HEADER SIGNALING PROTEIN/IMMUNE SYSTEM 07-OCT-22 8EQ6 TITLE PD1 SIGNALING RECEPTOR BOUND TO FAB COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN PD-1,HPD-1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ANTIBODY FAB LIGHT CHAIN; COMPND 8 CHAIN: L; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: ANTIBODY FAB HEAVY CHAIN; COMPND 12 CHAIN: H; COMPND 13 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: PDCD1, PD1; SOURCE 6 EXPRESSION_SYSTEM: EXPRESSION VECTOR PCDNA-INF; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 85704; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_TAXID: 10090; SOURCE 11 EXPRESSION_SYSTEM: EXPRESSION VECTOR PCDNA-INF; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 85704; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 15 ORGANISM_TAXID: 10090; SOURCE 16 EXPRESSION_SYSTEM: EXPRESSION VECTOR PCDNA-INF; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 85704 KEYWDS IMMUNE SIGNALING RECEPTOR FAB COMPLEX, SIGNALING PROTEIN, SIGNALING KEYWDS 2 PROTEIN-IMMUNE SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.BJORKELID,C.PALUCH,N.J.ROBERTSON REVDAT 2 06-MAR-24 8EQ6 1 JRNL REVDAT 1 11-OCT-23 8EQ6 0 JRNL AUTH A.H.LIPPERT,C.PALUCH,M.GAGLIONI,M.T.VUONG,J.MCCOLL, JRNL AUTH 2 E.JENKINS,M.FELLERMEYER,J.CLARKE,S.SHARMA, JRNL AUTH 3 S.MOREIRA DA SILVA,B.AKKAYA,C.ANZILOTTI,S.H.MORGAN, JRNL AUTH 4 C.F.JESSUP,M.KORBEL,U.GILEADI,J.LEITNER,R.KNOX,M.CHIRIFU, JRNL AUTH 5 J.HUO,S.YU,N.ASHMAN,Y.LUI,I.WILKINSON,K.E.ATTFIELD,L.FUGGER, JRNL AUTH 6 N.J.ROBERTSON,C.J.LYNCH,L.MURRAY,P.STEINBERGER,A.M.SANTOS, JRNL AUTH 7 S.F.LEE,R.J.CORNALL,D.KLENERMAN,S.J.DAVIS JRNL TITL ANTIBODY AGONISTS TRIGGER IMMUNE RECEPTOR SIGNALING THROUGH JRNL TITL 2 LOCAL EXCLUSION OF RECEPTOR-TYPE PROTEIN TYROSINE JRNL TITL 3 PHOSPHATASES. JRNL REF IMMUNITY V. 57 256 2024 JRNL REFN ISSN 1074-7613 JRNL PMID 38354703 JRNL DOI 10.1016/J.IMMUNI.2024.01.007 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 60052 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.029 REMARK 3 FREE R VALUE TEST SET COUNT : 3020 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3712 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.42 REMARK 3 BIN R VALUE (WORKING SET) : 0.3900 REMARK 3 BIN FREE R VALUE SET COUNT : 199 REMARK 3 BIN FREE R VALUE : 0.3950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3877 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 183 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.35900 REMARK 3 B22 (A**2) : 0.60100 REMARK 3 B33 (A**2) : -1.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.40400 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.121 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.119 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.150 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.284 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3985 ; 0.009 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3532 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5421 ; 1.599 ; 1.653 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8272 ; 0.540 ; 1.558 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 502 ; 8.077 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 20 ; 7.661 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 639 ;16.000 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 610 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4494 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 794 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 595 ; 0.212 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 166 ; 0.195 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1891 ; 0.181 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 209 ; 0.154 ; 0.200 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): 2011 ; 2.306 ; 2.499 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2011 ; 2.306 ; 2.498 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2503 ; 3.329 ; 3.735 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2504 ; 3.329 ; 3.736 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1974 ; 3.126 ; 2.788 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1975 ; 3.125 ; 2.788 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2915 ; 4.605 ; 4.047 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2916 ; 4.604 ; 4.047 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8EQ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1000269209. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60066 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 49.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.15600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.8600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 2.32900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.200 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: 6K0Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20.5% PEG 3350, 0.4M MGCL2, 0.1M BIS REMARK 280 -TRIS PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 33.37200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.25500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 33.37200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 39.25500 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 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, L, 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 GLY A 1 REMARK 465 PRO A 2 REMARK 465 SER A 3 REMARK 465 GLY A 4 REMARK 465 ALA A 5 REMARK 465 LEU A 6 REMARK 465 ASP A 7 REMARK 465 SER A 8 REMARK 465 PRO A 9 REMARK 465 ASP A 10 REMARK 465 ARG A 11 REMARK 465 PRO A 12 REMARK 465 TRP A 13 REMARK 465 ASN A 14 REMARK 465 SER A 38 REMARK 465 ASN A 39 REMARK 465 THR A 40 REMARK 465 SER A 41 REMARK 465 GLU A 42 REMARK 465 SER A 43 REMARK 465 PHE A 44 REMARK 465 SER A 52 REMARK 465 PRO A 53 REMARK 465 SER A 54 REMARK 465 ASN A 55 REMARK 465 GLN A 56 REMARK 465 THR A 57 REMARK 465 ASP A 58 REMARK 465 LYS A 59 REMARK 465 LEU A 60 REMARK 465 ALA A 61 REMARK 465 ALA A 62 REMARK 