HEADER IMMUNE SYSTEM 02-OCT-25 9YIR TITLE HPV_2-1 TCR IN COMPLEX WITH HLA-A*01:01 PRESENTING HPV16 E2 9MER TITLE 2 PEPTIDE (151-QVDYYGLYY-159) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN A ALPHA CHAIN; COMPND 3 CHAIN: C; COMPND 4 SYNONYM: MHC CLASS I ANTIGEN,MAJOR HISTOCOMPATIBILITY COMPLEX,CLASS COMPND 5 I,A; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 9 CHAIN: D; COMPND 10 FRAGMENT: UNP RESIDUES 21-119; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: REGULATORY PROTEIN E2; COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: TCR ALPHA CHAIN (TRAV21); COMPND 18 CHAIN: A; COMPND 19 ENGINEERED: YES; COMPND 20 MOL_ID: 5; COMPND 21 MOLECULE: TCR BETA CHAIN (TRBV27); COMPND 22 CHAIN: B; COMPND 23 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-A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: B2M, CDABP0092, HDCMA22P; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: HUMAN PAPILLOMAVIRUS 16; SOURCE 18 ORGANISM_TAXID: 333760; SOURCE 19 MOL_ID: 4; SOURCE 20 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 21 ORGANISM_TAXID: 9606; SOURCE 22 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 23 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 24 MOL_ID: 5; SOURCE 25 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 26 ORGANISM_TAXID: 9606; SOURCE 27 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 28 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS T CELL RECEPTOR, TCR, HLA, PHLA, MHC, PMHC, HPV, HPV16, E2, A*01:01, KEYWDS 2 IMMUNE SYSTEM, VIRAL EXPDTA X-RAY DIFFRACTION AUTHOR H.A.MILLER,G.M.PALOWITCH,C.L.DULBERGER REVDAT 1 16-SEP-26 9YIR 0 JRNL AUTH E.JACKSON JRNL TITL HPV16 E2-SPECIFIC TCR IN COMPLEX WITH HLA-A*01:01 PRESENTING JRNL TITL 2 HPV16 E2 9MER PEPTIDE (151-QVDYYGLYY-159) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0430 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) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 90.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 45417 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) : 0.255 REMARK 3 R VALUE (WORKING SET) : 0.253 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2326 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3253 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.28 REMARK 3 BIN R VALUE (WORKING SET) : 0.3860 REMARK 3 BIN FREE R VALUE SET COUNT : 175 REMARK 3 BIN FREE R VALUE : 0.4320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6340 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 25 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.90000 REMARK 3 B22 (A**2) : 0.90000 REMARK 3 B33 (A**2) : 0.56000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.85000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.333 