNL PMID 23939911 JRNL DOI 10.1002/EJI.201343456 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 28732 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) : 0.252 REMARK 3 R VALUE (WORKING SET) : 0.249 REMARK 3 FREE R VALUE : 0.305 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1537 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2132 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.68 REMARK 3 BIN R VALUE (WORKING SET) : 0.3880 REMARK 3 BIN FREE R VALUE SET COUNT : 109 REMARK 3 BIN FREE R VALUE : 0.4380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6251 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 106 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.77000 REMARK 3 B22 (A**2) : 10.08000 REMARK 3 B33 (A**2) : -5.31000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.956 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.411 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.381 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.931 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.908 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.855 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6377 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8656 ; 1.447 ; 1.940 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 752 ; 6.976 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 328 ;36.637 ;23.415 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1019 ;21.492 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 50 ;19.406 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 864 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5030 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4IHO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1000076764. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-SEP-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.93927 REMARK 200 MONOCHROMATOR : CHANNEL-CUT DOUBLE-CRYSTAL REMARK 200 SILICON [111] REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30269 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 42.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 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: PHASER REMARK 200 STARTING MODEL: 3CH1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6-1.8M NH4SO4, 100MM TRIS HCL, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 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+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 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 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 45.33050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 73.00550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 93.79250 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 45.33050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 73.00550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 93.79250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 