HEADER IMMUNE SYSTEM 15-JUL-14 4U1N 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-42 ALPHA CHAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MHC CLASS I ANTIGEN B*42; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: PROTEIN NEF; COMPND 12 CHAIN: C; COMPND 13 FRAGMENT: RESIDUES 69-77; COMPND 14 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_VARIANT: 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_VARIANT: 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: RM9 PEPTIDE 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 4U1N 1 REMARK REVDAT 2 30-AUG-17 4U1N 1 SITE ATOM REVDAT 1 08-APR-15 4U1N 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. 1.77 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 81.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 45492 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2299 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) : 1.77 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3148 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 REMARK 3 BIN FREE R VALUE SET COUNT : 169 REMARK 3 BIN FREE R VALUE : 0.2470 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3179 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 295 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : -0.01000 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): 0.104 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.103 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.068 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.225 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3380 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3065 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4574 ; 2.040 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7055 ; 0.937 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 398 ; 6.067 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 186 ;31.754 ;23.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 545 ;14.654 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;20.580 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 459 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3861 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 833 ; 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): 1574 ; 1.124 ; 1.116 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1573 ; 1.124 ; 1.116 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1972 ; 1.780 ; 1.662 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): 4.6060 -12.0913 -30.9502 REMARK 3 T TENSOR REMARK 3 T11: 0.0138 T22: 0.0161 REMARK 3 T33: 0.0037 T12: 0.0020 REMARK 3 T13: -0.0056 T23: -0.0050 REMARK 3 L TENSOR REMARK 3 L11: 2.2550 L22: 1.0204 REMARK 3 L33: 0.6892 L12: 0.1034 REMARK 3 L13: -0.4469 L23: 0.0348 REMARK 3 S TENSOR REMARK 3 S11: 0.0099 S12: 0.1826 S13: -0.0445 REMARK 3 S21: -0.1110 S22: 0.0105 S23: 0.0331 REMARK 3 S31: 0.0220 S32: -0.0078 S33: -0.0204 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): 25.9538 -15.0037 -1.7433 REMARK 3 T TENSOR REMARK 3 T11: 0.0794 T22: 0.0931 REMARK 3 T33: 0.0634 T12: 0.0322 REMARK 3 T13: -0.0160 T23: -0.0173 REMARK 3 L TENSOR REMARK 3 L11: 0.1136 L22: 0.5548 REMARK 3 L33: 6.7906 L12: -0.1003 REMARK 3 L13: 0.5051 L23: -1.0664 REMARK 3 S TENSOR REMARK 3 S11: 0.0181 S12: -0.0459 S13: -0.0330 REMARK 3 S21: 0.1122 S22: 0.0293 S23: -0.0290 REMARK 3 S31: 0.3011 S32: 0.2357 S33: -0.0474 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): 14.9630 2.9527 -10.4934 REMARK 3 T TENSOR REMARK 3 T11: 0.0677 T22: 0.0545 REMARK 3 T33: 0.0529 T12: 0.0149 REMARK 3 T13: -0.0149 T23: -0.0425 REMARK 3 L TENSOR REMARK 3 L11: 3.7051 L22: 2.7353 REMARK 3 L33: 2.4194 L12: 1.4025 REMARK 3 L13: 1.2735 L23: 0.9601 REMARK 3 S TENSOR REMARK 3 S11: -0.0849 S12: -0.3731 S13: 0.4003 REMARK 3 S21: 0.0809 S22: -0.0276 S23: 0.0252 REMARK 3 S31: -0.2382 S32: -0.0393 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 4U1N 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_1000202656. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 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 0.1.27, GDA REMARK 200 DATA SCALING SOFTWARE : AIMLESS 2.1.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45559 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 81.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.75200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 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 (%): 51.