HEADER IMMUNE SYSTEM 15-NOV-21 7VYT TITLE CRYSTAL STRUCTURE OF HUMAN TIGIT(23-129) IN COMPLEX WITH THE SCFV TITLE 2 FRAGMENT OF ANTI-TIGIT ANTIBODY MG1131 COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-CELL IMMUNORECEPTOR WITH IG AND ITIM DOMAINS; COMPND 3 CHAIN: A, T; COMPND 4 SYNONYM: V-SET AND IMMUNOGLOBULIN DOMAIN-CONTAINING PROTEIN 9,V-SET COMPND 5 AND TRANSMEMBRANE DOMAIN-CONTAINING PROTEIN 3; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: MG1131 HEAVY CHAIN VARIABLE REGION; COMPND 9 CHAIN: B, H; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: MG1131 LIGHT CHAIN VARIABLE REGION; COMPND 13 CHAIN: L, C; COMPND 14 ENGINEERED: YES; COMPND 15 OTHER_DETAILS: (G4S)4 IS A LINKER. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TIGIT, VSIG9, VSTM3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 MOL_ID: 3; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 ORGANISM_TAXID: 9606; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ANTIBODY, IMMUNE CHECKPOINT, TIGIT, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR B.-S.JEONG,H.NAM,M.KIM,B.-H.OH REVDAT 2 29-NOV-23 7VYT 1 REMARK REVDAT 1 02-MAR-22 7VYT 0 JRNL AUTH B.S.JEONG,H.NAM,J.LEE,H.Y.PARK,K.J.CHO,J.H.SHEEN,E.SONG, JRNL AUTH 2 M.OH,S.LEE,H.CHOI,J.E.YANG,M.KIM,B.H.OH JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF A MONOCLONAL JRNL TITL 2 ANTIBODY BLOCKING TIGIT. JRNL REF MABS V. 14 13750 2022 JRNL REFN ESSN 1942-0870 JRNL PMID 35090381 JRNL DOI 10.1080/19420862.2021.2013750 REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 126313 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6315 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 29.3300 - 4.7500 1.00 4111 217 0.1708 0.2116 REMARK 3 2 4.7500 - 3.7700 1.00 4049 213 0.1516 0.1494 REMARK 3 3 3.7700 - 3.2900 1.00 4030 212 0.1864 0.1955 REMARK 3 4 3.2900 - 2.9900 1.00 4033 212 0.2024 0.1936 REMARK 3 5 2.9900 - 2.7800 1.00 3975 209 0.2080 0.2421 REMARK 3 6 2.7800 - 2.6200 1.00 4060 214 0.2062 0.2166 REMARK 3 7 2.6200 - 2.4800 1.00 3973 209 0.2152 0.2579 REMARK 3 8 2.4800 - 2.3800 1.00 4028 212 0.2103 0.2391 REMARK 3 9 2.3800 - 2.2900 1.00 3986 210 0.2065 0.2186 REMARK 3 10 2.2900 - 2.2100 1.00 3999 211 0.2088 0.2295 REMARK 3 11 2.2100 - 2.1400 1.00 4021 211 0.1998 0.2088 REMARK 3 12 2.1400 - 2.0800 1.00 4012 211 0.2104 0.2273 REMARK 3 13 2.0800 - 2.0200 1.00 4007 211 0.2008 0.2494 REMARK 3 14 2.0200 - 1.9700 1.00 3992 210 0.2078 0.2244 REMARK 3 15 1.9700 - 1.9300 1.00 3952 209 0.2076 0.2326 REMARK 3 16 1.9300 - 1.8900 1.00 3998 210 0.2103 0.2246 REMARK 3 17 1.8900 - 1.8500 1.00 3989 210 0.2105 0.2205 REMARK 3 18 1.8500 - 1.8100 1.00 4004 211 0.2141 0.2184 REMARK 3 19 1.8100 - 1.7800 1.00 3994 210 0.2132 0.2407 REMARK 3 20 1.7800 - 1.7500 1.00 3975 208 0.2164 0.2700 REMARK 3 21 1.7500 - 1.7200 