HEADER IMMUNE SYSTEM 30-OCT-12 2YPK TITLE STRUCTURAL FEATURES UNDERLYING T-CELL RECEPTOR SENSITIVITY TO TITLE 2 CONCEALED MHC CLASS I MICROPOLYMORPHISMS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-57 ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 25-298; COMPND 5 SYNONYM: BW-57, MHC CLASS I ANTIGEN B*57, HLA-B5701; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: RESIDUES 21-119; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: KF11 P24 GAG PEPTIDE; COMPND 14 CHAIN: C; COMPND 15 FRAGMENT: RESIDUES 162-172 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET22B; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_VECTOR: PET22B; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS; SOURCE 22 ORGANISM_COMMON: HIV; SOURCE 23 ORGANISM_TAXID: 12721 KEYWDS IMMUNE SYSTEM, MICROPOLYMORPHISM EXPDTA X-RAY DIFFRACTION AUTHOR G.B.STEWART-JONES,P.SIMPSON,P.A.VAN DER MERWE,P.EASTERBROOK, AUTHOR 2 A.J.MCMICHAEL,S.L.ROWLAND-JONES,E.Y.JONES,G.M.GILLESPIE REVDAT 3 16-JAN-13 2YPK 1 JRNL REVDAT 2 19-DEC-12 2YPK 1 JRNL REVDAT 1 28-NOV-12 2YPK 0 JRNL AUTH G.B.STEWART-JONES,P.SIMPSON,P.ANTON VAN DER MERWE, JRNL AUTH 2 P.EASTERBROOK,A.J.MCMICHAEL,S.L.ROWLAND-JONES,E.Y.JONES, JRNL AUTH 3 G.M.GILLESPIE JRNL TITL STRUCTURAL FEATURES UNDERLYING T-CELL RECEPTOR SENSITIVITY JRNL TITL 2 TO CONCEALED MHC CLASS I MICROPOLYMORPHISMS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 E3483 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 23161907 JRNL DOI 10.1073/PNAS.1207896109 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 99.92 REMARK 3 NUMBER OF REFLECTIONS : 32685 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) : 0.19427 REMARK 3 R VALUE (WORKING SET) : 0.19125 REMARK 3 FREE R VALUE : 0.25182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 1737 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.950 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.001 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2358 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.261 REMARK 3 BIN FREE R VALUE SET COUNT : 122 REMARK 3 BIN FREE R VALUE : 0.301 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3139 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 494 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.235 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.33 REMARK 3 B22 (A**2) : -2.13 REMARK 3 B33 (A**2) : 3.46 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.170 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.167 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.115 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.705 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3229 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4387 ; 1.539 ; 1.936 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 381 ; 6.363 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 172 ;32.436 ;23.198 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 523 ;16.228 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;18.765 