HEADER CELL CYCLE 31-MAY-17 5O4Y TITLE STRUCTURE OF HUMAN PD-L1 IN COMPLEX WITH INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1; COMPND 3 CHAIN: B, C, E; COMPND 4 SYNONYM: PROGRAMMED DEATH LIGAND 1,B7 HOMOLOG 1,B7-H1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PHE-MAA-ASN-PRO-HIS-LEU-SER-TRP-SER-TRP-9KK-9KK-ARG-CCS- COMPND 8 GLY-NH2; COMPND 9 CHAIN: A, D, F; COMPND 10 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 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS PD-1, PROGRAMMED DEATH 1, PD-L1, PROGRAMMED DEATH LIGAND 1, IMMUNE KEYWDS 2 CHECKPOINT, CANCER, CELL CYCLE EXPDTA X-RAY DIFFRACTION AUTHOR K.MAGIERA,P.GRUDNIK,G.DUBIN,T.A.HOLAK REVDAT 4 17-JAN-24 5O4Y 1 LINK REVDAT 3 11-DEC-19 5O4Y 1 REMARK REVDAT 2 25-OCT-17 5O4Y 1 JRNL REVDAT 1 20-SEP-17 5O4Y 0 JRNL AUTH K.MAGIERA-MULARZ,L.SKALNIAK,K.M.ZAK,B.MUSIELAK, JRNL AUTH 2 E.RUDZINSKA-SZOSTAK,J.KOCIK,P.GRUDNIK,D.SALA, JRNL AUTH 3 T.ZARGANES-TZITZIKAS,S.SHAABANI,A.DOMLING,G.DUBIN,T.A.HOLAK JRNL TITL BIOACTIVE MACROCYCLIC INHIBITORS OF THE PD-1/PD-L1 IMMUNE JRNL TITL 2 CHECKPOINT. JRNL REF ANGEW. CHEM. INT. ED. ENGL. V. 56 13732 2017 JRNL REFN ESSN 1521-3773 JRNL PMID 28881104 JRNL DOI 10.1002/ANIE.201707707 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 18474 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 935 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.7828 - 4.3957 0.97 2549 127 0.1546 0.1986 REMARK 3 2 4.3957 - 3.4908 0.98 2508 122 0.1617 0.2296 REMARK 3 3 3.4908 - 3.0500 0.99 2523 147 0.2000 0.2775 REMARK 3 4 3.0500 - 2.7714 0.97 2496 120 0.2308 0.2934 REMARK 3 5 2.7714 - 2.5728 0.97 2472 126 0.2634 0.3546 REMARK 3 6 2.5728 - 2.4212 0.99 2493 161 0.2739 0.3066 REMARK 3 7 2.4212 - 2.3000 0.99 2498 132 0.3085 0.4039 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5O4Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1200005195. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-17 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18522 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 29.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.55200 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: 5C3T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE (PH 5.5), 0.1 M REMARK 280 BIS-TRIS, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 40.47500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, F 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: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, 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 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 GLU B 45 CB CG CD OE1 OE2 REMARK 470 LYS B 46 CB CG CD CE NZ REMARK 470 GLN B 47 CG CD OE1 NE2 REMARK 470 LEU B 50 CD1 CD2 REMARK 470 GLU B 71 CG CD OE1 OE2 REMARK 470 LEU B 74 CG CD1 CD2 REMARK 470 LYS B 75 NZ REMARK 470 VAL B 76 CG1 REMARK 470 ARG B 82 NE CZ NH1 NH2 REMARK 470 GLN B 107 CG CD OE1 NE2 REMARK 470 LYS B 129 CG CD CE NZ REMARK 470 LYS C 25 CE NZ REMARK 470 ILE C 38 CG2 