HEADER IMMUNE SYSTEM 30-NOV-07 3BIS TITLE CRYSTAL STRUCTURE OF THE PD-L1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: EXTRACELLULAR REGION; COMPND 5 SYNONYM: PROGRAMMED DEATH LIGAND 1, PD-L1, PDCD1 LIGAND 1, B7 HOMOLOG COMPND 6 1, B7-H1, CD274 ANTIGEN; COMPND 7 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: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PLM1 KEYWDS CO-STIMULATION, IMMUNOGLOBULIN-LIKE BETA-SANDWICH, T CELL, B CELL, KEYWDS 2 PROGRAMMED DEATH, IMMUNE SYSTEM, TRANSMEMBRANE, INHIBITORY RECEPTOR, KEYWDS 3 GLYCOPROTEIN, IMMUNOGLOBULIN DOMAIN EXPDTA X-RAY DIFFRACTION AUTHOR D.Y.LIN,Y.TANAKA,M.IWASAKI,A.G.GITTIS,H.P.SU,B.MIKAMI,T.OKAZAKI, AUTHOR 2 T.HONJO,N.MINATO,D.N.GARBOCZI REVDAT 4 13-JUL-11 3BIS 1 VERSN REVDAT 3 24-FEB-09 3BIS 1 VERSN REVDAT 2 11-NOV-08 3BIS 1 JRNL REVDAT 1 26-FEB-08 3BIS 0 JRNL AUTH D.Y.LIN,Y.TANAKA,M.IWASAKI,A.G.GITTIS,H.P.SU,B.MIKAMI, JRNL AUTH 2 T.OKAZAKI,T.HONJO,N.MINATO,D.N.GARBOCZI JRNL TITL THE PD-1/PD-L1 COMPLEX RESEMBLES THE ANTIGEN-BINDING FV JRNL TITL 2 DOMAINS OF ANTIBODIES AND T CELL RECEPTORS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 3011 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18287011 JRNL DOI 10.1073/PNAS.0712278105 REMARK 2 REMARK 2 RESOLUTION. 2.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 13406 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) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 700 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) : 2.64 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.71 REMARK 3 REFLECTION IN BIN (WORKING SET) : 700 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.3840 REMARK 3 BIN FREE R VALUE SET COUNT : 34 REMARK 3 BIN FREE R VALUE : 0.5000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3412 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 45 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.44000 REMARK 3 B22 (A**2) : -0.07000 REMARK 3 B33 (A**2) : -0.37000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.401 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.327 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 30.871 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.905 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3481 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4729 ; 1.526 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 422 ; 6.846 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 166 ;40.132 ;24.819 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 626 ;20.075 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;15.959 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 548 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2600 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1178 ; 0.236 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2228 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 105 ; 0.163 ; 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): 53 ; 0.269 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.245 ; 0.200 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): 2187 ; 0.811 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3466 ; 1.117 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1471 ; 1.699 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1263 ; 2.612 ; 4.500 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 133 A 230 REMARK 3 ORIGIN FOR THE GROUP (A): -12.0610 6.9730 -33.4130 REMARK 3 T TENSOR REMARK 3 T11: 0.1126 T22: 0.1359 REMARK 3 T33: 0.1657 