HEADER IMMUNE SYSTEM 13-MAR-17 5V52 TITLE STRUCTURE OF TIGIT BOUND TO NECTIN-2 (CD112) COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-CELL IMMUNORECEPTOR WITH IG AND ITIM DOMAINS; COMPND 3 CHAIN: A, B; 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: NECTIN-2; COMPND 9 CHAIN: C, D; COMPND 10 SYNONYM: HERPES VIRUS ENTRY MEDIATOR B,HVEB,NECTIN CELL ADHESION COMPND 11 MOLECULE 2,POLIOVIRUS RECEPTOR-RELATED PROTEIN 2; COMPND 12 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: 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 GENE: NECTIN2, HVEB, PRR2, PVRL2; SOURCE 13 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS IMMUNE RECEPTOR, ADHESION MOLECULE, IMMUNOGLOBULIN FOLD, IMMUNE KEYWDS 2 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR F.A.DEUSS,B.S.GULLY,J.ROSSJOHN,R.BERRY REVDAT 8 04-OCT-23 5V52 1 HETSYN REVDAT 7 29-JUL-20 5V52 1 COMPND REMARK HETNAM LINK REVDAT 7 2 1 SITE REVDAT 6 26-FEB-20 5V52 1 REMARK REVDAT 5 08-JAN-20 5V52 1 REMARK REVDAT 4 20-SEP-17 5V52 1 REMARK REVDAT 3 19-JUL-17 5V52 1 JRNL REVDAT 2 07-JUN-17 5V52 1 JRNL REVDAT 1 24-MAY-17 5V52 0 JRNL AUTH F.A.DEUSS,B.S.GULLY,J.ROSSJOHN,R.BERRY JRNL TITL RECOGNITION OF NECTIN-2 BY THE NATURAL KILLER CELL RECEPTOR JRNL TITL 2 T CELL IMMUNOGLOBULIN AND ITIM DOMAIN (TIGIT). JRNL REF J. BIOL. CHEM. V. 292 11413 2017 JRNL REFN ESSN 1083-351X JRNL PMID 28515320 JRNL DOI 10.1074/JBC.M117.786483 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.0 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 11685 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 563 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 : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 3.40 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.76 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2715 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2451 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2578 REMARK 3 BIN R VALUE (WORKING SET) : 0.2444 REMARK 3 BIN FREE R VALUE : 0.2588 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.05 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 137 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 : 3406 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 65.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 71.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.48390 REMARK 3 B22 (A**2) : -6.48390 REMARK 3 B33 (A**2) : 12.96770 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) : 0.666 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.398 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL 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 : 0.894 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.845 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 3535 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 4858 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1518 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 74 