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 448 ; 0.119 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2553 ; 0.008 ; 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 181 REMARK 3 ORIGIN FOR THE GROUP (A): -4.6052 -12.5318 30.7099 REMARK 3 T TENSOR REMARK 3 T11: 0.1367 T22: 0.1343 REMARK 3 T33: 0.0015 T12: 0.0060 REMARK 3 T13: 0.0016 T23: -0.0028 REMARK 3 L TENSOR REMARK 3 L11: 0.7736 L22: 0.4480 REMARK 3 L33: 0.0667 L12: 0.1527 REMARK 3 L13: -0.1976 L23: -0.0237 REMARK 3 S TENSOR REMARK 3 S11: -0.0064 S12: -0.0509 S13: -0.0063 REMARK 3 S21: 0.0606 S22: 0.0074 S23: -0.0209 REMARK 3 S31: -0.0023 S32: -0.0059 S33: -0.0010 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 182 A 274 REMARK 3 ORIGIN FOR THE GROUP (A): -25.0301 -15.5917 1.8585 REMARK 3 T TENSOR REMARK 3 T11: 0.1433 T22: 0.1594 REMARK 3 T33: 0.0163 T12: -0.0207 REMARK 3 T13: -0.0134 T23: 0.0091 REMARK 3 L TENSOR REMARK 3 L11: 0.1261 L22: 0.4926 REMARK 3 L33: 1.7684 L12: -0.0457 REMARK 3 L13: 0.3091 L23: 0.1647 REMARK 3 S TENSOR REMARK 3 S11: 0.0208 S12: 0.0083 S13: 0.0115 REMARK 3 S21: -0.0671 S22: 0.0169 S23: 0.0427 REMARK 3 S31: 0.0382 S32: 0.0183 S33: -0.0377 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 99 REMARK 3 ORIGIN FOR THE GROUP (A): -15.2057 2.5851 10.9116 REMARK 3 T TENSOR REMARK 3 T11: 0.1272 T22: 0.1281 REMARK 3 T33: 0.0272 T12: -0.0187 REMARK 3 T13: -0.0262 T23: 0.0325 REMARK 3 L TENSOR REMARK 3 L11: 1.3875 L22: 0.7029 REMARK 3 L33: 0.2716 L12: -0.4918 REMARK 3 L13: 0.4338 L23: -0.0804 REMARK 3 S TENSOR REMARK 3 S11: -0.0767 S12: 0.0859 S13: 0.1269 REMARK 3 S21: -0.0279 S22: 0.0341 S23: 0.0367 REMARK 3 S31: 0.0063 S32: 0.0426 S33: 0.0426 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 11 REMARK 3 ORIGIN FOR THE GROUP (A): 1.0231 -13.7681 37.9432 REMARK 3 T TENSOR REMARK 3 T11: 0.1546 T22: 0.1530 REMARK 3 T33: 0.0277 T12: -0.0185 REMARK 3 T13: -0.0330 T23: -0.0035 REMARK 3 L TENSOR REMARK 3 L11: 4.8405 L22: 1.8948 REMARK 3 L33: 2.4980 L12: -2.1298 REMARK 3 L13: -1.8326 L23: -0.5068 REMARK 3 S TENSOR REMARK 3 S11: 0.0392 S12: -0.3052 S13: -0.1770 REMARK 3 S21: 0.1247 S22: 0.0200 S23: 0.1572 REMARK 3 S31: -0.2126 S32: 0.2346 S33: -0.0592 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2YPK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-OCT-12. REMARK 100 THE PDBE ID CODE IS EBI-54663. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34422 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.95 REMARK 200 RESOLUTION RANGE LOW (A) : 30.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 2.99 REMARK 200 R MERGE (I) : 0.05 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.40 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.31 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.40 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: PDB ENTRY 2BVO REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 8000, 50MM MES PH6.5 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 