HEADER IMMUNE SYSTEM 02-SEP-17 6AVF TITLE CRYSTAL STRUCTURE OF THE KFJ5 TCR-NY-ESO-1-HLA-B*07:02 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 3 CHAIN: M; COMPND 4 FRAGMENT: UNP RESIDUES 13-119; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: T-CELL RECEPTOR ALPHA VARIABLE 4,TCR ALPHA CHAIN; COMPND 8 CHAIN: A; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: T-CELL RECEPTOR BETA VARIABLE 28,TCR BETA CHAIN; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: V_SEGMENT TRANSLATION PRODUCT; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: ALA-PRO-ARG-GLY-PRO-HIS-GLY-GLY-ALA-ALA-SER-GLY-LEU; COMPND 17 CHAIN: P; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 5; COMPND 20 MOLECULE: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-7 ALPHA CHAIN; COMPND 21 CHAIN: H; COMPND 22 SYNONYM: MHC CLASS I ANTIGEN B*7; 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: B2M, CDABP0092, HDCMA22P; 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: TRAV4; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 GENE: TCRBV3S1, TRBV28; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 22 MOL_ID: 4; SOURCE 23 SYNTHETIC: YES; SOURCE 24 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 25 ORGANISM_TAXID: 9606; SOURCE 26 MOL_ID: 5; SOURCE 27 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 28 ORGANISM_COMMON: HUMAN; SOURCE 29 ORGANISM_TAXID: 9606; SOURCE 30 GENE: HLA-B, HLAB; SOURCE 31 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 32 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HUMAN LEUKOCYTE ANTIGEN, MAJOR HISTOCOMPATIBILITY COMPLEX, KEYWDS 2 IMMUNOGLOBULIN, T CELL RECEPTOR, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR B.S.GULLY,S.GRAS,J.ROSSJOHN REVDAT 3 17-APR-19 6AVF 1 REMARK REVDAT 2 28-MAR-18 6AVF 1 JRNL REVDAT 1 28-FEB-18 6AVF 0 JRNL AUTH K.F.CHAN,B.S.GULLY,S.GRAS,D.X.BERINGER,L.KJER-NIELSEN, JRNL AUTH 2 J.CEBON,J.MCCLUSKEY,W.CHEN,J.ROSSJOHN JRNL TITL DIVERGENT T-CELL RECEPTOR RECOGNITION MODES OF A HLA-I JRNL TITL 2 RESTRICTED EXTENDED TUMOUR-ASSOCIATED PEPTIDE. JRNL REF NAT COMMUN V. 9 1026 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 29531227 JRNL DOI 10.1038/S41467-018-03321-W REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 109701 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.510 REMARK 3 FREE R VALUE TEST SET COUNT : 3854 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 46.0202 - 6.1524 0.93 3636 121 0.1671 0.2095 REMARK 3 2 6.1524 - 4.8851 0.95 3675 