HEADER SIGNALING PROTEIN 17-APR-07 2PKD TITLE CRYSTAL STRUCTURE OF CD84: INSITE INTO SLAM FAMILY FUNCTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SLAM FAMILY MEMBER 5; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 FRAGMENT: CD84; COMPND 5 SYNONYM: SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE 5, LEUKOCYTE COMPND 6 DIFFERENTIATION ANTIGEN CD84, CD84 ANTIGEN, CELL SURFACE ANTIGEN COMPND 7 MAX.3, HLY9-BETA; COMPND 8 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: CD84, SLAMF5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS SLAM, SIGNALING LYMPHOCYTE ACTIVATION MOLECULE, IGV, IMMUNOGLOBULIN KEYWDS 2 VARIABLE, IGC, IMMUNOGLOBULIN CONSTANT, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Q.YAN,V.N.MALASHKEVICH,A.FEDOROV,E.CAO,J.W.LARY,J.L.COLE, AUTHOR 2 S.G.NATHENSON,S.C.ALMO REVDAT 5 21-FEB-24 2PKD 1 REMARK SEQADV REVDAT 4 18-OCT-17 2PKD 1 REMARK REVDAT 3 24-FEB-09 2PKD 1 VERSN REVDAT 2 25-DEC-07 2PKD 1 JRNL REVDAT 1 26-JUN-07 2PKD 0 JRNL AUTH Q.YAN,V.N.MALASHKEVICH,A.FEDOROV,E.FEDOROV,E.CAO,J.W.LARY, JRNL AUTH 2 J.L.COLE,S.G.NATHENSON,S.C.ALMO JRNL TITL STRUCTURE OF CD84 PROVIDES INSIGHT INTO SLAM FAMILY JRNL TITL 2 FUNCTION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 10583 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17563375 JRNL DOI 10.1073/PNAS.0703893104 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 80.0 REMARK 3 NUMBER OF REFLECTIONS : 39654 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 862 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 25.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.2410 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5186 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 393 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.08000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.269 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.240 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.161 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.841 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5366 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7344 ; 1.938 ; 1.947 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 649 ; 7.821 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 264 ;35.466 ;23.712 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 855 ;18.910 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;21.592 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 836 ; 0.136 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4166 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2280 ; 0.241 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3523 ; 0.321 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 306 ; 0.180 ; 0.200 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): 80 ; 0.266 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 30 ; 0.234 ; 0.200 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): 3346 ; 1.560 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5371 ; 2.680 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2329 ; 3.412 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1973 ; 5.370 ; 4.500 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 2PKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-APR-07. REMARK 100 THE DEPOSITION ID IS D_1000042471. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-05; 26-SEP-05 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : NSLS; NSLS REMARK 200 BEAMLINE : X9A; X29A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.961, 0.9797, 0.9794; 1.1 REMARK 200 MONOCHROMATOR : X9A; X29A REMARK 200 OPTICS : X9A; X29A REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM; ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39739 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.2 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 15.