HEADER IMMUNE SYSTEM 29-FEB-24 8YJ2 TITLE N17.1.2 RECOGNITION OF NRAS NEOANTIGENS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HUMAN LEUKOCYTE ANTIGEN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: ILE-LEU-ASP-THR-ALA-GLY-ARG-GLU-GLU-TYR; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: TCR BETA; COMPND 15 CHAIN: E; COMPND 16 ENGINEERED: YES; COMPND 17 MOL_ID: 5; COMPND 18 MOLECULE: TCR ALPHA; COMPND 19 CHAIN: D; COMPND 20 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; 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: HOMO SAPIENS; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 MOL_ID: 4; SOURCE 20 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 21 ORGANISM_TAXID: 9606; SOURCE 22 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 23 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 24 MOL_ID: 5; SOURCE 25 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 26 ORGANISM_TAXID: 9606; SOURCE 27 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 28 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS T CELL RECEPTOR, P-MHC, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR D.C.WU,R.A.MARIUZZA REVDAT 1 04-DEC-24 8YJ2 0 JRNL AUTH D.WU,R.YIN,G.CHEN,H.V.RIBEIRO-FILHO,M.CHEUNG,P.F.ROBBINS, JRNL AUTH 2 R.A.MARIUZZA,B.G.PIERCE JRNL TITL STRUCTURAL CHARACTERIZATION AND ALPHAFOLD MODELING OF HUMAN JRNL TITL 2 T CELL RECEPTOR RECOGNITION OF NRAS CANCER NEOANTIGENS. JRNL REF SCI ADV V. 10 Q6150 2024 JRNL REFN ESSN 2375-2548 JRNL PMID 39576860 JRNL DOI 10.1126/SCIADV.ADQ6150 REMARK 2 REMARK 2 RESOLUTION. 2.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.16_3549: ???) 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) : 2.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 49611 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2476 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 42.7760 - 5.9213 0.97 2770 131 0.1846 0.2016 REMARK 3 2 5.9213 - 4.7018 1.00 2689 170 0.1535 0.1903 REMARK 3 3 4.7018 - 4.1080 0.98 2652 150 0.1462 0.1775 REMARK 3 4 4.1080 - 3.7326 0.99 2657 127 0.1735 0.2193 REMARK 3 5 3.7326 - 3.4652 1.00 2640 156 0.1872 0.2306 REMARK 3 6 3.4652 - 3.2610 1.00 2665 119 0.1875 0.2332 REMARK 3 7 3.2610 - 3.0977 1.00 2671 121 0.2037 0.2565 REMARK 3 8 3.0977 - 2.9629 0.98 2614 125 0.2112 0.2439 REMARK 3 9 2.9629 - 2.8489 1.00 2669 112 0.2135 0.2542 REMARK 3 10 2.8489 - 2.7506 1.00 2639 112 0.2141 0.2834 REMARK 3 11 2.7506 - 2.6646 0.99 2623 153 0.2069 0.2483 REMARK 3 12 2.6646 - 2.5885 1.00 2611 124 0.2136 0.2548 REMARK 3 13 2.5885 - 2.5203 1.00 2613 170 0.2152 0.2660 REMARK 3 14 2.5203 - 2.4588 1.00 