131 0.1541 0.2336 REMARK 3 3 4.8851 - 4.2681 0.94 3644 137 0.1374 0.1728 REMARK 3 4 4.2681 - 3.8781 0.96 3758 136 0.1535 0.2102 REMARK 3 5 3.8781 - 3.6002 0.96 3719 134 0.1641 0.1751 REMARK 3 6 3.6002 - 3.3880 0.96 3707 141 0.1755 0.2649 REMARK 3 7 3.3880 - 3.2184 0.97 3771 125 0.1861 0.2516 REMARK 3 8 3.2184 - 3.0783 0.98 3810 145 0.2091 0.2904 REMARK 3 9 3.0783 - 2.9599 0.99 3858 147 0.2092 0.2173 REMARK 3 10 2.9599 - 2.8577 0.99 3862 132 0.2073 0.3031 REMARK 3 11 2.8577 - 2.7684 0.99 3847 141 0.2361 0.2851 REMARK 3 12 2.7684 - 2.6893 0.99 3813 142 0.2498 0.3931 REMARK 3 13 2.6893 - 2.6185 0.98 3836 146 0.2416 0.3072 REMARK 3 14 2.6185 - 2.5546 0.99 3858 125 0.2231 0.2464 REMARK 3 15 2.5546 - 2.4965 0.99 3780 148 0.2298 0.3155 REMARK 3 16 2.4965 - 2.4434 0.99 3918 135 0.2317 0.2829 REMARK 3 17 2.4434 - 2.3945 0.99 3805 170 0.2457 0.3066 REMARK 3 18 2.3945 - 2.3493 0.99 3878 124 0.2423 0.2851 REMARK 3 19 2.3493 - 2.3074 0.99 3836 137 0.2468 0.2990 REMARK 3 20 2.3074 - 2.2683 0.99 3866 120 0.2576 0.2992 REMARK 3 21 2.2683 - 2.2317 0.96 3726 157 0.2674 0.3113 REMARK 3 22 2.2317 - 2.1974 0.99 3847 126 0.2678 0.2851 REMARK 3 23 2.1974 - 2.1650 0.99 3810 147 0.2672 0.3128 REMARK 3 24 2.1650 - 2.1345 0.99 3868 148 0.2778 0.3168 REMARK 3 25 2.1345 - 2.1057 0.99 3814 147 0.2773 0.3038 REMARK 3 26 2.1057 - 2.0783 0.99 3840 152 0.3010 0.3164 REMARK 3 27 2.0783 - 2.0524 0.96 3753 106 0.3129 0.3471 REMARK 3 28 2.0524 - 2.0276 0.85 3312 134 0.3349 0.3467 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 6761 REMARK 3 ANGLE : 1.171 9176 REMARK 3 CHIRALITY : 0.049 967 REMARK 3 PLANARITY : 0.006 1205 REMARK 3 DIHEDRAL : 15.408 2467 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6AVF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1000229896. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 109701 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.028 REMARK 200 RESOLUTION RANGE LOW (A) : 46.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.57000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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 (%): 41.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MIB PH 7.0 AND 25 % (W/V) PEG REMARK 280 1500, VAPOR DIFFUSION, HANGING 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 33.83950 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: M, A, B, P, H 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 SER M 20 REMARK 465 ASN M 21 REMARK 465 GLU M 74 REMARK 465 LYS M 