REMARK 470 LYS C 41 CE NZ REMARK 470 GLU C 45 CB CG CD OE1 OE2 REMARK 470 LYS C 46 CB CG CD CE NZ REMARK 470 GLN C 47 CG CD OE1 NE2 REMARK 470 LEU C 48 CG CD1 CD2 REMARK 470 ILE C 54 O REMARK 470 GLU C 71 CG CD OE1 OE2 REMARK 470 LEU C 74 CG CD1 CD2 REMARK 470 LYS C 75 CG CD CE NZ REMARK 470 SER C 93 OG REMARK 470 GLN C 107 CG CD OE1 NE2 REMARK 470 VAL C 111 CG1 CG2 REMARK 470 GLY C 120 O REMARK 470 ARG C 125 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 129 CG CD CE NZ REMARK 470 GLU E 45 CD OE1 OE2 REMARK 470 LYS E 46 CB CG CD CE NZ REMARK 470 GLU E 71 CG CD OE1 OE2 REMARK 470 LYS E 75 CG CD CE NZ REMARK 470 ARG E 82 CG CD NE CZ NH1 NH2 REMARK 470 LEU E 94 CG CD1 CD2 REMARK 470 LYS E 105 CG CD CE NZ REMARK 470 GLN E 107 CG CD OE1 NE2 REMARK 470 LYS E 129 NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HE22 GLN B 77 O HOH B 305 1.24 REMARK 500 OE1 GLN C 91 HD22 ASN C 96 1.51 REMARK 500 H GLN C 83 O HOH C 304 1.52 REMARK 500 O HOH B 308 O HOH B 322 1.87 REMARK 500 N PHE D 1 OZ1 CCS D 14 1.99 REMARK 500 O ALA B 52 O HOH B 301 2.01 REMARK 500 OE1 GLU B 31 O HOH B 302 2.03 REMARK 500 O ASN B 35 O HOH B 303 2.03 REMARK 500 OE1 GLU B 60 O HOH B 304 2.05 REMARK 500 NE2 GLN B 77 O HOH B 305 2.07 REMARK 500 O TYR C 118 O HOH C 301 2.07 REMARK 500 OD1 ASP E 103 O HOH E 301 2.08 REMARK 500 O HOH B 304 O HOH B 309 2.10 REMARK 500 O GLU B 45 O HOH B 306 2.11 REMARK 500 N PHE F 1 OZ1 CCS F 14 2.13 REMARK 500 O HOH C 305 O HOH C 309 2.14 REMARK 500 OD2 ASP B 73 O HOH B 307 2.14 REMARK 500 O ASP E 103 O HOH E 302 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 HH TYR E 134 HH21 ARG F 13 1556 1.34 REMARK 500 OH TYR E 134 HH21 ARG F 13 1556 1.40 REMARK 500 O 9KK A 12 HE ARG F 13 2555 1.57 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 9 CA SER A 9 CB -0.101 REMARK 500 ARG A 13 CZ ARG A 13 NH1 -0.092 REMARK 500 HIS D 5 CG HIS D 5 ND1 -0.093 REMARK 500 TRP D 8 NE1 TRP D 8 CE2 -0.101 REMARK 500 ARG D 13 CZ ARG D 13 NH1 -0.130 REMARK 500 ARG F 13 CZ ARG F 13 NH1 -0.132 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 PRO A 4 C - N - CA ANGL. DEV. = 9.6 DEGREES REMARK 500 PRO A 4 N - CA - C ANGL. DEV. = 16.4 DEGREES REMARK 500 PRO A 4 CA - C - N ANGL. DEV. = 25.1 DEGREES REMARK 500 PRO A 4 O - C - N ANGL. DEV. = -12.5 DEGREES REMARK 500 HIS A 5 C - N - CA ANGL. DEV. = 24.5 DEGREES REMARK 500 HIS A 5 N - CA - CB ANGL. DEV. = 18.3 DEGREES REMARK 500 SER A 9 C - N - CA ANGL. DEV. = 17.9 DEGREES REMARK 500 SER A 9 N - CA - CB ANGL. DEV. = -11.8 DEGREES REMARK 500 SER A 9 N - CA - C ANGL. DEV. = 22.0 DEGREES REMARK 500 TRP A 10 C - N - CA ANGL. DEV. = 16.2 DEGREES REMARK 500 PHE D 1 N - CA - CB ANGL. DEV. = 16.5 DEGREES REMARK 500 PRO D 4 CA - C - N ANGL. DEV. = 26.9 DEGREES REMARK 500 PRO D 4 O - C - N ANGL. DEV. = -15.4 DEGREES REMARK 500 HIS D 5 C - N - CA ANGL. DEV. = 27.1 DEGREES REMARK 500 HIS D 5 N - CA - CB ANGL. DEV. = 21.5 DEGREES REMARK 500 9KK D 12 CA - C - N ANGL. DEV. = 15.9 DEGREES REMARK 500 9KK D 12 O - C - N ANGL. DEV. = -14.8 DEGREES REMARK 500 ARG D 13 C - N - CA ANGL. DEV. = 20.9 DEGREES REMARK 500 ARG D 13 CB - CA - C ANGL. DEV. = 16.6 DEGREES REMARK 500 ARG D 13 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 PHE F 1 N - CA - CB ANGL. DEV. = 16.1 DEGREES REMARK 500 PRO F 4 CA - C - N ANGL. DEV. = 21.9 DEGREES REMARK 500 HIS F 5 C - N - CA ANGL. DEV. = 19.3 DEGREES REMARK 500 ARG F 13 C - N - CA ANGL. DEV. = 16.2 DEGREES REMARK 500 ARG F 13 NE - CZ - NH2 ANGL. DEV. = 5.4 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 B 46 -123.30 -124.56 REMARK 500 GLU B 60 71.53 44.37 REMARK 500 GLN B 83 -21.06 83.78 REMARK 500 LEU B 88 89.79 -69.08 REMARK 500 LYS C 46 -115.64 66.47 REMARK 500 GLU C 60 70.67 32.14 REMARK 500 GLN C 83 -4.21 74.66 REMARK 500 ASP C 103 77.28 49.84 REMARK 500 TYR C 118 77.19 -152.61 REMARK 500 LYS E 46 -117.36 -110.90 REMARK 500 GLU E 60 55.61 38.23 REMARK 500 TYR E 118 66.70 -150.16 REMARK 500 ALA E 133 -86.25 16.91 REMARK 500 PRO A 4 -63.51 -14.20 REMARK 500 HIS A 5 -33.18 117.47 REMARK 500 LEU A 6 -93.13 -111.41 REMARK 500 SER A 7 121.31 158.50 REMARK 500 SER A 9 -148.96 21.41 REMARK 500 9KK A 11 -63.74 -91.04 REMARK 500 ARG A 13 117.36 108.63 REMARK 500 HIS D 5 -52.75 102.94 REMARK 500 9KK D 12 73.97 -151.76 REMARK 500 ARG D 13 132.45 108.40 REMARK 500 MAA F 2 51.76 -102.44 REMARK 500 PRO F 4 -56.37 -4.75 REMARK 500 HIS F 5 -55.42 132.71 REMARK 500 9KK F 12 89.18 -168.15 REMARK 500 ARG F 13 113.23 101.08 REMARK 500 CCS F 14 -151.96 -102.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PHE A 1 MAA A 2 -145.55 REMARK 500 REMARK 500 REMARK: NULL DBREF 5O4Y B 18 132 UNP Q9NZQ7 PD1L1_HUMAN 18 132 DBREF 5O4Y C 18 132 UNP Q9NZQ7 PD1L1_HUMAN 18 132 DBREF 5O4Y E 18 132 UNP Q9NZQ7 PD1L1_HUMAN 18 132 DBREF 5O4Y A 1 16 PDB 5O4Y 5O4Y 1 16 DBREF 5O4Y D 1 16 PDB 5O4Y 5O4Y 1 16 DBREF 5O4Y F 1 16 PDB 5O4Y 5O4Y 1 16 SEQADV 5O4Y ALA B 133 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5O4Y TYR B 134 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5O4Y ALA B 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5O4Y ALA C 133 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5O4Y TYR C 134 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5O4Y ALA C 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5O4Y ALA E 133 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5O4Y TYR E 134 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5O4Y ALA E 135 UNP Q9NZQ7 EXPRESSION TAG SEQRES 1 B 118 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL SEQRES 2 B 118 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO SEQRES 3 B 118 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR SEQRES 4 B 118 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS SEQRES 5 B 118 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG SEQRES 6 B 118 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY SEQRES 7 B 118 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP SEQRES 8 B 118 