45.33050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 73.00550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 93.79250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 45.33050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 73.00550 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 93.79250 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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: 4420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 LEU A 179 REMARK 465 LEU A 219 REMARK 465 ASN A 220 REMARK 465 GLY A 221 REMARK 465 ILE B 1 REMARK 465 GLN B 2 REMARK 465 LEU D 179 REMARK 465 LEU D 180 REMARK 465 LEU D 219 REMARK 465 ASN D 220 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 ASN A 176 CB CG OD1 ND2 REMARK 480 VAL A 199 CG1 CG2 REMARK 480 LEU A 201 CG CD1 CD2 REMARK 480 TRP A 217 CB CG CD1 CD2 NE1 CE2 CE3 REMARK 480 TRP A 217 CZ2 CZ3 CH2 REMARK 480 GLN A 218 CB CG CD OE1 NE2 REMARK 480 GLU A 223 CG CD OE1 OE2 REMARK 480 THR A 225 OG1 CG2 REMARK 480 GLN A 226 CG CD OE1 NE2 REMARK 480 ASP A 227 CG OD1 OD2 REMARK 480 LYS A 243 CB CG CD CE NZ REMARK 480 LEU A 251 CB CG CD1 CD2 REMARK 480 LYS A 253 CG CD CE NZ REMARK 480 GLU A 254 CG CD OE1 OE2 REMARK 480 GLU A 264 CG CD OE1 OE2 REMARK 480 GLU A 268 CG CD OE1 OE2 REMARK 480 TRP A 274 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 480 TRP A 274 CZ3 CH2 REMARK 480 THR D 178 OG1 CG2 REMARK 480 ARG D 194 CG CD NE CZ NH1 NH2 REMARK 480 VAL D 199 CG1 CG2 REMARK 480 GLN D 218 CG CD OE1 NE2 REMARK 480 GLU D 222 CG CD OE1 OE2 REMARK 480 GLU D 223 CB CG CD OE1 OE2 REMARK 480 THR D 225 OG1 CG2 REMARK 480 GLN D 226 CG CD OE1 NE2 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 OH TYR A 85 OD2 ASP A 137 2.14 REMARK 500 NH1 ARG A 62 OE2 GLU C 1 2.18 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 LEU A 17 -140.24 55.38 REMARK 500 GLU A 18 -136.49 61.03 REMARK 500 ASP A 137 164.15 91.23 REMARK 500 TRP B 60 -10.52 84.24 REMARK 500 GLN C 6 -116.18 -110.40 REMARK 500 LEU D 17 -139.49 57.20 REMARK 500 GLU D 18 -133.40 60.84 REMARK 500 PRO D 43 87.31 -66.43 REMARK 500 ASP D 137 167.10 91.25 REMARK 500 TRP E 60 -3.84 84.37 REMARK 500 GLN F 6 -132.32 -73.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3CH1 RELATED DB: PDB REMARK 900 H-2DB COMPLEX WITH CHIMERIC GP100 REMARK 900 RELATED ID: 3CCH RELATED DB: PDB REMARK 900 H-2DB COMPLEX WITH MURINE GP100 REMARK 999 REMARK 999 SEQUENCE REMARK 999 ASP 85 IS NATURAL VARIANT, ALLELE A. DBREF 4IHO A 1 276 UNP P01899 HA11_MOUSE 25 300 DBREF 4IHO B 1 99 UNP P01887 B2MG_MOUSE 21 119 DBREF 4IHO D 1 276 UNP P01899 HA11_MOUSE 25 300 DBREF 4IHO E 1 99 UNP P01887 B2MG_MOUSE 21 119 DBREF 4IHO C 1 9 PDB 4IHO 4IHO 1 9 DBREF 4IHO F 1 9 PDB 4IHO 4IHO 1 9 SEQADV 4IHO PHE A 159 UNP P01899 TYR 183 ENGINEERED MUTATION SEQADV 4IHO ASP B 85 UNP P01887 ALA 105 SEE REMARK 999 SEQADV 4IHO PHE D 159 UNP P01899 TYR 183 ENGINEERED MUTATION SEQADV 4IHO ASP E 