75 REMARK 465 ASP M 98 REMARK 465 MET M 99 REMARK 465 MET A 2 REMARK 465 PRO A 205 REMARK 465 GLU A 206 REMARK 465 SER A 207 REMARK 465 SER A 208 REMARK 465 MET B 0 REMARK 465 ASP B 1 REMARK 465 MET H -23 REMARK 465 LEU H -22 REMARK 465 VAL H -21 REMARK 465 MET H -20 REMARK 465 ALA H -19 REMARK 465 PRO H -18 REMARK 465 ARG H -17 REMARK 465 THR H -16 REMARK 465 VAL H -15 REMARK 465 LEU H -14 REMARK 465 LEU H -13 REMARK 465 LEU H -12 REMARK 465 LEU H -11 REMARK 465 SER H -10 REMARK 465 ALA H -9 REMARK 465 ALA H -8 REMARK 465 LEU H -7 REMARK 465 ALA H -6 REMARK 465 LEU H -5 REMARK 465 THR H -4 REMARK 465 GLU H -3 REMARK 465 THR H -2 REMARK 465 TRP H -1 REMARK 465 ALA H 0 REMARK 465 ARG H 219 REMARK 465 ASP H 220 REMARK 465 GLY H 221 REMARK 465 GLU H 222 REMARK 465 ASP H 223 REMARK 465 GLN H 224 REMARK 465 PRO H 276 REMARK 465 SER H 277 REMARK 465 SER H 278 REMARK 465 GLN H 279 REMARK 465 SER H 280 REMARK 465 THR H 281 REMARK 465 VAL H 282 REMARK 465 PRO H 283 REMARK 465 ILE H 284 REMARK 465 VAL H 285 REMARK 465 GLY H 286 REMARK 465 ILE H 287 REMARK 465 VAL H 288 REMARK 465 ALA H 289 REMARK 465 GLY H 290 REMARK 465 LEU H 291 REMARK 465 ALA H 292 REMARK 465 VAL H 293 REMARK 465 LEU H 294 REMARK 465 ALA H 295 REMARK 465 VAL H 296 REMARK 465 VAL H 297 REMARK 465 VAL H 298 REMARK 465 ILE H 299 REMARK 465 GLY H 300 REMARK 465 ALA H 301 REMARK 465 VAL H 302 REMARK 465 VAL H 303 REMARK 465 ALA H 304 REMARK 465 ALA H 305 REMARK 465 VAL H 306 REMARK 465 MET H 307 REMARK 465 CYS H 308 REMARK 465 ARG H 309 REMARK 465 ARG H 310 REMARK 465 LYS H 311 REMARK 465 SER H 312 REMARK 465 SER H 313 REMARK 465 GLY H 314 REMARK 465 GLY H 315 REMARK 465 LYS H 316 REMARK 465 GLY H 317 REMARK 465 GLY H 318 REMARK 465 SER H 319 REMARK 465 TYR H 320 REMARK 465 SER H 321 REMARK 465 GLN H 322 REMARK 465 ALA H 323 REMARK 465 ALA H 324 REMARK 465 CYS H 325 REMARK 465 SER H 326 REMARK 465 ASP H 327 REMARK 465 SER H 328 REMARK 465 ALA H 329 REMARK 465 GLN H 330 REMARK 465 GLY H 331 REMARK 465 SER H 332 REMARK 465 ASP H 333 REMARK 465 VAL H 334 REMARK 465 SER H 335 REMARK 465 LEU H 336 REMARK 465 THR H 337 REMARK 465 ALA H 338 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 ASN M 17 CG OD1 ND2 REMARK 470 LYS M 19 CG CD CE NZ REMARK 470 ASP M 76 CG OD1 OD2 REMARK 470 GLU M 77 CG CD OE1 OE2 REMARK 470 LYS M 94 CG CD CE NZ REMARK 470 ASP B 243 CG OD1 OD2 REMARK 470 GLU H 173 CG CD OE1 OE2 REMARK 470 LYS H 176 CG CD CE NZ REMARK 470 ASP H 177 CG OD1 OD2 REMARK 470 ASP H 196 CG