HEADER IMMUNE SYSTEM 17-APR-16 5JDR TITLE STRUCTURE OF PD-L1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 18-239; COMPND 5 SYNONYM: PROGRAMMED DEATH LIGAND 1,B7 HOMOLOG 1,B7-H1; COMPND 6 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 KEYWDS IMMUNOSUPPRESSION, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.ZHOU,H.WEI REVDAT 3 13-NOV-24 5JDR 1 REMARK REVDAT 2 08-NOV-23 5JDR 1 REMARK REVDAT 1 12-APR-17 5JDR 0 JRNL AUTH F.ZHANG,H.WEI,X.WANG,Y.BAI,P.WANG,J.WU,X.JIANG,Y.WANG,H.CAI, JRNL AUTH 2 T.XU,A.ZHOU JRNL TITL STRUCTURAL BASIS OF A NOVEL PD-L1 NANOBODY FOR IMMUNE JRNL TITL 2 CHECKPOINT BLOCKADE. JRNL REF CELL DISCOV V. 3 17004 2017 JRNL REFN ESSN 2056-5968 JRNL PMID 28280600 JRNL DOI 10.1038/CELLDISC.2017.4 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12575 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) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 683 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 934 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3460 REMARK 3 BIN FREE R VALUE SET COUNT : 42 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3365 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 7 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.21000 REMARK 3 B22 (A**2) : -3.20000 REMARK 3 B33 (A**2) : 1.99000 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): 0.393 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.362 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 42.071 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.925 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.894 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3440 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3291 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4668 ; 1.188 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7580 ; 0.831 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 418 ; 6.401 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 164 ;38.148 ;24.817 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 622 ;14.329 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;14.522 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 540 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3842 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 766 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1675 ; 0.849 ; 3.885 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1674 ; 0.849 ; 3.885 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2092 ; 1.558 ; 5.825 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2093 ; 1.558 ; 5.825 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1765 ; 0.594 ; 3.950 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1766 ; 0.594 ; 3.950 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2577 ; 1.124 ; 5.878 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3364 ; 2.808 ;28.937 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3364 ; 2.808 ;28.937 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 19 A 131 4 REMARK 3 1 B 19 B 131 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1747 ; 0.44 ; 0.50 REMARK 3 MEDIUM THERMAL 1 B (A**2): 1747 ; 4.39 ; 2.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 3 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 132 A 168 4 REMARK 3 1 B 132 B 168 4 REMARK 3 2 A 176 A 228 4 REMARK 3 2 B 176 B 228 4 REMARK 3 3 A 169 A 175 6 REMARK 3 3 B 169 B 175 6 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 A (A): 1406 ; 0.51 ; 0.50 REMARK 3 LOOSE POSITIONAL 2 A (A): 102 ; 0.89 ; 5.00 REMARK 3 MEDIUM THERMAL 2 B (A**2): 1406 ; 9.58 ; 2.00 REMARK 3 LOOSE THERMAL 2 B (A**2): 102 ; 15.42 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 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 22 A 230 REMARK 3 ORIGIN FOR THE GROUP (A): 28.219 5.519 16.648 REMARK 3 T TENSOR REMARK 3 T11: 0.3654 T22: 0.0562 REMARK 3 T33: 0.0760 T12: 0.0373 REMARK 3 T13: 0.0347 T23: 0.0591 REMARK 3 L TENSOR REMARK 3 L11: 1.3710 L22: 1.4050 REMARK 3 L33: 0.6992 L12: 0.1801 REMARK 3 L13: -0.3327 L23: -0.3944 REMARK 3 S TENSOR REMARK 3 S11: 0.1539 S12: 0.2722 S13: 0.2884 REMARK 3 S21: -0.2552 S22: 0.0089 S23: 0.1320 REMARK 3 S31: -0.1364 S32: -0.0871 S33: -0.1629 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5JDR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220302. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-15 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 : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13282 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 70.