1.00 3985 210 0.2346 0.2694 REMARK 3 22 1.7200 - 1.7000 1.00 3951 208 0.2516 0.2977 REMARK 3 23 1.7000 - 1.6700 1.00 4022 212 0.2631 0.2661 REMARK 3 24 1.6700 - 1.6500 1.00 4008 210 0.2650 0.2913 REMARK 3 25 1.6500 - 1.6300 1.00 3959 208 0.2549 0.2757 REMARK 3 26 1.6300 - 1.6000 1.00 3984 210 0.2672 0.2565 REMARK 3 27 1.6000 - 1.5800 1.00 3990 210 0.2813 0.3176 REMARK 3 28 1.5800 - 1.5700 1.00 3986 210 0.2949 0.3084 REMARK 3 29 1.5700 - 1.5500 1.00 3979 209 0.3135 0.3549 REMARK 3 30 1.5500 - 1.5300 1.00 3946 208 0.3292 0.3557 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.197 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.812 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.78 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 : 0.012 5252 REMARK 3 ANGLE : 1.197 7132 REMARK 3 CHIRALITY : 0.093 782 REMARK 3 PLANARITY : 0.008 916 REMARK 3 DIHEDRAL : 11.581 742 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 : 2 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and (resid 25 through 35 or REMARK 3 resid 37 through 43 or resid 45 through REMARK 3 62 or resid 65 through 81 or resid 83 REMARK 3 through 128)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "T" and (resid 25 through 35 or REMARK 3 resid 37 through 43 or resid 45 through REMARK 3 62 or resid 65 through 81 or resid 83 REMARK 3 through 128)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS GROUP : ens_2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "H" and (resid 2 through 12 or REMARK 3 resid 14 through 42 or resid 44 through REMARK 3 82C or resid 84 through 112)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "B" and (resid 2 through 12 or REMARK 3 resid 14 through 42 or resid 44 through REMARK 3 86 or resid 88 through 120)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7VYT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1300025664. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-20 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 : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97957 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 126325 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 29.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.06538 REMARK 200 R SYM (I) : 0.07068 REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHENIX REMARK 200 STARTING MODEL: 6EHV, 3UCR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200MM AMMONIUM CITRATE, 20% (V/V) REMARK 280 POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.15K 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 39.91000 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 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: T, L, H 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 MET A 23 REMARK 465 THR A 24 REMARK 465 