PDB Short entry for 5C3T HEADER IMMUNE SYSTEM 17-JUN-15 5C3T TITLE PD-1 BINDING DOMAIN FROM HUMAN PD-L1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 18-134; COMPND 5 SYNONYM: PROGRAMMED DEATH LIGAND 1,B7 HOMOLOG 1,B7-H1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS IMMUNOLOGY, LIGAND, PD1/PDL1 AXIS, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR K.M.ZAK,G.DUBIN,T.A.HOLAK REVDAT 4 10-JAN-24 5C3T 1 REMARK REVDAT 3 16-DEC-15 5C3T 1 JRNL REVDAT 2 09-DEC-15 5C3T 1 JRNL REVDAT 1 04-NOV-15 5C3T 0 JRNL AUTH K.M.ZAK,R.KITEL,S.PRZETOCKA,P.GOLIK,K.GUZIK,B.MUSIELAK, JRNL AUTH 2 A.DOMLING,G.DUBIN,T.A.HOLAK JRNL TITL STRUCTURE OF THE COMPLEX OF HUMAN PROGRAMMED DEATH 1, PD-1, JRNL TITL 2 AND ITS LIGAND PD-L1. JRNL REF STRUCTURE V. 23 2341 2015 JRNL REFN ISSN 0969-2126 JRNL PMID 26602187 JRNL DOI 10.1016/J.STR.2015.09.010 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 11217 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) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 559 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 809 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1760 REMARK 3 BIN FREE R VALUE SET COUNT : 43 REMARK 3 BIN FREE R VALUE : 0.2610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 992 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 75 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.48000 REMARK 3 B22 (A**2) : 1.46000 REMARK 3 B33 (A**2) : -0.98000 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): 0.113 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.102 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.658 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1062 ; 0.023 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1007 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1446 ; 2.223 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2320 ; 1.043 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 136 ; 6.622 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 51 ;33.632 ;24.902 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 185 ;13.732 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;14.711 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 160 ; 0.180 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1221 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 243 ; 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): 523 ; 1.656 ; 1.463 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 522 ; 1.657 ; 1.460 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 657 ; 2.497 ; 2.182 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 18 A 143 REMARK 3 ORIGIN FOR THE GROUP (A): 6.7859 12.5744 -6.5134 REMARK 3 T TENSOR REMARK 3 T11: 0.0023 T22: 0.0041 REMARK 3 T33: 0.0056 T12: 0.0002 REMARK 3 T13: 0.0021 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 0.0497 L22: 0.2934 REMARK 3 L33: 0.2295 L12: -0.0809 REMARK 3 L13: 0.1057 L23: -0.1998 REMARK 3 S TENSOR REMARK 3 S11: -0.0082 S12: -0.0002 S13: -0.0007 REMARK 3 S21: 0.0086 S22: 0.0077 S23: -0.0119 REMARK 3 S31: -0.0180 S32: -0.0013 S33: 0.0005 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 5C3T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1000210978. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 193.15 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) : 0.91842 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS V2.0 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.2.8 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11799 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 42.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.450 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.39100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.900 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: 3BIS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.84 NA FORMATE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 295.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.45350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.45350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 26.50200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.35500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.50200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.35500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 42.45350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.50200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 27.35500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 42.45350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.50200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 27.35500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 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 A 45 CB CG CD OE1 OE2 REMARK 470 LYS A 46 CB CG CD CE NZ REMARK 470 GLU A 47 CG CD OE1 OE2 REMARK 470 ARG A 82 CG CD NE CZ NH1 NH2 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 O HOH A 207 O HOH A 264 1.68 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 ASP A 26 CB ASP A 26 CG -0.156 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 ASP A 26 CB - CG - OD1 ANGL. DEV. = -10.2 DEGREES REMARK 500 ASP A 49 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 LEU A 88 CB - CG - CD1 ANGL. DEV. = 12.4 DEGREES REMARK 500 ARG A 113 NE - CZ - NH2 ANGL. DEV. = -4.0 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 GLU A 45 -73.91 -55.80 REMARK 500 LYS A 46 -90.30 -107.82 REMARK 500 TYR A 118 86.46 -164.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ZQK RELATED DB: PDB DBREF 5C3T A 18 134 UNP Q9NZQ7 PD1L1_HUMAN 18 134 SEQADV 5C3T GLU A 47 UNP Q9NZQ7 GLN 47 ENGINEERED MUTATION SEQADV 5C3T ALA A 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5C3T ALA A 136 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5C3T ALA A 137 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5C3T LEU A 138 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5C3T GLU A 139 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5C3T HIS A 140 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5C3T HIS A 141 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5C3T HIS A 142 UNP Q9NZQ7 EXPRESSION TAG SEQADV 5C3T HIS A 143 UNP Q9NZQ7 EXPRESSION TAG SEQRES 1 A 126 ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL VAL SEQRES 2 A 126 GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE PRO SEQRES 3 A 126 VAL GLU LYS GLU LEU ASP LEU ALA ALA LEU ILE VAL TYR SEQRES 4 A 126 TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL HIS SEQRES 5 A 126 GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR ARG SEQRES 6 A 126 GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU GLY SEQRES 7 A 126 ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN ASP SEQRES 8 A 126 ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY ALA SEQRES 9 A 126 ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO TYR SEQRES 10 A 126 ALA ALA ALA LEU GLU HIS HIS HIS HIS FORMUL 2 HOH *75(H2 O) HELIX 1 AA1 ASP A 49 ALA A 51 5 3 HELIX 2 AA2 HIS A 78 ARG A 82 5 5 HELIX 3 AA3 LYS A 89 LEU A 94 5 6 HELIX 4 AA4 LYS A 105 ALA A 109 5 5 HELIX 5 AA5 PRO A 133 HIS A 140 1 8 SHEET 1 AA1 6 LEU A 27 GLU A 31 0 SHEET 2 AA1 6 ALA A 121 ASN A 131 1 O ASN A 131 N VAL A 30 SHEET 3 AA1 6 GLY A 110 TYR A 118 -1 N TYR A 112 O ILE A 126 SHEET 4 AA1 6 LEU A 53 MET A 59 -1 N TYR A 56 O MET A 115 SHEET 5 AA1 6 LYS A 62 VAL A 68 -1 O PHE A 67 N VAL A 55 SHEET 6 AA1 6 GLU A 71 GLU A 72 -1 O GLU A 71 N VAL A 68 SHEET 1 AA2 3 MET A 36 LYS A 41 0 SHEET 2 AA2 3 ASN A 96 ILE A 101 -1 O ALA A 97 N CYS A 40 SHEET 3 AA2 3 ALA A 85 LEU A 87 -1 N ARG A 86 O GLN A 100 SSBOND 1 CYS A 40 CYS A 114 1555 1555 2.06 CRYST1 53.004 54.710 84.907 90.00 90.00 90.00 C 2 2 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 0.018866 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018278 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011778 0.00000