HEADER IMMUNE SYSTEM 16-JUL-14 4U1S TITLE HLA CLASS I MICROPOLYMORPHISMS DETERMINE PEPTIDE-HLA LANDSCAPE AND TITLE 2 DICTATE DIFFERENTIAL HIV-1 ESCAPE THROUGH IDENTICAL EPITOPES COMPND MOL_ID: 1; COMPND 2 MOLECULE: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-81 ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 25-301; COMPND 5 SYNONYM: B'DT,MHC CLASS I ANTIGEN B*81; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UNP RESIDUES 21-119; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: VPR PROTEIN; COMPND 14 CHAIN: C; COMPND 15 SYNONYM: FL9; COMPND 16 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-B, HLAB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGMT7; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: B2M, CDABP0092, HDCMA22P; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PGMT7; SOURCE 21 MOL_ID: 3; SOURCE 22 SYNTHETIC: YES; SOURCE 23 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 24 ORGANISM_TAXID: 11676; SOURCE 25 OTHER_DETAILS: SYNTHETIC KEYWDS IMMUNOGLOBULIN, HLA, HIV, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR P.J.RIZKALLAH,D.K.COLE,A.FULLER,A.K.SEWELL REVDAT 3 20-DEC-23 4U1S 1 REMARK REVDAT 2 30-AUG-17 4U1S 1 REMARK SITE ATOM REVDAT 1 08-APR-15 4U1S 0 JRNL AUTH H.N.KLVERPRIS,D.K.COLE,A.FULLER,J.CARLSON,K.BECK, JRNL AUTH 2 A.J.SCHAUENBURG,P.J.RIZKALLAH,S.BUUS,A.K.SEWELL,P.GOULDER JRNL TITL A MOLECULAR SWITCH IN IMMUNODOMINANT HIV-1-SPECIFIC CD8 JRNL TITL 2 T-CELL EPITOPES SHAPES DIFFERENTIAL HLA-RESTRICTED ESCAPE. JRNL REF RETROVIROLOGY V. 12 20 2015 JRNL REFN ESSN 1742-4690 JRNL PMID 25808313 JRNL DOI 10.1186/S12977-015-0149-5 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 46542 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2350 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) : 1.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3224 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE SET COUNT : 158 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3185 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 59 REMARK 3 SOLVENT ATOMS : 244 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.29000 REMARK 3 B22 (A**2) : -0.13000 REMARK 3 B33 (A**2) : -0.15000 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): 0.107 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.104 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.073 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.547 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3354 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3036 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4536 ; 1.961 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6984 ; 0.950 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 390 ; 6.811 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 181 ;31.396 ;23.204 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 536 ;14.959 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;17.142 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 455 ; 0.138 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3803 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 829 ; 0.001 ; 0.020 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): 1560 ; 1.410 ; 1.263 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1559 ; 1.411 ; 1.263 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1950 ; 2.218 ; 1.882 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 181 REMARK 