HEADER CELL ADHESION 20-JUN-12 4FOM TITLE CRYSTAL STRUCTURE OF HUMAN NECTIN-3 FULL ECTODOMAIN (D1-D3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLIOVIRUS RECEPTOR-RELATED PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ECTODOMAIN (D1-D3, UNP RESIDUES 58-359); COMPND 5 SYNONYM: NECTIN-3, CDW113; 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: PVRL3, PRR3; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK 293F; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PCEP4 KEYWDS IMMUNOGLOBULIN-LIKE DOMAIN, IG DOMAIN, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR O.J.HARRISON,X.JIN,J.BRASCH,L.SHAPIRO REVDAT 5 13-SEP-23 4FOM 1 HETSYN REVDAT 4 29-JUL-20 4FOM 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 26-SEP-12 4FOM 1 JRNL REVDAT 2 05-SEP-12 4FOM 1 JRNL REVDAT 1 22-AUG-12 4FOM 0 JRNL AUTH O.J.HARRISON,J.VENDOME,J.BRASCH,X.JIN,S.HONG,P.S.KATSAMBA, JRNL AUTH 2 G.AHLSEN,R.B.TROYANOVSKY,S.M.TROYANOVSKY,B.HONIG,L.SHAPIRO JRNL TITL NECTIN ECTODOMAIN STRUCTURES REVEAL A CANONICAL ADHESIVE JRNL TITL 2 INTERFACE. JRNL REF NAT.STRUCT.MOL.BIOL. V. 19 906 2012 JRNL REFN ISSN 1545-9993 JRNL PMID 22902367 JRNL DOI 10.1038/NSMB.2366 REMARK 2 REMARK 2 RESOLUTION. 3.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 3.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 11210 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) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 558 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) : 3.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 4.03 REMARK 3 REFLECTION IN BIN (WORKING SET) : 659 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.3250 REMARK 3 BIN FREE R VALUE SET COUNT : 34 REMARK 3 BIN FREE R VALUE : 0.3740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2342 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 246 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 170.5 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.45000 REMARK 3 B22 (A**2) : 4.45000 REMARK 3 B33 (A**2) : -6.68000 REMARK 3 B12 (A**2) : 2.23000 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): 1.721 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.538 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.467 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 62.326 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2656 ; 0.016 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1735 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3628 ; 1.295 ; 2.041 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4206 ; 0.934 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 301 ; 8.555 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 101 ;41.454 ;24.455 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 381 ;22.382 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;22.335 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 452 ; 0.058 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2742 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 488 ; 0.005 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 3 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 58 A 168 REMARK 3 ORIGIN FOR THE GROUP (A): -38.0574 38.2624 -18.6403 REMARK 3 T TENSOR REMARK 3 T11: 1.9288 T22: 0.3630 REMARK 3 T33: 2.2114 T12: 0.8083 REMARK 3 T13: 0.1545 T23: -0.0733 REMARK 3 L TENSOR REMARK 3 L11: 23.7302 L22: 3.3393 REMARK 3 L33: 5.1183 L12: -8.4941 REMARK 3 L13: 1.7204 L23: -0.3595 REMARK 3 S TENSOR REMARK 3 S11: -0.1647 S12: -0.4974 S13: -0.6993 REMARK 3 S21: 0.2556 S22: 0.1807 S23: 1.0239 REMARK 3 