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA SEQRES 9 B 118 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA ALA TYR SEQRES 10 B 118 ALA SEQRES 1 C 118 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL SEQRES 2 C 118 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO SEQRES 3 C 118 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR SEQRES 4 C 118 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS SEQRES 5 C 118 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG SEQRES 6 C 118 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY SEQRES 7 C 118 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP SEQRES 8 C 118 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA SEQRES 9 C 118 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA ALA TYR SEQRES 10 C 118 ALA SEQRES 1 E 118 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL SEQRES 2 E 118 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO SEQRES 3 E 118 VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL TYR SEQRES 4 E 118 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS SEQRES 5 E 118 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG SEQRES 6 E 118 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY SEQRES 7 E 118 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP SEQRES 8 E 118 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA SEQRES 9 E 118 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA ALA TYR SEQRES 10 E 118 ALA SEQRES 1 A 16 PHE MAA ASN PRO HIS LEU SER TRP SER TRP 9KK 9KK ARG SEQRES 2 A 16 CCS GLY NH2 SEQRES 1 D 16 PHE MAA ASN PRO HIS LEU SER TRP SER TRP 9KK 9KK ARG SEQRES 2 D 16 CCS GLY NH2 SEQRES 1 F 16 PHE MAA ASN PRO HIS LEU SER TRP SER TRP 9KK 9KK ARG SEQRES 2 F 16 CCS GLY NH2 HET MAA A 2 13 HET 9KK A 11 22 HET 9KK A 12 22 HET CCS A 14 15 HET NH2 A 16 3 HET MAA D 2 13 HET 9KK D 11 22 HET 9KK D 12 22 HET CCS D 14 15 HET NH2 D 16 3 HET MAA F 2 13 HET 9KK F 11 22 HET 9KK F 12 22 HET CCS F 14 15 HET NH2 F 16 3 HETNAM MAA N-METHYL-L-ALANINE HETNAM 9KK N-METHYL NORLEUCINE HETNAM CCS CARBOXYMETHYLATED CYSTEINE HETNAM NH2 AMINO GROUP FORMUL 4 MAA 3(C4 H9 N O2) FORMUL 4 9KK 6(C7 H15 N O2) FORMUL 4 CCS 3(C5 H9 N O4 S) FORMUL 4 NH2 3(H2 N) FORMUL 7 HOH *105(H2 O) HELIX 1 AA1 ASP B 49 ALA B 51 5 3 HELIX 2 AA2 ASP B 73 GLN B 77 5 5 HELIX 3 AA3 HIS B 78 ARG B 82 5 5 HELIX 4 AA4 GLN B 91 GLY B 95 5 5 HELIX 5 AA5 LYS B 105 ALA B 109 5 5 HELIX 6 AA6 ASP C 49 LEU C 53 5 5 HELIX 7 AA7 ASP C 73 GLN C 77 5 5 HELIX 8 AA8 HIS C 78 ARG C 82 5 5 HELIX 9 AA9 LYS C 89 LEU C 92 5 4 HELIX 10 AB1 LYS C 105 ALA C 109 5 5 HELIX 11 AB2 ASP E 49 ALA E 51 5 3 HELIX 12 AB3 LEU E 74 GLN E 77 5 4 HELIX 13 AB4 HIS E 78 ARG E 82 5 5 HELIX 14 AB5 LYS E 89 SER E 93 5 5 HELIX 15 AB6 LYS E 105 ALA E 109 5 5 SHEET 1 AA1 5 LEU B 27 GLU B 31 0 SHEET 2 AA1 5 ALA B 121 ASN B 131 1 O LYS B 129 N TYR B 28 SHEET 3 AA1 5 GLY B 110 TYR B 118 -1 N TYR B 112 O ILE B 126 SHEET 4 AA1 5 LEU B 53 MET B 59 -1 N TYR B 56 O MET B 115 SHEET 5 AA1 5 ASN B 63 VAL B 68 -1 O PHE B 67 N VAL B 55 SHEET 1 AA2 3 MET B 36 ILE B 38 0 SHEET 2 AA2 3 ALA B 98 ILE B 101 -1 O ILE B 101 N MET B 36 SHEET 3 AA2 3 ALA B 85 LEU B 88 -1 N ARG B 86 O GLN B 100 SHEET 1 AA3 5 LEU C 27 GLU C 31 0 SHEET 2 AA3 5 ASP C 122 ASN C 131 1 O THR C 127 N TYR C 28 SHEET 3 AA3 5 GLY C 110 ILE C 116 -1 N TYR C 112 O ILE C 126 SHEET 4 AA3 5 TYR C 56 MET C 59 -1 N TYR C 56 O MET C 115 SHEET 5 AA3 5 LYS C 62 GLN C 66 -1 O LYS C 62 N MET C 59 SHEET 1 AA4 3 MET C 36 LYS C 41 0 SHEET 2 AA4 3 ASN C 96 ILE C 101 -1 O ALA C 97 N CYS C 40 SHEET 3 AA4 3 ALA C 85 LEU C 88 -1 N ARG C 86 O GLN C 100 SHEET 1 AA5 6 LEU E 27 GLU E 31 0 SHEET 2 AA5 6 ALA E 121 ASN E 131 1 O THR E 127 N TYR E 28 SHEET 3 AA5 6 GLY E 110 TYR E 118 -1 N TYR E 112 O ILE E 126 SHEET 4 AA5 6 LEU E 53 MET E 59 -1 N TYR E 56 O MET E 115 SHEET 5 AA5 6 LYS E 62 VAL E 68 -1 O PHE E 67 N VAL E 55 SHEET 6 AA5 6 GLU E 71 GLU E 72 -1 O GLU E 71 N VAL E 68 SHEET 1 AA6 3 MET E 36 LYS E 41 0 SHEET 2 AA6 3 ASN E 96 ILE E 101 -1 O LEU E 99 N ILE E 38 SHEET 3 AA6 3 ALA E 85 LEU E 87 -1 N ARG E 86 O GLN E 100 SSBOND 1 CYS B 40 CYS B 114 1555 1555 2.01 SSBOND 2 CYS C 40 CYS C 114 1555 1555 2.02 SSBOND 3 CYS E 40 CYS E 114 1555 1555 2.01 LINK C PHE A 1 N MAA A 2 1555 1555 1.28 LINK N PHE A 1 CE CCS A 14 1555 1555 1.29 LINK C MAA A 2 N ASN A 3 1555 1555 1.28 LINK C TRP A 10 N 9KK A 11 1555 1555 1.33 LINK C 9KK A 11 N 9KK A 12 1555 1555 1.28 LINK C 9KK A 12 N ARG A 13 1555 1555 1.28 LINK C ARG A 13 N CCS A 14 1555 1555 1.29 LINK C CCS A 14 N GLY A 15 1555 1555 1.28 LINK C GLY A 15 N NH2 A 16 1555 1555 1.31 LINK C PHE D 1 N MAA D 2 1555 1555 1.29 LINK N PHE D 1 CE CCS D 14 1555 1555 1.25 LINK C MAA D 2 N ASN D 3 1555 1555 1.31 LINK C TRP D 10 N 9KK D 11 1555 1555 1.32 LINK C 9KK D 11 N 9KK D 12 1555 1555 1.29 LINK C 9KK D 12 N ARG D 13 1555 1555 1.29 LINK C ARG D 13 N CCS D 14 1555 1555 1.31 LINK C CCS D 14 N GLY D 15 1555 1555 1.31 LINK C GLY D 15 N NH2 D 16 1555 1555 1.32 LINK C PHE F 1 N MAA F 2 1555 1555 1.31 LINK N PHE F 1 CE CCS F 14 1555 1555 1.29 LINK C MAA F 2 N ASN F 3 1555 1555 1.28 LINK C TRP F 10 N 9KK F 11 1555 1555 1.29 LINK C 9KK F 11 N 9KK F 12 1555 1555 1.28 LINK C 9KK F 12 N ARG F 13 1555 1555 1.32 LINK C ARG F 13 N CCS F 14 1555 1555 1.30 LINK C CCS F 14 N GLY F 15 1555 1555 1.31 LINK C GLY F 15 N NH2 F 16 1555 1555 1.32 CISPEP 1 PRO A 4 HIS A 5 0 -1.68 CISPEP 2 SER A 9 TRP A 10 0 -5.31 CISPEP 3 TRP A 10 9KK A 11 0 19.97 CISPEP 4 9KK A 12 ARG A 13 0 -16.63 CISPEP 5 PHE D 1 MAA D 2 0 -2.67 CISPEP 6 PRO D 4 HIS D 5 0 -2.46 CISPEP 7 TRP D 10 9KK D 11 0 -10.86 CISPEP 8 9KK D 12 ARG D 13 0 -7.97 CISPEP 9 PHE F 1 MAA F 2 0 -3.55 CISPEP 10 PRO F 4 HIS F 5 0 -15.76 CISPEP 11 TRP F 10 9KK F 11 0 -27.95 CISPEP 12 9KK F 12 ARG F 13 0 -6.06 CRYST1 50.550 80.950 54.230 90.00 104.49 90.00 P 1 21 1 6 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 0.019782 0.000000 0.005112 0.00000 SCALE2 0.000000 0.012353 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019046 0.00000