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 522 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 3535 ; 20.000 ; 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 : 486 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 3640 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 0.93 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.18 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 2.73 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { *|* } REMARK 3 ORIGIN FOR THE GROUP (A): -8.8222 8.0780 -28.4634 REMARK 3 T TENSOR REMARK 3 T11: 0.0982 T22: -0.1164 REMARK 3 T33: -0.1881 T12: -0.0308 REMARK 3 T13: 0.1492 T23: 0.0387 REMARK 3 L TENSOR REMARK 3 L11: 2.2736 L22: 0.3219 REMARK 3 L33: 2.6036 L12: -0.7912 REMARK 3 L13: -2.0189 L23: 0.7520 REMARK 3 S TENSOR REMARK 3 S11: -0.0361 S12: -0.1277 S13: -0.0245 REMARK 3 S21: 0.1448 S22: -0.0931 S23: 0.0560 REMARK 3 S31: 0.0328 S32: 0.2051 S33: 0.1293 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5V52 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1000226862. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-15 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : .9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11784 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 85.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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: 3UCR, 3R0N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3 M LITHIUM SULFATE 0.1M TRIS PH7, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 126.95500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.25000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.25000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 190.43250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.25000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.25000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 63.47750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.25000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.25000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 190.43250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.25000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.25000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 63.47750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 126.95500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A 22 REMARK 465 MET A 23 REMARK 465 LEU A 127 REMARK 465 GLU A 128 REMARK 465 MET B 22 REMARK 465 MET B 23 REMARK 465 GLU B 128 REMARK 465 GLN C 32 REMARK 465 GLY C 113 REMARK 465 GLN C 114 REMARK 465 ASP C 115 REMARK 465 PRO C 161 REMARK 465 ARG C 162 REMARK 465 GLY C 163 REMARK 465 SER C 164 REMARK 465 GLY C 165 REMARK 465 HIS C 166 REMARK 465 HIS C 167 REMARK 465 HIS C 168 REMARK 465 HIS C 169 REMARK 465 HIS C 170 REMARK 465 HIS C 171 REMARK 465 GLN D 32 REMARK 465 GLY D 113 REMARK 465 GLN D 114 REMARK 465 ASP D 115 REMARK 465 GLY D 163 REMARK 465 SER D 164 