T12: -0.0169 REMARK 3 T13: 0.0107 T23: -0.0015 REMARK 3 L TENSOR REMARK 3 L11: 3.3033 L22: 3.5499 REMARK 3 L33: 2.1478 L12: -1.3033 REMARK 3 L13: 1.3742 L23: -0.8657 REMARK 3 S TENSOR REMARK 3 S11: 0.1415 S12: -0.0182 S13: -0.1233 REMARK 3 S21: -0.1094 S22: -0.1185 S23: 0.1844 REMARK 3 S31: -0.0595 S32: -0.0421 S33: -0.0575 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 19 A 129 REMARK 3 ORIGIN FOR THE GROUP (A): -4.2790 -16.7680 -1.8580 REMARK 3 T TENSOR REMARK 3 T11: 0.1640 T22: 0.1548 REMARK 3 T33: 0.1514 T12: 0.0834 REMARK 3 T13: 0.0216 T23: 0.1575 REMARK 3 L TENSOR REMARK 3 L11: 3.9277 L22: 4.9149 REMARK 3 L33: 10.2487 L12: -0.0053 REMARK 3 L13: 1.7511 L23: -4.2008 REMARK 3 S TENSOR REMARK 3 S11: 0.1449 S12: 0.3369 S13: -0.4818 REMARK 3 S21: -0.4355 S22: -0.3689 S23: 0.2159 REMARK 3 S31: 0.2301 S32: -0.4711 S33: -0.5405 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 133 B 229 REMARK 3 ORIGIN FOR THE GROUP (A): -21.2350 23.9540 -24.4000 REMARK 3 T TENSOR REMARK 3 T11: 0.1819 T22: 0.1204 REMARK 3 T33: 0.1880 T12: 0.0350 REMARK 3 T13: 0.1118 T23: -0.0235 REMARK 3 L TENSOR REMARK 3 L11: 2.3281 L22: 13.0841 REMARK 3 L33: 2.2620 L12: 1.7545 REMARK 3 L13: 0.4623 L23: -1.6782 REMARK 3 S TENSOR REMARK 3 S11: 0.0968 S12: -0.2517 S13: 0.1548 REMARK 3 S21: -0.2591 S22: 0.0725 S23: 0.6231 REMARK 3 S31: 1.1918 S32: -0.0425 S33: -0.0582 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 18 B 129 REMARK 3 ORIGIN FOR THE GROUP (A): -27.5650 -15.0830 -13.8280 REMARK 3 T TENSOR REMARK 3 T11: 0.1760 T22: 0.1822 REMARK 3 T33: 0.2483 T12: -0.1564 REMARK 3 T13: 0.0434 T23: 0.0337 REMARK 3 L TENSOR REMARK 3 L11: 3.4650 L22: 6.3896 REMARK 3 L33: 6.0989 L12: 0.5513 REMARK 3 L13: -1.9302 L23: -2.5921 REMARK 3 S TENSOR REMARK 3 S11: 0.6055 S12: -0.0354 S13: -0.5701 REMARK 3 S21: -0.1398 S22: -0.1930 S23: 0.8604 REMARK 3 S31: -0.1609 S32: -0.3848 S33: 0.4152 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3BIS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-DEC-07. REMARK 100 THE RCSB ID CODE IS RCSB045571. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0722, 0.97948, 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-3 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14169 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.640 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.73 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.27200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.1 M NACACODYLATE, 0.2 REMARK 280 M AMMONIUM FORMATE OR AMMONIUM FLUORIDE, PH 6.50, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 70.86000 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 70.86000 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 36.54000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.35000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.54000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.35000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 70.86000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.54000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.35000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 70.86000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.54000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.35000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 A 266 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 ALA A 18 REMARK 465 LEU A 231 REMARK 465 ALA A 232 REMARK 465 HIS A 233 REMARK 465 PRO A 234 REMARK 465 PRO A 235 REMARK 465 ASN A 