PDB Short entry for 3SBW HEADER IMMUNE SYSTEM 06-JUN-11 3SBW TITLE CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE EXTRACELLULAR DOMAINS OF TITLE 2 MOUSE PD-1 MUTANT AND HUMAN PD-L1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 34-150; COMPND 5 SYNONYM: PROTEIN PD-1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1; COMPND 10 CHAIN: C; COMPND 11 FRAGMENT: UNP RESIDUES 19-239; COMPND 12 SYNONYM: PD-L1, PDCD1 LIGAND 1, PROGRAMMED DEATH LIGAND 1, B7 HOMOLOG COMPND 13 1, B7-H1; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PDCD1, PD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3) PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-3A; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3) PLYSS; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET-3A KEYWDS PD-1; PD-L1; B7-H1; PROGRAMMED DEATH-1 LIGAND 1, COMPLEX, KEYWDS 2 COSTIMULATORY, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR E.LAZAR-MOLNAR,U.A.RAMAGOPAL,E.CAO,S.G.NATHENSON,S.C.ALMO REVDAT 5 13-SEP-23 3SBW 1 SEQADV REVDAT 4 03-AUG-16 3SBW 1 REMARK REVDAT 3 25-DEC-13 3SBW 1 SEQADV REVDAT 2 18-SEP-13 3SBW 1 REMARK REVDAT 1 13-JUL-11 3SBW 0 JRNL AUTH E.LAZAR-MOLNAR,U.A.RAMAGOPAL,E.CAO,S.G.NATHENSON,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE EXTRACELLULAR JRNL TITL 2 DOMAINS OF MOUSE PD-1 MUTANT AND HUMAN PD-L1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 26756 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1339 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) : 2.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1630 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.35 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE SET COUNT : 91 REMARK 3 BIN FREE R VALUE : 0.2960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3429 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.33000 REMARK 3 B22 (A**2) : -1.72000 REMARK 3 B33 (A**2) : 2.05000 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): 0.236 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.170 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.222 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.899 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3521 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4792 ; 1.421 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 432 ; 6.423 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 168 ;37.774 ;24.821 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 598 ;16.418 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;21.329 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 545 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2665 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2166 ; 0.690 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3520 ; 1.295 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1355 ; 1.840 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1271 ; 2.969 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 3 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 34 A 145 REMARK 3 ORIGIN FOR THE GROUP (A): -5.4740 -8.1180 4.0440 REMARK 3 T TENSOR REMARK 3 T11: 0.0268 T22: 0.0624 REMARK 3 T33: 0.0978 T12: 0.0000 REMARK 3 T13: -0.0185 T23: -0.0200 REMARK 3 L TENSOR REMARK 3 L11: 3.0615 L22: 2.0291 REMARK 