S31: -0.3135 S32: -0.3375 S33: -0.0160 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 169 A 266 REMARK 3 ORIGIN FOR THE GROUP (A): -1.7516 17.5426 -13.5384 REMARK 3 T TENSOR REMARK 3 T11: 0.9577 T22: 0.3490 REMARK 3 T33: 0.5263 T12: -0.0074 REMARK 3 T13: 0.1391 T23: -0.1416 REMARK 3 L TENSOR REMARK 3 L11: 10.9489 L22: 8.8400 REMARK 3 L33: 6.1239 L12: -8.4624 REMARK 3 L13: 5.1878 L23: -3.6662 REMARK 3 S TENSOR REMARK 3 S11: -0.2099 S12: -0.9265 S13: 0.6322 REMARK 3 S21: 0.3906 S22: 0.1480 S23: 0.0974 REMARK 3 S31: -1.2822 S32: -0.1170 S33: 0.0619 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 267 A 359 REMARK 3 ORIGIN FOR THE GROUP (A): 22.0198 -17.6716 0.5228 REMARK 3 T TENSOR REMARK 3 T11: 0.7843 T22: 0.8690 REMARK 3 T33: 0.7482 T12: 0.4524 REMARK 3 T13: 0.0882 T23: 0.0939 REMARK 3 L TENSOR REMARK 3 L11: 4.9135 L22: 12.1116 REMARK 3 L33: 15.0762 L12: -5.6370 REMARK 3 L13: 6.4061 L23: -9.3634 REMARK 3 S TENSOR REMARK 3 S11: 0.2104 S12: -0.1544 S13: -0.4447 REMARK 3 S21: 0.2378 S22: -0.4041 S23: -0.5041 REMARK 3 S31: 1.3336 S32: 1.7918 S33: 0.1938 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 4FOM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000073160. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : BENT SINGLE SI(111) CRYSTAL REMARK 200 (HORIZONTAL FOCUSING AND REMARK 200 DEFLECTION) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11776 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.930 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07000 REMARK 200 FOR THE DATA SET : 34.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.61000 REMARK 200 FOR SHELL : 3.200 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: PDB ENTRY 3ALP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 86.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 9.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4.6 M AMMONIUM ACETATE, 0.1 M SODIUM REMARK 280 ACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.15K, PH REMARK 280 4.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 165.02867 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 82.51433 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 123.77150 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 41.25717 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 206.28583 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 165.02867 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 82.51433 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 41.25717 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 123.77150 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 206.28583 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 BIOMT1 2 0.500000 0.866025 0.000000 -65.93350 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 114.20017 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -41.25717 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 HIS A 360 REMARK 465 HIS A 361 REMARK 465 HIS A 362 REMARK 465 HIS A 363 REMARK 465 HIS A 364 REMARK 465 HIS A 365 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 OD1 ASN A 186 C1 NAG D 1 1.84 REMARK 500 ND2 ASN A 186 O5 NAG D 1 1.92 REMARK 500 CG ASN A 186 C1 NAG D 1 1.93 REMARK 500 O4 NAG C 1 C2 NAG C 2 2.05 REMARK 500 ND2 ASN A 222 O5 NAG E 1 2.18 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 ASN A 186 CG ASN A 186 ND2 -0.151 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 PHE A 153 CB - CA - C ANGL. DEV. = -13.1 DEGREES REMARK 500 PRO A 154 N - CA - CB ANGL. DEV. = -16.6 DEGREES REMARK 500 PRO A 154 N - CD - CG ANGL. DEV. = -16.2 DEGREES REMARK 500 PRO A 154 N - CA - C ANGL. DEV. = 21.8 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 81 83.46 -65.71 REMARK 500 ASN A 83 0.11 -58.18 REMARK 500 LYS A 97 -9.40 69.88 REMARK 500 TYR A 109 54.08 -107.92 REMARK 500 TYR A 117 1.35 -67.40 REMARK 500 ASN A 137 75.64 63.16 REMARK 500 LEU A 155 -37.76 -33.47 REMARK 500 ASN A 186 153.01 -43.71 REMARK 500 GLU A 187 139.08 -38.13 REMARK 500 ASP A 205 134.26 -174.50 REMARK 500 GLU A 214 153.84 175.34 REMARK 500 ASN A 222 -6.20 -55.19 REMARK 500 CYS A 291 32.42 -95.86 REMARK 500 ASN A 292 132.96 -35.54 REMARK 500 PHE A 300 -51.12 -122.69 REMARK 500 SER A 302 47.17 -145.03 REMARK 500 TRP A 304 61.16 -114.35 REMARK 500 ALA A 317 65.11 -116.40 REMARK 500 ASP A 319 -117.15 57.57 REMARK 500 PHE A 324 75.63 -116.13 REMARK 500 PRO A 327 150.25 -48.06 REMARK 500 TYR A 332 -6.35 84.51 REMARK 500 SER A 343 -38.05 -36.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4FMF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN NECTIN-1 FULL ECTODOMAIN D1-D3 REMARK 900 RELATED ID: 4FMK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURINE NECTIN-2 FRAGMENT D1-D2 REMARK 900 RELATED ID: 4FN0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURINE NECTIN-2 FRAGMENT D1-D2, 2ND CRYSTAL REMARK 900 FORM REMARK 900 RELATED ID: 4FQP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN NECTIN-LIKE 5 FULL ECTODOMAIN D1-D3 REMARK 900 RELATED ID: 4FRW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN NECTIN-4 FRAGMENT D1-D2 REMARK 900 RELATED ID: 4FS0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MUTANT F136D OF MOUSE NECTIN-2 FRAGMENT D1-D2 DBREF 4FOM A 58 359 UNP Q9NQS3 PVRL3_HUMAN 58 359 SEQADV 4FOM HIS A 360 UNP Q9NQS3 EXPRESSION TAG SEQADV 4FOM HIS A 361 UNP Q9NQS3 EXPRESSION TAG SEQADV 4FOM HIS A 362 UNP Q9NQS3 EXPRESSION TAG SEQADV 4FOM HIS A 363 UNP Q9NQS3 EXPRESSION TAG SEQADV 4FOM HIS A 364 UNP Q9NQS3 EXPRESSION TAG SEQADV 4FOM HIS A 365 UNP Q9NQS3 EXPRESSION TAG SEQRES 1 A 308 GLY PRO ILE ILE VAL GLU PRO HIS VAL THR ALA VAL TRP SEQRES 2 A 308 GLY LYS ASN VAL SER LEU LYS CYS LEU ILE GLU VAL ASN SEQRES 3 A 308 GLU THR ILE THR GLN ILE SER TRP GLU LYS ILE HIS GLY SEQRES 4 A 308 LYS SER SER GLN THR VAL ALA VAL HIS HIS PRO GLN TYR SEQRES 5 A 308 GLY PHE SER VAL GLN GLY GLU TYR GLN GLY ARG VAL LEU SEQRES 6 A 308 PHE LYS ASN TYR SER LEU ASN ASP ALA THR ILE THR LEU SEQRES 7 A 308 HIS ASN ILE GLY PHE SER ASP SER GLY LYS TYR ILE CYS SEQRES 8 A 308 LYS ALA VAL THR PHE PRO LEU GLY ASN ALA GLN SER SER SEQRES 9 A 308 THR THR VAL THR VAL LEU VAL GLU PRO THR VAL SER LEU SEQRES 10 A 308 ILE LYS GLY PRO ASP SER LEU ILE ASP GLY GLY ASN GLU SEQRES 11 A 308 THR VAL ALA ALA ILE CYS ILE ALA ALA THR GLY LYS PRO SEQRES 12 A 308 VAL ALA HIS ILE ASP TRP GLU GLY ASP LEU GLY GLU MET SEQRES 13 A 308 GLU SER THR THR THR SER PHE PRO ASN GLU THR ALA THR SEQRES 14 A 308 ILE ILE SER GLN TYR LYS LEU PHE PRO THR ARG PHE ALA SEQRES 15 A 308 ARG GLY ARG ARG ILE THR CYS VAL VAL LYS HIS PRO ALA SEQRES 16 A 308 LEU GLU LYS ASP ILE ARG TYR SER PHE ILE LEU ASP ILE SEQRES 17 A 308 GLN TYR ALA PRO GLU VAL SER VAL THR GLY TYR ASP GLY SEQRES 18 A 308 ASN TRP PHE VAL GLY ARG LYS GLY VAL ASN LEU LYS CYS SEQRES 19 A 308 ASN ALA ASP ALA ASN PRO PRO PRO PHE LYS SER VAL TRP SEQRES 20 A 308 SER ARG LEU ASP GLY GLN TRP PRO ASP GLY LEU LEU ALA SEQRES 21 A 308 SER ASP ASN THR LEU HIS PHE VAL HIS PRO LEU THR PHE SEQRES 22 A 308 ASN TYR SER GLY VAL TYR ILE CYS LYS VAL THR ASN SER SEQRES 23 A 308 LEU GLY GLN ARG SER ASP GLN LYS VAL ILE TYR ILE SER SEQRES 24 A 