2597 149 0.2131 0.2671 REMARK 3 15 2.4588 - 2.4029 1.00 2596 159 0.2201 0.2918 REMARK 3 16 2.4029 - 2.3518 0.99 2624 145 0.2195 0.2547 REMARK 3 17 2.3518 - 2.3048 0.96 2472 125 0.2280 0.2883 REMARK 3 18 2.3048 - 2.2613 0.88 2333 128 0.2274 0.2601 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.930 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 : 0.008 6860 REMARK 3 ANGLE : 0.929 9316 REMARK 3 CHIRALITY : 0.054 983 REMARK 3 PLANARITY : 0.006 1223 REMARK 3 DIHEDRAL : 7.671 4099 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 8YJ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-MAR-24. REMARK 100 THE DEPOSITION ID IS D_1300045750. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-22 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 : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 464104 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.260 REMARK 200 RESOLUTION RANGE LOW (A) : 42.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MG/ML, 0.2 M NH4 CITRATE TRIBASIC, REMARK 280 16% PEG3350, PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 111.06400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 111.06400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 35.76200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 67.07900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.76200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 67.07900 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 111.06400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.76200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 67.07900 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 111.06400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.76200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 67.07900 REMARK 290 SMTRY3 8 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: A, B, C, E, D 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH E 327 LIES ON A SPECIAL POSITION. 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 MET A 0 REMARK 465 MET E 0 REMARK 465 GLU E 1 REMARK 465 MET D 0 REMARK 465 PRO D 203 REMARK 465 GLU D 204 REMARK 465 SER D 205 REMARK 465 SER D 206 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 A 17 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 227 CG OD1 OD2 REMARK 470 LYS B 19 CG CD CE NZ REMARK 470 LYS B 48 CG CD CE NZ REMARK 470 LYS B 75 CG CD CE NZ REMARK 470 LYS D 150 CG CD CE NZ 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 OE1 GLU A 232 OG SER B 28 1.19 REMARK 500 O HOH E 450 O HOH E 451 1.80 REMARK 500 NH1 ARG E 244 O HOH E 301 1.81 REMARK 500 NE2 GLN D 148 O HOH