MET B 0 REMARK 465 SER B 121 REMARK 465 MET T 23 REMARK 465 THR T 24 REMARK 465 SER T 129 REMARK 465 GLY L -19 REMARK 465 GLY L -18 REMARK 465 GLY L -17 REMARK 465 GLY L -16 REMARK 465 SER L -15 REMARK 465 GLY L -14 REMARK 465 GLY L -13 REMARK 465 GLY L -12 REMARK 465 GLY L -11 REMARK 465 SER L -10 REMARK 465 GLY L -9 REMARK 465 GLY L -8 REMARK 465 GLY L -7 REMARK 465 GLY L -6 REMARK 465 SER L -5 REMARK 465 GLY L -4 REMARK 465 GLY L -3 REMARK 465 GLY L -2 REMARK 465 GLY L -1 REMARK 465 VAL L 109 REMARK 465 ASP L 110 REMARK 465 LYS L 111 REMARK 465 LEU L 112 REMARK 465 ALA L 113 REMARK 465 SER H 113 REMARK 465 GLY C -19 REMARK 465 GLY C -18 REMARK 465 GLY C -17 REMARK 465 GLY C -16 REMARK 465 SER C -15 REMARK 465 GLY C -14 REMARK 465 GLY C -13 REMARK 465 GLY C -12 REMARK 465 GLY C -11 REMARK 465 SER C -10 REMARK 465 GLY C -9 REMARK 465 GLY C -8 REMARK 465 GLY C -7 REMARK 465 GLY C -6 REMARK 465 SER C -5 REMARK 465 GLY C -4 REMARK 465 GLY C -3 REMARK 465 VAL C 111 REMARK 465 ASP C 112 REMARK 465 LYS C 113 REMARK 465 LEU C 114 REMARK 465 ALA C 115 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 NE2 GLN A 62 O HOH A 201 2.09 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 GLU T 60 CD GLU T 60 OE2 -0.075 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 ARG A 84 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 MET B 81 CG - SD - CE ANGL. DEV. = -12.6 DEGREES REMARK 500 LYS T 37 CD - CE - NZ ANGL. DEV. = 14.3 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 ALA L 51 -36.81 68.09 REMARK 500 ALA C 52 -37.42 71.24 REMARK 500 REMARK 500 REMARK: NULL DBREF 7VYT A 23 129 UNP Q495A1 TIGIT_HUMAN 23 129 DBREF 7VYT B 0 121 PDB 7VYT 7VYT 0 121 DBREF 7VYT T 23 129 UNP Q495A1 TIGIT_HUMAN 23 129 DBREF 7VYT L -19 113 PDB 7VYT 7VYT -19 113 DBREF 7VYT H 0 113 PDB 7VYT 7VYT 0 113 DBREF 7VYT C -19 115 PDB 7VYT 7VYT -19 115 SEQRES 1 A 107 MET THR GLY THR ILE GLU THR THR GLY ASN ILE SER ALA SEQRES 2 A 107 GLU LYS GLY GLY SER ILE ILE LEU GLN CYS HIS LEU SER SEQRES 3 A 107 SER THR THR ALA GLN VAL THR GLN VAL ASN TRP GLU GLN SEQRES 4 A 107 GLN ASP GLN LEU LEU ALA ILE CYS ASN ALA ASP LEU GLY SEQRES 5 A 107 TRP HIS ILE SER PRO SER PHE LYS ASP ARG VAL ALA PRO SEQRES 6 A 107 GLY PRO GLY LEU GLY LEU THR LEU GLN SER LEU THR VAL SEQRES 7 A 107 ASN ASP THR GLY GLU TYR PHE CYS ILE TYR HIS THR TYR SEQRES 8 A 107 PRO ASP GLY THR TYR THR GLY ARG ILE PHE LEU GLU VAL SEQRES 9 A 107 LEU GLU SER SEQRES 1 B 122 MET GLU VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS SEQRES 2 B 122 LYS PRO GLY ALA SER VAL LYS VAL SER CYS LYS ALA SER SEQRES 3 B 122 GLY TYR THR PHE THR SER TYR TYR MET HIS TRP VAL ARG SEQRES 4 B 122 GLN ALA PRO GLY GLN GLY LEU GLU TRP MET GLY ILE ILE SEQRES 5 B 122 ASN PRO SER GLY GLY SER THR SER TYR ALA GLN LYS PHE SEQRES 6 B 122 GLN GLY ARG