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.261 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.295 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.554 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.915 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.875 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6507 ; 0.003 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 5688 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8882 ; 1.131 ; 1.802 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13032 ; 0.409 ; 1.752 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 816 ; 7.466 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 41 ; 5.588 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 937 ;13.782 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 961 ; 0.053 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7935 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1597 ; 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): 3279 ; 1.824 ; 3.708 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3279 ; 1.824 ; 3.708 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4090 ; 3.080 ; 6.663 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4091 ; 3.080 ; 6.662 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3228 ; 1.772 ; 3.793 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3229 ; 1.772 ; 3.793 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4793 ; 2.999 ; 6.907 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6768 ; 4.695 ;35.040 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6768 ; 4.695 ;35.040 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 9YIR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-25. REMARK 100 THE DEPOSITION ID IS D_1000300636. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97626 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45417 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 96.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.23700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 1.66500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.700 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 3000, 0.1 M TRIS PH 8.5, 0.2 M REMARK 280 LITHIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 27.49200 REMARK 290 SMTRY3 2 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 AUTHOR DETERMINED BIOLOGICAL UNIT: PENTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, P, A, B 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 GLY C 1 REMARK 465 MET D 0 REMARK 465 ILE D 1 REMARK 465 PRO A 201 REMARK 465 GLU A 202 REMARK 465 SER A 203 REMARK 465 SER A 204 REMARK 465 CYS A 205 REMARK 465 GLY A 206 REMARK 465 SER A 207 REMARK 465 LEU A 208 REMARK 465 GLU A 209 REMARK 465 VAL A 210 REMARK 