HEADER IMMUNE SYSTEM 15-JAN-24 8RPB TITLE STRUCTURE OF S79 FAB IN COMPLEX WITH IGV DOMAIN OF HUMAN PD-L1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEAVY CHAIN OF S79 FAB; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: LIGHT CHAIN OF S79 FAB; COMPND 7 CHAIN: L; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: PROGRAMMED CELL DEATH 1 LIGAND 1; COMPND 11 CHAIN: P; COMPND 12 SYNONYM: PD-L1,PDCD1 LIGAND 1,PROGRAMMED DEATH LIGAND 1,HPD-L1,B7 COMPND 13 HOMOLOG 1,B7-H1; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 11 MOL_ID: 3; 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: 562 KEYWDS IMMUNE SYSTEM, FAB EXPDTA X-RAY DIFFRACTION AUTHOR A.SVENSSON,V.KELPSAS,M.LAURSEN,N.ROSE REVDAT 2 16-OCT-24 8RPB 1 REMARK REVDAT 1 19-JUN-24 8RPB 0 JRNL AUTH P.MALINGE,X.CHAUCHET,J.BOURGUIGNON,N.BOSSON,S.CALLOUD, JRNL AUTH 2 T.BAUTZOVA,M.BORLET,M.LAURSEN,V.KELPSAS,N.ROSE,F.GUENEAU, JRNL AUTH 3 U.RAVN,G.MAGISTRELLI,N.FISCHER JRNL TITL STRUCTURAL ANALYSIS OF LIGHT CHAIN-DRIVEN BISPECIFIC JRNL TITL 2 ANTIBODIES TARGETING CD47 AND PD-L1. JRNL REF MABS V. 16 62432 2024 JRNL REFN ESSN 1942-0870 JRNL PMID 38849989 JRNL DOI 10.1080/19420862.2024.2362432 REMARK 2 REMARK 2 RESOLUTION. 2.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.8 (8-JUN-2022) REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 28249 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) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1385 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.79 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.51 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3414 REMARK 3 BIN FREE R VALUE : 0.3519 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 24 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4124 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 17 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 119.0 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.02030 REMARK 3 B22 (A**2) : -3.02030 REMARK 3 B33 (A**2) : 6.04060 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.410 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.383 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.266 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.385 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.269 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 4263 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 5799 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1397 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES : 703 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 4263 ; 10.