3 L33: 1.3895 L12: -1.1360 REMARK 3 L13: 0.1172 L23: -0.0273 REMARK 3 S TENSOR REMARK 3 S11: -0.1619 S12: -0.1397 S13: 0.1784 REMARK 3 S21: 0.1569 S22: 0.0790 S23: -0.1439 REMARK 3 S31: -0.1357 S32: 0.0797 S33: 0.0829 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 : B 34 B 145 REMARK 3 ORIGIN FOR THE GROUP (A): -14.9960 2.5790 -17.7160 REMARK 3 T TENSOR REMARK 3 T11: 0.0613 T22: 0.0978 REMARK 3 T33: 0.1411 T12: -0.0089 REMARK 3 T13: -0.0233 T23: 0.0011 REMARK 3 L TENSOR REMARK 3 L11: 3.0584 L22: 2.9170 REMARK 3 L33: 2.8297 L12: 1.1432 REMARK 3 L13: -0.0287 L23: -0.1552 REMARK 3 S TENSOR REMARK 3 S11: -0.1110 S12: 0.3169 S13: 0.0544 REMARK 3 S21: -0.3339 S22: 0.1532 S23: 0.2481 REMARK 3 S31: -0.1429 S32: -0.2117 S33: -0.0422 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 : C 18 C 229 REMARK 3 ORIGIN FOR THE GROUP (A): -8.9860 -11.5460 -49.9210 REMARK 3 T TENSOR REMARK 3 T11: 0.3029 T22: 0.2798 REMARK 3 T33: 0.2441 T12: 0.0148 REMARK 3 T13: 0.0208 T23: -0.0376 REMARK 3 L TENSOR REMARK 3 L11: 2.0882 L22: 0.0340 REMARK 3 L33: 6.1208 L12: -0.0807 REMARK 3 L13: -3.3147 L23: 0.0757 REMARK 3 S TENSOR REMARK 3 S11: -0.1196 S12: 0.1244 S13: 0.0595 REMARK 3 S21: 0.0630 S22: 0.0344 S23: -0.0621 REMARK 3 S31: 0.2824 S32: -0.5542 S33: 0.0852 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 U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 3SBW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1000066014. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-AUG-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.071 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26816 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.72900 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: MOLREP REMARK 200 STARTING MODEL: 1NPU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CITRATE PH 5, 20% PEG REMARK 280 8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K, PH 4.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 28.38900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 80.43150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.42150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 80.43150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.38900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.42150 REMARK 290 SMTRY3 4 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 300 REMARK: THE CRYSTAL CORRESPONDING TO THIS PARTICULAR PDB HAS THE REMARK 300 CORRECT 1:1 PD-1:PD-L1 STRUCTURE, AS WELL AS AN ADDITIONAL REMARK 300 ARTIFACTUAL PD-1 THAT IS INCORPORATED INTO THE LATTICE. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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: 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 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 GLU A 146 REMARK 465 ARG A 147 REMARK 465 ILE A 148 REMARK 465 LEU A 149 REMARK 465 GLU A 150 REMARK 465 GLU B 146 REMARK 465 ARG B 147 REMARK 465 ILE B 148 REMARK 465 LEU B 149 REMARK 465 GLU B 150 REMARK 465 LYS C 185 REMARK 465 ARG C 186 REMARK 465 GLU C 187 REMARK 465 GLU C 188 REMARK 465 PRO C 230 REMARK 465 LEU C 231 REMARK 465 ALA C 232 REMARK 465 HIS C 233 REMARK 465 PRO C 234 REMARK 465 PRO C 235 REMARK 465 ASN C 236 REMARK 465 GLU C 237 REMARK 465 ARG C 238 REMARK 465 THR C 239 