OD1 OD2 REMARK 470 GLU H 254 CG CD OE1 OE2 REMARK 470 ARG H 256 CG CD NE CZ NH1 NH2 REMARK 470 GLN H 262 CG CD OE1 NE2 REMARK 470 LYS H 268 CG CD CE NZ REMARK 470 ARG H 273 CG CD NE CZ NH1 NH2 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 B 306 O HOH B 449 2.06 REMARK 500 O HOH M 103 O HOH M 116 2.14 REMARK 500 O HOH H 488 O HOH H 489 2.15 REMARK 500 OD1 ASN A 111 O HOH A 301 2.15 REMARK 500 NH2 ARG H 6 OD1 ASP H 102 2.17 REMARK 500 O GLY M 43 O HOH M 101 2.18 REMARK 500 O HOH B 466 O HOH B 467 2.19 REMARK 500 O HOH B 496 O HOH B 500 2.19 REMARK 500 O HOH A 435 O HOH B 489 2.19 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 LEU A 164 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 ALA M 15 70.91 -68.38 REMARK 500 ASN M 42 26.64 49.88 REMARK 500 THR M 68 -167.48 -123.77 REMARK 500 PRO M 90 151.79 -41.45 REMARK 500 TRP M 95 -69.70 -92.73 REMARK 500 HIS A 26 69.25 -152.84 REMARK 500 TYR A 53 -58.08 -123.51 REMARK 500 LYS A 54 -47.47 -141.51 REMARK 500 ARG A 79 104.13 -14.63 REMARK 500 ASP A 97 -131.78 50.58 REMARK 500 LYS A 101 48.41 -104.83 REMARK 500 SER A 132 107.10 -58.38 REMARK 500 ASP A 184 30.49 -92.45 REMARK 500 LYS B 53 -12.64 72.97 REMARK 500 SER B 80 89.13 -150.88 REMARK 500 GLU B 98 63.93 -151.41 REMARK 500 ARG H 14 63.86 -157.48 REMARK 500 ASP H 29 -129.00 52.78 REMARK 500 GLU H 89 -5.68 -58.27 REMARK 500 ASP H 114 98.66 -162.76 REMARK 500 TYR H 123 -74.59 -114.08 REMARK 500 LYS H 176 -64.63 -28.00 REMARK 500 PRO H 269 104.44 -56.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 501 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH B 502 DISTANCE = 6.81 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6AT5 RELATED DB: PDB REMARK 900 RELATED ID: 6AT6 RELATED DB: PDB REMARK 900 RELATED ID: 6AVG RELATED DB: PDB DBREF 6AVF M 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF1 6AVF A 3 94 UNP A0A0B4J268_HUMAN DBREF2 6AVF A A0A0B4J268 18 109 DBREF 6AVF A 94 208 PDB 6AVF 6AVF 94 208 DBREF 6AVF B 1 95 UNP A0A5B6 A0A5B6_HUMAN 20 114 DBREF 6AVF B 96 243 PDB 6AVF 6AVF 96 243 DBREF 6AVF P 1 13 PDB 6AVF 6AVF 1 13 DBREF 6AVF H -23 338 UNP P01889 1B07_HUMAN 1 362 SEQADV 6AVF MET A 2 UNP A0A0B4J26 INITIATING METHIONINE SEQADV 6AVF MET B 0 UNP A0A5B6 INITIATING METHIONINE SEQADV 6AVF GLN B 95 UNP A0A5B6 LEU 114 CONFLICT SEQRES 1 M 99 ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG HIS SEQRES 2 M 99 PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS TYR SEQRES 3 M 99 VAL SER GLY PHE HIS PRO SER ASP