465 LEU A 211 REMARK 465 PHE A 212 REMARK 465 GLN A 213 REMARK 465 GLU B -1 REMARK 465 ALA B 0 REMARK 465 ASP B 241 REMARK 465 CYS B 242 REMARK 465 GLY B 243 REMARK 465 SER B 244 REMARK 465 LEU B 245 REMARK 465 GLU B 246 REMARK 465 VAL B 247 REMARK 465 LEU B 248 REMARK 465 PHE B 249 REMARK 465 GLN B 250 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG C 17 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 19 CG CD OE1 OE2 REMARK 470 GLN C 43 CG CD OE1 NE2 REMARK 470 LYS C 44 CG CD CE NZ REMARK 470 GLU C 46 CG CD OE1 OE2 REMARK 470 GLU C 58 CG CD OE1 OE2 REMARK 470 ASP C 90 CG OD1 OD2 REMARK 470 ASP C 106 CG OD1 OD2 REMARK 470 ARG C 108 CG CD NE CZ NH1 NH2 REMARK 470 LEU C 110 CG CD1 CD2 REMARK 470 ARG C 111 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 128 CG CD OE1 OE2 REMARK 470 GLU C 154 CG CD OE1 OE2 REMARK 470 ARG C 181 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 186 CG CD CE NZ REMARK 470 HIS C 197 CG ND1 CD2 CE1 NE2 REMARK 470 GLU C 222 CG CD OE1 OE2 REMARK 470 THR C 225 OG1 CG2 REMARK 470 GLN C 226 CG CD OE1 NE2 REMARK 470 ASP C 227 CG OD1 OD2 REMARK 470 GLU C 232 CG CD OE1 OE2 REMARK 470 LYS C 268 CG CD CE NZ REMARK 470 ARG C 273 CG CD NE CZ NH1 NH2 REMARK 470 GLU D 16 CG CD OE1 OE2 REMARK 470 ASN D 17 CG OD1 ND2 REMARK 470 LYS D 19 CG CD CE NZ REMARK 470 ARG D 45 CG CD NE CZ NH1 NH2 REMARK 470 GLU D 47 CG CD OE1 OE2 REMARK 470 LYS D 48 CG CD CE NZ REMARK 470 GLU D 50 CG CD OE1 OE2 REMARK 470 LYS D 58 CG CD CE NZ REMARK 470 GLU D 74 CG CD OE1 OE2 REMARK 470 LYS D 75 CG CD CE NZ REMARK 470 ILE A 6 CG1 CG2 CD1 REMARK 470 SER A 23 OG REMARK 470 LYS A 41 CG CD CE NZ REMARK 470 ARG A 54 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 55 CG CD OE1 OE2 REMARK 470 LYS A 67 CG CD CE NZ REMARK 470 SER A 68 OG REMARK 470 ARG A 71 CG CD NE CZ NH1 NH2 REMARK 470 SER A 79 OG REMARK 470 LYS A 97 CG CD CE NZ REMARK 470 LYS A 148 CG CD CE NZ REMARK 470 ARG A 163 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 168 CG CD CE NZ REMARK 470 GLU A 194 CG CD OE1 OE2 REMARK 470 GLN B 1 CG CD OE1 NE2 REMARK 470 LYS B 15 CG CD CE NZ REMARK 470 LYS B 16 CG CD CE NZ REMARK 470 ASN B 26 CG OD1 ND2 REMARK 470 GLU B 60 CG CD OE1 OE2 REMARK 470 LYS B 63 CG CD CE NZ REMARK 470 SER B 65 OG REMARK 470 ARG B 70 CG CD NE CZ NH1 NH2 REMARK 470 SER B 92 OG REMARK 470 LYS B 115 CG CD CE NZ REMARK 470 LYS B 129 CG CD CE NZ REMARK 470 LYS B 161 CG CD CE NZ REMARK 470 GLN B 172 CG CD OE1 NE2 REMARK 470 LYS B 175 CG CD CE NZ REMARK 470 GLN B 177 CG CD OE1 NE2 REMARK 470 ASP B 182 CG OD1 OD2 REMARK 470 GLU B 216 CG CD OE1 OE2 REMARK 470 ASN B 217 CG OD1 ND2 REMARK 470 GLU B 219 CG CD OE1 OE2 REMARK 470 GLN B 222 CG CD OE1 NE2 REMARK 470 ASP B 223 CG OD1 OD2 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 ASP