VAL THR MET THR ARG ASP THR SER THR SER SEQRES 7 B 122 THR VAL TYR MET GLU LEU SER SER LEU ARG SER GLU ASP SEQRES 8 B 122 THR ALA VAL TYR TYR CYS ALA SER ARG SER GLY SER GLY SEQRES 9 B 122 TRP PHE GLY ALA LEU ASP TYR TRP GLY GLN GLY THR LEU SEQRES 10 B 122 VAL THR VAL SER SER SEQRES 1 T 107 MET THR GLY THR ILE GLU THR THR GLY ASN ILE SER ALA SEQRES 2 T 107 GLU LYS GLY GLY SER ILE ILE LEU GLN CYS HIS LEU SER SEQRES 3 T 107 SER THR THR ALA GLN VAL THR GLN VAL ASN TRP GLU GLN SEQRES 4 T 107 GLN ASP GLN LEU LEU ALA ILE CYS ASN ALA ASP LEU GLY SEQRES 5 T 107 TRP HIS ILE SER PRO SER PHE LYS ASP ARG VAL ALA PRO SEQRES 6 T 107 GLY PRO GLY LEU GLY LEU THR LEU GLN SER LEU THR VAL SEQRES 7 T 107 ASN ASP THR GLY GLU TYR PHE CYS ILE TYR HIS THR TYR SEQRES 8 T 107 PRO ASP GLY THR TYR THR GLY ARG ILE PHE LEU GLU VAL SEQRES 9 T 107 LEU GLU SER SEQRES 1 L 135 GLY GLY GLY GLY SER GLY GLY GLY GLY SER GLY GLY GLY SEQRES 2 L 135 GLY SER GLY GLY GLY GLY SER GLU ILE VAL LEU THR GLN SEQRES 3 L 135 SER PRO GLY THR LEU SER LEU SER PRO GLY GLU ARG ALA SEQRES 4 L 135 THR LEU SER CYS ARG ALA SER GLN SER VAL SER SER SER SEQRES 5 L 135 TYR LEU ALA TRP TYR GLN GLN LYS PRO GLY GLN ALA PRO SEQRES 6 L 135 ARG LEU LEU ILE TYR GLY ALA SER SER ARG ALA THR GLY SEQRES 7 L 135 ILE PRO ASP ARG PHE SER GLY SER GLY SER GLY THR ASP SEQRES 8 L 135 PHE THR LEU THR ILE SER ARG LEU GLU PRO GLU ASP PHE SEQRES 9 L 135 ALA VAL TYR TYR CYS GLN GLN TYR GLY SER SER PRO GLY SEQRES 10 L 135 GLY THR PHE GLY GLN GLY THR LYS VAL GLU ILE LYS ARG SEQRES 11 L 135 VAL ASP LYS LEU ALA SEQRES 1 H 122 MET GLU VAL GLN LEU VAL GLN SER GLY ALA GLU VAL LYS SEQRES 2 H 122 LYS PRO GLY ALA SER VAL LYS VAL SER CYS LYS ALA SER SEQRES 3 H 122 GLY TYR THR PHE THR SER TYR TYR MET HIS TRP VAL ARG SEQRES 4 H 122 GLN ALA PRO GLY GLN GLY LEU GLU TRP MET GLY ILE ILE SEQRES 5 H 122 ASN PRO SER GLY GLY SER THR SER TYR ALA GLN LYS PHE SEQRES 6 H 122 GLN GLY ARG VAL THR MET THR ARG ASP THR SER THR SER SEQRES 7 H 122 THR VAL TYR MET GLU LEU SER SER LEU ARG SER GLU ASP SEQRES 8 H 122 THR ALA VAL TYR TYR CYS ALA SER ARG SER GLY SER GLY SEQRES 9 H 122 TRP PHE GLY ALA LEU ASP TYR TRP GLY GLN GLY THR LEU SEQRES 10 H 122 VAL THR VAL SER SER SEQRES 1 C 135 GLY GLY GLY GLY SER GLY GLY GLY GLY SER GLY GLY GLY SEQRES 2 C 135 GLY SER GLY GLY GLY GLY SER GLU ILE VAL LEU THR GLN SEQRES 3 C 135 SER PRO GLY THR LEU SER LEU SER PRO GLY GLU ARG ALA SEQRES 4 C 135 THR LEU SER CYS ARG ALA SER GLN SER VAL SER SER SER SEQRES 5 C 135 TYR LEU ALA TRP TYR GLN GLN LYS PRO GLY GLN ALA PRO SEQRES 6 C 135 ARG LEU LEU ILE TYR GLY ALA SER SER ARG ALA THR GLY SEQRES 7 C 135 ILE PRO ASP ARG PHE SER GLY SER GLY SER GLY THR ASP SEQRES 8 C 135 PHE THR LEU THR ILE SER ARG LEU GLU PRO GLU ASP PHE SEQRES 9 C 135 ALA VAL TYR TYR CYS GLN GLN TYR GLY SER SER PRO GLY SEQRES 