465 PHE A 63 REMARK 465 PRO A 64 REMARK 465 GLU A 65 REMARK 465 ASP A 66 REMARK 465 ARG A 67 REMARK 465 SER A 68 REMARK 465 GLN A 69 REMARK 465 PRO A 70 REMARK 465 GLY A 71 REMARK 465 GLN A 72 REMARK 465 ASP A 73 REMARK 465 ILE A 107 REMARK 465 SER A 108 REMARK 465 LEU A 109 REMARK 465 ALA A 110 REMARK 465 PRO A 111 REMARK 465 LYS A 112 REMARK 465 ALA A 113 REMARK 465 GLN A 114 REMARK 465 ARG A 129 REMARK 465 GLY L 213 REMARK 465 GLU L 214 REMARK 465 CYS L 215 REMARK 465 SER H 135 REMARK 465 LYS H 136 REMARK 465 SER H 137 REMARK 465 THR H 138 REMARK 465 SER H 139 REMARK 465 GLY H 140 REMARK 465 LYS H 221 REMARK 465 SER H 222 REMARK 465 CYS H 223 REMARK 465 ASP H 224 REMARK 465 LYS H 225 REMARK 465 THR H 226 REMARK 465 HIS H 227 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 HE21 GLN L 91 H ASN L 93 1.07 REMARK 500 HD21 ASN H 100 O HOH H 301 1.13 REMARK 500 HH TYR H 60 H LEU H 70 1.21 REMARK 500 HG1 THR H 91 H VAL H 118 1.32 REMARK 500 H VAL L 15 O HOH L 303 1.51 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 124 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 GLN L 91 N - CA - CB ANGL. DEV. = -11.2 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 75 -29.47 93.34 REMARK 500 THR L 52 -49.08 80.61 REMARK 500 SER L 53 -1.73 -140.11 REMARK 500 SER L 78 87.88 -166.71 REMARK 500 PRO L 142 -168.61 -79.67 REMARK 500 PRO H 41 -46.16 -29.50 REMARK 500 THR H 77 50.71 38.41 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 H 87 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8EQ6 A 6 129 UNP Q15116 PDCD1_HUMAN 25 148 DBREF 8EQ6 L 1 215 PDB 8EQ6 8EQ6 1 215 DBREF 8EQ6 H 1 227 PDB 8EQ6 8EQ6 1 227 SEQADV 8EQ6 GLY A 1 UNP Q15116 EXPRESSION TAG SEQADV 8EQ6 PRO A 2 UNP Q15116 EXPRESSION TAG SEQADV 8EQ6 SER A 3 UNP Q15116 EXPRESSION TAG SEQADV 8EQ6 GLY A 4 UNP Q15116 EXPRESSION TAG SEQADV 8EQ6 ALA A 5 UNP Q15116 EXPRESSION TAG SEQADV 8EQ6 SER A 74 UNP Q15116 CYS 93 CONFLICT SEQRES 1 A 129 GLY PRO SER GLY ALA LEU ASP SER PRO ASP ARG PRO TRP SEQRES 2 A 129 ASN PRO PRO THR PHE SER PRO ALA LEU LEU VAL VAL THR SEQRES 3 A 129 GLU GLY ASP ASN ALA THR PHE THR CYS SER PHE SER ASN SEQRES 4 A 129 THR SER GLU SER PHE VAL LEU ASN TRP TYR ARG MET SER SEQRES 5 A 129 PRO SER ASN GLN THR ASP LYS LEU ALA ALA PHE PRO GLU SEQRES 6 A 129 ASP ARG SER GLN PRO GLY GLN ASP SER ARG PHE ARG VAL SEQRES 7 A 129 THR GLN LEU PRO ASN GLY ARG ASP PHE HIS MET SER VAL SEQRES 8 A 129 VAL ARG ALA ARG ARG ASN ASP SER GLY THR TYR LEU CYS SEQRES 9 A 129 GLY ALA ILE SER LEU ALA PRO LYS ALA GLN ILE LYS GLU SEQRES 10 A 129 SER LEU ARG ALA GLU LEU ARG VAL THR GLU ARG ARG SEQRES 1 L 215 GLU ASN GLN LEU THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 215 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 215 SER SER VAL ILE SER SER TYR LEU HIS TRP TYR GLN GLN SEQRES 4 L 215 LYS PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR SER THR SEQRES 5 L 215 SER ASN LEU ALA SER GLY VAL PRO SER ARG PHE SER GLY SEQRES 6 L 215 SER GLY SER GLY THR ASP TYR THR LEU THR ILE SER SER