C 29 -115.76 51.65 REMARK 500 ARG C 48 26.18 -144.08 REMARK 500 GLU C 161 31.67 -80.73 REMARK 500 SER C 195 -158.54 -130.02 REMARK 500 ASP C 227 61.69 74.27 REMARK 500 HIS C 263 140.28 -173.54 REMARK 500 GLU D 16 76.71 -167.02 REMARK 500 ASN D 17 98.16 -35.82 REMARK 500 LYS D 48 86.29 61.33 REMARK 500 TRP D 60 1.46 92.14 REMARK 500 PRO A 7 118.76 14.44 REMARK 500 SER A 58 113.73 -170.08 REMARK 500 ALA A 85 -179.39 -177.33 REMARK 500 SER B 85 -178.89 -172.76 REMARK 500 PRO B 178 2.61 -60.74 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 ILE A 6 PRO A 7 -121.11 REMARK 500 PRO B 120 GLU B 121 149.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 60 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 9YIR C 1 275 UNP Q5SUL5 Q5SUL5_HUMAN 25 299 DBREF 9YIR D 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 9YIR P 1 9 UNP P03120 VE2_HPV16 151 159 DBREF 9YIR A 1 213 PDB 9YIR 9YIR 1 213 DBREF 9YIR B -1 250 PDB 9YIR 9YIR -1 250 SEQADV 9YIR MET D 0 UNP P61769 INITIATING METHIONINE SEQRES 1 C 275 GLY SER HIS SER MET ARG TYR PHE PHE THR SER VAL SER SEQRES 2 C 275 ARG PRO GLY ARG GLY GLU PRO ARG PHE ILE ALA VAL GLY SEQRES 3 C 275 TYR VAL ASP ASP THR GLN PHE VAL ARG PHE ASP SER ASP SEQRES 4 C 275 ALA ALA SER GLN LYS MET GLU PRO ARG ALA PRO TRP ILE SEQRES 5 C 275 GLU GLN GLU GLY PRO GLU TYR TRP ASP GLN GLU THR ARG SEQRES 6 C 275 ASN MET LYS ALA HIS SER GLN THR ASP ARG ALA ASN LEU SEQRES 7 C 275 GLY THR LEU ARG GLY TYR TYR ASN GLN SER GLU ASP GLY SEQRES 8 C 275 SER HIS THR ILE GLN ILE MET TYR GLY CYS ASP VAL GLY SEQRES 9 C 275 PRO ASP GLY ARG PHE LEU ARG GLY TYR ARG GLN ASP ALA SEQRES 10 C 275 TYR ASP GLY LYS ASP TYR ILE ALA LEU ASN GLU ASP LEU SEQRES 11 C 275 ARG SER TRP THR ALA ALA ASP MET ALA ALA GLN ILE THR SEQRES 12 C 275 LYS ARG LYS TRP GLU ALA VAL HIS ALA ALA GLU GLN ARG SEQRES 13 C 275 ARG VAL TYR LEU GLU GLY ARG CYS VAL ASP GLY LEU ARG SEQRES 14 C 275 ARG TYR LEU GLU ASN GLY LYS GLU THR LEU GLN ARG THR SEQRES 15 C 275 ASP PRO PRO LYS THR HIS MET THR HIS HIS PRO ILE SER SEQRES 16 C 275 ASP HIS GLU ALA THR LEU ARG CYS TRP ALA LEU GLY PHE SEQRES 17 C 275 TYR PRO ALA GLU ILE THR LEU THR TRP GLN ARG ASP GLY SEQRES 18 C 275 GLU ASP GLN THR GLN ASP THR GLU LEU VAL GLU THR ARG SEQRES 19 C 275 PRO ALA GLY ASP GLY THR PHE GLN LYS TRP ALA ALA VAL SEQRES 20 C 275 VAL VAL PRO SER GLY GLU GLU GLN ARG TYR THR CYS HIS SEQRES 21 C 275 VAL GLN HIS GLU GLY LEU PRO LYS PRO LEU THR LEU ARG SEQRES 22 C 275 TRP GLU SEQRES 1 D 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG SEQRES 2 D 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS SEQRES 3 D 100 TYR VAL SER GLY PHE HIS PRO SER ASP ILE GLU VAL ASP SEQRES 4 D 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SEQRES 5 D 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU SEQRES 6 D 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU SEQRES 7 D 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO SEQRES 8 D 100 LYS ILE VAL LYS TRP ASP ARG ASP MET SEQRES 1 P 9 GLN VAL ASP TYR TYR GLY LEU TYR TYR SEQRES 1 A 213 GLN GLU VAL THR GLN ILE PRO ALA ALA LEU SER VAL PRO SEQRES 2 A 213 GLU GLY GLU ASN LEU VAL LEU ASN CYS SER PHE THR ASP SEQRES 3 A 213 SER ALA ILE TYR ASN LEU GLN TRP PHE ARG GLN ASP PRO SEQRES 4 A 213 GLY LYS GLY LEU THR SER LEU LEU LEU ILE GLN SER SER SEQRES 5 A 213 GLN ARG GLU GLN THR SER GLY ARG LEU ASN ALA SER LEU SEQRES 6 A 213 ASP LYS SER SER GLY ARG SER THR LEU TYR ILE ALA ALA SEQRES 7 A 213 SER GLN PRO GLY ASP SER ALA THR TYR LEU CYS ALA VAL SEQRES 8 A 213 ASP THR GLY GLY PHE LYS THR ILE PHE GLY ALA GLY THR SEQRES 9 A 213 ARG LEU PHE VAL LYS ALA TYR ILE GLN ASN PRO ASP PRO SEQRES 10 A 213 ALA VAL TYR GLN LEU ARG ASP SER LYS SER SER ASP LYS SEQRES 11 A 213 PHE VAL CYS LEU PHE THR ASP PHE ASP SER GLN ILE GLN SEQRES 12 A 213 VAL SER GLN SER LYS ASP SER ASP VAL TYR ILE THR ASP SEQRES 13 A 213 LYS CYS VAL LEU ASP MET ARG SER MET ASP PHE LYS SER SEQRES 14 A 213 ASN SER ALA VAL ALA TRP SER GLN LYS SER ASP PHE THR SEQRES 15 A 213 CYS ALA ASN ALA PHE GLN ASN SER ILE ILE PRO GLU ASP SEQRES 16 A 213 THR PHE PHE PRO SER PRO GLU SER SER CYS GLY SER LEU SEQRES 17 A 213 GLU VAL LEU PHE GLN SEQRES 1 B 252 GLU ALA GLN VAL THR GLN ASN PRO ARG TYR LEU ILE THR SEQRES 2 B 252 VAL THR GLY LYS LYS LEU THR VAL THR CYS SER GLN ASN SEQRES 3 B 252 MET ASN HIS GLU TYR MET SER TRP TYR ARG GLN ASP PRO SEQRES 4 B 252 GLY LEU GLY LEU ARG GLN ILE TYR TYR SER MET ASN VAL SEQRES 5 B 252 GLU VAL THR ASP LYS GLY ASP VAL PRO GLU GLY TYR LYS SEQRES 6 B 252 VAL SER ARG LYS GLU LYS ARG ASN PHE PRO LEU ILE LEU SEQRES 7 B 252 GLU SER PRO SER PRO ASN GLN THR SER LEU TYR PHE CYS SEQRES 8 B 252 ALA SER SER SER GLY ASP GLY ASN TYR GLY TYR THR PHE SEQRES 9 B 252 GLY SER GLY THR ARG LEU THR VAL VAL GLU ASP LEU LYS SEQRES 10 B 252 ASN VAL PHE PRO PRO GLU VAL ALA VAL PHE GLU PRO SER SEQRES 11 B 252 LYS ALA GLU ILE SER ARG THR GLN LYS ALA THR LEU VAL SEQRES 12 B 252 CYS LEU ALA THR GLY PHE TYR PRO PRO HIS VAL GLU LEU SEQRES 13 B 252 SER TRP TRP VAL ASN GLY LYS GLU VAL HIS ASP GLY VAL SEQRES 14 B 252 CYS THR ASP PRO GLN PRO LEU LYS GLU GLN PRO ALA LEU SEQRES 15 B 252 GLN ASP SER ARG TYR ALA LEU SER SER ARG LEU ARG VAL SEQRES 16 B 252 SER ALA THR PHE TRP GLN ASP PRO ARG ASN HIS PHE ARG SEQRES 17 B 252 CYS GLN VAL GLN PHE TYR GLY LEU SER GLU ASN ASP GLU SEQRES 18 B 252 TRP THR GLN ASP ARG ALA LYS PRO VAL THR GLN ILE VAL SEQRES 19 B 252 SER ALA GLU ALA TRP GLY ARG ALA ASP CYS GLY SER LEU SEQRES 20 B 252 GLU VAL LEU PHE GLN FORMUL 6 HOH *25(H2 O) HELIX 1 AA1 GLY C 56 TYR C 85 1 30 HELIX 2 AA2 ASP C 137 VAL C 150 1 14 