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: 4Z18 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 20% PEG 3350, REMARK 280 LIQUID DIFFUSION, TEMPERATURE 295K 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 70.91500 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 70.91500 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 36.12000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.75500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.12000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.75500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 70.91500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.12000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 45.75500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 70.91500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.12000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 45.75500 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 17 REMARK 465 ALA A 18 REMARK 465 PHE A 19 REMARK 465 THR A 20 REMARK 465 VAL A 21 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 ASP A 240 REMARK 465 LYS A 241 REMARK 465 LEU A 242 REMARK 465 ALA A 243 REMARK 465 ALA A 244 REMARK 465 ALA A 245 REMARK 465 LEU A 246 REMARK 465 GLU A 247 REMARK 465 HIS A 248 REMARK 465 HIS A 249 REMARK 465 HIS A 250 REMARK 465 HIS A 251 REMARK 465 HIS A 252 REMARK 465 HIS A 253 REMARK 465 MET B 17 REMARK 465 ALA B 18 REMARK 465 GLU B 228 REMARK 465 LEU B 229 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 465 ASP B 240 REMARK 465 LYS B 241 REMARK 465 LEU B 242 REMARK 465 ALA B 243 REMARK 465 ALA B 244 REMARK 465 ALA B 245 REMARK 465 LEU B 246 REMARK 465 GLU B 247 REMARK 465 HIS B 248 REMARK 465 HIS B 249 REMARK 465 HIS B 250 REMARK 465 HIS B 251 REMARK 465 HIS B 252 REMARK 465 HIS B 253 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 46 -159.96 -100.88 REMARK 500 ASP A 103 73.42 61.85 REMARK 500 PRO A 161 -153.22 -76.18 REMARK 500 THR A 203 135.13 -33.60 REMARK 500 ASN A 204 -11.30 75.92 REMARK 500 LYS B 46 -100.98 -107.19 REMARK 500 ASP B 103 74.56 55.26 REMARK 500 ALA B 132 72.55 -118.51 REMARK 500 PRO B 161 -155.48 -80.62 REMARK 500 ARG B 186 -60.44 -91.37 REMARK 500 ASN B 204 -14.41 72.57 REMARK 500 REMARK 500 REMARK: NULL DBREF 5JDR A 18 239 UNP Q9NZQ7 PD1L1_HUMAN 18 239 DBREF 5JDR B 18 239 UNP Q9NZQ7 PD1L1_HUMAN 18 239 SEQADV 5JDR MET A 17 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR ASP A 240 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR LYS A 241 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR LEU A 242 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR ALA A 243 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR ALA A 244 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR ALA A 245 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR LEU A 246 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR GLU A 247 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR HIS A 248 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR HIS A 249 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR HIS A 250 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR HIS A 251 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR HIS A 252 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR HIS A 253 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR MET B 17 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR ASP B 240 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR LYS B 241 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR LEU B 242 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR ALA B 243 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR ALA B 244 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR ALA B 245 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR LEU B 246 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR GLU B 247 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR HIS B 248 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR HIS B 249 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR HIS B 250 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR HIS B 251 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR HIS B 252 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5JDR HIS B 253 UNP Q9NZQ7 EXPRESSION TAG SEQRES 1 A 237 MET ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL SEQRES 2 A 237 VAL GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE SEQRES 3 A 237 PRO VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL SEQRES 4 A 237 TYR TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL SEQRES 5 A 237 HIS GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR SEQRES 6 A 237 ARG GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU SEQRES 7 A 237 GLY ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN SEQRES 8 A 237 ASP ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY SEQRES 9 A 237 ALA ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO SEQRES 10 A 237 TYR ASN LYS ILE ASN GLN ARG ILE LEU VAL VAL ASP PRO SEQRES 11 A 237 VAL THR SER GLU HIS GLU LEU THR CYS GLN ALA GLU GLY SEQRES 12 A 237 TYR PRO LYS ALA GLU VAL ILE TRP THR SER SER ASP HIS SEQRES 13 A 237 GLN VAL LEU SER GLY LYS THR THR THR THR ASN SER LYS SEQRES 14 A 237 ARG GLU GLU LYS LEU PHE ASN VAL THR SER THR LEU ARG SEQRES 15 A 237 ILE ASN THR THR THR ASN GLU ILE PHE TYR CYS THR PHE SEQRES 16 A 237 ARG ARG LEU ASP PRO GLU GLU ASN HIS THR ALA GLU LEU SEQRES 17 A 237 VAL ILE PRO GLU LEU PRO LEU ALA HIS PRO PRO ASN GLU SEQRES 18 A 237 ARG THR ASP LYS LEU ALA ALA ALA LEU GLU HIS HIS HIS SEQRES 19 A 237 HIS HIS HIS SEQRES 1 B 237 MET ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL SEQRES 2 B 237 VAL GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE SEQRES 3 B 237 PRO VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL SEQRES 4 B 237 TYR TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL SEQRES 5 B 237 HIS GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR SEQRES 6 B 237 ARG GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU SEQRES 7 B 237 GLY ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN SEQRES 8 B 237 ASP ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY SEQRES 9 B 237 ALA ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO SEQRES 10 B 237 TYR ASN LYS ILE ASN GLN ARG ILE LEU VAL VAL ASP PRO SEQRES 11 B 237 VAL THR SER GLU HIS GLU LEU THR CYS GLN ALA GLU GLY SEQRES 12 B 237 TYR PRO LYS ALA GLU VAL ILE TRP THR SER SER ASP HIS SEQRES 13 B 237 GLN VAL LEU SER GLY LYS THR THR THR THR ASN SER LYS SEQRES 14 B 237 ARG GLU GLU LYS LEU PHE ASN VAL THR SER THR LEU ARG SEQRES 15 B 237 ILE ASN THR THR THR ASN GLU ILE PHE TYR CYS THR PHE SEQRES 16 B 237 ARG ARG LEU ASP PRO GLU GLU ASN HIS THR ALA GLU LEU SEQRES 17 B 237 VAL ILE PRO GLU LEU PRO LEU ALA HIS PRO PRO ASN GLU SEQRES 18 B 237 ARG THR ASP LYS LEU ALA ALA ALA LEU GLU HIS HIS HIS SEQRES 19 B 237 HIS HIS HIS FORMUL 3 HOH *7(H2 O) HELIX 1 AA1 HIS A 78 ARG A 82 5 5 HELIX 2 AA2 LYS A 89 LEU A 92 5 4 HELIX 3 AA3 LYS A 105 ALA A 109 5 5 HELIX 4 AA4 HIS B 78 ARG B 82 5 5 HELIX 5 AA5 GLN B 91 GLY B 95 5 5 SHEET 1 AA1 5 LEU A 27 GLU A 31 0 SHEET 2 AA1 5 ALA A 121 ASN A 131 1 O LYS A 129 N VAL A 30 SHEET 3 AA1 5 GLY A 110 SER A 117 -1 N TYR A 112 O ILE A 126 SHEET 4 AA1 5 ILE A 54 MET A 59 -1 N TYR A 56 O MET A 115 SHEET 5 AA1 5 LYS A 62 VAL A 68 -1 O ILE A 64 N TRP A 57 SHEET 1 AA2 3 ASN A 35 LYS A 41 0 SHEET 2 AA2 3 ASN A 96 THR A 102 -1 O LEU A 99 N ILE A 38 SHEET 3 AA2 3 ALA A 85 LEU A 87 -1 N ARG A 86 O GLN A 100 SHEET 1 AA3 8 LYS A 178 ASN A 183 0 SHEET 2 AA3 8 PHE A 191 ASN A 200 -1 O THR A 194 N THR A 180 SHEET 3 AA3 8 GLU A 150 GLY A 159 -1 N HIS A 151 O ILE A 199 SHEET 4 AA3 8 ASN A 138 ASP A 145 -1 N LEU A 142 O GLU A 152 SHEET 5 AA3 8 ILE B 137 ASP B 145 1 O GLN B 139 N VAL A 143 SHEET 6 AA3 8 GLU B 150 GLY B 159 -1 O GLN B 156 N ASN B 138 SHEET 7 AA3 8 PHE B 191 ASN B 200 -1 O ILE B 199 N HIS B 151 SHEET 8 AA3 8 LYS B 178 ASN B 183 -1 N THR B 182 O ASN B 192 SHEET 1 AA4 4 VAL A 174 LEU A 175 0 SHEET 2 AA4 4 GLU A 164 SER A 169 -1 N TRP A 167 O LEU A 175 SHEET 3 AA4 4 ILE A 206 ARG A 213 -1 O TYR A 208 N THR A 168 SHEET 4 AA4 4 GLU A 218 VAL A 225 -1 O HIS A 220 N PHE A 211 SHEET 1 AA5 6 LEU B 27 GLU B 31 0 SHEET 2 AA5 6 ALA B 121 ASN B 131 1 O LYS B 129 N TYR B 28 SHEET 3 AA5 6 GLY B 110 SER B 117 -1 N TYR B 112 O ILE B 126 SHEET 4 AA5 6 ILE B 54 MET B 59 -1 N TYR B 56 O MET B 115 SHEET 5 AA5 6 LYS B 62 VAL B 68 -1 O PHE B 67 N VAL B 55 SHEET 6 AA5 6 GLU B 71 GLU B 72 -1 O GLU B 71 N VAL B 68 SHEET 1 AA6 3 MET B 36 ILE B 38 0 SHEET 2 AA6 3 ALA B 98 ILE B 101 -1 O LEU B 99 N ILE B 38 SHEET 3 AA6 3 ALA B 85 LEU B 88 -1 N ARG B 86 O GLN B 100 SHEET 1 AA7 3 GLU B 164 SER B 169 0 SHEET 2 AA7 3 ILE B 206 ARG B 213 -1 O ARG B 212 N GLU B 164 SHEET 3 AA7 3 GLU B 218 VAL B 225 -1 O HIS B 220 N PHE B 211 SSBOND 1 CYS A 40 CYS A 114 1555 1555 2.03 SSBOND 2 CYS A 155 CYS A 209 1555 1555 2.04 SSBOND 3 CYS B 40 CYS B 114 1555 1555 2.03 SSBOND 4 CYS B 155 CYS B 209 1555 1555 2.05 CISPEP 1 TYR A 160 PRO A 161 0 -10.54 CISPEP 2 ASP A 215 PRO A 216 0 -0.38 CISPEP 3 TYR B 160 PRO B 161 0 -1.08 CISPEP 4 ASP B 215 PRO B 216 0 -3.17 CRYST1 72.240 91.510 141.830 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 0.013843 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010928 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007051 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -0.919523 -0.175797 -0.351528 47.28728 1 MTRIX2 2 0.270907 0.364509 -0.890923 19.90837 1 MTRIX3 2 0.284757 -0.914456 -0.287549 16.50082 1