ILE GLU VAL ASP LEU SEQRES 4 M 99 LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SER SEQRES 5 M 99 ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU LEU SEQRES 6 M 99 TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU TYR SEQRES 7 M 99 ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO LYS SEQRES 8 M 99 ILE VAL LYS TRP ASP ARG ASP MET SEQRES 1 A 207 MET LEU ALA LYS THR THR GLN PRO ILE SER MET ASP SER SEQRES 2 A 207 TYR GLU GLY GLN GLU VAL ASN ILE THR CYS SER HIS ASN SEQRES 3 A 207 ASN ILE ALA THR ASN ASP TYR ILE THR TRP TYR GLN GLN SEQRES 4 A 207 PHE PRO SER GLN GLY PRO ARG PHE ILE ILE GLN GLY TYR SEQRES 5 A 207 LYS THR LYS VAL THR ASN GLU VAL ALA SER LEU PHE ILE SEQRES 6 A 207 PRO ALA ASP ARG LYS SER SER THR LEU SER LEU PRO ARG SEQRES 7 A 207 VAL SER LEU SER ASP THR ALA VAL TYR TYR CYS LEU VAL SEQRES 8 A 207 GLY GLU ILE LEU ASP ASN PHE ASN LYS PHE TYR PHE GLY SEQRES 9 A 207 SER GLY THR LYS LEU ASN VAL LYS PRO ASN ILE GLN ASN SEQRES 10 A 207 PRO ASP PRO ALA VAL TYR GLN LEU ARG ASP SER LYS SER SEQRES 11 A 207 SER ASP LYS SER VAL CYS LEU PHE THR ASP PHE ASP SER SEQRES 12 A 207 GLN THR ASN VAL SER GLN SER LYS ASP SER ASP VAL TYR SEQRES 13 A 207 ILE THR ASP LYS CYS VAL LEU ASP MET ARG SER MET ASP SEQRES 14 A 207 PHE LYS SER ASN SER ALA VAL ALA TRP SER ASN LYS SER SEQRES 15 A 207 ASP PHE ALA CYS ALA ASN ALA PHE ASN ASN SER ILE ILE SEQRES 16 A 207 PRO GLU ASP THR PHE PHE PRO SER PRO GLU SER SER SEQRES 1 B 244 MET ASP VAL LYS VAL THR GLN SER SER ARG TYR LEU VAL SEQRES 2 B 244 LYS ARG THR GLY GLU LYS VAL PHE LEU GLU CYS VAL GLN SEQRES 3 B 244 ASP MET ASP HIS GLU ASN MET PHE TRP TYR ARG GLN ASP SEQRES 4 B 244 PRO GLY LEU GLY LEU ARG LEU ILE TYR PHE SER TYR ASP SEQRES 5 B 244 VAL LYS MET LYS GLU LYS GLY ASP ILE PRO GLU GLY TYR SEQRES 6 B 244 SER VAL SER ARG GLU LYS LYS GLU ARG PHE SER LEU ILE SEQRES 7 B 244 LEU GLU SER ALA SER THR ASN GLN THR SER MET TYR LEU SEQRES 8 B 244 CYS ALA SER SER GLN ARG GLN GLU GLY ASP THR GLN TYR SEQRES 9 B 244 PHE GLY PRO GLY THR ARG LEU THR VAL LEU GLU ASP LEU SEQRES 10 B 244 LYS ASN VAL PHE PRO PRO GLU VAL ALA VAL PHE GLU PRO SEQRES 11 B 244 SER GLU ALA GLU ILE SER HIS THR GLN LYS ALA THR LEU SEQRES 12 B 244 VAL CYS LEU ALA THR GLY PHE TYR PRO ASP HIS VAL GLU SEQRES 13 B 244 LEU SER TRP TRP VAL ASN GLY LYS GLU VAL HIS SER GLY SEQRES 14 B 244 VAL CYS THR ASP PRO GLN PRO LEU LYS GLU GLN PRO ALA SEQRES 15 B 244 LEU ASN ASP SER ARG TYR ALA LEU SER SER ARG LEU ARG SEQRES 16 B 244 VAL SER ALA THR PHE TRP