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 558 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : 2 ; 1.000 ; HARMONIC REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 2908 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 0.96 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.26 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.79 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { H|1 - H|116 L|1 - L|113 } REMARK 3 ORIGIN FOR THE GROUP (A): -17.4374 -74.7604 -9.3984 REMARK 3 T TENSOR REMARK 3 T11: -0.2457 T22: 0.1993 REMARK 3 T33: 0.1313 T12: 0.1743 REMARK 3 T13: -0.1932 T23: -0.0256 REMARK 3 L TENSOR REMARK 3 L11: 6.4416 L22: 2.0523 REMARK 3 L33: 2.6844 L12: -0.074 REMARK 3 L13: 0.9485 L23: 0.7404 REMARK 3 S TENSOR REMARK 3 S11: -0.397 S12: -0.1112 S13: -0.3155 REMARK 3 S21: -0.1112 S22: -0.0355 S23: 0.5856 REMARK 3 S31: -0.3155 S32: 0.5856 S33: 0.4326 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { H|117 - H|218 L|114 - L|215 } REMARK 3 ORIGIN FOR THE GROUP (A): -40.2809 -60.9584 12.792 REMARK 3 T TENSOR REMARK 3 T11: 0.0284 T22: 0.5367 REMARK 3 T33: -0.2772 T12: 0.8038 REMARK 3 T13: -0.3664 T23: -0.5064 REMARK 3 L TENSOR REMARK 3 L11: 6.8902 L22: 8.32 REMARK 3 L33: 5.0447 L12: -0.876 REMARK 3 L13: 1.3021 L23: 2.2508 REMARK 3 S TENSOR REMARK 3 S11: -1.2115 S12: 1.5701 S13: -0.434 REMARK 3 S21: 1.5701 S22: 1.191 S23: -0.2982 REMARK 3 S31: -0.434 S32: -0.2982 S33: 0.0205 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { P|* } REMARK 3 ORIGIN FOR THE GROUP (A): 2.3222 -71.1313 -29.0013 REMARK 3 T TENSOR REMARK 3 T11: -0.7768 T22: 1.1164 REMARK 3 T33: -0.3712 T12: -0.1817 REMARK 3 T13: -0.0474 T23: 0.8076 REMARK 3 L TENSOR REMARK 3 L11: 11.6712 L22: 6.8222 REMARK 3 L33: 8.8733 L12: -2.5393 REMARK 3 L13: 1.6282 L23: -2.3429 REMARK 3 S TENSOR REMARK 3 S11: -0.6184 S12: -0.6389 S13: -0.7085 REMARK 3 S21: -0.6389 S22: -0.2701 S23: 2.4728 REMARK 3 S31: -0.7085 S32: 2.4728 S33: 0.8885 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8RPB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JAN-24. REMARK 100 THE DEPOSITION ID IS D_1292135379. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-22 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 : MAX IV REMARK 200 BEAMLINE : BIOMAX REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28276 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.790 REMARK 200 RESOLUTION RANGE LOW (A) : 48.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 24.00 REMARK 200 R MERGE (I) : 0.20500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 23.90 REMARK 200 R MERGE FOR SHELL (I) : 3.08900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH 8.0, 1.6M LI2SO4, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.49133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.74567 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 73.49133 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 36.74567 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 73.49133 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 36.74567 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 73.49133 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 36.74567 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: 6840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -110.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, L, P 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 S SO4 H 306 LIES ON A SPECIAL POSITION. REMARK 375 O1 SO4 H 306 LIES ON A SPECIAL POSITION. 