3 RESIDUE RANGE : C 1 C 9 REMARK 3 ORIGIN FOR THE GROUP (A): 4.8133 -12.0665 -31.1346 REMARK 3 T TENSOR REMARK 3 T11: 0.0167 T22: 0.0289 REMARK 3 T33: 0.0130 T12: 0.0029 REMARK 3 T13: -0.0075 T23: -0.0076 REMARK 3 L TENSOR REMARK 3 L11: 2.5271 L22: 1.9287 REMARK 3 L33: 1.2279 L12: -0.1160 REMARK 3 L13: -0.6329 L23: 0.3382 REMARK 3 S TENSOR REMARK 3 S11: 0.0247 S12: 0.2509 S13: -0.0892 REMARK 3 S21: -0.1692 S22: 0.0066 S23: 0.0560 REMARK 3 S31: 0.0088 S32: -0.0191 S33: -0.0313 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 181 A 277 REMARK 3 ORIGIN FOR THE GROUP (A): 25.6612 -15.2537 -1.7498 REMARK 3 T TENSOR REMARK 3 T11: 0.0955 T22: 0.1639 REMARK 3 T33: 0.0971 T12: 0.0389 REMARK 3 T13: -0.0187 T23: -0.0336 REMARK 3 L TENSOR REMARK 3 L11: 0.3006 L22: 1.1716 REMARK 3 L33: 6.6246 L12: -0.3913 REMARK 3 L13: 1.2596 L23: -0.9078 REMARK 3 S TENSOR REMARK 3 S11: 0.0554 S12: 0.0481 S13: -0.0412 REMARK 3 S21: 0.1282 S22: 0.0135 S23: -0.0212 REMARK 3 S31: 0.4695 S32: 0.3716 S33: -0.0689 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 0 B 99 REMARK 3 ORIGIN FOR THE GROUP (A): 15.0521 2.9405 -10.5723 REMARK 3 T TENSOR REMARK 3 T11: 0.0832 T22: 0.0860 REMARK 3 T33: 0.1161 T12: -0.0094 REMARK 3 T13: 0.0114 T23: -0.0886 REMARK 3 L TENSOR REMARK 3 L11: 3.8528 L22: 2.4121 REMARK 3 L33: 2.8228 L12: 1.1406 REMARK 3 L13: 1.8069 L23: 0.7673 REMARK 3 S TENSOR REMARK 3 S11: -0.0699 S12: -0.3705 S13: 0.5273 REMARK 3 S21: 0.1384 S22: -0.0427 S23: 0.0682 REMARK 3 S31: -0.3278 S32: 0.0274 S33: 0.1126 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 ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 4U1S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000202668. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 3.3.20, GDA REMARK 200 DATA SCALING SOFTWARE : SCALA 2.1.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46617 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 40.625 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09600 REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 1.01400 REMARK 200 R SYM FOR SHELL (I) : 1.01400 REMARK 200 FOR SHELL : 0.600 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: 4I4W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM CHLORIDE, PH 8, 20% PEG REMARK 280 6000, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 25.58500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.38500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.62500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.38500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.58500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.62500 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 300 REMARK: CHAINS A, B AND C FORM ONE BIOLOGICAL ENTITY. ONLY ONE COPY REMARK 300 IS PRESENT IN THE A.U. 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: 7430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 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 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 HOH A 524 O HOH A 536 2.11 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 GLY A 175 C - N - CA ANGL. DEV. = 15.9 DEGREES REMARK 500 ASP A 177 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 239 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 3 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG B 3 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ASP B 34 CB - CG - OD1 ANGL. DEV. = 7.0 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 67.65 -155.57 REMARK 500 ASP A 29 -125.85 52.29 REMARK 500 ASN A 174 78.58 -152.86 REMARK 500 ARG A 239 -18.93 90.03 REMARK 500 PRO A 276 96.77 -61.34 REMARK 500 PRO B 32 -177.56 -69.59 REMARK 500 TRP B 60 -2.59 75.39 REMARK 500 LEU C 6 -111.85 79.62 REMARK 500 LEU C 6 -111.85 77.