25.41450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.24450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.03350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.24450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.41450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.03350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.2 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 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 NE2 GLN A 96 O HOH A 2203 2.07 REMARK 500 NZ LYS A 186 O HOH A 2292 2.06 REMARK 500 CB SER B 55 O HOH B 2070 2.07 REMARK 500 O HOH A 2024 O HOH A 2064 2.10 REMARK 500 O HOH A 2306 O HOH A 2308 1.95 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 NH2 ARG A 83 OE1 GLU A 177 1655 1.86 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 VAL A 25 CG1 - CB - CG2 ANGL. DEV. = 11.2 DEGREES REMARK 500 ASP A 129 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 LEU A 272 CA - CB - CG 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 ARG A 14 68.23 -155.57 REMARK 500 ASP A 29 -125.32 53.37 REMARK 500 ARG A 239 -23.56 84.05 REMARK 500 SER A 251 134.34 -30.46 REMARK 500 TRP B 60 -9.01 83.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YPL RELATED DB: PDB REMARK 900 STRUCTURAL FEATURES UNDERLYING T-CELL RECEPTOR SENSITIVITY REMARK 900 TO CONCEALED MHC CLASS I MICROPOLYMORPHISMS DBREF 2YPK A 1 274 UNP P18465 1B57_HUMAN 25 298 DBREF 2YPK B 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 2YPK C 1 11 UNP Q70XD7 Q70XD7_9HIV1 162 172 SEQRES 1 A 274 GLY SER HIS SER MET ARG TYR PHE TYR THR ALA MET SER SEQRES 2 A 274 ARG PRO GLY ARG GLY GLU PRO ARG PHE ILE ALA VAL GLY SEQRES 3 A 274 TYR VAL ASP ASP THR GLN PHE VAL ARG PHE ASP SER ASP SEQRES 4 A 274 ALA ALA SER PRO ARG MET ALA PRO ARG ALA PRO TRP ILE SEQRES 5 A 274 GLU GLN GLU GLY PRO GLU TYR TRP ASP GLY GLU THR ARG SEQRES 6 A 274 ASN MET LYS ALA SER ALA GLN THR TYR ARG GLU ASN LEU SEQRES 7 A 274 ARG ILE ALA LEU ARG TYR TYR ASN GLN SER GLU ALA GLY SEQRES 8 A 274 SER HIS ILE ILE GLN VAL MET TYR GLY CYS ASP VAL GLY SEQRES 9 A 274 PRO ASP GLY ARG LEU LEU ARG GLY HIS ASP GLN SER ALA SEQRES 10 A 274 TYR ASP GLY LYS ASP TYR ILE ALA LEU ASN GLU ASP LEU SEQRES 11 A 274 SER SER TRP THR ALA ALA ASP THR ALA ALA GLN ILE THR SEQRES 12 A 274 GLN ARG LYS TRP GLU ALA ALA ARG VAL ALA GLU GLN LEU SEQRES 13 A 274 ARG ALA TYR LEU GLU GLY LEU CYS VAL GLU TRP LEU ARG SEQRES 14 A 274 ARG TYR LEU GLU ASN GLY LYS GLU THR LEU GLN ARG ALA SEQRES 15 A 274 ASP PRO PRO LYS THR HIS VAL THR HIS HIS PRO ILE SER SEQRES 16 A 274 ASP HIS GLU ALA THR LEU ARG CYS TRP ALA LEU GLY PHE SEQRES 17 A 274 TYR PRO ALA GLU ILE THR LEU THR TRP GLN ARG ASP GLY SEQRES 18 A 274 GLU ASP GLN THR GLN ASP THR GLU LEU VAL GLU THR ARG SEQRES 19 A 274 PRO ALA GLY ASP ARG THR PHE GLN LYS TRP ALA ALA VAL SEQRES 20 A 274 VAL VAL PRO SER GLY GLU GLU GLN ARG TYR THR CYS HIS SEQRES 21 A 274 VAL GLN HIS GLU GLY LEU PRO LYS PRO LEU THR LEU ARG SEQRES 22 A 274 TRP SEQRES 1 B 99 ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG HIS SEQRES 2 B 99 PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS TYR SEQRES 3 B 99 VAL SER GLY PHE HIS