GLN ASN PRO ARG ASN HIS PHE SEQRES 17 B 244 ARG CYS GLN VAL GLN PHE TYR GLY LEU SER GLU ASN ASP SEQRES 18 B 244 GLU TRP THR GLN ASP ARG ALA LYS PRO VAL THR GLN ILE SEQRES 19 B 244 VAL SER ALA GLU ALA TRP GLY ARG ALA ASP SEQRES 1 P 13 ALA PRO ARG GLY PRO HIS GLY GLY ALA ALA SER GLY LEU SEQRES 1 H 362 MET LEU VAL MET ALA PRO ARG THR VAL LEU LEU LEU LEU SEQRES 2 H 362 SER ALA ALA LEU ALA LEU THR GLU THR TRP ALA GLY SER SEQRES 3 H 362 HIS SER MET ARG TYR PHE TYR THR SER VAL SER ARG PRO SEQRES 4 H 362 GLY ARG GLY GLU PRO ARG PHE ILE SER VAL GLY TYR VAL SEQRES 5 H 362 ASP ASP THR GLN PHE VAL ARG PHE ASP SER ASP ALA ALA SEQRES 6 H 362 SER PRO ARG GLU GLU PRO ARG ALA PRO TRP ILE GLU GLN SEQRES 7 H 362 GLU GLY PRO GLU TYR TRP ASP ARG ASN THR GLN ILE TYR SEQRES 8 H 362 LYS ALA GLN ALA GLN THR ASP ARG GLU SER LEU ARG ASN SEQRES 9 H 362 LEU ARG GLY TYR TYR ASN GLN SER GLU ALA GLY SER HIS SEQRES 10 H 362 THR LEU GLN SER MET TYR GLY CYS ASP VAL GLY PRO ASP SEQRES 11 H 362 GLY ARG LEU LEU ARG GLY HIS ASP GLN TYR ALA TYR ASP SEQRES 12 H 362 GLY LYS ASP TYR ILE ALA LEU ASN GLU ASP LEU ARG SER SEQRES 13 H 362 TRP THR ALA ALA ASP THR ALA ALA GLN ILE THR GLN ARG SEQRES 14 H 362 LYS TRP GLU ALA ALA ARG GLU ALA GLU GLN ARG ARG ALA SEQRES 15 H 362 TYR LEU GLU GLY GLU CYS VAL GLU TRP LEU ARG ARG TYR SEQRES 16 H 362 LEU GLU ASN GLY LYS ASP LYS LEU GLU ARG ALA ASP PRO SEQRES 17 H 362 PRO LYS THR HIS VAL THR HIS HIS PRO ILE SER ASP HIS SEQRES 18 H 362 GLU ALA THR LEU ARG CYS TRP ALA LEU GLY PHE TYR PRO SEQRES 19 H 362 ALA GLU ILE THR LEU THR TRP GLN ARG ASP GLY GLU ASP SEQRES 20 H 362 GLN THR GLN ASP THR GLU LEU VAL GLU THR ARG PRO ALA SEQRES 21 H 362 GLY ASP ARG THR PHE GLN LYS TRP ALA ALA VAL VAL VAL SEQRES 22 H 362 PRO SER GLY GLU GLU GLN ARG TYR THR CYS HIS VAL GLN SEQRES 23 H 362 HIS GLU GLY LEU PRO LYS PRO LEU THR LEU ARG TRP GLU SEQRES 24 H 362 PRO SER SER GLN SER THR VAL PRO ILE VAL GLY ILE VAL SEQRES 25 H 362 ALA GLY LEU ALA VAL LEU ALA VAL VAL VAL ILE GLY ALA SEQRES 26 H 362 VAL VAL ALA ALA VAL MET CYS ARG ARG LYS SER SER GLY SEQRES 27 H 362 GLY LYS GLY GLY SER TYR SER GLN ALA ALA CYS SER ASP SEQRES 28 H 362 SER ALA GLN GLY SER ASP VAL SER LEU THR ALA FORMUL 6 HOH *447(H2 O) HELIX 1 AA1 SER A 81 THR A 85 5 5 HELIX 2 AA2 ALA A 186 PHE A 191 1 6 HELIX 3 AA3 SER B 82 THR B 86 5 5 HELIX 4 AA4 ASP B 115 VAL B 119 5 5 HELIX 5 AA5 SER B 130 GLN B 138 1 9 HELIX 6 AA6 ALA B 197 GLN B 201 1 5 HELIX 7 AA7 GLY P 4 GLY P 8 5 5 HELIX 8 AA8 ALA H 49 GLU H 53 5 5 HELIX 9 