10 C 135 GLY THR PHE GLY GLN GLY THR LYS VAL GLU ILE LYS ARG SEQRES 11 C 135 VAL ASP LYS LEU ALA HET FLC H 201 13 HET FLC C 201 13 HETNAM FLC CITRATE ANION FORMUL 7 FLC 2(C6 H5 O7 3-) FORMUL 9 HOH *388(H2 O) HELIX 1 AA1 PRO A 79 LYS A 82 5 4 HELIX 2 AA2 THR A 99 THR A 103 5 5 HELIX 3 AA3 GLN B 62 GLN B 65 5 4 HELIX 4 AA4 THR B 74 THR B 76 5 3 HELIX 5 AA5 ARG B 87 THR B 91 5 5 HELIX 6 AA6 PRO T 79 LYS T 82 5 4 HELIX 7 AA7 THR T 99 THR T 103 5 5 HELIX 8 AA8 SER L 29 SER L 31 5 3 HELIX 9 AA9 GLU L 79 PHE L 83 5 5 HELIX 10 AB1 GLN H 61 GLN H 64 5 4 HELIX 11 AB2 ARG H 83 THR H 87 5 5 HELIX 12 AB3 SER C 30 SER C 32 5 3 HELIX 13 AB4 GLU C 80 PHE C 84 5 5 SHEET 1 AA1 2 THR A 26 GLU A 28 0 SHEET 2 AA1 2 HIS A 46 SER A 48 -1 O HIS A 46 N GLU A 28 SHEET 1 AA2 6 ASN A 32 GLU A 36 0 SHEET 2 AA2 6 GLY A 116 LEU A 127 1 O LEU A 127 N ALA A 35 SHEET 3 AA2 6 GLY A 104 TYR A 113 -1 N TYR A 106 O ILE A 122 SHEET 4 AA2 6 GLN A 53 GLN A 61 -1 N GLN A 53 O TYR A 113 SHEET 5 AA2 6 GLN A 64 ASN A 70 -1 O ALA A 67 N TRP A 59 SHEET 6 AA2 6 GLY A 74 ILE A 77 -1 O HIS A 76 N ILE A 68 SHEET 1 AA3 3 ILE A 41 LEU A 43 0 SHEET 2 AA3 3 LEU A 93 LEU A 95 -1 O LEU A 93 N LEU A 43 SHEET 3 AA3 3 VAL A 85 PRO A 87 -1 N ALA A 86 O THR A 94 SHEET 1 AA4 4 GLN B 3 GLN B 6 0 SHEET 2 AA4 4 VAL B 18 SER B 25 -1 O SER B 25 N GLN B 3 SHEET 3 AA4 4 THR B 78 LEU B 83 -1 O MET B 81 N VAL B 20 SHEET 4 AA4 4 VAL B 68 ASP B 73 -1 N ASP B 73 O THR B 78 SHEET 1 AA5 6 GLU B 10 LYS B 12 0 SHEET 2 AA5 6 THR B 115 VAL B 119 1 O THR B 118 N GLU B 10 SHEET 3 AA5 6 ALA B 92 SER B 98 -1 N TYR B 94 O THR B 115 SHEET 4 AA5 6 MET B 34 GLN B 39 -1 N VAL B 37 O TYR B 95 SHEET 5 AA5 6 LEU B 45 ILE B 51 -1 O MET B 48 N TRP B 36 SHEET 6 AA5 6 THR B 58 TYR B 60 -1 O SER B 59 N ILE B 50 SHEET 1 AA6 4 GLU B 10 LYS B 12 0 SHEET 2 AA6 4 THR B 115 VAL B 119 1 O THR B 118 N GLU B 10 SHEET 3 AA6 4 ALA B 92 SER B 98 -1 N TYR B 94 O THR B 115 SHEET 4 AA6 4 TYR B 110 TRP B 111 -1 O TYR B 110 N SER B 98 SHEET 1 AA7 2 THR T 26 GLU T 28 0 SHEET 2 AA7 2 HIS T 46 SER T 48 -1 O SER T 48 N THR T 26 SHEET 1 AA8 6 ASN T 32 GLU T 36 0 SHEET 2 AA8 6 GLY T 116 LEU T 127 1 O LEU T 127 N ALA T 35 SHEET 3 AA8 6 GLY T 104 TYR T 113 -1 N TYR T 110 O TYR T 118 SHEET 4 AA8 6 GLN T 53 GLN T 61 -1 N GLN T 56 O HIS T 111 SHEET 5 AA8 6 GLN T 64 ASN T 70 -1 O ALA T 67 N TRP T 59 SHEET 6 AA8 6 GLY T 74 ILE T 77 -1 O HIS T 76 N ILE T 68 SHEET 1 AA9 3 ILE T 41 LEU T 43 0 SHEET 2 AA9 3 LEU T 93 LEU T 95 -1 O LEU T 93 N LEU T 43 SHEET 3 AA9 3 VAL T 85 PRO T 87 -1 N ALA T 86 O THR T 94 SHEET 1 AB1 4 LEU L 4 SER L 7 0 SHEET 2 AB1 4 ALA L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 AB1 4 ASP L 70 ILE L 75 -1 O LEU L 73 N LEU L 21 SHEET 4 AB1 4 PHE L 62 SER L 67 -1 N SER L 63 O THR L 74 SHEET 1 AB2 6 THR L 10 LEU L 13 0 SHEET 2 AB2 6 