REMARK 465 GLY D 165 REMARK 465 HIS D 166 REMARK 465 HIS D 167 REMARK 465 HIS D 168 REMARK 465 HIS D 169 REMARK 465 HIS D 170 REMARK 465 HIS D 171 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 36 CG CD OE1 OE2 REMARK 470 LYS A 37 CG CD CE NZ REMARK 470 GLN A 53 CG CD OE1 NE2 REMARK 470 LYS A 82 CG CD CE NZ REMARK 470 ARG A 84 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 36 CG CD OE1 OE2 REMARK 470 LYS B 37 CG CD CE NZ REMARK 470 ASP B 63 CG OD1 OD2 REMARK 470 LYS B 82 CG CD CE NZ REMARK 470 GLU B 125 CG CD OE1 OE2 REMARK 470 LEU B 127 CG CD1 CD2 REMARK 470 ARG C 35 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 41 CG CD OE1 OE2 REMARK 470 ARG C 43 CG CD NE CZ NH1 NH2 REMARK 470 ASN C 78 CG OD1 ND2 REMARK 470 LYS C 88 CG CD CE NZ REMARK 470 LYS C 97 CG CD CE NZ REMARK 470 LYS C 147 CG CD CE NZ REMARK 470 ARG C 157 CG CD NE CZ NH1 NH2 REMARK 470 ASN D 78 CG OD1 ND2 REMARK 470 LYS D 97 CG CD CE NZ REMARK 470 GLU D 101 CG CD OE1 OE2 REMARK 470 LYS D 109 CG CD CE NZ REMARK 470 GLU D 133 CG CD OE1 OE2 REMARK 470 ARG D 162 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 ND2 ASN C 137 O5 NAG C 200 2.04 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 ASP A 63 50.89 -140.01 REMARK 500 GLN C 80 -73.23 -68.89 REMARK 500 PRO D 161 -86.75 -86.69 REMARK 500 REMARK 500 REMARK: NULL DBREF 5V52 A 22 128 UNP Q495A1 TIGIT_HUMAN 22 128 DBREF 5V52 B 22 128 UNP Q495A1 TIGIT_HUMAN 22 128 DBREF 5V52 C 32 158 UNP Q92692 NECT2_HUMAN 32 158 DBREF 5V52 D 32 158 UNP Q92692 NECT2_HUMAN 32 158 SEQADV 5V52 SER A 69 UNP Q495A1 CYS 69 ENGINEERED MUTATION SEQADV 5V52 SER B 69 UNP Q495A1 CYS 69 ENGINEERED MUTATION SEQADV 5V52 LEU C 159 UNP Q92692 EXPRESSION TAG SEQADV 5V52 VAL C 160 UNP Q92692 EXPRESSION TAG SEQADV 5V52 PRO C 161 UNP Q92692 EXPRESSION TAG SEQADV 5V52 ARG C 162 UNP Q92692 EXPRESSION TAG SEQADV 5V52 GLY C 163 UNP Q92692 EXPRESSION TAG SEQADV 5V52 SER C 164 UNP Q92692 EXPRESSION TAG SEQADV 5V52 GLY C 165 UNP Q92692 EXPRESSION TAG SEQADV 5V52 HIS C 166 UNP Q92692 EXPRESSION TAG SEQADV 5V52 HIS C 167 UNP Q92692 EXPRESSION TAG SEQADV 5V52 HIS C 168 UNP Q92692 EXPRESSION TAG SEQADV 5V52 HIS C 169 UNP Q92692 EXPRESSION TAG SEQADV 5V52 HIS C 170 UNP Q92692 EXPRESSION TAG SEQADV 5V52 HIS C 171 UNP Q92692 EXPRESSION TAG SEQADV 5V52 LEU D 159 UNP Q92692 EXPRESSION TAG SEQADV 5V52 VAL D 160 UNP Q92692 EXPRESSION TAG SEQADV 5V52 PRO D 161 UNP Q92692 EXPRESSION TAG SEQADV 5V52 ARG D 162 UNP Q92692 EXPRESSION TAG SEQADV 5V52 GLY D 163 UNP Q92692 EXPRESSION TAG SEQADV 5V52 SER D 164 UNP Q92692 EXPRESSION TAG SEQADV 5V52 GLY D 165 UNP Q92692 EXPRESSION TAG SEQADV 5V52 HIS D 166 UNP Q92692 EXPRESSION TAG SEQADV 5V52 HIS D 167 UNP Q92692 EXPRESSION TAG SEQADV 5V52 HIS D 168 UNP Q92692 EXPRESSION TAG SEQADV 5V52 HIS D 169 UNP Q92692 EXPRESSION TAG SEQADV 5V52 HIS D 170 UNP Q92692 EXPRESSION TAG SEQADV 5V52 HIS D 171 UNP Q92692 EXPRESSION TAG SEQRES 1 A 107 MET MET THR GLY THR ILE GLU THR THR GLY ASN ILE