HELIX 3 AA3 HIS C 151 GLU C 161 1 11 HELIX 4 AA4 GLY C 162 GLY C 175 1 14 HELIX 5 AA5 GLY C 175 GLN C 180 1 6 HELIX 6 AA6 GLU C 253 GLN C 255 5 3 HELIX 7 AA7 GLN A 80 SER A 84 5 5 HELIX 8 AA8 SER B 80 THR B 84 5 5 HELIX 9 AA9 SER B 128 GLN B 136 1 9 HELIX 10 AB1 ALA B 195 GLN B 199 1 5 SHEET 1 AA1 8 GLU C 46 PRO C 47 0 SHEET 2 AA1 8 THR C 31 ASP C 37 -1 N ARG C 35 O GLU C 46 SHEET 3 AA1 8 ARG C 21 VAL C 28 -1 N VAL C 28 O THR C 31 SHEET 4 AA1 8 HIS C 3 VAL C 12 -1 N PHE C 8 O VAL C 25 SHEET 5 AA1 8 THR C 94 VAL C 103 -1 O TYR C 99 N TYR C 7 SHEET 6 AA1 8 PHE C 109 TYR C 118 -1 O GLN C 115 N MET C 98 SHEET 7 AA1 8 LYS C 121 LEU C 126 -1 O ILE C 124 N ASP C 116 SHEET 8 AA1 8 TRP C 133 ALA C 135 -1 O THR C 134 N ALA C 125 SHEET 1 AA2 4 LYS C 186 PRO C 193 0 SHEET 2 AA2 4 GLU C 198 PHE C 208 -1 O TRP C 204 N HIS C 188 SHEET 3 AA2 4 PHE C 241 PRO C 250 -1 O VAL C 249 N ALA C 199 SHEET 4 AA2 4 THR C 228 LEU C 230 -1 N GLU C 229 O ALA C 246 SHEET 1 AA3 4 LYS C 186 PRO C 193 0 SHEET 2 AA3 4 GLU C 198 PHE C 208 -1 O TRP C 204 N HIS C 188 SHEET 3 AA3 4 PHE C 241 PRO C 250 -1 O VAL C 249 N ALA C 199 SHEET 4 AA3 4 ARG C 234 PRO C 235 -1 N ARG C 234 O GLN C 242 SHEET 1 AA4 3 THR C 214 ARG C 219 0 SHEET 2 AA4 3 TYR C 257 GLN C 262 -1 O HIS C 260 N THR C 216 SHEET 3 AA4 3 LEU C 270 LEU C 272 -1 O LEU C 272 N CYS C 259 SHEET 1 AA5 4 LYS D 6 SER D 11 0 SHEET 2 AA5 4 ASN D 21 PHE D 30 -1 O ASN D 24 N TYR D 10 SHEET 3 AA5 4 PHE D 62 PHE D 70 -1 O TYR D 66 N CYS D 25 SHEET 4 AA5 4 GLU D 50 HIS D 51 -1 N GLU D 50 O TYR D 67 SHEET 1 AA6 4 LYS D 6 SER D 11 0 SHEET 2 AA6 4 ASN D 21 PHE D 30 -1 O ASN D 24 N TYR D 10 SHEET 3 AA6 4 PHE D 62 PHE D 70 -1 O TYR D 66 N CYS D 25 SHEET 4 AA6 4 SER D 55 PHE D 56 -1 N SER D 55 O TYR D 63 SHEET 1 AA7 4 GLU D 44 ARG D 45 0 SHEET 2 AA7 4 GLU D 36 LYS D 41 -1 N LYS D 41 O GLU D 44 SHEET 3 AA7 4 TYR D 78 ASN D 83 -1 O ARG D 81 N ASP D 38 SHEET 4 AA7 4 LYS D 91 LYS D 94 -1 O VAL D 93 N CYS D 80 SHEET 1 AA8 5 VAL A 3 GLN A 5 0 SHEET 2 AA8 5 LEU A 18 PHE A 24 -1 O SER A 23 N THR A 4 SHEET 3 AA8 5 ARG A 71 ILE A 76 -1 O LEU A 74 N LEU A 20 SHEET 4 AA8 5 LEU A 61 ASP A 66 -1 N ASN A 62 O TYR A 75 SHEET 5 AA8 5 GLU A 55 SER A 58 -1 N SER A 58 O LEU A 61 SHEET 1 AA9 5 ALA A 9 PRO A 13 0 SHEET 2 AA9 5 THR A 104 LYS A 109 1 O LYS A 109 N VAL A 12 SHEET 3 AA9 5 ALA A 85 ASP A 92 -1 N ALA A 85 O LEU A 106 SHEET 4 AA9 5 ASN A 31 ASP A 38 -1 N PHE A 35 O LEU A 88 SHEET 5 AA9 5 GLY A 42 GLN A 50 -1 O ILE A 49 N LEU A 32 SHEET 1 AB1 4 ALA A 9 PRO A 13 0 SHEET 2 AB1 4 THR A 104 LYS A 109 1 O LYS A 109 N VAL A 12 SHEET 3 AB1 4 ALA A 85 ASP A 92 -1 N ALA A 85 O LEU A 106 SHEET 4 AB1 4 THR A 98 PHE A 100 -1 O ILE A 99 N VAL A 91 SHEET 1 AB2 4 ALA A 118 ARG A 123 0 SHEET 2 AB2 4 PHE A 131 THR A 136 -1 O LEU A 134 N TYR A 120 