D 301 1.86 REMARK 500 O HOH E 372 O HOH E 445 1.86 REMARK 500 OH TYR E 190 O HOH E 302 1.89 REMARK 500 NZ LYS A 176 O HOH A 301 1.93 REMARK 500 O VAL A 231 NZ LYS A 243 1.93 REMARK 500 O HOH A 354 O HOH B 146 1.98 REMARK 500 O SER D 133 O HOH D 302 1.99 REMARK 500 O HOH B 131 O HOH B 140 2.00 REMARK 500 OG SER D 73 O HOH D 303 2.04 REMARK 500 O SER D 202 O HOH D 304 2.07 REMARK 500 OH TYR E 35 O HOH E 303 2.07 REMARK 500 O HOH D 371 O HOH D 390 2.07 REMARK 500 O HOH D 313 O HOH D 388 2.09 REMARK 500 O HIS B 84 O HOH B 101 2.09 REMARK 500 NZ LYS D 99 O HOH D 305 2.10 REMARK 500 O ILE D 193 O HOH D 306 2.15 REMARK 500 O HOH B 127 O HOH B 133 2.18 REMARK 500 OG1 THR D 107 O HOH D 307 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH E 372 O HOH E 428 3654 2.05 REMARK 500 NH1 ARG A 108 O SER D 129 7554 2.07 REMARK 500 O HOH E 430 O HOH E 445 3654 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 E 103 CD GLU E 103 OE1 -0.083 REMARK 500 GLU E 103 CD GLU E 103 OE2 -0.077 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 ARG A 108 NE - CZ - NH2 ANGL. DEV. = -4.5 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 17 21.69 -153.09 REMARK 500 ASP A 29 -124.68 52.74 REMARK 500 TYR A 123 -61.01 -109.05 REMARK 500 SER A 195 -151.48 -112.30 REMARK 500 THR A 225 34.57 -98.02 REMARK 500 PRO B 32 -167.99 -76.36 REMARK 500 TRP B 60 -0.22 80.01 REMARK 500 GLU C 8 28.08 -141.94 REMARK 500 ILE E 46 -63.04 -94.50 REMARK 500 HIS E 156 78.76 -103.42 REMARK 500 ARG D 16 -5.39 71.84 REMARK 500 ALA D 97 43.69 -150.46 REMARK 500 ASP D 118 58.01 -154.01 REMARK 500 PHE D 189 33.79 -98.37 REMARK 500 ASP D 197 30.41 -89.84 REMARK 500 REMARK 500 REMARK: NULL DBREF 8YJ2 A 1 275 UNP F6IQR9 F6IQR9_HUMAN 25 299 DBREF 8YJ2 B 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 8YJ2 C 1 10 PDB 8YJ2 8YJ2 1 10 DBREF 8YJ2 E 0 246 PDB 8YJ2 8YJ2 0 246 DBREF 8YJ2 D 0 206 PDB 8YJ2 8YJ2 0 206 SEQADV 8YJ2 MET A 0 UNP F6IQR9 INITIATING METHIONINE SEQADV 8YJ2 MET B 0 UNP P61769 EXPRESSION TAG SEQRES 1 A 276 MET GLY SER HIS SER MET ARG TYR PHE PHE THR SER VAL SEQRES 2 A 276 SER ARG PRO GLY ARG GLY GLU PRO ARG PHE ILE ALA VAL SEQRES 3 A 276 GLY TYR VAL ASP ASP THR GLN PHE VAL ARG PHE ASP SER SEQRES 4 A 276 ASP ALA ALA SER GLN LYS MET GLU PRO ARG ALA PRO TRP SEQRES 5 A 276 ILE GLU GLN GLU GLY PRO GLU TYR TRP ASP GLN GLU THR SEQRES 6 A 276 ARG ASN MET LYS ALA HIS SER GLN THR ASP ARG ALA ASN SEQRES 7 A 276 LEU GLY THR LEU ARG GLY TYR TYR ASN GLN SER GLU ASP SEQRES 8 A 276 GLY SER HIS THR ILE GLN ILE MET TYR GLY CYS ASP VAL SEQRES 9 A 276 GLY PRO ASP GLY ARG PHE LEU ARG GLY TYR ARG GLN ASP SEQRES 10 A 276 ALA