SER SEQRES 2 A 107 ALA GLU LYS GLY GLY SER ILE ILE LEU GLN CYS HIS LEU SEQRES 3 A 107 SER SER THR THR ALA GLN VAL THR GLN VAL ASN TRP GLU SEQRES 4 A 107 GLN GLN ASP GLN LEU LEU ALA ILE SER ASN ALA ASP LEU SEQRES 5 A 107 GLY TRP HIS ILE SER PRO SER PHE LYS ASP ARG VAL ALA SEQRES 6 A 107 PRO GLY PRO GLY LEU GLY LEU THR LEU GLN SER LEU THR SEQRES 7 A 107 VAL ASN ASP THR GLY GLU TYR PHE CYS ILE TYR HIS THR SEQRES 8 A 107 TYR PRO ASP GLY THR TYR THR GLY ARG ILE PHE LEU GLU SEQRES 9 A 107 VAL LEU GLU SEQRES 1 B 107 MET MET THR GLY THR ILE GLU THR THR GLY ASN ILE SER SEQRES 2 B 107 ALA GLU LYS GLY GLY SER ILE ILE LEU GLN CYS HIS LEU SEQRES 3 B 107 SER SER THR THR ALA GLN VAL THR GLN VAL ASN TRP GLU SEQRES 4 B 107 GLN GLN ASP GLN LEU LEU ALA ILE SER ASN ALA ASP LEU SEQRES 5 B 107 GLY TRP HIS ILE SER PRO SER PHE LYS ASP ARG VAL ALA SEQRES 6 B 107 PRO GLY PRO GLY LEU GLY LEU THR LEU GLN SER LEU THR SEQRES 7 B 107 VAL ASN ASP THR GLY GLU TYR PHE CYS ILE TYR HIS THR SEQRES 8 B 107 TYR PRO ASP GLY THR TYR THR GLY ARG ILE PHE LEU GLU SEQRES 9 B 107 VAL LEU GLU SEQRES 1 C 140 GLN ASP VAL ARG VAL GLN VAL LEU PRO GLU VAL ARG GLY SEQRES 2 C 140 GLN LEU GLY GLY THR VAL GLU LEU PRO CYS HIS LEU LEU SEQRES 3 C 140 PRO PRO VAL PRO GLY LEU TYR ILE SER LEU VAL THR TRP SEQRES 4 C 140 GLN ARG PRO ASP ALA PRO ALA ASN HIS GLN ASN VAL ALA SEQRES 5 C 140 ALA PHE HIS PRO LYS MET GLY PRO SER PHE PRO SER PRO SEQRES 6 C 140 LYS PRO GLY SER GLU ARG LEU SER PHE VAL SER ALA LYS SEQRES 7 C 140 GLN SER THR GLY GLN ASP THR GLU ALA GLU LEU GLN ASP SEQRES 8 C 140 ALA THR LEU ALA LEU HIS GLY LEU THR VAL GLU ASP GLU SEQRES 9 C 140 GLY ASN TYR THR CYS GLU PHE ALA THR PHE PRO LYS GLY SEQRES 10 C 140 SER VAL ARG GLY MET THR TRP LEU ARG VAL LEU VAL PRO SEQRES 11 C 140 ARG GLY SER GLY HIS HIS HIS HIS HIS HIS SEQRES 1 D 140 GLN ASP VAL ARG VAL GLN VAL LEU PRO GLU VAL ARG GLY SEQRES 2 D 140 GLN LEU GLY GLY THR VAL GLU LEU PRO CYS HIS LEU LEU SEQRES 3 D 140 PRO PRO VAL PRO GLY LEU TYR ILE SER LEU VAL THR TRP SEQRES 4 D 140 GLN ARG PRO ASP ALA PRO ALA ASN HIS GLN ASN VAL ALA SEQRES 5 D 140 ALA PHE HIS PRO LYS MET GLY PRO SER PHE PRO SER PRO SEQRES 6 D 140 LYS PRO GLY SER GLU ARG LEU SER PHE VAL SER ALA LYS SEQRES 7 D 140 GLN SER THR GLY GLN ASP THR GLU ALA GLU LEU GLN ASP SEQRES 8 D 140 ALA THR LEU ALA LEU HIS GLY LEU THR VAL GLU ASP GLU SEQRES 9 D 140 GLY ASN TYR THR CYS GLU PHE ALA THR PHE PRO LYS GLY SEQRES 10 D 140 SER VAL ARG GLY MET THR TRP LEU ARG VAL LEU VAL PRO SEQRES 11 D 140 ARG GLY SER GLY HIS HIS HIS HIS HIS HIS HET GOL A 200 6 HET SO4 B 201 5 HET NAG C 200 14 HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 5 GOL C3 H8 O3 FORMUL 6 SO4 O4 S 2- FORMUL 7 NAG C8 H15 N O6 HELIX 1 AA1 THR A 99 THR A 103 5 5 HELIX 2 AA2 THR B 99 THR B 103 5 5 HELIX 3 AA3 PRO C 76 HIS C 79 5 4 HELIX 4 AA4 THR C 131 GLU C 135 5 5 HELIX 5 AA5 PRO D 76 HIS D 79 5 4 HELIX 6 AA6 THR D 131 GLU D 135 5 5 SHEET 1 AA1 2 THR A 26 THR A 29 0 SHEET 2 AA1 2 CYS A 45 SER