236 REMARK 465 GLU A 237 REMARK 465 ARG A 238 REMARK 465 THR A 239 REMARK 465 PRO B 230 REMARK 465 LEU B 231 REMARK 465 ALA B 232 REMARK 465 HIS B 233 REMARK 465 PRO B 234 REMARK 465 PRO B 235 REMARK 465 ASN B 236 REMARK 465 GLU B 237 REMARK 465 ARG B 238 REMARK 465 THR B 239 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 LYS A 46 CE LYS A 46 NZ 0.157 REMARK 500 LYS B 162 CD LYS B 162 CE 0.229 REMARK 500 ASP B 215 CG ASP B 215 OD1 0.247 REMARK 500 ASP B 215 CG ASP B 215 OD2 0.231 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP B 215 CB - CG - OD1 ANGL. DEV. = -8.9 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 LYS A 25 133.80 -172.92 REMARK 500 LYS A 46 -125.39 44.11 REMARK 500 GLU A 60 45.26 35.56 REMARK 500 ASP A 61 -12.33 82.06 REMARK 500 TYR A 81 -98.12 -111.63 REMARK 500 ARG A 82 -160.96 67.94 REMARK 500 GLN A 83 6.36 -47.01 REMARK 500 SER A 93 -23.36 -39.34 REMARK 500 TYR A 118 85.91 -160.75 REMARK 500 ASP A 145 108.62 -161.52 REMARK 500 HIS A 172 16.54 81.87 REMARK 500 THR A 203 137.36 -39.55 REMARK 500 ASN A 204 -1.31 78.53 REMARK 500 TYR B 32 130.93 -35.88 REMARK 500 LYS B 46 -51.88 -121.01 REMARK 500 MET B 59 -59.47 -131.64 REMARK 500 GLU B 60 -109.49 -138.11 REMARK 500 HIS B 69 48.54 36.40 REMARK 500 LEU B 74 -74.47 -50.82 REMARK 500 LYS B 75 -64.37 -13.24 REMARK 500 GLN B 77 87.32 -42.57 REMARK 500 SER B 79 -125.39 52.47 REMARK 500 TYR B 81 7.60 -60.39 REMARK 500 TYR B 118 92.22 -161.92 REMARK 500 PRO B 161 -125.89 -73.29 REMARK 500 SER B 170 -89.47 -43.55 REMARK 500 HIS B 172 -122.08 -55.09 REMARK 500 GLN B 173 124.94 65.87 REMARK 500 GLU B 188 -76.68 -31.58 REMARK 500 ASN B 204 -9.36 83.72 REMARK 500 LEU B 214 -75.63 -93.29 REMARK 500 ASP B 215 -73.75 -78.99 REMARK 500 PRO B 216 73.32 -55.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 THR A 179 23.5 L L OUTSIDE RANGE REMARK 500 LEU B 214 24.3 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BIK RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH PD-1 (CD279) DBREF 3BIS A 18 239 UNP Q9NZQ7 PD1L1_HUMAN 18 239 DBREF 3BIS B 18 239 UNP Q9NZQ7 PD1L1_HUMAN 18 239 SEQRES 1 A 222 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL SEQRES 2 A 222 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO SEQRES 3 A 222 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR SEQRES 4 A 222 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS SEQRES 5 A 222 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG SEQRES 6 A 222 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY SEQRES 7 A 222 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP SEQRES 8 A 222 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA SEQRES 9 A 222 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR SEQRES 10 A 222 ASN LYS ILE ASN GLN ARG ILE LEU VAL VAL ASP PRO VAL SEQRES 11 A 222 THR SER GLU HIS GLU LEU THR CYS GLN ALA GLU GLY TYR SEQRES 12 A 222 PRO LYS ALA GLU VAL ILE TRP THR SER SER ASP HIS GLN SEQRES 13 A 222 VAL LEU SER GLY LYS THR THR THR THR ASN SER LYS ARG SEQRES 14 A 222 GLU GLU LYS LEU PHE ASN VAL THR SER THR LEU ARG ILE SEQRES 15 A 222 ASN THR THR THR ASN GLU ILE PHE TYR CYS THR PHE ARG SEQRES 16 A 222 ARG LEU ASP PRO GLU GLU ASN HIS THR ALA GLU LEU VAL SEQRES 17 A 222 ILE PRO GLU LEU PRO LEU ALA HIS PRO PRO ASN GLU ARG SEQRES 18 A 222 THR SEQRES 1 B 222 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL SEQRES 2 B 222 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO SEQRES 3 B 222 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR SEQRES 4 B 