TYR ASP GLY LYS ASP TYR ILE ALA LEU ASN GLU ASP SEQRES 11 A 276 LEU ARG SER TRP THR ALA ALA ASP MET ALA ALA GLN ILE SEQRES 12 A 276 THR LYS ARG LYS TRP GLU ALA VAL HIS ALA ALA GLU GLN SEQRES 13 A 276 ARG ARG VAL TYR LEU GLU GLY ARG CYS VAL ASP GLY LEU SEQRES 14 A 276 ARG ARG TYR LEU GLU ASN GLY LYS GLU THR LEU GLN ARG SEQRES 15 A 276 THR ASP PRO PRO LYS THR HIS MET THR HIS HIS PRO ILE SEQRES 16 A 276 SER ASP HIS GLU ALA THR LEU ARG CYS TRP ALA LEU GLY SEQRES 17 A 276 PHE TYR PRO ALA GLU ILE THR LEU THR TRP GLN ARG ASP SEQRES 18 A 276 GLY GLU ASP GLN THR GLN ASP THR GLU LEU VAL GLU THR SEQRES 19 A 276 ARG PRO ALA GLY ASP GLY THR PHE GLN LYS TRP ALA ALA SEQRES 20 A 276 VAL VAL VAL PRO SER GLY GLU GLU GLN ARG TYR THR CYS SEQRES 21 A 276 HIS VAL GLN HIS GLU GLY LEU PRO LYS PRO LEU THR LEU SEQRES 22 A 276 ARG TRP GLU 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 10 ILE LEU ASP THR ALA GLY ARG GLU GLU TYR SEQRES 1 E 247 MET GLU ALA GLN VAL THR GLN ASN PRO ARG TYR LEU ILE SEQRES 2 E 247 THR VAL THR GLY LYS LYS LEU THR VAL THR CYS SER GLN SEQRES 3 E 247 ASN MET ASN HIS GLU TYR MET SER TRP TYR ARG GLN ASP SEQRES 4 E 247 PRO GLY LEU GLY LEU ARG GLN ILE TYR TYR SER MET ASN SEQRES 5 E 247 VAL GLU VAL THR ASP LYS GLY ASP VAL PRO GLU GLY TYR SEQRES 6 E 247 LYS VAL SER ARG LYS GLU LYS ARG ASN PHE PRO LEU ILE SEQRES 7 E 247 LEU GLU SER PRO SER PRO ASN GLN THR SER LEU TYR PHE SEQRES 8 E 247 CYS ALA SER SER LEU VAL SER THR PRO LEU PRO LYS GLU SEQRES 9 E 247 THR GLN TYR PHE GLY PRO GLY THR ARG LEU LEU VAL LEU SEQRES 10 E 247 GLU ASP LEU LYS ASN VAL PHE PRO PRO GLU VAL ALA VAL SEQRES 11 E 247 PHE GLU PRO SER GLU ALA GLU ILE SER HIS THR GLN LYS SEQRES 12 E 247 ALA THR LEU VAL CYS LEU ALA THR GLY PHE TYR PRO ASP SEQRES 13 E 247 HIS VAL GLU LEU SER TRP TRP VAL ASN GLY LYS GLU VAL SEQRES 14 E 247 HIS SER GLY VAL CYS THR ASP PRO GLN PRO LEU LYS GLU SEQRES 15 E 247 GLN PRO ALA LEU ASN ASP SER ARG TYR ALA LEU SER SER SEQRES 16 E 247 ARG LEU ARG VAL SER ALA THR PHE TRP GLN ASN PRO ARG SEQRES 17 E 247 ASN HIS PHE ARG CYS GLN VAL GLN PHE TYR GLY LEU SER SEQRES 18 E 247 GLU ASN ASP GLU TRP THR GLN ASP ARG ALA LYS PRO VAL SEQRES 19 E 247 THR GLN ILE VAL SER ALA GLU ALA TRP GLY ARG ALA ASP SEQRES 1 D 207 MET ALA GLN LYS VAL THR GLN ALA GLN SER SER VAL SER SEQRES 2 D 207 MET PRO VAL ARG LYS ALA VAL THR LEU ASN CYS LEU TYR SEQRES 3 D 207 GLU THR SER TRP TRP SER TYR TYR ILE PHE TRP TYR LYS SEQRES 4 D 207 GLN LEU PRO SER LYS GLU MET ILE PHE LEU ILE ARG GLN SEQRES 5 D 207 GLY SER ASP GLU GLN ASN ALA LYS SER GLY ARG TYR SER SEQRES 6 D 207 VAL ASN PHE LYS LYS ALA ALA LYS SER VAL ALA LEU THR SEQRES 7 D 