85 UNP P01887 ALA 105 SEE REMARK 999 SEQRES 1 A 276 GLY PRO HIS SER MET ARG TYR PHE GLU THR ALA VAL SER SEQRES 2 A 276 ARG PRO GLY LEU GLU GLU PRO ARG TYR ILE SER VAL GLY SEQRES 3 A 276 TYR VAL ASP ASN LYS GLU PHE VAL ARG PHE ASP SER ASP SEQRES 4 A 276 ALA GLU ASN PRO ARG TYR GLU PRO ARG ALA PRO TRP MET SEQRES 5 A 276 GLU GLN GLU GLY PRO GLU TYR TRP GLU ARG GLU THR GLN SEQRES 6 A 276 LYS ALA LYS GLY GLN GLU GLN TRP PHE ARG VAL SER LEU SEQRES 7 A 276 ARG ASN LEU LEU GLY TYR TYR ASN GLN SER ALA GLY GLY SEQRES 8 A 276 SER HIS THR LEU GLN GLN MET SER GLY CYS ASP LEU GLY SEQRES 9 A 276 SER ASP TRP ARG LEU LEU ARG GLY TYR LEU GLN PHE ALA SEQRES 10 A 276 TYR GLU GLY ARG ASP TYR ILE ALA LEU ASN GLU ASP LEU SEQRES 11 A 276 LYS THR TRP THR ALA ALA ASP MET ALA ALA GLN ILE THR SEQRES 12 A 276 ARG ARG LYS TRP GLU GLN SER GLY ALA ALA GLU HIS TYR SEQRES 13 A 276 LYS ALA PHE LEU GLU GLY GLU CYS VAL GLU TRP LEU HIS SEQRES 14 A 276 ARG TYR LEU LYS ASN GLY ASN ALA THR LEU LEU ARG THR SEQRES 15 A 276 ASP SER PRO LYS ALA HIS VAL THR HIS HIS PRO ARG SER SEQRES 16 A 276 LYS GLY GLU VAL THR LEU ARG CYS TRP ALA LEU GLY PHE SEQRES 17 A 276 TYR PRO ALA ASP ILE THR LEU THR TRP GLN LEU ASN GLY SEQRES 18 A 276 GLU GLU LEU THR GLN ASP MET GLU LEU VAL GLU THR ARG SEQRES 19 A 276 PRO ALA GLY ASP GLY THR PHE GLN LYS TRP ALA SER VAL SEQRES 20 A 276 VAL VAL PRO LEU GLY LYS GLU GLN ASN TYR THR CYS ARG SEQRES 21 A 276 VAL TYR HIS GLU GLY LEU PRO GLU PRO LEU THR LEU ARG SEQRES 22 A 276 TRP GLU PRO SEQRES 1 B 99 ILE GLN LYS THR PRO GLN ILE GLN VAL TYR SER ARG HIS SEQRES 2 B 99 PRO PRO GLU ASN GLY LYS PRO ASN ILE LEU ASN CYS TYR SEQRES 3 B 99 VAL THR GLN PHE HIS PRO PRO HIS ILE GLU ILE GLN MET SEQRES 4 B 99 LEU LYS ASN GLY LYS LYS ILE PRO LYS VAL GLU MET SER SEQRES 5 B 99 ASP MET SER PHE SER LYS ASP TRP SER PHE TYR ILE LEU SEQRES 6 B 99 ALA HIS THR GLU PHE THR PRO THR GLU THR ASP THR TYR SEQRES 7 B 99 ALA CYS ARG VAL LYS HIS ASP SER MET ALA GLU PRO LYS SEQRES 8 B 99 THR VAL TYR TRP ASP ARG ASP MET SEQRES 1 C 9 GLU GLY PRO ARG ASN GLN ASP TRP LEU SEQRES 1 D 276 GLY PRO HIS SER MET ARG TYR PHE GLU THR ALA VAL SER SEQRES 2 D 276 ARG PRO GLY LEU GLU GLU PRO ARG TYR ILE SER VAL GLY SEQRES 3 D 276 TYR VAL ASP ASN LYS GLU PHE VAL ARG PHE ASP SER ASP SEQRES 4 D 276 ALA GLU ASN PRO ARG TYR GLU PRO ARG ALA PRO TRP MET SEQRES 5 D 276 GLU GLN GLU GLY PRO GLU TYR TRP GLU ARG GLU THR GLN SEQRES 6 D 276 LYS ALA LYS GLY GLN GLU GLN TRP PHE ARG VAL SER LEU SEQRES 7 D 276 ARG ASN LEU LEU GLY TYR TYR ASN GLN SER ALA GLY GLY SEQRES 8 D 276 SER HIS THR LEU GLN GLN MET SER GLY CYS ASP LEU GLY SEQRES 9 D 276 SER ASP TRP ARG LEU LEU ARG GLY TYR LEU GLN PHE ALA SEQRES 10 D 276 TYR GLU GLY ARG ASP TYR ILE ALA LEU ASN GLU ASP LEU SEQRES 11 D 276 LYS THR TRP THR ALA ALA ASP MET ALA ALA GLN ILE THR SEQRES 12 D 276 ARG ARG LYS TRP GLU GLN SER GLY ALA ALA GLU HIS TYR SEQRES 13 D 276 LYS ALA PHE LEU GLU GLY GLU CYS VAL GLU TRP LEU HIS SEQRES 14 D 276 ARG