222 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS SEQRES 5 B 222 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG SEQRES 6 B 222 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY SEQRES 7 B 222 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP SEQRES 8 B 222 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA SEQRES 9 B 222 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR SEQRES 10 B 222 ASN LYS ILE ASN GLN ARG ILE LEU VAL VAL ASP PRO VAL SEQRES 11 B 222 THR SER GLU HIS GLU LEU THR CYS GLN ALA GLU GLY TYR SEQRES 12 B 222 PRO LYS ALA GLU VAL ILE TRP THR SER SER ASP HIS GLN SEQRES 13 B 222 VAL LEU SER GLY LYS THR THR THR THR ASN SER LYS ARG SEQRES 14 B 222 GLU GLU LYS LEU PHE ASN VAL THR SER THR LEU ARG ILE SEQRES 15 B 222 ASN THR THR THR ASN GLU ILE PHE TYR CYS THR PHE ARG SEQRES 16 B 222 ARG LEU ASP PRO GLU GLU ASN HIS THR ALA GLU LEU VAL SEQRES 17 B 222 ILE PRO GLU LEU PRO LEU ALA HIS PRO PRO ASN GLU ARG SEQRES 18 B 222 THR FORMUL 3 HOH *45(H2 O) HELIX 1 1 LEU A 74 GLN A 77 5 4 HELIX 2 2 LYS A 89 LEU A 94 5 6 HELIX 3 3 LYS A 105 ALA A 109 5 5 HELIX 4 4 ASP B 49 LEU B 53 5 5 HELIX 5 5 HIS B 78 ARG B 82 5 5 HELIX 6 6 ASP B 90 LEU B 94 5 5 SHEET 1 A 6 LEU A 27 GLU A 31 0 SHEET 2 A 6 ALA A 121 ASN A 131 1 O LYS A 129 N TYR A 28 SHEET 3 A 6 GLY A 110 SER A 117 -1 N TYR A 112 O ILE A 126 SHEET 4 A 6 ILE A 54 MET A 59 -1 N TYR A 56 O MET A 115 SHEET 5 A 6 LYS A 62 VAL A 68 -1 O PHE A 67 N VAL A 55 SHEET 6 A 6 GLU A 71 GLU A 72 -1 O GLU A 71 N VAL A 68 SHEET 1 B 3 MET A 36 LYS A 41 0 SHEET 2 B 3 ASN A 96 ILE A 101 -1 O ILE A 101 N MET A 36 SHEET 3 B 3 ALA A 85 LEU A 87 -1 N ARG A 86 O GLN A 100 SHEET 1 C 8 LYS A 178 ASN A 183 0 SHEET 2 C 8 PHE A 191 ASN A 200 -1 O ASN A 192 N THR A 182 SHEET 3 C 8 GLU A 150 GLY A 159 -1 N GLY A 159 O PHE A 191 SHEET 4 C 8 ASN A 138 ASP A 145 -1 N ARG A 140 O THR A 154 SHEET 5 C 8 ILE B 137 ASP B 145 1 O GLN B 139 N VAL A 143 SHEET 6 C 8 GLU B 150 GLY B 159 -1 O GLU B 152 N LEU B 142 SHEET 7 C 8 PHE B 191 ASN B 200 -1 O ILE B 199 N HIS B 151 SHEET 8 C 8 LYS B 178 ASN B 183 -1 N THR B 180 O THR B 194 SHEET 1 D 4 VAL A 174 LEU A 175 0 SHEET 2 D 4 GLU A 164 SER A 169 -1 N TRP A 167 O LEU A 175 SHEET 3 D 4 ILE A 206 ARG A 213 -1 O TYR A 208 N THR A 168 SHEET 4 D 4 GLU A 218 VAL A 225 -1 O HIS A 220 N PHE A 211 SHEET 1 E 6 LEU B 27 GLU B 31 0 SHEET 2 E 6 ALA B 121 ASN B 131 1 O LYS B 129 N VAL B 30 SHEET 3 E 6 GLY B 110 SER B 117 -1 N TYR B 112 O ILE B 126 SHEET 4 E 6 ILE B 54 GLU B 58 -1 N TYR B 56 O MET B 115 SHEET 5 E 6 ASN B 63 VAL B 68 -1 O PHE B 67 N VAL B 55 SHEET 6 E 6 GLU B 71 GLU B 72 -1 O GLU B 71 N VAL B 68 SHEET 1 F 3 MET B 36 LYS B 41 0 SHEET 2 F 3 ASN B 96 ILE B 101 -1 O ILE B 101 N MET B 36 SHEET 3 F 3 ALA B 85 LEU B 87 -1 N ARG B 86 O GLN B 100 SHEET 1 G 4 VAL B 174 LEU B 175 0 SHEET 2 G 4 GLU B 164 SER B 169 -1 N TRP B 167 O LEU B 175 SHEET 3 G 4 ILE B 206 ARG B 213 -1 O THR B 210 N ILE B 166 SHEET 4 G 4 GLU B 218 VAL B 225 -1 O LEU B 224 N PHE B 207 SSBOND 1 CYS A 40 CYS A 114 1555 1555 2.06 SSBOND 2 CYS A 155 CYS A 209 1555 1555 2.08 SSBOND 3 CYS B 40 CYS B 114 1555 1555 2.03 SSBOND 4 CYS B 155 CYS B 209 1555 1555 2.06 CISPEP 1 TYR A 160 PRO A 161 0 1.50 CISPEP 2 ASP A 215 PRO A 216 0 1.44 CISPEP 3 TYR B 160 PRO B 161 0 -2.52 CRYST1 73.080 92.700 141.720 90.00 90.00 90.00 C 2 2 21 16 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 0.013680 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010790 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007060 0.00000