AA9 GLY H 56 TYR H 85 1 30 HELIX 10 AB1 ASP H 137 ARG H 151 1 15 HELIX 11 AB2 ARG H 151 GLY H 162 1 12 HELIX 12 AB3 GLY H 162 GLY H 175 1 14 HELIX 13 AB4 GLY H 175 GLU H 180 1 6 HELIX 14 AB5 GLU H 253 TYR H 257 5 5 SHEET 1 AA1 4 LYS M 6 SER M 11 0 SHEET 2 AA1 4 LEU M 23 PHE M 30 -1 O SER M 28 N LYS M 6 SHEET 3 AA1 4 PHE M 62 TYR M 67 -1 O TYR M 66 N CYS M 25 SHEET 4 AA1 4 GLU M 50 HIS M 51 -1 N GLU M 50 O TYR M 67 SHEET 1 AA2 4 LYS M 6 SER M 11 0 SHEET 2 AA2 4 LEU M 23 PHE M 30 -1 O SER M 28 N LYS M 6 SHEET 3 AA2 4 PHE M 62 TYR M 67 -1 O TYR M 66 N CYS M 25 SHEET 4 AA2 4 SER M 55 PHE M 56 -1 N SER M 55 O TYR M 63 SHEET 1 AA3 4 GLU M 44 ARG M 45 0 SHEET 2 AA3 4 GLU M 36 LYS M 41 -1 N LYS M 41 O GLU M 44 SHEET 3 AA3 4 TYR M 78 ASN M 83 -1 O ARG M 81 N ASP M 38 SHEET 4 AA3 4 LYS M 91 LYS M 94 -1 O LYS M 91 N VAL M 82 SHEET 1 AA4 5 SER A 11 TYR A 15 0 SHEET 2 AA4 5 THR A 108 LYS A 113 1 O LYS A 113 N SER A 14 SHEET 3 AA4 5 ALA A 86 GLY A 93 -1 N ALA A 86 O LEU A 110 SHEET 4 AA4 5 TYR A 34 GLN A 40 -1 N THR A 36 O LEU A 91 SHEET 5 AA4 5 ARG A 47 GLY A 52 -1 O ARG A 47 N GLN A 39 SHEET 1 AA5 4 VAL A 20 SER A 25 0 SHEET 2 AA5 4 SER A 72 LEU A 77 -1 O LEU A 77 N VAL A 20 SHEET 3 AA5 4 SER A 63 PHE A 65 -1 N SER A 63 O SER A 76 SHEET 4 AA5 4 VAL A 57 THR A 58 -1 N VAL A 57 O LEU A 64 SHEET 1 AA6 2 ILE A 95 LEU A 96 0 SHEET 2 AA6 2 PHE A 99 ASN A 100 -1 O PHE A 99 N LEU A 96 SHEET 1 AA7 4 ALA A 122 ARG A 127 0 SHEET 2 AA7 4 SER A 135 THR A 140 -1 O LEU A 138 N TYR A 124 SHEET 3 AA7 4 PHE A 171 SER A 180 -1 O ALA A 178 N CYS A 137 SHEET 4 AA7 4 VAL A 156 ILE A 158 -1 N TYR A 157 O TRP A 179 SHEET 1 AA8 4 ALA A 122 ARG A 127 0 SHEET 2 AA8 4 SER A 135 THR A 140 -1 O LEU A 138 N TYR A 124 SHEET 3 AA8 4 PHE A 171 SER A 180 -1 O ALA A 178 N CYS A 137 SHEET 4 AA8 4 CYS A 162 MET A 166 -1 N LEU A 164 O SER A 173 SHEET 1 AA9 2 VAL B 4 GLN B 6 0 SHEET 2 AA9 2 CYS B 23 GLN B 25 -1 O VAL B 24 N THR B 5 SHEET 1 AB1 6 TYR B 10 ARG B 14 0 SHEET 2 AB1 6 THR B 108 LEU B 113 1 O THR B 111 N LEU B 11 SHEET 3 AB1 6 SER B 87 GLN B 95 -1 N TYR B 89 O THR B 108 SHEET 4 AB1 6 ASN B 31 ASP B 38 -1 N ASN B 31 O SER B 94 SHEET 5 AB1 6 GLY B 42 SER B 49 -1 O ARG B 44 N ARG B 36 SHEET 6 AB1 6 GLU B 56 LYS B 57 -1 O GLU B 56 N PHE B 48 SHEET 1 AB2 4 TYR B 10 ARG B 14 0 SHEET 2 AB2 4 THR B 108 LEU B 113 1 O THR B 111 N LEU B 11 SHEET 3 AB2 4 SER B 87 GLN B 95 -1 N TYR B 89 O THR B 108 SHEET 4 AB2 4 GLU B 98 PHE B 104 -1 O TYR B 103 N SER B 93 SHEET 1 AB3 3 VAL B 19 LEU B 21 0 SHEET 