SEQRES 7 L 215 LEU GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN SEQRES 8 L 215 TYR ASN SER TYR PRO LEU THR PHE GLY GLY GLY THR LYS SEQRES 9 L 215 LEU GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE SEQRES 10 L 215 ILE PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR SEQRES 11 L 215 ALA SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG SEQRES 12 L 215 GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SEQRES 13 L 215 SER GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER SEQRES 14 L 215 LYS ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SEQRES 15 L 215 SER LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS SEQRES 16 L 215 GLU VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SEQRES 17 L 215 SER PHE ASN ARG GLY GLU CYS SEQRES 1 H 227 GLN VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS LYS SEQRES 2 H 227 PRO GLY ALA SER VAL LYS VAL SER CYS LYS ALA PHE GLY SEQRES 3 H 227 TYR THR PHE THR THR TYR PRO ILE GLU TRP MET ARG GLN SEQRES 4 H 227 ALA PRO GLY LYS GLY LEU GLU TRP ILE GLY ASN PHE HIS SEQRES 5 H 227 PRO TYR ASN ASP ASP THR LYS TYR ASN GLU LYS PHE GLN SEQRES 6 H 227 GLY ARG VAL THR LEU THR VAL ASP LYS SER SER THR THR SEQRES 7 H 227 VAL TYR MET GLU LEU SER SER LEU ARG SER GLU ASP THR SEQRES 8 H 227 ALA VAL TYR TYR CYS ALA ARG GLU ASN TYR GLY SER HIS SEQRES 9 H 227 GLY GLY PHE VAL TYR TRP GLY GLN GLY THR LEU VAL THR SEQRES 10 H 227 VAL SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO SEQRES 11 H 227 LEU ALA PRO SER SER LYS SER THR SER GLY GLY THR ALA SEQRES 12 H 227 ALA LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO SEQRES 13 H 227 VAL THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY SEQRES 14 H 227 VAL HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU SEQRES 15 H 227 TYR SER LEU SER SER VAL VAL THR VAL PRO SER SER SER SEQRES 16 H 227 LEU GLY THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS SEQRES 17 H 227 PRO SER ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SEQRES 18 H 227 SER CYS ASP LYS THR HIS FORMUL 4 HOH *183(H2 O) HELIX 1 AA1 ARG A 95 SER A 99 5 5 HELIX 2 AA2 ILE L 30 SER L 32 5 3 HELIX 3 AA3 GLN L 80 PHE L 84 5 5 HELIX 4 AA4 SER L 122 LYS L 127 1 6 HELIX 5 AA5 LYS L 184 HIS L 190 1 7 HELIX 6 AA6 THR H 28 TYR H 32 5 5 HELIX 7 AA7 GLU H 62 GLN H 65 5 4 HELIX 8 AA8 LYS H 74 SER H 76 5 3 HELIX 9 AA9 ARG H 87 THR H 91 5 5 HELIX 10 AB1 SER H 163 ALA H 165 5 3 HELIX 11 AB2 SER H 194 LEU H 196 5 3 HELIX 12 AB3 LYS H 208 ASN H 211 5 4 SHEET 1 AA1 4 THR A 17 SER A 19 0 SHEET 2 AA1 4 ALA A 31 SER A 36 -1 O THR A 34 N SER A 19 SHEET 3 AA1 4 ASP A 86 VAL A 91 -1 O PHE A 87 N CYS A 35 SHEET 4 AA1 4 PHE A 76 GLN A 80 -1 N THR A 79 O HIS A 88 SHEET 1 AA2 4 LEU A 22 THR A 26 0 SHEET 2 AA2 4 ALA A 121 THR A 126 1 O ARG A 124 N VAL A 25 SHEET 3 AA2 4 GLY A 100 GLY A 105 -1 N GLY A 100 O LEU A 123 SHEET 4 AA2 4 ASN A 47 ARG A 50 -1 N ASN A 47 O GLY A 105 SHEET 1 AA3 3 LEU L 4 SER L 7 0 SHEET 2 AA3 3 VAL L 19 VAL L 29 -1 O THR L 22 N SER L 7 SHEET 3 AA3 3 PHE