PDB Short entry for 4FQP HEADER CELL ADHESION 25-JUN-12 4FQP TITLE CRYSTAL STRUCTURE OF HUMAN NECTIN-LIKE 5 FULL ECTODOMAIN (D1-D3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLIOVIRUS RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ECTODOMAIN (D1-D3, UNP RESIDUES 28-334); COMPND 5 SYNONYM: NECTIN-LIKE PROTEIN 5, NECL-5; 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: PVR, PVS; 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, VIRAL ENTRY RECEPTOR, CELL KEYWDS 2 ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR O.J.HARRISON,X.JIN,J.BRASCH,L.SHAPIRO REVDAT 5 13-SEP-23 4FQP 1 HETSYN REVDAT 4 29-JUL-20 4FQP 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 26-SEP-12 4FQP 1 JRNL REVDAT 2 05-SEP-12 4FQP 1 JRNL REVDAT 1 22-AUG-12 4FQP 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. 3.60 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) : 3.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 17687 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) : 0.250 REMARK 3 R VALUE (WORKING SET) : 0.248 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 963 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) : 3.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1034 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.31 REMARK 3 BIN R VALUE (WORKING SET) : 0.5080 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.4740 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 : 257 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) : 116.4 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.81000 REMARK 3 B22 (A**2) : 6.81000 REMARK 3 B33 (A**2) : -10.21000 REMARK 3 B12 (A**2) : 3.40000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.548 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.385 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.285 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 40.773 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.919 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2685 ; 0.013 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1751 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3692 ; 1.761 ; 2.071 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4245 ; 3.064 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 305 ; 7.599 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 101 ;42.044 ;24.653 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 371 ;20.406 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;13.525 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 468 ; 0.403 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2782 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 470 ; 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 28 A 142 REMARK 3 ORIGIN FOR THE GROUP (A): -58.7149 -19.0715 -19.7168 REMARK 3 T TENSOR REMARK 3 T11: 0.0566 T22: 0.0650 REMARK 3 T33: 0.1124 T12: 0.0083 REMARK 3 T13: 0.0750 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 2.0985 L22: 13.5613 REMARK 3 L33: 6.4049 L12: 0.8514 REMARK 3 L13: 0.8110 L23: 6.0329 REMARK 3 S TENSOR REMARK 3 S11: -0.2383 S12: 0.1184 S13: -0.2559 REMARK 3 S21: 0.1706 S22: -0.2549 S23: 0.4338 REMARK 3 S31: 0.1669 S32: -0.1537 S33: 0.4932 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 143 A 241 REMARK 3 ORIGIN FOR THE GROUP (A): -51.6785 20.6901 -11.2038 REMARK 3 T TENSOR REMARK 3 T11: 0.0439 T22: 0.2004 REMARK 3 T33: 0.1231 T12: -0.0078 REMARK 3 T13: -0.0528 T23: 0.1173 REMARK 3 L TENSOR REMARK 3 L11: 0.1668 L22: 17.1127 REMARK 3 L33: 3.4617 L12: 0.2016 REMARK 3 L13: 0.6769 L23: -2.1928 REMARK 3 S TENSOR REMARK 3 S11: -0.0332 S12: 0.0605 S13: 0.0575 REMARK 3 S21: 0.1539 S22: -0.1442 S23: -0.3769 REMARK 3 S31: -0.0821 S32: 0.1341 S33: 0.1775 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 242 A 333 REMARK 3 ORIGIN FOR THE GROUP (A): -58.3767 63.3116 -15.2561 REMARK 3 T TENSOR REMARK 3 T11: 0.4521 T22: 0.0417 REMARK 3 T33: 0.5876 T12: 0.0016 REMARK 3 T13: -0.3844 T23: 0.0485 REMARK 3 L TENSOR REMARK 3 L11: 3.3290 L22: 9.1905 REMARK 3 L33: 6.9608 L12: -4.5609 REMARK 3 L13: 2.7078 L23: -4.4704 REMARK 3 S TENSOR REMARK 3 S11: -0.2794 S12: 0.3313 S13: 0.8032 REMARK 3 S21: 0.9560 S22: -0.3409 S23: -1.2082 REMARK 3 S31: -0.9531 S32: 0.3482 S33: 0.6203 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 4FQP 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_1000073235. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 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 : 19387 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.563 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.55000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 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 3EOW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 88.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 11.1 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 55% V/V TACSIMATE, 0.1 M BICINE, PH REMARK 280 9.0, WITH ADDITIONAL 10% TACSIMATE AS CRYOPROTECTANT, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.15K 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 182.43000 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 91.21500 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 136.82250 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 45.60750 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 228.03750 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 182.43000 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 91.21500 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 45.60750 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 136.82250 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 228.03750 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G 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 PRO A 334 REMARK 465 HIS A 335 REMARK 465 HIS A 336 REMARK 465 HIS A 337 REMARK 465 HIS A 338 REMARK 465 HIS A 339 REMARK 465 HIS A 340 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 A 120 C2 NAG C 1 1.75 REMARK 500 O4 NAG B 2 O5 BMA B 3 1.90 REMARK 500 CG ASN A 120 C1 NAG C 1 1.98 REMARK 500 CG ASN A 307 C1 NAG G 1 2.07 REMARK 500 OD1 ASN A 120 C1 NAG C 1 2.09 REMARK 500 ND2 ASN A 307 O5 NAG G 1 2.16 REMARK 500 ND2 ASN A 237 O5 NAG F 1 2.16 REMARK 500 O4 NAG E 1 O5 NAG E 2 2.18 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 43 -159.85 -97.53 REMARK 500 ASN A 55 -6.68 -53.18 REMARK 500 ARG A 104 -31.69 -137.01 REMARK 500 LEU A 156 46.13 -103.03 REMARK 500 ASN A 253 -14.56 -46.28 REMARK 500 GLU A 261 105.42 -57.87 REMARK 500 LEU A 325 112.26 -166.08 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: 4FOM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN NECTIN-3 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 4FQP A 28 334 UNP P15151 PVR_HUMAN 28 334 SEQADV 4FQP HIS A 335 UNP P15151 EXPRESSION TAG SEQADV 4FQP HIS A 336 UNP P15151 EXPRESSION TAG SEQADV 4FQP HIS A 337 UNP P15151 EXPRESSION TAG SEQADV 4FQP HIS A 338 UNP P15151 EXPRESSION TAG SEQADV 4FQP HIS A 339 UNP P15151 EXPRESSION TAG SEQADV 4FQP HIS A 340 UNP P15151 EXPRESSION TAG SEQRES 1 A 313 ASP VAL VAL VAL GLN ALA PRO THR GLN VAL PRO GLY PHE SEQRES 2 A 313 LEU GLY ASP SER VAL THR LEU PRO CYS TYR LEU GLN VAL SEQRES 3 A 313 PRO ASN MET GLU VAL THR HIS VAL SER GLN LEU THR TRP SEQRES 4 A 313 ALA ARG HIS GLY GLU SER GLY SER MET ALA VAL PHE HIS SEQRES 5 A 313 GLN THR GLN GLY PRO SER TYR SER GLU SER LYS ARG LEU SEQRES 6 A 313 GLU PHE VAL ALA ALA ARG LEU GLY ALA GLU LEU ARG ASN SEQRES 7 A 313 ALA SER LEU ARG MET PHE GLY LEU ARG VAL GLU ASP GLU SEQRES 8 A 313 GLY ASN TYR THR CYS LEU PHE VAL THR PHE PRO GLN GLY SEQRES 9 A 313 SER ARG SER VAL ASP ILE TRP LEU ARG VAL LEU ALA LYS SEQRES 10 A 313 PRO GLN ASN THR ALA GLU VAL GLN LYS VAL GLN LEU THR SEQRES 11 A 313 GLY GLU PRO VAL PRO MET ALA ARG CYS VAL SER THR GLY SEQRES 12 A 313 GLY ARG PRO PRO ALA GLN ILE THR TRP HIS SER ASP LEU SEQRES 13 A 313 GLY GLY MET PRO ASN THR SER GLN VAL PRO GLY PHE LEU SEQRES 14 A 313 SER GLY THR VAL THR VAL THR SER LEU TRP ILE LEU VAL SEQRES 15 A 313 PRO SER SER GLN VAL ASP GLY LYS ASN VAL THR CYS LYS SEQRES 16 A 313 VAL GLU HIS GLU SER PHE GLU LYS PRO GLN LEU LEU THR SEQRES 17 A 313 VAL ASN LEU THR VAL TYR TYR PRO PRO GLU VAL SER ILE