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 AB2 6 ALA L 84 GLN L 90 -1 N ALA L 84 O VAL L 104 SHEET 4 AB2 6 LEU L 33 GLN L 38 -1 N ALA L 34 O GLN L 89 SHEET 5 AB2 6 ARG L 45 TYR L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 AB2 6 SER L 53 ARG L 54 -1 O SER L 53 N TYR L 49 SHEET 1 AB3 4 THR L 10 LEU L 13 0 SHEET 2 AB3 4 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 AB3 4 ALA L 84 GLN L 90 -1 N ALA L 84 O VAL L 104 SHEET 4 AB3 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 AB4 4 GLN H 3 GLN H 6 0 SHEET 2 AB4 4 VAL H 18 SER H 25 -1 O LYS H 23 N VAL H 5 SHEET 3 AB4 4 THR H 77 LEU H 82 -1 O MET H 80 N VAL H 20 SHEET 4 AB4 4 VAL H 67 ASP H 72 -1 N THR H 70 O TYR H 79 SHEET 1 AB5 6 GLU H 10 LYS H 12 0 SHEET 2 AB5 6 THR H 107 VAL H 111 1 O THR H 110 N LYS H 12 SHEET 3 AB5 6 ALA H 88 SER H 94 -1 N TYR H 90 O THR H 107 SHEET 4 AB5 6 MET H 34 GLN H 39 -1 N VAL H 37 O TYR H 91 SHEET 5 AB5 6 LEU H 45 ILE H 51 -1 O MET H 48 N TRP H 36 SHEET 6 AB5 6 THR H 57 TYR H 59 -1 O SER H 58 N ILE H 50 SHEET 1 AB6 4 GLU H 10 LYS H 12 0 SHEET 2 AB6 4 THR H 107 VAL H 111 1 O THR H 110 N LYS H 12 SHEET 3 AB6 4 ALA H 88 SER H 94 -1 N TYR H 90 O THR H 107 SHEET 4 AB6 4 TYR H 102 TRP H 103 -1 O TYR H 102 N SER H 94 SHEET 1 AB7 3 LEU C 4 SER C 7 0 SHEET 2 AB7 3 ALA C 19 VAL C 29 -1 O ARG C 24 N THR C 5 SHEET 3 AB7 3 PHE C 63 ILE C 76 -1 O LEU C 74 N LEU C 21 SHEET 1 AB8 6 THR C 10 LEU C 13 0 SHEET 2 AB8 6 THR C 104 ILE C 108 1 O GLU C 107 N LEU C 11 SHEET 3 AB8 6 ALA C 85 GLN C 91 -1 N ALA C 85 O VAL C 106 SHEET 4 AB8 6 LEU C 34 GLN C 39 -1 N ALA C 35 O GLN C 90 SHEET 5 AB8 6 ARG C 46 TYR C 50 -1 O LEU C 48 N TRP C 36 SHEET 6 AB8 6 SER C 54 ARG C 55 -1 O SER C 54 N TYR C 50 SHEET 1 AB9 4 THR C 10 LEU C 13 0 SHEET 2 AB9 4 THR C 104 ILE C 108 1 O GLU C 107 N LEU C 11 SHEET 3 AB9 4 ALA C 85 GLN C 91 -1 N ALA C 85 O VAL C 106 SHEET 4 AB9 4 THR C 99 PHE C 100 -1 O THR C 99 N GLN C 91 CISPEP 1 GLY A 88 PRO A 89 0 0.92 CISPEP 2 TYR A 113 PRO A 114 0 4.90 CISPEP 3 GLY T 88 PRO T 89 0 0.27 CISPEP 4 TYR T 113 PRO T 114 0 4.29 CISPEP 5 SER L 7 PRO L 8 0 -6.19 CISPEP 6 SER C 7 PRO C 8 0 -8.41 CRYST1 69.670 79.820 77.970 90.00 100.55 90.00 P 1 21 1 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 0.014353 0.000000 0.002674 0.00000 SCALE2 0.000000 0.012528 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013046 0.00000 MTRIX1 1 -0.088983 -0.007704 0.996003 -11.43471 1 MTRIX2 1 -0.017661 -0.999801 -0.009311 160.96817 1 MTRIX3 1 0.995877 -0.018419 0.088829 12.48749 1 MTRIX1 2 -0.065734 -0.011343 0.997773 -12.50643 1 MTRIX2 2 -0.017820 -0.999763 -0.012540 161.03808 1 MTRIX3 2 0.997678 -0.018605 0.065516 13.32000 1 MTRIX1 3 -0.146514 -0.018903 0.989028 -7.93451 1 MTRIX2 3 -0.030734 -0.999248 -0.023651 162.27046 1 MTRIX3 3 0.988731 -0.033862 0.145823 10.44103 1