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 174 GLY A 175 -141.29 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 EDO A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 104 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4U1H RELATED DB: PDB REMARK 900 RELATED ID: 4U1I RELATED DB: PDB REMARK 900 RELATED ID: 4U1J RELATED DB: PDB REMARK 900 RELATED ID: 4U1K RELATED DB: PDB REMARK 900 RELATED ID: 4U1L RELATED DB: PDB REMARK 900 RELATED ID: 4U1M RELATED DB: PDB REMARK 900 RELATED ID: 4U1N RELATED DB: PDB DBREF 4U1S A 1 277 UNP Q31610 1B81_HUMAN 25 301 DBREF 4U1S B 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 4U1S C 1 9 UNP T2D0U8 T2D0U8_9HIV1 34 42 SEQADV 4U1S MET A 0 UNP Q31610 INITIATING METHIONINE SEQADV 4U1S MET B 0 UNP P61769 INITIATING METHIONINE SEQRES 1 A 278 MET GLY SER HIS SER MET ARG TYR PHE TYR THR SER VAL SEQRES 2 A 278 SER ARG PRO GLY ARG GLY GLU PRO ARG PHE ILE SER VAL SEQRES 3 A 278 GLY TYR VAL ASP ASP THR GLN PHE VAL ARG PHE ASP SER SEQRES 4 A 278 ASP ALA ALA SER PRO ARG GLU GLU PRO ARG ALA PRO TRP SEQRES 5 A 278 ILE GLU GLN GLU GLY PRO GLU TYR TRP ASP ARG ASN THR SEQRES 6 A 278 GLN ILE TYR LYS ALA GLN ALA GLN THR ASP ARG GLU SER SEQRES 7 A 278 LEU ARG ASN LEU ARG GLY TYR TYR ASN GLN SER GLU ALA SEQRES 8 A 278 GLY SER HIS THR LEU GLN SER MET TYR GLY CYS ASP VAL SEQRES 9 A 278 GLY PRO ASP GLY ARG LEU LEU ARG GLY HIS ASN GLN TYR SEQRES 10 A 278 ALA TYR ASP GLY LYS ASP TYR ILE ALA LEU ASN GLU ASP SEQRES 11 A 278 LEU ARG SER TRP THR ALA ALA ASP THR ALA ALA GLN ILE SEQRES 12 A 278 SER GLN ARG LYS LEU GLU ALA ALA ARG VAL ALA GLU GLN SEQRES 13 A 278 LEU ARG ALA TYR LEU GLU GLY GLU CYS VAL GLU TRP LEU SEQRES 14 A 278 ARG ARG TYR LEU GLU ASN GLY LYS ASP LYS LEU GLU ARG SEQRES 15 A 278 ALA ASP PRO PRO LYS THR HIS VAL THR HIS HIS PRO ILE SEQRES 16 A 278 SER ASP HIS GLU ALA THR LEU ARG CYS TRP ALA LEU GLY SEQRES 17 A 278 PHE TYR PRO ALA GLU ILE THR LEU THR TRP GLN ARG ASP SEQRES 18 A 278 GLY GLU ASP GLN THR GLN ASP THR GLU LEU VAL GLU THR SEQRES 19 A 278 ARG PRO ALA GLY ASP ARG THR PHE GLN LYS TRP THR ALA SEQRES 20 A 278 VAL VAL VAL PRO SER GLY GLU GLU GLN ARG TYR THR CYS SEQRES 21 A 278 HIS VAL GLN HIS GLU GLY LEU PRO LYS PRO LEU THR LEU SEQRES 22 A 278 ARG TRP GLU PRO SER SEQRES 1 B 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG SEQRES 2 B 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS SEQRES 3 B 100 TYR VAL SER GLY PHE HIS PRO SER ASP ILE GLU VAL ASP SEQRES 4 B 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SEQRES 5 B 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU SEQRES 6 B 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU SEQRES 7 B 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO SEQRES 8 B 100 LYS ILE VAL LYS TRP ASP ARG ASP MET SEQRES 1 C 9 PHE PRO ARG PRO TRP LEU HIS GLY LEU HET EDO A 301 4 HET EDO A 302 4 HET EDO A 303 4 HET EDO A 304 4 HET EDO A 305 4 HET EDO A 306 4 HET EDO A 307 4 HET EDO A 308 4 HET EDO A 309 4 HET SO4 A 310 5 HET EDO B 101 4 HET EDO B 102 4 HET EDO B 103 4 HET GOL B 104 6 HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 EDO 12(C2 H6 O2) FORMUL 