HEADER IMMUNE SYSTEM 08-MAY-19 6K0Y TITLE STUDY OF THE INTERACTIONS OF A NOVEL MONOCLONAL ANTIBODY, MAB059C, TITLE 2 WITH THE HPD-1 RECEPTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTIBODY HEAVY CHAIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ANTIBODY LIGHT CHAIN; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PROGRAMMED CELL DEATH PROTEIN 1; COMPND 11 CHAIN: C; COMPND 12 SYNONYM: HPD-1; 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 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 6 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM_CELL_LINE: HEK293; SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606; SOURCE 21 GENE: PDCD1, PD1; SOURCE 22 EXPRESSION_SYSTEM: ESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR SOURCE 23 PPPARG4; SOURCE 24 EXPRESSION_SYSTEM_TAXID: 1182032; SOURCE 25 EXPRESSION_SYSTEM_VARIANT: BL21 KEYWDS PD-1 COMPLEX, IMMUNE CHECKPOINT, INHIBITOR, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR J.X.LIU,G.Q.WANG REVDAT 2 22-NOV-23 6K0Y 1 REMARK REVDAT 1 11-DEC-19 6K0Y 0 JRNL AUTH J.LIU,G.WANG,L.LIU,R.WU,Y.WU,C.FANG,X.ZHOU,J.JIAO,Y.GU, JRNL AUTH 2 H.ZHOU,Z.XIE,Z.SUN,D.CHEN,K.DAI,D.WANG,W.TANG,T.T.C.YANG JRNL TITL STUDY OF THE INTERACTIONS OF A NOVEL MONOCLONAL ANTIBODY, JRNL TITL 2 MAB059C, WITH THE HPD-1 RECEPTOR. JRNL REF SCI REP V. 9 17830 2019 JRNL REFN ESSN 2045-2322 JRNL PMID 31780710 JRNL DOI 10.1038/S41598-019-54231-W REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 59148 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3095 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3633 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.1910 REMARK 3 BIN FREE R VALUE SET COUNT : 199 REMARK 3 BIN FREE R VALUE : 0.2580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4176 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 492 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.48000 REMARK 3 B22 (A**2) : 1.14000 REMARK 3 B33 (A**2) : 0.34000 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): 0.156 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.105 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.339 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4287 ; 0.004 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3846 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5830 ; 1.246 ; 1.650 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8964 ; 1.194 ; 1.570 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 544 ; 7.379 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 199 ;31.137 ;22.111 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 681 ;12.041 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;16.494 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 576 ; 0.046 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4795 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 888 ; 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): 2185 ; 1.046 ; 1.654 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2184 ; 1.045 ; 1.653 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2726 ; 1.536 ; 2.479 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2727 ; 1.536 ; 2.480 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2102 ; 1.098 ; 1.805 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2103 ; 1.097 ; 1.806 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3105 ; 1.455 ; 2.616 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4585 ; 2.796 ;20.014 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4485 ; 2.568 ;19.605 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 8133 ; 0.869 ; 3.000 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 : 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 6K0Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1300012087. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 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) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : Q315R REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 R CDTE 300K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62244 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 41.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.16600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 1.06100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 5GGS REMARK 200 REMARK 200 REMARK: SINGLE LONG SHAPE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NACL , 0.1M TRIS PH 8, 14% PEG REMARK 280 4K, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 19.97600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.86150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.29500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.86150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.97600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.29500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 CYS B 214 REMARK 465 LEU C 25 REMARK 465 ASP C 26 REMARK 465 SER C 27 REMARK 465 PRO C 28 REMARK 465 ASP C 29 REMARK 465 ARG C 30 REMARK 465 PRO C 31 REMARK 465 TRP C 32 REMARK 465 ALA C 149 REMARK 465 GLU C 150 REMARK 465 VAL C 151 REMARK 465 PRO C 152 REMARK 465 THR C 153 REMARK 465 ALA C 154 REMARK 465 HIS C 155 REMARK 465 PRO C 156 REMARK 465 SER C 157 REMARK 465 PRO C 158 REMARK 465 SER C 159 REMARK 465 PRO C 160 REMARK 465 ARG C 161 REMARK 465 PRO C 162 REMARK 465 ALA C 163 REMARK 465 GLY C 164 REMARK 465 GLN C 165 REMARK 465 PHE C 166 REMARK 465 GLN C 167 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 ASN C 58 CG OD1 ND2 REMARK 470 THR C 59 OG1 CG2 REMARK 470 SER C 60 OG REMARK 470 ARG C 96 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 148 CG CD NE CZ NH1 NH2 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 SER A 15 -11.55 88.23 REMARK 500 ASP A 150 62.24 70.56 REMARK 500 ASN B 30 -127.54 55.47 REMARK 500 ALA B 51 -41.38 70.50 REMARK 500 ALA B 84 170.42 177.57 REMARK 500 ARG C 112 70.51 50.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 629 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH B 630 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH B 631 DISTANCE = 7.09 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 201 DBREF 6K0Y A 1 218 PDB 6K0Y 6K0Y 1 218 DBREF 6K0Y B 1 214 PDB 6K0Y 6K0Y 1 214 DBREF 6K0Y C 25 167 UNP Q15116 PDCD1_HUMAN 25 167 SEQADV 6K0Y SER C 93 UNP Q15116 CYS 93 ENGINEERED MUTATION SEQRES 1 A 218 GLN VAL GLN LEU GLN GLU SER GLY PRO GLY LEU VAL LYS SEQRES 2 A 218 PRO SER GLU THR LEU SER LEU THR CYS ALA VAL SER GLY SEQRES 3 A 218 HIS SER ILE ARG GLY SER TYR PHE TRP GLY TRP ILE ARG SEQRES 4 A 218 GLN PRO PRO GLY ARG GLY LEU GLU TRP ILE GLY SER ILE SEQRES 5 A 218 TYR HIS SER GLY SER THR TYR THR ASN PRO SER LEU LYS SEQRES 6 A 218 SER ARG ALA THR ILE SER VAL ASP THR SER LYS ASN GLN SEQRES 7 A 218 PHE SER LEU LYS LEU ASN SER VAL THR ALA ALA ASP THR SEQRES 8 A 218 ALA VAL TYR TYR CYS ALA ARG ASP LEU ASP ILE ALA THR SEQRES 9 A 218 THR ARG ASP TYR TRP GLY GLN GLY THR LEU VAL THR VAL SEQRES 10 A 218 SER SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU SEQRES 11 A 218 ALA PRO CYS SER ARG SER THR SER GLU SER THR ALA ALA SEQRES 12 A 218 LEU GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL SEQRES 13 A 218 THR VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL SEQRES 14 A 218 HIS THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SEQRES 15 A 218 SER LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU SEQRES 16 A 218 GLY THR LYS THR TYR THR CYS ASN VAL ASP HIS LYS PRO SEQRES 17 A 218 SER ASN THR LYS VAL ASP LYS ARG VAL GLU SEQRES 1 B 214 ASP ILE GLN LEU THR GLN SER PRO SER PHE LEU SER ALA SEQRES 2 B 214 SER VAL GLY ASP ARG VAL THR ILE ILE CYS ARG ALA SER SEQRES 3 B 214 GLN GLY ILE ASN ASN TYR LEU ALA TRP TYR GLN GLN LYS SEQRES 4 B 214 PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR ALA ALA SER SEQRES 5 B 214 THR LEU GLN SER GLY VAL PRO SER ARG PHE SER GLY SER SEQRES 6 B 214 GLY SER GLY THR GLU PHE THR LEU THR ILE SER SER LEU SEQRES 7 B 214 GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN GLN LEU SEQRES 8 B 214 ASP SER TYR PRO ARG THR PHE GLY GLN GLY THR LYS VAL SEQRES 9 B 214 GLU ILE LYS ARG THR VAL ALA ALA PRO SER VAL PHE ILE SEQRES 10 B 214 PHE PRO PRO SER ASP GLU GLN LEU LYS SER GLY THR ALA SEQRES 11 B 214 SER VAL VAL CYS LEU LEU ASN ASN PHE TYR PRO ARG GLU SEQRES 12 B 214 ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA LEU GLN SER SEQRES 13 B 214 GLY ASN SER GLN GLU SER VAL THR GLU GLN ASP SER LYS SEQRES 14 B 214 ASP SER THR TYR SER LEU SER SER THR LEU THR LEU SER SEQRES 15 B 214 LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR ALA CYS GLU SEQRES 16 B 214 VAL THR HIS GLN GLY LEU SER SER PRO VAL THR LYS SER SEQRES 17 B 214 PHE ASN ARG GLY GLU CYS SEQRES 1 C 143 LEU ASP SER PRO ASP ARG PRO TRP ASN PRO PRO THR PHE SEQRES 2 C 143 SER PRO ALA LEU LEU VAL VAL THR GLU GLY ASP ASN ALA SEQRES 3 C 143 THR PHE THR CYS SER PHE SER ASN THR SER GLU SER PHE SEQRES 4 C 143 VAL LEU ASN TRP TYR ARG MET SER PRO SER ASN GLN THR SEQRES 5 C 143 ASP LYS LEU ALA ALA PHE PRO GLU ASP ARG SER GLN PRO SEQRES 6 C 143 GLY GLN ASP SER ARG PHE ARG VAL THR GLN LEU PRO ASN SEQRES 7 C 143 GLY ARG ASP PHE HIS MET SER VAL VAL ARG ALA ARG ARG SEQRES 8 C 143 ASN ASP SER GLY THR TYR LEU CYS GLY ALA ILE SER LEU SEQRES 9 C 143 ALA PRO LYS ALA GLN ILE LYS GLU SER LEU ARG ALA GLU SEQRES 10 C 143 LEU ARG VAL THR GLU ARG ARG ALA GLU VAL PRO THR ALA SEQRES 11 C 143 HIS PRO SER PRO SER PRO ARG PRO ALA GLY GLN PHE GLN HET EDO A 501 4 HET EDO A 502 4 HET EDO B 301 4 HET EDO C 201 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 4 EDO 4(C2 H6 O2) FORMUL 8 HOH *492(H2 O) HELIX 1 AA1 PRO A 62 LYS A 65 5 4 HELIX 2 AA2 THR A 74 LYS A 76 5 3 HELIX 3 AA3 THR A 87 THR A 91 5 5 HELIX 4 AA4 SER A 162 ALA A 164 5 3 HELIX 5 AA5 SER A 193 LEU A 195 5 3 HELIX 6 AA6 LYS A 207 ASN A 210 5 4 HELIX 7 AA7 GLN B 79 PHE B 83 5 5 HELIX 8 AA8 SER B 121 LYS B 126 1 6 HELIX 9 AA9 LYS B 183 LYS B 188 1 6 HELIX 10 AB1 PRO C 83 SER C 87 5 5 HELIX 11 AB2 ARG C 114 SER C 118 5 5 SHEET 1 AA1 4 GLN A 3 SER A 7 0 SHEET 2 AA1 4 LEU A 18 SER A 25 -1 O SER A 25 N GLN A 3 SHEET 3 AA1 4 GLN A 78 LEU A 83 -1 O PHE A 79 N CYS A 22 SHEET 4 AA1 4 ALA A 68 ASP A 73 -1 N THR A 69 O LYS A 82 SHEET 1 AA2 6 LEU A 11 VAL A 12 0 SHEET 2 AA2 6 THR A 113 VAL A 117 1 O THR A 116 N VAL A 12 SHEET 3 AA2 6 ALA A 92 ARG A 98 -1 N TYR A 94 O THR A 113 SHEET 4 AA2 6 TRP A 35 GLN A 40 -1 N ILE A 38 O TYR A 95 SHEET 5 AA2 6 GLU A 47 ILE A 52 -1 O ILE A 49 N TRP A 37 SHEET 6 AA2 6 THR A 58 THR A 60 -1 O TYR A 59 N SER A 51 SHEET 1 AA3 4 LEU A 11 VAL A 12 0 SHEET 2 AA3 4 THR A 113 VAL A 117 1 O THR A 116 N VAL A 12 SHEET 3 AA3 4 ALA A 92 ARG A 98 -1 N TYR A 94 O THR A 113 SHEET 4 AA3 4 TYR A 108 TRP A 109 -1 O TYR A 108 N ARG A 98 