PDB Short entry for 3BIK HEADER IMMUNE SYSTEM 30-NOV-07 3BIK TITLE CRYSTAL STRUCTURE OF THE PD-1/PD-L1 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1; COMPND 3 CHAIN: A; 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; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PROGRAMMED CELL DEATH PROTEIN 1; COMPND 10 CHAIN: B, C; COMPND 11 FRAGMENT: EXTRACELLULAR DOMAIN; COMPND 12 SYNONYM: PROTEIN PD-1, MPD-1, CD279 ANTIGEN; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: 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; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 14 ORGANISM_TAXID: 10090; SOURCE 15 GENE: PDCD1, PD1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2 (DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PLM1 KEYWDS CO-STIMULATION, RECEPTOR-LIGAND COMPLEX, IMMUNOGLOBULIN-LIKE BETA- KEYWDS 2 SANDWICH, T CELL, B CELL, PROGRAMMED DEATH, IMMUNE SYSTEM, KEYWDS 3 TRANSMEMBRANE, INHIBITORY RECEPTOR, GLYCOPROTEIN, IMMUNOGLOBULIN KEYWDS 4 DOMAIN, APOPTOSIS 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 6 30-AUG-23 3BIK 1 REMARK REVDAT 5 20-OCT-21 3BIK 1 REMARK SEQADV REVDAT 4 13-JUL-11 3BIK 1 VERSN REVDAT 3 24-FEB-09 3BIK 1 VERSN REVDAT 2 11-NOV-08 3BIK 1 JRNL REVDAT 1 26-FEB-08 3BIK 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. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 17225 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) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 898 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) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.72 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1050 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 52 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3562 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 76 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.96000 REMARK 3 B22 (A**2) : -1.41000 REMARK 3 B33 (A**2) : -0.55000 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): 0.826 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.343 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.888 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3649 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4960 ; 1.400 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 443 ; 6.569 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 178 ;38.473 ;24.494 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 622 ;17.421 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;17.544 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 556 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2776 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1294 ; 0.208 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2364 ; 0.309 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 134 ; 0.129 ; 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): 66 ; 0.171 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.207 ; 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): 2230 ; 2.322 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3622 ; 4.044 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1419 ; 2.842 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1338 ; 4.817 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 3BIK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045564. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-05 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.00 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) : 0.97943 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 : 17320 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.43400 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: PDB ENTRY 1NPU FOR CHAINS B,C, EARLY MODEL FOR REMARK 200 CHAIN A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 200MM NH4H2PO4, PH 6.00, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 28.23000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 79.96000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.97000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 79.96000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.23000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.97000 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 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: 1730 ANGSTROM**2 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 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: 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 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 PRO A 230 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 ALA B 24 REMARK 465 LEU B 25 REMARK 465 GLU B 26 REMARK 465 VAL B 27 REMARK 465 PRO B 28 REMARK 465 ASN B 29 REMARK 465 GLY B 30 REMARK 465 PRO B 31 REMARK 465 TRP B 32 REMARK 465 LEU B 149 REMARK 465 GLU B 150 REMARK 465 THR B 151 REMARK 465 SER B 152 REMARK 465 THR B 153 REMARK 465 ARG B 154 REMARK 465 TYR B 155 REMARK 465 PRO B 156 REMARK 465 SER B 157 REMARK 465 ALA C 24 REMARK 465 LEU C 25 REMARK 465 GLU C 26 REMARK 465 VAL C 27 REMARK 465 PRO C 28 REMARK 465 ASN C 29 REMARK 465 ILE C 148 REMARK 465 LEU C 149 REMARK 465 GLU C 150 REMARK 465 THR C 151 REMARK 465 SER C 152 REMARK 465 THR C 153 REMARK 465 ARG C 154 REMARK 465 TYR C 155 REMARK 465 PRO C 156 REMARK 465 SER C 157 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 -70.62 -6.82 REMARK 500 ASP A 61 -3.25 70.49 REMARK 500 SER A 80 26.17 -62.58 REMARK 500 TYR A 118 85.70 -159.66 REMARK 500 PRO A 146 33.34 -80.71 REMARK 500 VAL A 147 -50.08 -123.13 REMARK 500 PRO A 161 -156.73 -70.95 REMARK 500 HIS A 172 34.57 70.50 REMARK 500 GLU A 187 -109.07 -106.84 REMARK 500 GLU A 188 -109.86 -137.83 REMARK 500 ASP A 215 65.59 60.09 REMARK 500 PRO A 227 -168.13 -70.87 REMARK 500 ASN B 74 15.36 95.85 REMARK 500 GLN B 91 -12.76 -146.82 REMARK 500 ASN B 102 -36.43 -30.53 REMARK 500 ARG B 103 -28.54 77.77 REMARK 500 LEU C 128 56.89 -119.17 REMARK 500 LYS C 133 120.26 -170.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3BIS RELATED DB: PDB DBREF 3BIK A 18 239 UNP Q9NZQ7 PD1L1_HUMAN 18 239 DBREF 3BIK B 25 157 UNP Q02242 PDCD1_MOUSE 25 157 DBREF 3BIK C 25 157 UNP Q02242 PDCD1_MOUSE 25 157 SEQADV 3BIK ALA B 24 UNP Q02242 EXPRESSION TAG SEQADV 3BIK SER B 83 UNP Q02242 CYS 83 ENGINEERED MUTATION SEQADV 3BIK ALA C 24 UNP Q02242 EXPRESSION TAG SEQADV 3BIK SER C 83 UNP Q02242 CYS 83 ENGINEERED MUTATION 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 134 ALA LEU GLU VAL PRO ASN GLY PRO TRP ARG SER LEU THR SEQRES 2 B 134 PHE TYR PRO ALA TRP LEU THR VAL SER GLU GLY ALA ASN SEQRES 3 B 134 ALA THR PHE THR CYS SER LEU SER ASN TRP SER GLU ASP SEQRES 4 B 134 LEU MET LEU ASN TRP ASN ARG LEU SER PRO SER ASN GLN SEQRES 5 B 134 THR GLU LYS GLN ALA ALA PHE SER ASN GLY LEU SER GLN SEQRES 6 B 134 PRO VAL GLN ASP ALA ARG PHE GLN ILE ILE GLN LEU PRO SEQRES 7 B 134 ASN ARG HIS ASP PHE HIS MET ASN ILE LEU ASP THR ARG SEQRES 8 B 134 ARG ASN ASP SER GLY ILE TYR LEU CYS GLY ALA ILE SER SEQRES 9 B 134 LEU HIS PRO LYS ALA LYS ILE GLU GLU SER PRO GLY ALA SEQRES 10 B 134 GLU LEU VAL VAL THR GLU ARG ILE