207 ILE SER ALA LEU GLN LEU GLU ASP SER ALA LYS TYR PHE SEQRES 8 D 207 CYS ALA LEU GLY ASP THR ALA GLY LYS SER THR PHE GLY SEQRES 9 D 207 ASP GLY THR THR LEU THR VAL LYS PRO ASN ILE GLN ASN SEQRES 10 D 207 PRO ASP PRO ALA VAL TYR GLN LEU ARG ASP SER LYS SER SEQRES 11 D 207 SER ASP LYS SER VAL CYS LEU PHE THR ASP PHE ASP SER SEQRES 12 D 207 GLN THR ASN VAL SER GLN SER LYS ASP SER ASP VAL TYR SEQRES 13 D 207 ILE THR ASP LYS CYS VAL LEU ASP MET ARG SER MET ASP SEQRES 14 D 207 PHE LYS SER ASN SER ALA VAL ALA TRP SER ASN LYS SER SEQRES 15 D 207 ASP PHE ALA CYS ALA ASN ALA PHE ASN ASN SER ILE ILE SEQRES 16 D 207 PRO GLU ASP THR PHE PHE PRO SER PRO GLU SER SER FORMUL 6 HOH *426(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 VAL A 150 1 14 HELIX 4 AA4 HIS A 151 GLY A 162 1 12 HELIX 5 AA5 GLY A 162 GLY A 175 1 14 HELIX 6 AA6 GLY A 175 GLN A 180 1 6 HELIX 7 AA7 GLU A 253 GLN A 255 5 3 HELIX 8 AA8 SER E 82 THR E 86 5 5 HELIX 9 AA9 SER E 133 GLN E 141 1 9 HELIX 10 AB1 ALA E 200 GLN E 204 1 5 HELIX 11 AB2 GLN D 82 SER D 86 5 5 HELIX 12 AB3 ARG D 165 ASP D 168 5 4 HELIX 13 AB4 ALA D 184 PHE D 189 1 6 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 VAL A 28 O THR A 31 SHEET 4 AA1 8 HIS A 3 VAL A 12 -1 N THR A 10 O ILE A 23 SHEET 5 AA1 8 THR A 94 VAL A 103 -1 O ILE A 97 N PHE A 9 SHEET 6 AA1 8 PHE A 109 TYR A 118 -1 O ALA A 117 N GLN A 96 SHEET 7 AA1 8 LYS A 121 LEU A 126 -1 O ILE A 124 N ASP 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 THR A 200 N HIS A 192 SHEET 3 AA2 4 PHE A 241 PRO A 250 -1 O ALA 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 THR A 200 N HIS A 192 SHEET 3 AA3 4 PHE A 241 PRO A 250 -1 O ALA 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 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 ASN B 24 N TYR B 10 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 ASN B 24 N TYR B 10 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 SHEET 1 AA8 4 VAL E 4 ASN E 7 0 SHEET 2 AA8 4 LEU E 19 GLN E 25 -1 O SER E 24 N THR E 5 SHEET 3 AA8 4 LEU E 76 LEU E 78 -1 O LEU E 76 N VAL E 21 SHEET 4 AA8 4 LYS E 65 VAL E 66 -1 N LYS E 65 O ILE E 77 SHEET 1 AA9 6 TYR E 10 VAL E 14 0 SHEET 2 AA9 6 THR E 111 LEU E 116 1 O LEU E 116 N THR E 13 SHEET 3 AA9 6 SER E 87 SER E 94 -1 N TYR E 89 O THR E 111 SHEET 4 AA9 6 TYR E 31 GLN E 37 -1 N SER E 33 O ALA E 92 SHEET 5 AA9 6 LEU E 43 ASN E 51 -1 O SER E 49 N MET E 32 SHEET 6 AA9 6 VAL E 54 LYS E 57 -1 O ASP E 56 N TYR E 48 SHEET 1 AB1 4 TYR E 10 VAL E 14 0 SHEET 2 AB1 4 THR E 111 LEU E 116 1 O LEU E 116 N THR E 13 SHEET 3 AB1 4 SER E 87 SER E 94 -1 N TYR E 89 O THR E 111 SHEET 4 AB1 4 TYR E 106 PHE E 107 -1 O