PRO SER ASP ILE GLU VAL ASP LEU SEQRES 4 B 99 LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SER SEQRES 5 B 99 ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU LEU SEQRES 6 B 99 TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU TYR SEQRES 7 B 99 ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO LYS SEQRES 8 B 99 ILE VAL LYS TRP ASP ARG ASP MET SEQRES 1 C 11 LYS ALA PHE SER PRO GLU VAL ILE PRO MET PHE FORMUL 4 HOH *494(H2 O) HELIX 1 1 ALA A 49 GLU A 53 5 5 HELIX 2 2 GLY A 56 TYR A 85 1 30 HELIX 3 3 ASP A 137 ALA A 150 1 14 HELIX 4 4 ARG A 151 GLY A 162 1 12 HELIX 5 5 GLY A 162 GLY A 175 1 14 HELIX 6 6 GLY A 175 GLN A 180 1 6 HELIX 7 7 THR A 225 THR A 228 5 4 HELIX 8 8 GLU A 253 GLN A 255 5 3 SHEET 1 AA 8 ALA A 46 PRO A 47 0 SHEET 2 AA 8 THR A 31 ASP A 37 -1 O ARG A 35 N ALA A 46 SHEET 3 AA 8 ARG A 21 VAL A 28 -1 O ALA A 24 N PHE A 36 SHEET 4 AA 8 HIS A 3 MET A 12 -1 O ARG A 6 N TYR A 27 SHEET 5 AA 8 ILE A 94 VAL A 103 -1 O ILE A 95 N ALA A 11 SHEET 6 AA 8 LEU A 109 TYR A 118 -1 N LEU A 110 O ASP A 102 SHEET 7 AA 8 LYS A 121 LEU A 126 -1 O LYS A 121 N TYR A 118 SHEET 8 AA 8 TRP A 133 ALA A 135 -1 O THR A 134 N ALA A 125 SHEET 1 AB 4 LYS A 186 PRO A 193 0 SHEET 2 AB 4 GLU A 198 PHE A 208 -1 O THR A 200 N HIS A 192 SHEET 3 AB 4 PHE A 241 PRO A 250 -1 O PHE A 241 N PHE A 208 SHEET 4 AB 4 ARG A 234 PRO A 235 1 O ARG A 234 N GLN A 242 SHEET 1 AC 4 LYS A 186 PRO A 193 0 SHEET 2 AC 4 GLU A 198 PHE A 208 -1 O THR A 200 N HIS A 192 SHEET 3 AC 4 PHE A 241 PRO A 250 -1 O PHE A 241 N PHE A 208 SHEET 4 AC 4 GLU A 229 LEU A 230 -1 O GLU A 229 N ALA A 246 SHEET 1 AD 2 ARG A 234 PRO A 235 0 SHEET 2 AD 2 PHE A 241 PRO A 250 1 O GLN A 242 N ARG A 234 SHEET 1 AE 4 GLU A 222 ASP A 223 0 SHEET 2 AE 4 THR A 214 ARG A 219 -1 O ARG A 219 N GLU A 222 SHEET 3 AE 4 TYR A 257 GLN A 262 -1 O THR A 258 N GLN A 218 SHEET 4 AE 4 LEU A 270 LEU A 272 -1 O LEU A 270 N VAL A 261 SHEET 1 BA 4 LYS B 6 SER B 11 0 SHEET 2 BA 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 BA 4 PHE B 62 PHE B 70 -1 O PHE B 62 N PHE B 30 SHEET 4 BA 4 SER B 55 PHE B 56 1 O SER B 55 N TYR B 63 SHEET 1 BB 4 LYS B 6 SER B 11 0 SHEET 2 BB 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 BB 4 PHE B 62 PHE B 70 -1 O PHE B 62 N PHE B 30 SHEET 4 BB 4 GLU B 50 HIS B 51 -1 O GLU B 50 N TYR B 67 SHEET 1 BC 2 SER B 55 PHE B 56 0 SHEET 2 BC 2 PHE B 62 PHE B 70 1 O TYR B 63 N SER B 55 SHEET 1 BD 4 GLU B 44 ARG B 45 0 SHEET 2 BD 4 GLU B 36 LYS B 41 -1 O LYS B 41 N GLU B 44 SHEET 3 BD 4 TYR B 78 ASN B 83 -1 O ALA B 79 N LEU B 40 SHEET 4 BD 4 LYS B 91 LYS B 94 -1 O LYS B 91 N VAL B 82 SSBOND 1 CYS A 101 CYS A 164 1555 1555 2.07 SSBOND 2 CYS A 203 CYS A 259 1555 1555 2.02 SSBOND 3 CYS B 25 CYS B 80 1555 1555 2.00 CISPEP 1 TYR A 209 PRO A 210 0 6.35 CISPEP 2 HIS B 31 PRO B 32 0 4.34 CRYST1 50.829 82.067 110.489 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.019674 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012185 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009051 0.00000 MASTER 384 0 0 8 36 0 0 6 0 0 0 31 END