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 C 82 CG CD NE CZ NH1 NH2 REMARK 470 LEU C 229 CG CD1 CD2 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 THR A 76 135.02 -38.78 REMARK 500 GLN A 91 -5.75 -158.47 REMARK 500 ARG A 103 -36.42 74.46 REMARK 500 ASN B 74 38.24 72.14 REMARK 500 GLN B 91 -6.40 -147.61 REMARK 500 ARG B 103 -27.45 73.86 REMARK 500 GLU C 45 -72.23 -75.99 REMARK 500 HIS C 69 19.67 48.86 REMARK 500 TYR C 81 62.19 -108.04 REMARK 500 TYR C 118 76.23 -155.90 REMARK 500 ASN C 204 -4.57 82.52 REMARK 500 REMARK 500 REMARK: NULL DBREF 3SBW A 34 150 UNP Q02242 PDCD1_MOUSE 34 150 DBREF 3SBW B 34 150 UNP Q02242 PDCD1_MOUSE 34 150 DBREF 3SBW C 19 239 UNP Q9NZQ7 PD1L1_HUMAN 19 239 SEQADV 3SBW SER A 83 UNP Q02242 CYS 83 ENGINEERED MUTATION SEQADV 3SBW LEU A 132 UNP Q02242 ALA 132 ENGINEERED MUTATION SEQADV 3SBW SER B 83 UNP Q02242 CYS 83 ENGINEERED MUTATION SEQADV 3SBW LEU B 132 UNP Q02242 ALA 132 ENGINEERED MUTATION SEQADV 3SBW MET C 18 UNP Q9NZQ7 INITIATING METHIONINE SEQRES 1 A 117 SER LEU THR PHE TYR PRO ALA TRP LEU THR VAL SER GLU SEQRES 2 A 117 GLY ALA ASN ALA THR PHE THR CYS SER LEU SER ASN TRP SEQRES 3 A 117 SER GLU ASP LEU MET LEU ASN TRP ASN ARG LEU SER PRO SEQRES 4 A 117 SER ASN GLN THR GLU LYS GLN ALA ALA PHE SER ASN GLY SEQRES 5 A 117 LEU SER GLN PRO VAL GLN ASP ALA ARG PHE GLN ILE ILE SEQRES 6 A 117 GLN LEU PRO ASN ARG HIS ASP PHE HIS MET ASN ILE LEU SEQRES 7 A 117 ASP THR ARG ARG ASN ASP SER GLY ILE TYR LEU CYS GLY SEQRES 8 A 117 ALA ILE SER LEU HIS PRO LYS LEU LYS ILE GLU GLU SER SEQRES 9 A 117 PRO GLY ALA GLU LEU VAL VAL THR GLU ARG ILE LEU GLU SEQRES 1 B 117 SER LEU THR PHE TYR PRO ALA TRP LEU THR VAL SER GLU SEQRES 2 B 117 GLY ALA ASN ALA THR PHE THR CYS SER LEU SER ASN TRP SEQRES 3 B 117 SER GLU ASP LEU MET LEU ASN TRP ASN ARG LEU SER PRO SEQRES 4 B 117 SER ASN GLN THR GLU LYS GLN ALA ALA PHE SER ASN GLY SEQRES 5 B 117 LEU SER GLN PRO VAL GLN ASP ALA ARG PHE GLN ILE ILE SEQRES 6 B 117 GLN LEU PRO ASN ARG HIS ASP PHE HIS MET ASN ILE LEU SEQRES 7 B 117 ASP THR ARG ARG ASN ASP SER GLY ILE TYR LEU CYS GLY SEQRES 8 B 117 ALA ILE SER LEU HIS PRO LYS LEU LYS ILE GLU GLU SER SEQRES 9 B 117 PRO GLY ALA GLU LEU VAL VAL THR GLU ARG ILE LEU GLU SEQRES 1 C 222 MET PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL SEQRES 2 C 222 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO SEQRES 3 C 222 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR SEQRES 4 C 222 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS SEQRES 5 C 222 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG SEQRES 6 C 222 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY SEQRES 7 C 222 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP SEQRES 8 C 222 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA SEQRES 9 C 222 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR SEQRES 10 C 222 ASN LYS ILE ASN GLN ARG ILE LEU VAL VAL ASP PRO VAL SEQRES 11 C 222 THR SER GLU HIS GLU LEU THR CYS GLN ALA GLU GLY TYR SEQRES 12 C 222 PRO LYS ALA GLU VAL ILE TRP THR SER SER ASP HIS GLN SEQRES 13 C 222 VAL LEU SER GLY LYS THR THR THR THR ASN SER LYS ARG SEQRES 14 C 222 GLU GLU LYS LEU PHE ASN VAL THR SER THR LEU ARG ILE SEQRES 15 C 222 ASN THR THR THR ASN GLU ILE PHE TYR CYS THR PHE ARG SEQRES 16 C 222 ARG LEU ASP