SEQRES 18 A 313 SER GLY TYR ASP ASN ASN TRP TYR LEU GLY GLN ASN GLU SEQRES 19 A 313 ALA THR LEU THR CYS ASP ALA ARG SER ASN PRO GLU PRO SEQRES 20 A 313 THR GLY TYR ASN TRP SER THR THR MET GLY PRO LEU PRO SEQRES 21 A 313 PRO PHE ALA VAL ALA GLN GLY ALA GLN LEU LEU ILE ARG SEQRES 22 A 313 PRO VAL ASP LYS PRO ILE ASN THR THR LEU ILE CYS ASN SEQRES 23 A 313 VAL THR ASN ALA LEU GLY ALA ARG GLN ALA GLU LEU THR SEQRES 24 A 313 VAL GLN VAL LYS GLU GLY PRO PRO HIS HIS HIS HIS HIS SEQRES 25 A 313 HIS MODRES 4FQP ASN A 237 ASN GLYCOSYLATION SITE MODRES 4FQP ASN A 120 ASN GLYCOSYLATION SITE MODRES 4FQP ASN A 188 ASN GLYCOSYLATION SITE MODRES 4FQP ASN A 105 ASN GLYCOSYLATION SITE MODRES 4FQP ASN A 307 ASN GLYCOSYLATION SITE MODRES 4FQP ASN A 313 ASN GLYCOSYLATION SITE MODRES 4FQP ASN A 218 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET BMA B 3 11 HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET MAN C 4 11 HET FUC C 5 10 HET NAG D 1 14 HET NAG D 2 14 HET NAG E 1 14 HET NAG E 2 14 HET NAG F 1 14 HET NAG F 2 14 HET BMA F 3 11 HET NAG G 1 14 HET NAG G 2 14 HET BMA G 3 11 HET FUC G 4 10 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 13(C8 H15 N O6) FORMUL 2 BMA 4(C6 H12 O6) FORMUL 3 MAN C6 H12 O6 FORMUL 3 FUC 2(C6 H12 O5) HELIX 1 1 ARG A 114 GLU A 118 5 5 HELIX 2 2 SER A 211 ASP A 215 5 5 SHEET 1 A 2 VAL A 30 GLN A 32 0 SHEET 2 A 2 TYR A 50 GLN A 52 -1 O TYR A 50 N GLN A 32 SHEET 1 B 6 GLN A 36 VAL A 37 0 SHEET 2 B 6 SER A 132 LEU A 139 1 O TRP A 138 N VAL A 37 SHEET 3 B 6 GLY A 119 VAL A 126 -1 N TYR A 121 O ILE A 137 SHEET 4 B 6 GLN A 63 ARG A 68 -1 N GLN A 63 O VAL A 126 SHEET 5 B 6 ALA A 76 HIS A 79 -1 O ALA A 76 N TRP A 66 SHEET 6 B 6 GLY A 83 TYR A 86 -1 O SER A 85 N VAL A 77 SHEET 1 C 3 VAL A 45 LEU A 47 0 SHEET 2 C 3 LEU A 108 MET A 110 -1 O LEU A 108 N LEU A 47 SHEET 3 C 3 LEU A 92 PHE A 94 -1 N GLU A 93 O ARG A 109 SHEET 1 D 4 GLN A 146 VAL A 151 0 SHEET 2 D 4 VAL A 161 GLY A 171 -1 O VAL A 167 N THR A 148 SHEET 3 D 4 VAL A 200 LEU A 208 -1 O TRP A 206 N ALA A 164 SHEET 4 D 4 MET A 186 PRO A 193 -1 N SER A 190 O THR A 203 SHEET 1 E 3 GLN A 176 SER A 181 0 SHEET 2 E 3 ASN A 218 GLU A 224 -1 O LYS A 222 N THR A 178 SHEET 3 E 3 GLN A 232 ASN A 237 -1 O LEU A 234 N CYS A 221 SHEET 1 F 4 TYR A 242 SER A 249 0 SHEET 2 F 4 ALA A 262 ASN A 271 -1 O ASP A 267 N SER A 247 SHEET 3 F 4 GLN A 296 ILE A 299 -1 O ILE A 299 N ALA A 262 SHEET 4 F 4 ALA A 290 GLN A 293 -1 N GLN A 293 O GLN A 296 SHEET 1 G 4 TRP A 255 TYR A 256 0 SHEET 2 G 4 ALA A 320 LYS A 330 1 O LYS A 330 N TRP A 255 SHEET 3 G 4 ASN A 307 THR A 315 -1 N LEU A 310 O LEU A 325 SHEET 4 G 4 GLY A 276 THR A 281 -1 N SER A 280 O ILE A 311 SSBOND 1 CYS A 49 CYS A 123 1555 1555 2.04 SSBOND 2 CYS A 166 CYS A 221 1555 1555 2.04 SSBOND 3 CYS A 266 CYS A 312 1555 1555 2.05 LINK ND2 ASN A 105 C1 NAG B 1 1555 1555 1.42 LINK ND2 ASN A 120 C1 NAG C 1 1555 1555 1.39 LINK ND2 ASN A 188 C1 NAG D 1 1555 1555 1.42 LINK ND2 ASN A 218 C1 NAG E 1 1555 1555 1.49 LINK ND2 ASN A 237 C1 NAG F 1 1555 1555 1.38 LINK ND2 ASN A 307 C1 NAG G 1 1555 1555 1.40 LINK ND2 ASN A 313 C1 NAG A 420 1555 1555 1.47 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.49 LINK O4 NAG B 2 C1 BMA B 3 1555 1555 1.25 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.48 LINK O6 NAG C 1 C1 FUC C 5 1555 1555 1.45 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.43 LINK O3 BMA C 3 C1 MAN C 4 1555 1555 1.39 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.54 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.45 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.47 LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.46 LINK O4 NAG G 1 C1 NAG G 2 1555 1555 1.47 LINK O6 NAG G 1 C1 FUC G 4 1555 1555 1.43 LINK O4 NAG G 2 C1 BMA G 3 1555 1555 1.42 CISPEP 1 PRO A 38 GLY A 39 0 -2.66 CISPEP 2 PHE A 128 PRO A 129 0 11.44 CISPEP 3 ARG A 172 PRO A 173 0 -10.14 CISPEP 4 ASN A 271 PRO A 272 0 -3.17 CRYST1 138.919 138.919 273.645 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 0.007198 0.004156 0.000000 0.00000 SCALE2 0.000000 0.008312 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003654 0.00000