TYR E 106 N SER E 93 SHEET 1 AB2 4 GLU E 126 PHE E 130 0 SHEET 2 AB2 4 LYS E 142 PHE E 152 -1 O VAL E 146 N PHE E 130 SHEET 3 AB2 4 TYR E 190 SER E 199 -1 O VAL E 198 N ALA E 143 SHEET 4 AB2 4 VAL E 172 THR E 174 -1 N CYS E 173 O ARG E 195 SHEET 1 AB3 4 GLU E 126 PHE E 130 0 SHEET 2 AB3 4 LYS E 142 PHE E 152 -1 O VAL E 146 N PHE E 130 SHEET 3 AB3 4 TYR E 190 SER E 199 -1 O VAL E 198 N ALA E 143 SHEET 4 AB3 4 LEU E 179 LYS E 180 -1 N LEU E 179 O ALA E 191 SHEET 1 AB4 4 LYS E 166 VAL E 168 0 SHEET 2 AB4 4 VAL E 157 VAL E 163 -1 N VAL E 163 O LYS E 166 SHEET 3 AB4 4 HIS E 209 PHE E 216 -1 O GLN E 215 N GLU E 158 SHEET 4 AB4 4 GLN E 235 TRP E 242 -1 O GLN E 235 N PHE E 216 SHEET 1 AB5 2 LYS D 3 THR D 5 0 SHEET 2 AB5 2 LEU D 24 GLU D 26 -1 O LEU D 24 N THR D 5 SHEET 1 AB6 5 SER D 10 PRO D 14 0 SHEET 2 AB6 5 THR D 106 LYS D 111 1 O THR D 107 N VAL D 11 SHEET 3 AB6 5 ALA D 87 GLY D 94 -1 N ALA D 87 O LEU D 108 SHEET 4 AB6 5 TYR D 33 GLN D 39 -1 N PHE D 35 O ALA D 92 SHEET 5 AB6 5 MET D 45 GLY D 52 -1 O ILE D 46 N LYS D 38 SHEET 1 AB7 4 SER D 10 PRO D 14 0 SHEET 2 AB7 4 THR D 106 LYS D 111 1 O THR D 107 N VAL D 11 SHEET 3 AB7 4 ALA D 87 GLY D 94 -1 N ALA D 87 O LEU D 108 SHEET 4 AB7 4 SER D 100 PHE D 102 -1 O THR D 101 N LEU D 93 SHEET 1 AB8 4 VAL D 19 LEU D 21 0 SHEET 2 AB8 4 SER D 73 ILE D 78 -1 O LEU D 76 N LEU D 21 SHEET 3 AB8 4 TYR D 63 LYS D 68 -1 N LYS D 68 O SER D 73 SHEET 4 AB8 4 LYS D 59 SER D 60 -1 N SER D 60 O TYR D 63 SHEET 1 AB9 4 ALA D 120 ARG D 125 0 SHEET 2 AB9 4 SER D 133 THR D 138 -1 O LEU D 136 N TYR D 122 SHEET 3 AB9 4 PHE D 169 SER D 178 -1 O ALA D 176 N CYS D 135 SHEET 4 AB9 4 VAL D 154 ILE D 156 -1 N TYR D 155 O TRP D 177 SHEET 1 AC1 4 ALA D 120 ARG D 125 0 SHEET 2 AC1 4 SER D 133 THR D 138 -1 O LEU D 136 N TYR D 122 SHEET 3 AC1 4 PHE D 169 SER D 178 -1 O ALA D 176 N CYS D 135 SHEET 4 AC1 4 CYS D 160 MET D 164 -1 N MET D 164 O PHE D 169 SSBOND 1 CYS A 101 CYS A 164 1555 1555 2.10 SSBOND 2 CYS A 203 CYS A 259 1555 1555 2.04 SSBOND 3 CYS B 25 CYS B 80 1555 1555 2.05 SSBOND 4 CYS E 23 CYS E 91 1555 1555 2.03 SSBOND 5 CYS E 147 CYS E 212 1555 1555 2.00 SSBOND 6 CYS E 173 CYS D 160 1555 1555 2.05 SSBOND 7 CYS D 23 CYS D 91 1555 1555 2.05 SSBOND 8 CYS D 135 CYS D 185 1555 1555 2.05 CISPEP 1 TYR A 209 PRO A 210 0 1.63 CISPEP 2 HIS B 31 PRO B 32 0 3.66 CISPEP 3 ASN E 7 PRO E 8 0 4.83 CISPEP 4 TYR E 153 PRO E 154 0 -3.19 CRYST1 71.524 134.158 222.128 90.00 90.00 90.00 C 2 2 21 8 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 0.013981 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007454 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004502 0.00000