L 63 ILE L 76 -1 O TYR L 72 N CYS L 23 SHEET 1 AA4 6 SER L 10 ALA L 13 0 SHEET 2 AA4 6 THR L 103 ILE L 107 1 O GLU L 106 N LEU L 11 SHEET 3 AA4 6 THR L 86 GLN L 91 -1 N TYR L 87 O THR L 103 SHEET 4 AA4 6 LEU L 34 GLN L 39 -1 N GLN L 39 O THR L 86 SHEET 5 AA4 6 LYS L 46 TYR L 50 -1 O LEU L 48 N TRP L 36 SHEET 6 AA4 6 ASN L 54 LEU L 55 -1 O ASN L 54 N TYR L 50 SHEET 1 AA5 4 SER L 10 ALA L 13 0 SHEET 2 AA5 4 THR L 103 ILE L 107 1 O GLU L 106 N LEU L 11 SHEET 3 AA5 4 THR L 86 GLN L 91 -1 N TYR L 87 O THR L 103 SHEET 4 AA5 4 THR L 98 PHE L 99 -1 O THR L 98 N GLN L 91 SHEET 1 AA6 4 SER L 115 PHE L 119 0 SHEET 2 AA6 4 THR L 130 PHE L 140 -1 O LEU L 136 N PHE L 117 SHEET 3 AA6 4 TYR L 174 SER L 183 -1 O LEU L 176 N LEU L 137 SHEET 4 AA6 4 SER L 160 VAL L 164 -1 N GLN L 161 O THR L 179 SHEET 1 AA7 4 ALA L 154 LEU L 155 0 SHEET 2 AA7 4 LYS L 146 VAL L 151 -1 N VAL L 151 O ALA L 154 SHEET 3 AA7 4 VAL L 192 THR L 198 -1 O GLU L 196 N GLN L 148 SHEET 4 AA7 4 VAL L 206 ASN L 211 -1 O VAL L 206 N VAL L 197 SHEET 1 AA8 4 GLN H 3 GLN H 6 0 SHEET 2 AA8 4 VAL H 18 PHE H 25 -1 O LYS H 23 N VAL H 5 SHEET 3 AA8 4 THR H 78 LEU H 83 -1 O MET H 81 N VAL H 20 SHEET 4 AA8 4 VAL H 68 ASP H 73 -1 N THR H 69 O GLU H 82 SHEET 1 AA9 6 GLU H 10 LYS H 12 0 SHEET 2 AA9 6 THR H 114 VAL H 118 1 O THR H 117 N LYS H 12 SHEET 3 AA9 6 ALA H 92 ARG H 98 -1 N TYR H 94 O THR H 114 SHEET 4 AA9 6 ILE H 34 ALA H 40 -1 N GLU H 35 O ALA H 97 SHEET 5 AA9 6 GLY H 44 PHE H 51 -1 O ILE H 48 N TRP H 36 SHEET 6 AA9 6 THR H 58 TYR H 60 -1 O LYS H 59 N ASN H 50 SHEET 1 AB1 4 GLU H 10 LYS H 12 0 SHEET 2 AB1 4 THR H 114 VAL H 118 1 O THR H 117 N LYS H 12 SHEET 3 AB1 4 ALA H 92 ARG H 98 -1 N TYR H 94 O THR H 114 SHEET 4 AB1 4 TYR H 109 TRP H 110 -1 O TYR H 109 N ARG H 98 SHEET 1 AB2 4 SER H 127 LEU H 131 0 SHEET 2 AB2 4 THR H 142 TYR H 152 -1 O LEU H 148 N PHE H 129 SHEET 3 AB2 4 TYR H 183 PRO H 192 -1 O LEU H 185 N VAL H 149 SHEET 4 AB2 4 VAL H 170 THR H 172 -1 N HIS H 171 O VAL H 188 SHEET 1 AB3 4 SER H 127 LEU H 131 0 SHEET 2 AB3 4 THR H 142 TYR H 152 -1 O LEU H 148 N PHE H 129 SHEET 3 AB3 4 TYR H 183 PRO H 192 -1 O LEU H 185 N VAL H 149 SHEET 4 AB3 4 VAL H 176 LEU H 177 -1 N VAL H 176 O SER H 184 SHEET 1 AB4 3 THR H 158 TRP H 161 0 SHEET 2 AB4 3 ILE H 202 HIS H 207 -1 O ASN H 206 N THR H 158 SHEET 3 AB4 3 THR H 212 LYS H 217 -1 O VAL H 214 N VAL H 205 SSBOND 1 CYS A 35 CYS A 104 1555 1555 2.01 SSBOND 2 CYS L 23 CYS L 89 1555 1555 2.14 SSBOND 3 CYS L 135 CYS L 195 1555 1555 2.02 SSBOND 4 CYS H 22 CYS H 96 1555 1555 2.07 SSBOND 5 CYS H 147 CYS H 203 1555 1555 2.06 CISPEP 1 SER A 19 PRO A 20 0 -5.67 CISPEP 2 SER L 7 PRO L 8 0 -6.27 CISPEP 3 TYR L 95 PRO L 96 0 -5.87 CISPEP 4 TYR L 141 PRO L 142 0 -3.07 CISPEP 5 PHE H 153 PRO H 154 0 -12.68 CISPEP 6 GLU H 155 PRO H 156 0 -4.23 CRYST1 66.744 78.510 102.021 90.00 106.42 90.00 C 1 2 1 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 0.014983 0.000000 0.004416 0.00000 SCALE2 0.000000 0.012737 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010219 0.00000