13 SO4 O4 S 2- FORMUL 17 GOL C3 H8 O3 FORMUL 18 HOH *244(H2 O) HELIX 1 AA1 ALA A 49 GLU A 53 5 5 HELIX 2 AA2 GLY A 56 TYR A 85 1 30 HELIX 3 AA3 ASP A 137 ALA A 150 1 14 HELIX 4 AA4 ARG A 151 GLY A 162 1 12 HELIX 5 AA5 GLY A 162 ASN A 174 1 13 HELIX 6 AA6 GLY A 175 GLU A 180 1 6 HELIX 7 AA7 GLU A 253 GLN A 255 5 3 SHEET 1 AA1 8 GLU A 46 PRO A 47 0 SHEET 2 AA1 8 THR A 31 ASP A 37 -1 N ARG A 35 O GLU A 46 SHEET 3 AA1 8 ARG A 21 VAL A 28 -1 N GLY A 26 O PHE A 33 SHEET 4 AA1 8 HIS A 3 VAL A 12 -1 N ARG A 6 O TYR A 27 SHEET 5 AA1 8 THR A 94 VAL A 103 -1 O VAL A 103 N HIS A 3 SHEET 6 AA1 8 LEU A 109 TYR A 118 -1 O LEU A 110 N ASP A 102 SHEET 7 AA1 8 LYS A 121 LEU A 126 -1 O TYR A 123 N TYR A 116 SHEET 8 AA1 8 TRP A 133 ALA A 135 -1 O THR A 134 N ALA A 125 SHEET 1 AA2 4 LYS A 186 PRO A 193 0 SHEET 2 AA2 4 GLU A 198 PHE A 208 -1 O TRP A 204 N HIS A 188 SHEET 3 AA2 4 PHE A 241 PRO A 250 -1 O THR A 245 N CYS A 203 SHEET 4 AA2 4 THR A 228 LEU A 230 -1 N GLU A 229 O ALA A 246 SHEET 1 AA3 4 LYS A 186 PRO A 193 0 SHEET 2 AA3 4 GLU A 198 PHE A 208 -1 O TRP A 204 N HIS A 188 SHEET 3 AA3 4 PHE A 241 PRO A 250 -1 O THR A 245 N CYS A 203 SHEET 4 AA3 4 ARG A 234 PRO A 235 -1 N ARG A 234 O GLN A 242 SHEET 1 AA4 4 GLU A 222 GLN A 224 0 SHEET 2 AA4 4 THR A 214 ARG A 219 -1 N TRP A 217 O GLN A 224 SHEET 3 AA4 4 TYR A 257 GLN A 262 -1 O HIS A 260 N THR A 216 SHEET 4 AA4 4 LEU A 270 LEU A 272 -1 O LEU A 272 N CYS A 259 SHEET 1 AA5 4 LYS B 6 SER B 11 0 SHEET 2 AA5 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 AA5 4 PHE B 62 PHE B 70 -1 O PHE B 62 N PHE B 30 SHEET 4 AA5 4 GLU B 50 HIS B 51 -1 N GLU B 50 O TYR B 67 SHEET 1 AA6 4 LYS B 6 SER B 11 0 SHEET 2 AA6 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 AA6 4 PHE B 62 PHE B 70 -1 O PHE B 62 N PHE B 30 SHEET 4 AA6 4 SER B 55 PHE B 56 -1 N SER B 55 O TYR B 63 SHEET 1 AA7 4 GLU B 44 ARG B 45 0 SHEET 2 AA7 4 GLU B 36 LYS B 41 -1 N LYS B 41 O GLU B 44 SHEET 3 AA7 4 TYR B 78 ASN B 83 -1 O ARG B 81 N ASP B 38 SHEET 4 AA7 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 2.15 SSBOND 2 CYS A 203 CYS A 259 1555 1555 2.04 SSBOND 3 CYS B 25 CYS B 80 1555 1555 2.04 CISPEP 1 TYR A 209 PRO A 210 0 -0.42 CISPEP 2 HIS B 31 PRO B 32 0 -2.21 SITE 1 AC1 8 GLN A 70 THR A 73 ASP A 74 SER A 77 SITE 2 AC1 8 TYR A 116 TRP C 5 HIS C 7 HOH C 101 SITE 1 AC2 8 ASP A 39 ASN A 127 GLU A 128 ASP A 129 SITE 2 AC2 8 SER A 132 HIS A 197 HOH A 459 HOH A 473 SITE 1 AC3 6 ASP A 122 ALA A 125 THR A 134 ALA A 136 SITE 2 AC3 6 HOH A 499 HOH A 457 SITE 1 AC4 3 SER A 195 ASP A 196 HOH A 485 SITE 1 AC5 3 GLU A 46 PRO A 47 ARG A 48 SITE 1 AC6 3 TYR A 85 TYR A 118 ASP A 122 SITE 1 AC7 2 GLU A 166 ARG A 170 SITE 1 AC8 5 PRO A 47 ARG A 48 ALA A 49 PRO A 50 SITE 2 AC8 5 GLU A 53 SITE 1 AC9 4 LEU A 179 ARG A 181 ALA A 182 GLU A 264 SITE 1 AD1 5 GLN A 262 HIS A 263 LEU A 266 LYS A 268 SITE 2 AD1 5 PRO A 269 SITE 1 AD2 4 ASP A 37 ASP B 53 LEU B 54 HOH B 205 SITE 1 AD3 5 MET A 98 SER B 57 LYS B 58 TRP B 60 SITE 2 AD3 5 HOH B 232 SITE 1 AD4 10 LEU A 206 ARG A 234 GLN A 242 TYR B 10 SITE 2 AD4 10 SER B 11 HIS B 13 PRO B 14 HOH B 241 SITE 3 AD4 10 HOH B 252 HOH B 233 SITE 1 AD5 8 HIS B 13 PRO B 14 ALA B 15 GLU B 16 SITE 2 AD5 8 LYS B 19 SER B 20 ASN B 21 PRO B 72 CRYST1 51.170 81.250 110.770 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 0.019543 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012308 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009028 0.00000