SHEET 1 AA4 4 SER A 126 LEU A 130 0 SHEET 2 AA4 4 THR A 141 TYR A 151 -1 O LEU A 147 N PHE A 128 SHEET 3 AA4 4 TYR A 182 PRO A 191 -1 O LEU A 184 N VAL A 148 SHEET 4 AA4 4 VAL A 169 THR A 171 -1 N HIS A 170 O VAL A 187 SHEET 1 AA5 4 SER A 126 LEU A 130 0 SHEET 2 AA5 4 THR A 141 TYR A 151 -1 O LEU A 147 N PHE A 128 SHEET 3 AA5 4 TYR A 182 PRO A 191 -1 O LEU A 184 N VAL A 148 SHEET 4 AA5 4 VAL A 175 LEU A 176 -1 N VAL A 175 O SER A 183 SHEET 1 AA6 3 THR A 157 TRP A 160 0 SHEET 2 AA6 3 TYR A 200 HIS A 206 -1 O ASN A 203 N SER A 159 SHEET 3 AA6 3 THR A 211 VAL A 217 -1 O VAL A 213 N VAL A 204 SHEET 1 AA7 4 LEU B 4 SER B 7 0 SHEET 2 AA7 4 VAL B 19 ALA B 25 -1 O ILE B 22 N SER B 7 SHEET 3 AA7 4 GLU B 70 ILE B 75 -1 O LEU B 73 N ILE B 21 SHEET 4 AA7 4 PHE B 62 SER B 65 -1 N SER B 63 O THR B 74 SHEET 1 AA8 6 PHE B 10 SER B 14 0 SHEET 2 AA8 6 THR B 102 LYS B 107 1 O GLU B 105 N LEU B 11 SHEET 3 AA8 6 ALA B 84 GLN B 90 -1 N ALA B 84 O VAL B 104 SHEET 4 AA8 6 LEU B 33 GLN B 38 -1 N TYR B 36 O TYR B 87 SHEET 5 AA8 6 LYS B 45 TYR B 49 -1 O LEU B 47 N TRP B 35 SHEET 6 AA8 6 THR B 53 LEU B 54 -1 O THR B 53 N TYR B 49 SHEET 1 AA9 4 PHE B 10 SER B 14 0 SHEET 2 AA9 4 THR B 102 LYS B 107 1 O GLU B 105 N LEU B 11 SHEET 3 AA9 4 ALA B 84 GLN B 90 -1 N ALA B 84 O VAL B 104 SHEET 4 AA9 4 THR B 97 PHE B 98 -1 O THR B 97 N GLN B 90 SHEET 1 AB1 4 SER B 114 PHE B 118 0 SHEET 2 AB1 4 THR B 129 PHE B 139 -1 O LEU B 135 N PHE B 116 SHEET 3 AB1 4 TYR B 173 SER B 182 -1 O LEU B 181 N ALA B 130 SHEET 4 AB1 4 SER B 159 VAL B 163 -1 N GLN B 160 O THR B 178 SHEET 1 AB2 4 ALA B 153 LEU B 154 0 SHEET 2 AB2 4 LYS B 145 VAL B 150 -1 N VAL B 150 O ALA B 153 SHEET 3 AB2 4 VAL B 191 THR B 197 -1 O GLU B 195 N GLN B 147 SHEET 4 AB2 4 VAL B 205 ASN B 210 -1 O VAL B 205 N VAL B 196 SHEET 1 AB3 4 THR C 36 SER C 38 0 SHEET 2 AB3 4 ALA C 50 SER C 55 -1 O THR C 53 N SER C 38 SHEET 3 AB3 4 ASP C 105 VAL C 110 -1 O VAL C 110 N ALA C 50 SHEET 4 AB3 4 PHE C 95 GLN C 99 -1 N ARG C 96 O SER C 109 SHEET 1 AB4 5 LEU C 41 THR C 45 0 SHEET 2 AB4 5 ALA C 140 THR C 145 1 O ARG C 143 N LEU C 42 SHEET 3 AB4 5 GLY C 119 SER C 127 -1 N GLY C 119 O LEU C 142 SHEET 4 AB4 5 PHE C 63 MET C 70 -1 N VAL C 64 O ILE C 126 SHEET 5 AB4 5 THR C 76 PHE C 82 -1 O ASP C 77 N ARG C 69 SHEET 1 AB5 4 LEU C 41 THR C 45 0 SHEET 2 AB5 4 ALA C 140 THR C 145 1 O ARG C 143 N LEU C 42 SHEET 3 AB5 4 GLY C 119 SER C 127 -1 N GLY C 119 O LEU C 142 SHEET 4 AB5 4 GLN C 133 GLU C 136 -1 O LYS C 135 N ALA C 125 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.06 SSBOND 2 CYS A 146 CYS A 202 1555 1555 2.02 SSBOND 3 CYS B 23 CYS B 88 1555 1555 2.02 SSBOND 4 CYS B 134 CYS B 194 1555 1555 2.01 SSBOND 5 CYS C 54 CYS C 123 1555 1555 2.06 CISPEP 1 PHE A 152 PRO A 153 0 -6.56 CISPEP 2 GLU A 154 PRO A 155 0 -6.35 CISPEP 3 SER B 7 PRO B 8 0 -3.51 CISPEP 4 TYR B 94 PRO B 95 0 3.35 CISPEP 5 TYR B 140 PRO B 141 0 2.64 CISPEP 6 SER C 38 PRO C 39 0 -7.74 CISPEP 7 PHE C 82 PRO C 83 0 -2.00 CISPEP 8 ALA C 129 PRO C 130 0 -1.12 SITE 1 AC1 11 PHE A 172 PRO A 173 VAL A 175 SER A 183 SITE 2 AC1 11 LEU A 184 SER A 185 HOH A 602 HOH A 724 SITE 3 AC1 11 SER B 162 SER B 176 HOH B 401 SITE 1 AC2 6 VAL A 2 HIS A 27 TYR A 33 ARG A 98 SITE 2 AC2 6 HOH A 611 HOH A 686 SITE 1 AC3 5 LEU B 54 SER B 60 PHE B 62 SER B 63 SITE 2 AC3 5 HOH B 455 SITE 1 AC4 4 THR C 59 SER C 60 GLU C 61 PHE C 63 CRYST1 39.952 102.590 137.723 90.00 90.00 90.00 P 21 21 21 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 0.025030 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009748 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007261 0.00000