PRO GLU GLU ASN HIS THR ALA GLU LEU VAL SEQRES 17 C 222 ILE PRO GLU LEU PRO LEU ALA HIS PRO PRO ASN GLU ARG SEQRES 18 C 222 THR FORMUL 4 HOH *130(H2 O) HELIX 1 1 ARG A 114 SER A 118 5 5 HELIX 2 2 ARG B 114 SER B 118 5 5 HELIX 3 3 HIS C 78 ARG C 82 5 5 HELIX 4 4 LEU C 88 SER C 93 1 6 HELIX 5 5 LYS C 105 ALA C 109 5 5 SHEET 1 A 4 LEU A 35 TYR A 38 0 SHEET 2 A 4 ALA A 50 LEU A 56 -1 O THR A 53 N TYR A 38 SHEET 3 A 4 ASP A 105 ILE A 110 -1 O PHE A 106 N CYS A 54 SHEET 4 A 4 PHE A 95 GLN A 99 -1 N ILE A 98 O HIS A 107 SHEET 1 B 6 TRP A 41 SER A 45 0 SHEET 2 B 6 ALA A 140 THR A 145 1 O GLU A 141 N LEU A 42 SHEET 3 B 6 GLY A 119 SER A 127 -1 N TYR A 121 O ALA A 140 SHEET 4 B 6 MET A 64 ARG A 69 -1 N ASN A 66 O GLY A 124 SHEET 5 B 6 GLU A 77 SER A 83 -1 O GLN A 79 N TRP A 67 SHEET 6 B 6 LEU A 86 PRO A 89 -1 O GLN A 88 N ALA A 81 SHEET 1 C 4 TRP A 41 SER A 45 0 SHEET 2 C 4 ALA A 140 THR A 145 1 O GLU A 141 N LEU A 42 SHEET 3 C 4 GLY A 119 SER A 127 -1 N TYR A 121 O ALA A 140 SHEET 4 C 4 LYS A 133 GLU A 136 -1 O GLU A 135 N ALA A 125 SHEET 1 D 4 LEU B 35 TYR B 38 0 SHEET 2 D 4 ALA B 50 LEU B 56 -1 O THR B 53 N TYR B 38 SHEET 3 D 4 ASP B 105 ILE B 110 -1 O PHE B 106 N CYS B 54 SHEET 4 D 4 PHE B 95 GLN B 99 -1 N GLN B 96 O ASN B 109 SHEET 1 E 6 TRP B 41 SER B 45 0 SHEET 2 E 6 ALA B 140 THR B 145 1 O GLU B 141 N LEU B 42 SHEET 3 E 6 GLY B 119 SER B 127 -1 N GLY B 119 O LEU B 142 SHEET 4 E 6 MET B 64 LEU B 70 -1 N ASN B 66 O GLY B 124 SHEET 5 E 6 THR B 76 SER B 83 -1 O GLN B 79 N TRP B 67 SHEET 6 E 6 LEU B 86 PRO B 89 -1 O GLN B 88 N ALA B 81 SHEET 1 F 4 TRP B 41 SER B 45 0 SHEET 2 F 4 ALA B 140 THR B 145 1 O GLU B 141 N LEU B 42 SHEET 3 F 4 GLY B 119 SER B 127 -1 N GLY B 119 O LEU B 142 SHEET 4 F 4 LYS B 133 GLU B 136 -1 O LYS B 133 N SER B 127 SHEET 1 G 6 LEU C 27 GLU C 31 0 SHEET 2 G 6 ALA C 121 ASN C 131 1 O LYS C 129 N TYR C 28 SHEET 3 G 6 GLY C 110 SER C 117 -1 N TYR C 112 O ILE C 126 SHEET 4 G 6 ILE C 54 MET C 59 -1 N TYR C 56 O MET C 115 SHEET 5 G 6 LYS C 62 VAL C 68 -1 O PHE C 67 N VAL C 55 SHEET 6 G 6 GLU C 71 GLU C 72 -1 O GLU C 71 N VAL C 68 SHEET 1 H 3 MET C 36 LYS C 41 0 SHEET 2 H 3 ASN C 96 ILE C 101 -1 O ILE C 101 N MET C 36 SHEET 3 H 3 ALA C 85 LEU C 87 -1 N ARG C 86 O GLN C 100 SHEET 1 I 4 ASN C 138 ASP C 145 0 SHEET 2 I 4 GLU C 150 GLY C 159 -1 O GLU C 150 N VAL C 144 SHEET 3 I 4 PHE C 191 ASN C 200 -1 O ILE C 199 N HIS C 151 SHEET 4 I 4 LYS C 178 ASN C 183 -1 N THR C 180 O THR C 194 SHEET 1 J 4 VAL C 174 LEU C 175 0 SHEET 2 J 4 GLU C 164 SER C 169 -1 N TRP C 167 O LEU C 175 SHEET 3 J 4 ILE C 206 ARG C 213 -1 O ARG C 212 N GLU C 164 SHEET 4 J 4 GLU C 218 VAL C 225 -1 O HIS C 220 N PHE C 211 SSBOND 1 CYS A 54 CYS A 123 1555 1555 2.08 SSBOND 2 CYS B 54 CYS B 123 1555 1555 2.05 SSBOND 3 CYS C 40 CYS C 114 1555 1555 2.05 SSBOND 4 CYS C 155 CYS C 209 1555 1555 2.05 CISPEP 1 TYR A 38 PRO A 39 0 1.49 CISPEP 2 HIS A 129 PRO A 130 0 5.45 CISPEP 3 TYR B 38 PRO B 39 0 -2.78 CISPEP 4 HIS B 129 PRO B 130 0 -5.22 CISPEP 5 TYR C 160 PRO C 161 0 1.27 CISPEP 6 ASP C 215 PRO C 216 0 -8.04 CRYST1 56.778 62.843 160.863 90.00 90.00 90.00 P 21 21 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 0.017612 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015913 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006216 0.00000