SHEET 3 AB2 4 PHE A 167 SER A 176 -1 O ALA A 174 N CYS A 133 SHEET 4 AB2 4 VAL A 152 ILE A 154 -1 N TYR A 153 O TRP A 175 SHEET 1 AB3 4 ALA A 118 ARG A 123 0 SHEET 2 AB3 4 PHE A 131 THR A 136 -1 O LEU A 134 N TYR A 120 SHEET 3 AB3 4 PHE A 167 SER A 176 -1 O ALA A 174 N CYS A 133 SHEET 4 AB3 4 CYS A 158 MET A 162 -1 N MET A 162 O PHE A 167 SHEET 1 AB4 4 VAL B 2 ASN B 5 0 SHEET 2 AB4 4 LEU B 17 GLN B 23 -1 O SER B 22 N THR B 3 SHEET 3 AB4 4 LEU B 74 LEU B 76 -1 O LEU B 76 N LEU B 17 SHEET 4 AB4 4 LYS B 63 VAL B 64 -1 N LYS B 63 O ILE B 75 SHEET 1 AB5 6 TYR B 8 VAL B 12 0 SHEET 2 AB5 6 THR B 106 VAL B 111 1 O VAL B 111 N THR B 11 SHEET 3 AB5 6 SER B 85 SER B 92 -1 N TYR B 87 O THR B 106 SHEET 4 AB5 6 TYR B 29 ASP B 36 -1 N TYR B 33 O PHE B 88 SHEET 5 AB5 6 GLY B 40 ASN B 49 -1 O ILE B 44 N TRP B 32 SHEET 6 AB5 6 VAL B 52 LYS B 55 -1 O ASP B 54 N TYR B 46 SHEET 1 AB6 4 TYR B 8 VAL B 12 0 SHEET 2 AB6 4 THR B 106 VAL B 111 1 O VAL B 111 N THR B 11 SHEET 3 AB6 4 SER B 85 SER B 92 -1 N TYR B 87 O THR B 106 SHEET 4 AB6 4 THR B 101 PHE B 102 -1 O THR B 101 N SER B 91 SHEET 1 AB7 4 GLU B 121 PHE B 125 0 SHEET 2 AB7 4 LYS B 137 PHE B 147 -1 O VAL B 141 N PHE B 125 SHEET 3 AB7 4 TYR B 185 SER B 194 -1 O TYR B 185 N PHE B 147 SHEET 4 AB7 4 VAL B 167 THR B 169 -1 N CYS B 168 O ARG B 190 SHEET 1 AB8 4 GLU B 121 PHE B 125 0 SHEET 2 AB8 4 LYS B 137 PHE B 147 -1 O VAL B 141 N PHE B 125 SHEET 3 AB8 4 TYR B 185 SER B 194 -1 O TYR B 185 N PHE B 147 SHEET 4 AB8 4 LEU B 174 LYS B 175 -1 N LEU B 174 O ALA B 186 SHEET 1 AB9 4 LYS B 161 VAL B 163 0 SHEET 2 AB9 4 VAL B 152 VAL B 158 -1 N VAL B 158 O LYS B 161 SHEET 3 AB9 4 HIS B 204 PHE B 211 -1 O ARG B 206 N TRP B 157 SHEET 4 AB9 4 GLN B 230 TRP B 237 -1 O GLN B 230 N PHE B 211 SSBOND 1 CYS C 101 CYS C 164 1555 1555 2.43 SSBOND 2 CYS C 203 CYS C 259 1555 1555 2.45 SSBOND 3 CYS D 25 CYS D 80 1555 1555 2.23 SSBOND 4 CYS A 22 CYS A 89 1555 1555 2.01 SSBOND 5 CYS A 133 CYS A 183 1555 1555 2.35 SSBOND 6 CYS A 158 CYS B 168 1555 1555 2.10 SSBOND 7 CYS B 21 CYS B 89 1555 1555 2.11 SSBOND 8 CYS B 142 CYS B 207 1555 1555 2.02 CISPEP 1 TYR C 209 PRO C 210 0 6.96 CISPEP 2 HIS D 31 PRO D 32 0 0.27 CISPEP 3 ASN B 5 PRO B 6 0 -4.01 CISPEP 4 TYR B 148 PRO B 149 0 3.98 CRYST1 100.223 54.984 106.706 90.00 115.63 90.00 P 1 21 1 2 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 0.009978 0.000000 0.004787 0.00000 SCALE2 0.000000 0.018187 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010394 0.00000 CONECT 786 1274 CONECT 1274 786 CONECT 1577 2008 CONECT 2008 1577 CONECT 2320 2753 CONECT 2753 2320 CONECT 3161 3647 CONECT 3647 3161 CONECT 3982 4366 CONECT 4179 5785 CONECT 4366 3982 CONECT 4649 5195 CONECT 5195 4649 CONECT 5581 6095 CONECT 5785 4179 CONECT 6095 5581 MASTER 396 0 0 10 79 0 0 6 6365 5 16 68 END