LEU GLU THR SER THR SEQRES 11 B 134 ARG TYR PRO SER SEQRES 1 C 134 ALA LEU GLU VAL PRO ASN GLY PRO TRP ARG SER LEU THR SEQRES 2 C 134 PHE TYR PRO ALA TRP LEU THR VAL SER GLU GLY ALA ASN SEQRES 3 C 134 ALA THR PHE THR CYS SER LEU SER ASN TRP SER GLU ASP SEQRES 4 C 134 LEU MET LEU ASN TRP ASN ARG LEU SER PRO SER ASN GLN SEQRES 5 C 134 THR GLU LYS GLN ALA ALA PHE SER ASN GLY LEU SER GLN SEQRES 6 C 134 PRO VAL GLN ASP ALA ARG PHE GLN ILE ILE GLN LEU PRO SEQRES 7 C 134 ASN ARG HIS ASP PHE HIS MET ASN ILE LEU ASP THR ARG SEQRES 8 C 134 ARG ASN ASP SER GLY ILE TYR LEU CYS GLY ALA ILE SER SEQRES 9 C 134 LEU HIS PRO LYS ALA LYS ILE GLU GLU SER PRO GLY ALA SEQRES 10 C 134 GLU LEU VAL VAL THR GLU ARG ILE LEU GLU THR SER THR SEQRES 11 C 134 ARG TYR PRO SER HET GOL C 301 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *76(H2 O) HELIX 1 1 HIS A 78 ARG A 82 5 5 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 ARG B 114 SER B 118 5 5 HELIX 5 5 ARG C 114 SER C 118 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 ASN A 131 N VAL A 30 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 ALA A 97 N CYS A 40 SHEET 3 B 3 ALA A 85 LEU A 87 -1 N ARG A 86 O GLN A 100 SHEET 1 C 4 ASN A 138 ASP A 145 0 SHEET 2 C 4 GLU A 150 GLY A 159 -1 O GLN A 156 N ASN A 138 SHEET 3 C 4 PHE A 191 ASN A 200 -1 O ILE A 199 N HIS A 151 SHEET 4 C 4 LYS A 178 ASN A 183 -1 N THR A 182 O ASN A 192 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 4 LEU B 35 TYR B 38 0 SHEET 2 E 4 ALA B 50 LEU B 56 -1 O SER B 55 N THR B 36 SHEET 3 E 4 ASP B 105 ILE B 110 -1 O MET B 108 N PHE B 52 SHEET 4 E 4 PHE B 95 GLN B 99 -1 N GLN B 96 O ASN B 109 SHEET 1 F 6 TRP B 41 SER B 45 0 SHEET 2 F 6 ALA B 140 THR B 145 1 O GLU B 141 N LEU B 42 SHEET 3 F 6 GLY B 119 SER B 127 -1 N GLY B 119 O LEU B 142 SHEET 4 F 6 MET B 64 LEU B 70 -1 N ASN B 66 O GLY B 124 SHEET 5 F 6 THR B 76 SER B 83 -1 O ALA B 80 N TRP B 67 SHEET 6 F 6 LEU B 86 PRO B 89 -1 O GLN B 88 N ALA B 81 SHEET 1 G 4 TRP B 41 SER B 45 0 SHEET 2 G 4 ALA B 140 THR B 145 1 O GLU B 141 N LEU B 42 SHEET 3 G 4 GLY B 119 SER B 127 -1 N GLY B 119 O LEU B 142 SHEET 4 G 4 LYS B 133 GLU B 136 -1 O GLU B 135 N ALA B 125 SHEET 1 H 4 LEU C 35 TYR C 38 0 SHEET 2 H 4 ALA C 50 LEU C 56 -1 O THR C 53 N TYR C 38 SHEET 3 H 4 ASP C 105 ILE C 110 -1 O MET C 108 N PHE C 52 SHEET 4 H 4 PHE C 95 GLN C 99 -1 N GLN C 96 O ASN C 109 SHEET 1 I 6 TRP C 41 SER C 45 0 SHEET 2 I 6 ALA C 140 THR C 145 1 O GLU C 141 N LEU C 42 SHEET 3 I 6 GLY C 119 ILE C 126 -1 N TYR C 121 O ALA C 140 SHEET 4 I 6 MET C 64 ARG C 69 -1 N ASN C 68 O LEU C 122 SHEET 5 I 6 GLU C 77 SER C 83 -1 O GLN C 79 N TRP C 67 SHEET 6 I 6 LEU C 86 PRO C 89 -1 O GLN C 88 N ALA C 81 SHEET 1 J 4 TRP C 41 SER C 45 0 SHEET 2 J 4 ALA C 140 THR C 145 1 O GLU C 141 N LEU C 42 SHEET 3 J 4 GLY C 119 ILE C 126 -1 N TYR C 121 O ALA C 140 SHEET 4 J 4 ILE C 134 GLU C 136 -1 O GLU C 135 N ALA C 125 SSBOND 1 CYS A 40 CYS A 114 1555 1555 2.05 SSBOND 2 CYS A 155 CYS A 209 1555 1555 2.05 SSBOND 3 CYS B 54 CYS B 123 1555 1555 2.08 SSBOND 4 CYS C 54 CYS C 123 1555 1555 2.08 CISPEP 1 TYR A 160 PRO A 161 0 -4.94 CISPEP 2 ASP A 215 PRO A 216 0 -11.10 CISPEP 3 TYR B 38 PRO B 39 0 -3.68 CISPEP 4 HIS B 129 PRO B 130 0 -0.01 CISPEP 5 TYR C 38 PRO C 39 0 3.74 CISPEP 6 HIS C 129 PRO C 130 0 -20.56 SITE 1 AC1 4 LEU C 70 PRO C 72 GLY C 119 ILE C 120 CRYST1 56.460 63.940 159.920 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 0.017710 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015640 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006250 0.00000