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 H 219 REMARK 465 ASP H 220 REMARK 465 LYS H 221 REMARK 465 THR H 222 REMARK 465 HIS H 223 REMARK 465 CYS L 216 REMARK 465 SER L 217 REMARK 465 MET P 17 REMARK 465 ALA P 132 REMARK 465 PRO P 133 REMARK 465 GLY P 134 REMARK 465 SER P 135 REMARK 465 HIS P 136 REMARK 465 HIS P 137 REMARK 465 HIS P 138 REMARK 465 HIS P 139 REMARK 465 HIS P 140 REMARK 465 HIS P 141 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 TYR H 100 74.14 -153.18 REMARK 500 SER H 135 10.73 90.10 REMARK 500 ALA L 53 -34.90 65.85 REMARK 500 ASN L 71 51.29 -102.00 REMARK 500 GLN L 113 124.92 -30.16 REMARK 500 ASP L 156 61.17 23.92 REMARK 500 SER L 157 -19.64 104.45 REMARK 500 LYS P 46 -27.13 72.66 REMARK 500 GLN P 47 53.62 -110.84 REMARK 500 GLN P 83 -5.28 66.46 REMARK 500 TYR P 118 71.94 -157.68 REMARK 500 REMARK 500 REMARK: NULL DBREF 8RPB H 1 223 PDB 8RPB 8RPB 1 223 DBREF 8RPB L 1 217 PDB 8RPB 8RPB 1 217 DBREF 8RPB P 18 133 UNP Q9NZQ7 PD1L1_HUMAN 18 133 SEQADV 8RPB MET P 17 UNP Q9NZQ7 INITIATING METHIONINE SEQADV 8RPB GLY P 134 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8RPB SER P 135 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8RPB HIS P 136 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8RPB HIS P 137 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8RPB HIS P 138 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8RPB HIS P 139 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8RPB HIS P 140 UNP Q9NZQ7 EXPRESSION TAG SEQADV 8RPB HIS P 141 UNP Q9NZQ7 EXPRESSION TAG SEQRES 1 H 223 GLU VAL GLN LEU LEU GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 223 PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 H 223 PHE THR PHE SER SER TYR ALA MET SER TRP VAL ARG GLN SEQRES 4 H 223 ALA PRO GLY LYS GLY LEU GLU TRP VAL SER ALA ILE SER SEQRES 5 H 223 GLY SER GLY GLY SER THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 H 223 GLY ARG PHE THR ILE SER ARG ASP ASN SER LYS ASN THR SEQRES 7 H 223 LEU TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP THR SEQRES 8 H 223 ALA VAL TYR TYR CYS ALA LYS SER TYR GLY ALA PHE ASP SEQRES 9 H 223 TYR TRP GLY GLN GLY THR LEU VAL THR VAL SER SER ALA SEQRES 10 H 223 SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA PRO SER SEQRES 11 H 223 SER LYS SER THR SER GLY GLY THR ALA ALA LEU GLY CYS SEQRES 12 H 223 LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR VAL SER SEQRES 13 H 223 TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS THR PHE SEQRES 14 H 223 PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER LEU SER SEQRES 15 H 223 SER VAL VAL THR VAL PRO SER SER SER LEU GLY THR GLN SEQRES 16 H 223 THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER ASN THR SEQRES 17 H 223 LYS VAL ASP LYS ARG VAL GLU PRO LYS SER CYS ASP LYS SEQRES 18 H 223 THR HIS SEQRES 1 L 217 GLN SER ALA LEU THR GLN PRO ALA SER VAL SER GLY SER SEQRES 2 L 217 PRO GLY GLN SER ILE THR ILE SER CYS THR GLY THR SER SEQRES 3 L 217 SER ASP VAL