A 48 -1 O HIS A 46 N GLU A 28 SHEET 1 AA212 GLY A 74 ILE A 77 0 SHEET 2 AA212 GLN A 64 ASN A 70 -1 N ASN A 70 O GLY A 74 SHEET 3 AA212 GLN A 53 GLN A 61 -1 N TRP A 59 O ALA A 67 SHEET 4 AA212 GLY A 104 TYR A 113 -1 O PHE A 107 N GLU A 60 SHEET 5 AA212 GLY A 116 GLU A 125 -1 O GLY A 116 N THR A 112 SHEET 6 AA212 ASN A 32 SER A 34 1 N ILE A 33 O GLU A 125 SHEET 7 AA212 ASN B 32 GLU B 36 -1 O SER B 34 N ASN A 32 SHEET 8 AA212 GLY B 116 LEU B 127 1 O LEU B 127 N ALA B 35 SHEET 9 AA212 GLY B 104 TYR B 113 -1 N THR B 112 O GLY B 116 SHEET 10 AA212 GLN B 53 GLN B 61 -1 N GLU B 60 O PHE B 107 SHEET 11 AA212 GLN B 64 ASN B 70 -1 O ALA B 67 N TRP B 59 SHEET 12 AA212 GLY B 74 ILE B 77 -1 O GLY B 74 N ASN B 70 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 2 THR B 26 THR B 29 0 SHEET 2 AA4 2 CYS B 45 SER B 48 -1 O HIS B 46 N GLU B 28 SHEET 1 AA5 3 ILE B 41 LEU B 43 0 SHEET 2 AA5 3 LEU B 93 LEU B 95 -1 O LEU B 93 N LEU B 43 SHEET 3 AA5 3 VAL B 85 PRO B 87 -1 N ALA B 86 O THR B 94 SHEET 1 AA6 2 ARG C 35 VAL C 38 0 SHEET 2 AA6 2 CYS C 54 LEU C 57 -1 O LEU C 57 N ARG C 35 SHEET 1 AA7 6 GLU C 41 GLN C 45 0 SHEET 2 AA7 6 GLY C 148 LEU C 159 1 O TRP C 155 N VAL C 42 SHEET 3 AA7 6 GLY C 136 PHE C 145 -1 N GLY C 136 O LEU C 156 SHEET 4 AA7 6 TYR C 64 GLN C 71 -1 N GLN C 71 O THR C 139 SHEET 5 AA7 6 ASN C 81 HIS C 86 -1 O ALA C 83 N TRP C 70 SHEET 6 AA7 6 GLY C 90 SER C 92 -1 O GLY C 90 N HIS C 86 SHEET 1 AA8 3 VAL C 50 LEU C 52 0 SHEET 2 AA8 3 LEU C 125 LEU C 127 -1 O LEU C 125 N LEU C 52 SHEET 3 AA8 3 LEU C 103 PHE C 105 -1 N SER C 104 O ALA C 126 SHEET 1 AA9 2 ARG D 35 VAL D 38 0 SHEET 2 AA9 2 CYS D 54 LEU D 57 -1 O LEU D 57 N ARG D 35 SHEET 1 AB1 6 GLU D 41 GLN D 45 0 SHEET 2 AB1 6 GLY D 148 LEU D 159 1 O ARG D 157 N VAL D 42 SHEET 3 AB1 6 GLY D 136 PHE D 145 -1 N GLY D 136 O LEU D 156 SHEET 4 AB1 6 TYR D 64 GLN D 71 -1 N GLN D 71 O THR D 139 SHEET 5 AB1 6 ASN D 81 HIS D 86 -1 O ALA D 83 N TRP D 70 SHEET 6 AB1 6 GLY D 90 SER D 92 -1 O GLY D 90 N HIS D 86 SHEET 1 AB2 3 VAL D 50 LEU D 52 0 SHEET 2 AB2 3 LEU D 125 LEU D 127 -1 O LEU D 125 N LEU D 52 SHEET 3 AB2 3 LEU D 103 PHE D 105 -1 N SER D 104 O ALA D 126 SSBOND 1 CYS A 45 CYS A 108 1555 1555 2.03 SSBOND 2 CYS B 45 CYS B 108 1555 1555 2.04 SSBOND 3 CYS C 54 CYS C 140 1555 1555 2.03 SSBOND 4 CYS D 54 CYS D 140 1555 1555 2.03 LINK ND2 ASN C 137 C1 NAG C 200 1555 1555 1.38 CISPEP 1 GLY A 88 PRO A 89 0 0.42 CISPEP 2 TYR A 113 PRO A 114 0 3.03 CISPEP 3 GLY B 88 PRO B 89 0 0.14 CISPEP 4 TYR B 113 PRO B 114 0 3.01 CISPEP 5 LEU C 57 PRO C 58 0 0.70 CISPEP 6 LYS C 97 PRO C 98 0 3.01 CISPEP 7 PHE C 145 PRO C 146 0 3.33 CISPEP 8 LEU D 57 PRO D 58 0 -3.41 CISPEP 9 LYS D 97 PRO D 98 0 2.71 CISPEP 10 PHE D 145 PRO D 146 0 3.44 CRYST1 68.500 68.500 253.910 90.00 90.00 90.00 P 43 21 2 16 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 0.014599 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014599 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003938 0.00000