TYR LEU LYS ASN GLY ASN ALA THR LEU LEU ARG THR SEQRES 15 D 276 ASP SER PRO LYS ALA HIS VAL THR HIS HIS PRO ARG SER SEQRES 16 D 276 LYS GLY GLU VAL THR LEU ARG CYS TRP ALA LEU GLY PHE SEQRES 17 D 276 TYR PRO ALA ASP ILE THR LEU THR TRP GLN LEU ASN GLY SEQRES 18 D 276 GLU GLU LEU THR GLN ASP MET GLU LEU VAL GLU THR ARG SEQRES 19 D 276 PRO ALA GLY ASP GLY THR PHE GLN LYS TRP ALA SER VAL SEQRES 20 D 276 VAL VAL PRO LEU GLY LYS GLU GLN ASN TYR THR CYS ARG SEQRES 21 D 276 VAL TYR HIS GLU GLY LEU PRO GLU PRO LEU THR LEU ARG SEQRES 22 D 276 TRP GLU PRO SEQRES 1 E 99 ILE GLN LYS THR PRO GLN ILE GLN VAL TYR SER ARG HIS SEQRES 2 E 99 PRO PRO GLU ASN GLY LYS PRO ASN ILE LEU ASN CYS TYR SEQRES 3 E 99 VAL THR GLN PHE HIS PRO PRO HIS ILE GLU ILE GLN MET SEQRES 4 E 99 LEU LYS ASN GLY LYS LYS ILE PRO LYS VAL GLU MET SER SEQRES 5 E 99 ASP MET SER PHE SER LYS ASP TRP SER PHE TYR ILE LEU SEQRES 6 E 99 ALA HIS THR GLU PHE THR PRO THR GLU THR ASP THR TYR SEQRES 7 E 99 ALA CYS ARG VAL LYS HIS ASP SER MET ALA GLU PRO LYS SEQRES 8 E 99 THR VAL TYR TRP ASP ARG ASP MET SEQRES 1 F 9 GLU GLY PRO ARG ASN GLN ASP TRP LEU HET GOL A 301 6 HET GOL A 302 6 HET SO4 A 303 5 HET GOL B 101 6 HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 7 GOL 3(C3 H8 O3) FORMUL 9 SO4 O4 S 2- FORMUL 11 HOH *106(H2 O) HELIX 1 1 ALA A 49 GLU A 55 5 7 HELIX 2 2 GLY A 56 TYR A 85 1 30 HELIX 3 3 ASP A 137 SER A 150 1 14 HELIX 4 4 GLY A 151 GLY A 162 1 12 HELIX 5 5 GLY A 162 GLY A 175 1 14 HELIX 6 6 LYS A 253 TYR A 257 5 5 HELIX 7 7 ALA D 49 GLU D 55 5 7 HELIX 8 8 GLY D 56 TYR D 85 1 30 HELIX 9 9 ASP D 137 SER D 150 1 14 HELIX 10 10 GLY D 151 GLY D 162 1 12 HELIX 11 11 GLY D 162 GLY D 175 1 14 SHEET 1 A 8 TYR A 45 PRO A 47 0 SHEET 2 A 8 LYS A 31 ASP A 37 -1 N ARG A 35 O GLU A 46 SHEET 3 A 8 ARG A 21 VAL A 28 -1 N GLY A 26 O PHE A 33 SHEET 4 A 8 HIS A 3 SER A 13 -1 N VAL A 12 O ARG A 21 SHEET 5 A 8 HIS A 93 LEU A 103 -1 O LEU A 95 N ALA A 11 SHEET 6 A 8 LEU A 109 TYR A 118 -1 O TYR A 113 N GLY A 100 SHEET 7 A 8 ARG A 121 LEU A 126 -1 O TYR A 123 N PHE A 116 SHEET 8 A 8 TRP A 133 THR A 134 -1 O THR A 134 N ALA A 125 SHEET 1 B 4 LYS A 186 ARG A 194 0 SHEET 2 B 4 GLU A 198 PHE A 208 -1 O LEU A 206 N LYS A 186 SHEET 3 B 4 PHE A 241 SER A 246 -1 O ALA A 245 N CYS A 203 SHEET 4 B 4 ARG A 234 PRO A 235 -1 N ARG A 234 O GLN A 242 SHEET 1 C 4 GLU A 229 LEU A 230 0 SHEET 2 C 4 PHE A 241 SER A 246 -1 O SER A 246 N GLU A 229 SHEET 3 C 4 GLU A 198 PHE A 208 -1 N CYS A 203 O ALA A 245 SHEET 4 C 4 VAL A 248 PRO A 250 -1 O VAL A 249 N VAL A 199 SHEET 1 D 3 THR A 214 TRP A 217 0 SHEET 2 D 3 CYS A 259 TYR A 262 -1 O ARG A 260 N THR A 216 SHEET 3 D 3 LEU A 270 LEU A 272 -1 O LEU A 270 N VAL A 261 SHEET 1 E 4 GLN B 6 SER B 11 0 SHEET 2 E 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 E 4 PHE B 62 PHE B 70 -1 O PHE B 70 N ASN B 21 SHEET 4 E 4 GLU B 50 MET B 51 -1 N GLU B 50 O HIS B 67 SHEET 1 F 4 GLN B 6 SER B 11 0 SHEET 2 F 