PHE ARG PRO PRO LEU VAL SER TRP TYR GLN SEQRES 4 L 217 GLN HIS PRO GLY LYS ALA PRO LYS LEU MET ILE TYR PHE SEQRES 5 L 217 ALA SER LEU ARG PRO SER GLY VAL SER ASN ARG PHE SER SEQRES 6 L 217 GLY SER LYS SER GLY ASN THR ALA SER LEU THR ILE SER SEQRES 7 L 217 GLY LEU GLN ALA GLU ASP GLU ALA ASP TYR TYR CYS SER SEQRES 8 L 217 SER TRP ASP HIS THR GLY ASP GLY HIS VAL PHE GLY GLY SEQRES 9 L 217 GLY THR LYS LEU THR VAL LEU GLY GLN PRO LYS ALA ALA SEQRES 10 L 217 PRO SER VAL THR LEU PHE PRO PRO SER SER GLU GLU LEU SEQRES 11 L 217 GLN ALA ASN LYS ALA THR LEU VAL CYS LEU ILE SER ASP SEQRES 12 L 217 PHE TYR PRO GLY ALA VAL THR VAL ALA TRP LYS ALA ASP SEQRES 13 L 217 SER SER PRO VAL LYS ALA GLY VAL GLU THR THR THR PRO SEQRES 14 L 217 SER LYS GLN SER ASN ASN LYS TYR ALA ALA SER SER TYR SEQRES 15 L 217 LEU SER LEU THR PRO GLU GLN TRP LYS SER HIS ARG SER SEQRES 16 L 217 TYR SER CYS GLN VAL THR HIS GLU GLY SER THR VAL GLU SEQRES 17 L 217 LYS THR VAL ALA PRO THR GLU CYS SER SEQRES 1 P 125 MET ALA PHE THR VAL THR VAL PRO LYS ASP LEU TYR VAL SEQRES 2 P 125 VAL GLU TYR GLY SER ASN MET THR ILE GLU CYS LYS PHE SEQRES 3 P 125 PRO VAL GLU LYS GLN LEU ASP LEU ALA ALA LEU ILE VAL SEQRES 4 P 125 TYR TRP GLU MET GLU ASP LYS ASN ILE ILE GLN PHE VAL SEQRES 5 P 125 HIS GLY GLU GLU ASP LEU LYS VAL GLN HIS SER SER TYR SEQRES 6 P 125 ARG GLN ARG ALA ARG LEU LEU LYS ASP GLN LEU SER LEU SEQRES 7 P 125 GLY ASN ALA ALA LEU GLN ILE THR ASP VAL LYS LEU GLN SEQRES 8 P 125 ASP ALA GLY VAL TYR ARG CYS MET ILE SER TYR GLY GLY SEQRES 9 P 125 ALA ASP TYR LYS ARG ILE THR VAL LYS VAL ASN ALA PRO SEQRES 10 P 125 GLY SER HIS HIS HIS HIS HIS HIS HET CL H 301 1 HET GOL H 302 6 HET GOL H 303 6 HET GOL H 304 6 HET SO4 H 305 5 HET SO4 H 306 5 HET SO4 L 301 5 HET SO4 L 302 5 HET SO4 L 303 5 HET SO4 P 201 5 HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 CL CL 1- FORMUL 5 GOL 3(C3 H8 O3) FORMUL 8 SO4 6(O4 S 2-) FORMUL 14 HOH *17(H2 O) HELIX 1 AA1 THR H 28 TYR H 32 5 5 HELIX 2 AA2 ARG H 87 THR H 91 5 5 HELIX 3 AA3 SER H 130 THR H 134 5 5 HELIX 4 AA4 SER H 159 ALA H 161 5 3 HELIX 5 AA5 LYS H 204 ASN H 207 5 4 HELIX 6 AA6 ARG L 31 PRO L 33 5 3 HELIX 7 AA7 GLN L 81 GLU L 85 5 5 HELIX 8 AA8 SER L 126 ALA L 132 1 7 HELIX 9 AA9 THR L 186 SER L 192 1 7 HELIX 10 AB1 ASP P 49 LEU P 53 5 5 HELIX 11 AB2 LEU P 74 GLN P 77 5 4 HELIX 12 AB3 HIS P 78 ARG P 82 5 5 HELIX 13 AB4 LYS P 89 LEU P 94 5 6 HELIX 14 AB5 LYS P 105 ALA P 109 5 5 SHEET 1 AA1 4 GLN H 3 SER H 7 0 SHEET 2 AA1 4 LEU H 18 SER H 25 -1 O SER H 25 N GLN H 3 SHEET 3 AA1 4 THR H 78 MET H 83 -1 O MET H 83 N LEU H 18 SHEET 4 AA1 4 PHE H 68 ASP H 73 -1 N SER H 71 O TYR H 80 SHEET 1 AA2 6 GLY H 10 VAL H 12 0 SHEET 2 AA2 6 THR H 110 VAL H 114 1 O THR H 113 N VAL H 12 SHEET 3 AA2 6 ALA H 92 SER H 99 -1 N TYR H 94 O THR H 110 SHEET 4 AA2 6 ALA H 33 GLN H 39 -1 N VAL H 37 O TYR H 95 SHEET 5 AA2 6 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 AA2 6 THR H 58 TYR H 60 -1 O TYR H 59 N ALA H 50 SHEET 1 AA3 4 GLY H 10 VAL H 12 0 SHEET 2 AA3 4 THR H 110 VAL H 114 1 O THR H 113 N VAL H 12 SHEET 