308 ASP PRO PRO HIS HIS HIS HIS HIS HIS MODRES 4FOM ASN A 186 ASN GLYCOSYLATION SITE MODRES 4FOM ASN A 73 ASN GLYCOSYLATION SITE MODRES 4FOM ASN A 125 ASN GLYCOSYLATION SITE MODRES 4FOM ASN A 331 ASN GLYCOSYLATION SITE MODRES 4FOM ASN A 222 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET MAN B 4 11 HET MAN B 5 11 HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET NAG D 1 14 HET NAG D 2 14 HET BMA D 3 11 HET MAN D 4 11 HET MAN D 5 11 HET FUC D 6 10 HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET MAN E 4 11 HET MAN E 5 11 HET NAG A 420 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE 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 HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 2 NAG 9(C8 H15 N O6) FORMUL 2 BMA 4(C6 H12 O6) FORMUL 2 MAN 6(C6 H12 O6) FORMUL 4 FUC C6 H12 O5 HELIX 1 1 GLY A 139 SER A 143 5 5 HELIX 2 2 THR A 236 ARG A 240 5 5 SHEET 1 A 6 THR A 67 VAL A 69 0 SHEET 2 A 6 GLY A 156 LEU A 167 1 O LEU A 167 N ALA A 68 SHEET 3 A 6 GLY A 144 THR A 152 -1 N THR A 152 O GLY A 156 SHEET 4 A 6 ILE A 86 ILE A 94 -1 N GLU A 92 O ILE A 147 SHEET 5 A 6 SER A 99 HIS A 105 -1 O VAL A 102 N TRP A 91 SHEET 6 A 6 PHE A 111 VAL A 113 -1 O SER A 112 N VAL A 104 SHEET 1 B 3 VAL A 74 LEU A 76 0 SHEET 2 B 3 ILE A 133 LEU A 135 -1 O ILE A 133 N LEU A 76 SHEET 3 B 3 VAL A 121 PHE A 123 -1 N LEU A 122 O THR A 134 SHEET 1 C 4 THR A 171 LYS A 176 0 SHEET 2 C 4 THR A 188 GLY A 198 -1 O ILE A 194 N SER A 173 SHEET 3 C 4 ALA A 225 LEU A 233 -1 O TYR A 231 N ALA A 191 SHEET 4 C 4 SER A 215 SER A 219 -1 N THR A 218 O THR A 226 SHEET 1 D 3 HIS A 203 TRP A 206 0 SHEET 2 D 3 ARG A 243 LYS A 249 -1 O VAL A 247 N ASP A 205 SHEET 3 D 3 ILE A 257 ILE A 262 -1 O ILE A 257 N VAL A 248 SHEET 1 E 2 TYR A 267 VAL A 271 0 SHEET 2 E 2 ALA A 293 ASN A 296 -1 O ASN A 296 N TYR A 267 SHEET 1 F 2 TRP A 280 PHE A 281 0 SHEET 2 F 2 ILE A 355 SER A 356 1 O SER A 356 N TRP A 280 SHEET 1 G 2 ASN A 288 LYS A 290 0 SHEET 2 G 2 THR A 321 HIS A 323 -1 O LEU A 322 N LEU A 289 SHEET 1 H 3 PRO A 299 ARG A 306 0 SHEET 2 H 3 VAL A 335 ASN A 342 -1 O LYS A 339 N VAL A 303 SHEET 3 H 3 GLY A 345 VAL A 352 -1 O GLY A 345 N ASN A 342 SSBOND 1 CYS A 78 CYS A 148 1555 1555 2.79 SSBOND 2 CYS A 193 CYS A 246 1555 1555 2.05 SSBOND 3 CYS A 291 CYS A 338 1555 1555 2.05 LINK ND2 ASN A 73 C1 NAG B 1 1555 1555 1.42 LINK ND2 ASN A 125 C1 NAG C 1 1555 1555 1.43 LINK ND2 ASN A 186 C1 NAG D 1 1555 1555 1.71 LINK ND2 ASN A 222 C1 NAG E 1 1555 1555 1.45 LINK ND2 ASN A 331 C1 NAG A 420 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.44 LINK O3 BMA B 3 C1 MAN B 4 1555 1555 1.40 LINK O6 BMA B 3 C1 MAN B 5 1555 1555 1.40 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.40 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.42 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.52 LINK O6 NAG D 1 C1 FUC D 6 1555 1555 1.40 LINK O4 NAG D 2 C1 BMA D 3 1555 1555 1.43 LINK O3 BMA D 3 C1 MAN D 4 1555 1555 1.42 LINK O6 BMA D 3 C1 MAN D 5 1555 1555 1.41 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.47 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.46 LINK O3 BMA E 3 C1 MAN E 4 1555 1555 1.39 LINK O6 BMA E 3 C1 MAN E 5 1555 1555 1.41 CISPEP 1 GLY A 115 GLU A 116 0 4.02 CISPEP 2 PHE A 153 PRO A 154 0 3.06 CISPEP 3 LYS A 199 PRO A 200 0 -8.14 CISPEP 4 ASN A 296 PRO A 297 0 0.14 CRYST1 131.867 131.867 247.543 90.00 90.00 120.00 P 65 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 0.007583 0.004378 0.000000 0.00000 SCALE2 0.000000 0.008757 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004040 0.00000