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 F 4 PHE B 62 PHE B 70 -1 O PHE B 70 N ASN B 21 SHEET 4 F 4 SER B 55 PHE B 56 -1 N SER B 55 O TYR B 63 SHEET 1 G 4 LYS B 44 LYS B 45 0 SHEET 2 G 4 GLU B 36 LYS B 41 -1 N LYS B 41 O LYS B 44 SHEET 3 G 4 TYR B 78 LYS B 83 -1 O ALA B 79 N LEU B 40 SHEET 4 G 4 LYS B 91 TYR B 94 -1 O LYS B 91 N VAL B 82 SHEET 1 H 8 GLU D 46 PRO D 47 0 SHEET 2 H 8 LYS D 31 ASP D 37 -1 N ARG D 35 O GLU D 46 SHEET 3 H 8 ARG D 21 VAL D 28 -1 N SER D 24 O PHE D 36 SHEET 4 H 8 HIS D 3 SER D 13 -1 N VAL D 12 O ARG D 21 SHEET 5 H 8 HIS D 93 LEU D 103 -1 O LEU D 103 N HIS D 3 SHEET 6 H 8 LEU D 109 TYR D 118 -1 O TYR D 113 N GLY D 100 SHEET 7 H 8 ARG D 121 LEU D 126 -1 O TYR D 123 N PHE D 116 SHEET 8 H 8 TRP D 133 THR D 134 -1 O THR D 134 N ALA D 125 SHEET 1 I 4 LYS D 186 ARG D 194 0 SHEET 2 I 4 GLU D 198 PHE D 208 -1 O LEU D 206 N LYS D 186 SHEET 3 I 4 PHE D 241 SER D 246 -1 O LYS D 243 N ALA D 205 SHEET 4 I 4 ARG D 234 PRO D 235 -1 N ARG D 234 O GLN D 242 SHEET 1 J 4 GLU D 229 LEU D 230 0 SHEET 2 J 4 PHE D 241 SER D 246 -1 O SER D 246 N GLU D 229 SHEET 3 J 4 GLU D 198 PHE D 208 -1 N ALA D 205 O LYS D 243 SHEET 4 J 4 VAL D 248 PRO D 250 -1 O VAL D 249 N VAL D 199 SHEET 1 K 3 THR D 214 THR D 216 0 SHEET 2 K 3 CYS D 259 TYR D 262 -1 O ARG D 260 N THR D 216 SHEET 3 K 3 LEU D 270 LEU D 272 -1 O LEU D 270 N VAL D 261 SHEET 1 L 4 GLN E 6 SER E 11 0 SHEET 2 L 4 ASN E 21 PHE E 30 -1 O ASN E 24 N TYR E 10 SHEET 3 L 4 PHE E 62 PHE E 70 -1 O PHE E 70 N ASN E 21 SHEET 4 L 4 GLU E 50 MET E 51 -1 N GLU E 50 O HIS E 67 SHEET 1 M 4 GLN E 6 SER E 11 0 SHEET 2 M 4 ASN E 21 PHE E 30 -1 O ASN E 24 N TYR E 10 SHEET 3 M 4 PHE E 62 PHE E 70 -1 O PHE E 70 N ASN E 21 SHEET 4 M 4 SER E 55 PHE E 56 -1 N SER E 55 O TYR E 63 SHEET 1 N 4 LYS E 44 LYS E 45 0 SHEET 2 N 4 GLU E 36 LYS E 41 -1 N LYS E 41 O LYS E 44 SHEET 3 N 4 TYR E 78 LYS E 83 -1 O ALA E 79 N LEU E 40 SHEET 4 N 4 LYS E 91 TYR E 94 -1 O LYS E 91 N VAL E 82 SSBOND 1 CYS A 101 CYS A 164 1555 1555 2.06 SSBOND 2 CYS A 203 CYS A 259 1555 1555 2.03 SSBOND 3 CYS B 25 CYS B 80 1555 1555 2.01 SSBOND 4 CYS D 101 CYS D 164 1555 1555 1.19 SSBOND 5 CYS D 203 CYS D 259 1555 1555 2.03 SSBOND 6 CYS E 25 CYS E 80 1555 1555 2.03 CISPEP 1 TYR A 209 PRO A 210 0 2.89 CISPEP 2 HIS B 31 PRO B 32 0 -10.20 CISPEP 3 TYR D 209 PRO D 210 0 1.49 CISPEP 4 HIS E 31 PRO E 32 0 -10.13 SITE 1 AC1 3 TYR A 85 TYR A 118 GLU A 119 SITE 1 AC2 2 ARG A 21 GOL B 101 SITE 1 AC3 1 ARG A 111 SITE 1 AC4 6 ARG A 21 GOL A 302 MET B 51 SER B 52 SITE 2 AC4 6 ASP B 53 MET B 54 CRYST1 90.661 146.011 187.585 90.00 90.00 90.00 I 2 2 2 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 0.011030 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006849 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005331 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -0.355836 0.291955 0.887774 -61.10905 1 MTRIX2 2 -0.178342 -0.953706 0.242155 -91.97601 1 MTRIX3 2 0.917374 -0.072160 0.391431 21.08749 1