3 AA3 4 ALA H 92 SER H 99 -1 N TYR H 94 O THR H 110 SHEET 4 AA3 4 PHE H 103 TRP H 106 -1 O TYR H 105 N LYS H 98 SHEET 1 AA4 4 SER H 123 LEU H 127 0 SHEET 2 AA4 4 THR H 138 TYR H 148 -1 O LEU H 144 N PHE H 125 SHEET 3 AA4 4 TYR H 179 PRO H 188 -1 O TYR H 179 N TYR H 148 SHEET 4 AA4 4 VAL H 166 THR H 168 -1 N HIS H 167 O VAL H 184 SHEET 1 AA5 4 SER H 123 LEU H 127 0 SHEET 2 AA5 4 THR H 138 TYR H 148 -1 O LEU H 144 N PHE H 125 SHEET 3 AA5 4 TYR H 179 PRO H 188 -1 O TYR H 179 N TYR H 148 SHEET 4 AA5 4 VAL H 172 LEU H 173 -1 N VAL H 172 O SER H 180 SHEET 1 AA6 3 THR H 154 TRP H 157 0 SHEET 2 AA6 3 ILE H 198 HIS H 203 -1 O ASN H 200 N SER H 156 SHEET 3 AA6 3 THR H 208 ARG H 213 -1 O VAL H 210 N VAL H 201 SHEET 1 AA7 5 SER L 9 GLY L 12 0 SHEET 2 AA7 5 THR L 106 VAL L 110 1 O THR L 109 N VAL L 10 SHEET 3 AA7 5 ASP L 87 TRP L 93 -1 N TYR L 88 O THR L 106 SHEET 4 AA7 5 VAL L 35 GLN L 40 -1 N GLN L 40 O ASP L 87 SHEET 5 AA7 5 LYS L 47 ILE L 50 -1 O MET L 49 N TRP L 37 SHEET 1 AA8 4 SER L 9 GLY L 12 0 SHEET 2 AA8 4 THR L 106 VAL L 110 1 O THR L 109 N VAL L 10 SHEET 3 AA8 4 ASP L 87 TRP L 93 -1 N TYR L 88 O THR L 106 SHEET 4 AA8 4 HIS L 100 PHE L 102 -1 O VAL L 101 N SER L 92 SHEET 1 AA9 3 ILE L 18 CYS L 22 0 SHEET 2 AA9 3 THR L 72 ILE L 77 -1 O ALA L 73 N CYS L 22 SHEET 3 AA9 3 PHE L 64 SER L 69 -1 N SER L 65 O THR L 76 SHEET 1 AB1 4 SER L 119 PHE L 123 0 SHEET 2 AB1 4 ALA L 135 PHE L 144 -1 O LEU L 140 N THR L 121 SHEET 3 AB1 4 TYR L 177 LEU L 185 -1 O SER L 181 N CYS L 139 SHEET 4 AB1 4 VAL L 164 THR L 166 -1 N GLU L 165 O TYR L 182 SHEET 1 AB2 4 SER L 119 PHE L 123 0 SHEET 2 AB2 4 ALA L 135 PHE L 144 -1 O LEU L 140 N THR L 121 SHEET 3 AB2 4 TYR L 177 LEU L 185 -1 O SER L 181 N CYS L 139 SHEET 4 AB2 4 SER L 170 LYS L 171 -1 N SER L 170 O ALA L 178 SHEET 1 AB3 4 SER L 158 VAL L 160 0 SHEET 2 AB3 4 THR L 150 ALA L 155 -1 N ALA L 155 O SER L 158 SHEET 3 AB3 4 TYR L 196 HIS L 202 -1 O GLN L 199 N ALA L 152 SHEET 4 AB3 4 SER L 205 VAL L 211 -1 O VAL L 207 N VAL L 200 SHEET 1 AB4 6 LEU P 27 GLU P 31 0 SHEET 2 AB4 6 ALA P 121 ASN P 131 1 O LYS P 129 N VAL P 30 SHEET 3 AB4 6 GLY P 110 SER P 117 -1 N TYR P 112 O ILE P 126 SHEET 4 AB4 6 ILE P 54 MET P 59 -1 N TYR P 56 O MET P 115 SHEET 5 AB4 6 LYS P 62 VAL P 68 -1 O ILE P 64 N TRP P 57 SHEET 6 AB4 6 GLU P 71 GLU P 72 -1 O GLU P 71 N VAL P 68 SHEET 1 AB5 3 MET P 36 LYS P 41 0 SHEET 2 AB5 3 ASN P 96 ILE P 101 -1 O ALA P 97 N CYS P 40 SHEET 3 AB5 3 ALA P 85 LEU P 87 -1 N ARG P 86 O GLN P 100 SSBOND 1 CYS H 22 CYS H 96 1555 1555 2.06 SSBOND 2 CYS H 143 CYS H 199 1555 1555 2.04 SSBOND 3 CYS L 22 CYS L 90 1555 1555 2.04 SSBOND 4 CYS L 139 CYS L 198 1555 1555 2.04 SSBOND 5 CYS P 40 CYS P 114 1555 1555 2.03 CISPEP 1 PHE H 149 PRO H 150 0 -5.30 CISPEP 2 GLU H 151 PRO H 152 0 6.96 CISPEP 3 TYR L 145 PRO L 146 0 -1.58 CRYST1 185.852 185.852 110.237 90.00 90.00 120.00 P 62 2 2 12 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 0.005381 0.003107 0.000000 0.00000 SCALE2 0.000000 0.006213 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009071 0.00000