2 AB3 3 ARG B 73 LEU B 78 -1 O LEU B 76 N LEU B 21 SHEET 3 AB3 3 TYR B 64 LYS B 70 -1 N SER B 65 O ILE B 77 SHEET 1 AB4 4 GLU B 123 PHE B 127 0 SHEET 2 AB4 4 LYS B 139 PHE B 149 -1 O VAL B 143 N PHE B 127 SHEET 3 AB4 4 TYR B 187 SER B 196 -1 O VAL B 195 N ALA B 140 SHEET 4 AB4 4 VAL B 169 THR B 171 -1 N CYS B 170 O ARG B 192 SHEET 1 AB5 4 GLU B 123 PHE B 127 0 SHEET 2 AB5 4 LYS B 139 PHE B 149 -1 O VAL B 143 N PHE B 127 SHEET 3 AB5 4 TYR B 187 SER B 196 -1 O VAL B 195 N ALA B 140 SHEET 4 AB5 4 LEU B 176 LYS B 177 -1 N LEU B 176 O ALA B 188 SHEET 1 AB6 4 LYS B 163 VAL B 165 0 SHEET 2 AB6 4 VAL B 154 VAL B 160 -1 N VAL B 160 O LYS B 163 SHEET 3 AB6 4 HIS B 206 PHE B 213 -1 O GLN B 210 N SER B 157 SHEET 4 AB6 4 GLN B 232 TRP B 239 -1 O GLN B 232 N PHE B 213 SHEET 1 AB7 8 GLU H 46 PRO H 47 0 SHEET 2 AB7 8 THR H 31 ASP H 37 -1 N ARG H 35 O GLU H 46 SHEET 3 AB7 8 ARG H 21 VAL H 28 -1 N VAL H 28 O THR H 31 SHEET 4 AB7 8 HIS H 3 VAL H 12 -1 N ARG H 6 O TYR H 27 SHEET 5 AB7 8 THR H 94 VAL H 103 -1 O SER H 97 N TYR H 9 SHEET 6 AB7 8 LEU H 109 TYR H 118 -1 O LEU H 110 N ASP H 102 SHEET 7 AB7 8 LYS H 121 LEU H 126 -1 O TYR H 123 N TYR H 116 SHEET 8 AB7 8 TRP H 133 ALA H 135 -1 O THR H 134 N ALA H 125 SHEET 1 AB8 4 LYS H 186 PRO H 193 0 SHEET 2 AB8 4 GLU H 198 PHE H 208 -1 O THR H 200 N HIS H 192 SHEET 3 AB8 4 PHE H 241 PRO H 250 -1 O VAL H 249 N ALA H 199 SHEET 4 AB8 4 THR H 228 LEU H 230 -1 N GLU H 229 O ALA H 246 SHEET 1 AB9 4 LYS H 186 PRO H 193 0 SHEET 2 AB9 4 GLU H 198 PHE H 208 -1 O THR H 200 N HIS H 192 SHEET 3 AB9 4 PHE H 241 PRO H 250 -1 O VAL H 249 N ALA H 199 SHEET 4 AB9 4 ARG H 234 PRO H 235 -1 N ARG H 234 O GLN H 242 SHEET 1 AC1 3 THR H 214 GLN H 218 0 SHEET 2 AC1 3 THR H 258 GLN H 262 -1 O THR H 258 N GLN H 218 SHEET 3 AC1 3 LEU H 270 LEU H 272 -1 O LEU H 272 N CYS H 259 SSBOND 1 CYS M 25 CYS M 80 1555 1555 2.04 SSBOND 2 CYS A 24 CYS A 90 1555 1555 2.06 SSBOND 3 CYS A 137 CYS A 187 1555 1555 2.02 SSBOND 4 CYS A 162 CYS B 170 1555 1555 2.03 SSBOND 5 CYS B 23 CYS B 91 1555 1555 2.01 SSBOND 6 CYS B 144 CYS B 209 1555 1555 2.04 SSBOND 7 CYS H 101 CYS H 164 1555 1555 2.04 SSBOND 8 CYS H 203 CYS H 259 1555 1555 2.03 CISPEP 1 HIS M 31 PRO M 32 0 4.40 CISPEP 2 TYR B 150 PRO B 151 0 -2.31 CISPEP 3 TYR H 209 PRO H 210 0 -3.04 CRYST1 64.366 67.679 105.716 90.00 102.93 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 0.015536 0.000000 0.003567 0.00000 SCALE2 0.000000 0.014776 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009705 0.00000