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 6000, 10MM MAGNESIUM CHLORIDE, REMARK 280 PH 6.0, 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 25.49000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.23500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.61500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.23500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.49000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.61500 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. THERE IS ONLY REMARK 300 ONE COPY 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 15.0 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: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 173 CG GLU A 173 CD 0.119 REMARK 500 TRP A 204 CB TRP A 204 CG -0.109 REMARK 500 MET C 9 CG MET C 9 SD -0.157 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 ASP A 37 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 44 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 108 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP A 177 CB - CG - OD1 ANGL. DEV. = 5.4 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 75.96 -154.11 REMARK 500 ASP A 29 -124.73 51.23 REMARK 500 GLN A 224 56.64 -106.04 REMARK 500 ARG A 239 -20.68 85.45 REMARK 500 TRP B 60 -3.29 77.32 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 EDO A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4U1H RELATED DB: PDB REMARK 900 RELATED ID: 4U1J RELATED DB: PDB REMARK 900 RELATED ID: 4U1L RELATED DB: PDB DBREF 4U1N A 1 277 UNP P30480 1B42_HUMAN 25 301 DBREF 4U1N B 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 4U1N C 1 9 UNP Q90VG9 Q90VG9_9HIV1 69 77 SEQADV 4U1N MET A 0 UNP P30480 INITIATING METHIONINE SEQADV 4U1N HIS A 9 UNP P30480 TYR 33 CONFLICT SEQADV 4U1N MET B 0 UNP P61769 INITIATING METHIONINE SEQRES 1 A 278 MET GLY SER HIS SER MET ARG TYR PHE HIS 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 THR GLN ARG LYS TRP GLU ALA ALA ARG VAL ALA GLU GLN SEQRES 13 A 278 ASP ARG ALA TYR LEU GLU GLY THR CYS VAL GLU TRP LEU SEQRES 14 A 278 ARG ARG TYR LEU GLU ASN GLY LYS ASP THR 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 ALA 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 ARG PRO GLN VAL PRO LEU ARG PRO MET 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 EDO A 310 4 HET GOL A 311 6 HET GOL A 312 6 HET EDO B 101 4 HET EDO C 101 4 HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 EDO 12(C2 H6 O2) FORMUL 14 GOL 2(C3 H8 O3) FORMUL 18 HOH *295(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 GLY A 175 1 14 HELIX 6 AA6 GLY A 175 GLU A 180 1 6 HELIX 7 AA7 THR A 225 THR A 228 5 4 HELIX 8 AA8 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 VAL A 249 N ALA A 199 SHEET 4 AA2 4 GLU A 229 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 VAL A 249 N ALA A 199 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 ASP A 223 0 SHEET 2 AA4 4 THR A 214 ARG A 219 -1 N ARG A 219 O GLU A 222 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 SER B 28 N LYS B 6 SHEET 3 AA5 4 PHE B 62 PHE B 70 -1 O THR B 68 N LEU B 23 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 SER B 28 N LYS B 6 SHEET 3 AA6 4 PHE B 62 PHE B 70 -1 O THR B 68 N LEU B 23 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 ALA B 79 N LEU B 40 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 2.09 SSBOND 2 CYS A 203 CYS A 259 1555 1555 2.01 SSBOND 3 CYS B 25 CYS B 80 1555 1555 2.00 CISPEP 1 TYR A 209 PRO A 210 0 2.86 CISPEP 2 HIS B 31 PRO B 32 0 -2.81 SITE 1 AC1 7 GLN A 70 THR A 73 ASP A 74 SER A 77 SITE 2 AC1 7 HOH A 471 ARG C 7 EDO C 101 SITE 1 AC2 6 ASP A 39 ASN A 127 GLU A 128 ASP A 129 SITE 2 AC2 6 HIS A 197 HOH A 447 SITE 1 AC3 5 HIS A 3 LEU A 179 GLU A 180 GLU A 264 SITE 2 AC3 5 HOH A 552 SITE 1 AC4 8 ASP A 122 TYR A 123 ILE A 124 ALA A 125 SITE 2 AC4 8 THR A 134 ALA A 136 HOH A 456 HOH A 484 SITE 1 AC5 4 SER A 195 ASP A 196 HOH A 415 HOH A 448 SITE 1 AC6 7 PRO A 235 ALA A 236 GLY A 237 ASP A 238 SITE 2 AC6 7 ARG A 239 THR A 240 HOH A 571 SITE 1 AC7 3 GLU A 166 TRP A 167 ARG A 170 SITE 1 AC8 4 ARG A 6 MET A 98 HIS A 113 GLN A 115 SITE 1 AC9 6 TYR A 85 TYR A 118 LYS A 121 ASP A 122 SITE 2 AC9 6 ASP A 137 HOH A 578 SITE 1 AD1 4 ARG A 35 GLU A 46 PRO A 47 ARG A 48 SITE 1 AD2 6 SER A 4 PHE A 8 TYR A 27 ASP A 29 SITE 2 AD2 6 ASP A 30 HOH B 203 SITE 1 AD3 9 THR A 138 GLN A 141 ILE A 142 GLU A 180 SITE 2 AD3 9 ARG A 181 ALA A 182 HOH A 408 HOH A 409 SITE 3 AD3 9 HOH A 535 SITE 1 AD4 10 TRP A 204 LEU A 206 ARG A 234 GLN A 242 SITE 2 AD4 10 TYR B 10 SER B 11 HIS B 13 PRO B 14 SITE 3 AD4 10 HOH B 241 HOH B 238 SITE 1 AD5 6 TYR A 116 VAL A 152 ASP A 156 EDO A 301 SITE 2 AD5 6 LEU C 6 ARG C 7 CRYST1 50.980 81.230 110.470 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 0.019616 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012311 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009052 0.00000