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.30 REMARK 200 R MERGE FOR SHELL (I) : 0.40600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, RESOLVE 2.09, SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.3 M MGCL2, 0.1 M, REMARK 280 HEPES, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 74.26350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 74.26350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 30.50650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 85.49100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.50650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 85.49100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 74.26350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.50650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 85.49100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 74.26350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.50650 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 85.49100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 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 APPLY THE FOLLOWING TO CHAINS: C, 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, F REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH C 556 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 LYS A 2 REMARK 465 ASP A 3 REMARK 465 SER A 4 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 465 ASP B 3 REMARK 465 MET C 1 REMARK 465 LYS C 2 REMARK 465 ASP C 3 REMARK 465 SER C 4 REMARK 465 MET D 1 REMARK 465 LYS D 2 REMARK 465 ASP D 3 REMARK 465 SER D 4 REMARK 465 MET E 1 REMARK 465 LYS E 2 REMARK 465 MET F 1 REMARK 465 LYS F 2 REMARK 465 ASP F 3 REMARK 465 SER F 4 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 O HOH C 531 O HOH C 564 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH E 641 O HOH F 128 5345 2.16 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 F 82 CG GLU F 82 CD 0.091 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 LEU E 13 CA - CB - CG 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 GLU A 15 -160.74 -107.38 REMARK 500 VAL A 21 -56.52 -120.78 REMARK 500 SER A 36 -139.09 -145.36 REMARK 500 ASP A 47 -150.48 -155.56 REMARK 500 PRO A 97 1.99 -58.46 REMARK 500 TYR A 98 -49.39 69.80 REMARK 500 LEU B 13 135.38 -36.20 REMARK 500 GLU B 15 -159.95 -103.79 REMARK 500 GLU B 25 68.61 -170.67 REMARK 500 ARG B 27 -2.86 -58.56 REMARK 500 SER B 36 -140.65 -136.89 REMARK 500 VAL B 40 -70.62 -125.46 REMARK 500 GLU B 49 -174.50 -170.45 REMARK 500 GLU B 63 3.62 59.38 REMARK 500 ASP B 96 139.50 -35.31 REMARK 500 TYR B 98 -33.38 69.62 REMARK 500 GLU C 15 -158.01 -107.13 REMARK 500 VAL C 21 -55.12 -122.67 REMARK 500 SER C 36 -137.14 -149.13 REMARK 500 VAL C 40 -66.11 -122.06 REMARK 500 ASP C 78 50.76 38.05 REMARK 500 ARG C 110 145.88 -30.36 REMARK 500 LEU D 13 128.69 -38.19 REMARK 500 GLU D 15 -166.07 -105.36 REMARK 500 SER D 36 -131.87 -139.54 REMARK 500 VAL D 40 -65.42 -120.27 REMARK 500 SER D 48 -142.10 -118.19 REMARK 500 GLN D 94 35.74 -87.48 REMARK 500 ALA D 95 149.30 -179.42 REMARK 500 TYR D 98 -41.06 80.95 REMARK 500 GLU E 5 29.79 -70.97 REMARK 500 LEU E 13 127.00 -38.81 REMARK 500 GLU E 15 -157.95 -93.81 REMARK 500 GLU E 25 78.43 -111.34 REMARK 500 SER E 36 -138.83 -142.54 REMARK 500 TYR E 98 -38.34 62.95 REMARK 500 GLU F 15 -158.80 -110.20 REMARK 500 GLU F 25 60.01 -113.47 REMARK 500 SER F 36 -133.88 -147.97 REMARK 500 THR F 50 42.92 -69.36 REMARK 500 GLU F 63 -0.18 76.16 REMARK 500 ASP F 96 133.04 -36.83 REMARK 500 TYR F 98 -48.42 83.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 48 GLU A 49 148.21 REMARK 500 GLU A 49 THR A 50 148.49 REMARK 500 GLU B 49 THR B 50 149.20 REMARK 500 THR B 50 ALA B 51 -144.93 REMARK 500 SER F 48 GLU F 49 -41.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL C 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL E 600 DBREF 2PKD A 2 111 UNP Q9UIB8 SLAF5_HUMAN 22 131 DBREF 2PKD B 2 111 UNP Q9UIB8 SLAF5_HUMAN 22 131 DBREF 2PKD C 2 111 UNP Q9UIB8 SLAF5_HUMAN 22 131 DBREF 2PKD D 2 111 UNP Q9UIB8 SLAF5_HUMAN 22 131 DBREF 2PKD E 2 111 UNP Q9UIB8 SLAF5_HUMAN 22 131 DBREF 2PKD F 2 111 UNP Q9UIB8 SLAF5_HUMAN 22 131 SEQADV 2PKD MET A 1 UNP Q9UIB8 INITIATING METHIONINE SEQADV 2PKD MET B 1 UNP Q9UIB8 INITIATING METHIONINE SEQADV 2PKD MET C 1 UNP Q9UIB8 INITIATING METHIONINE SEQADV 2PKD MET D 1 UNP Q9UIB8 INITIATING METHIONINE SEQADV 2PKD MET E 1 UNP Q9UIB8 INITIATING METHIONINE SEQADV 2PKD MET F 1 UNP Q9UIB8 INITIATING METHIONINE SEQRES 1 A 111 MET LYS ASP SER GLU ILE PHE THR VAL ASN GLY ILE LEU SEQRES 2 A 111 GLY GLU SER VAL THR PHE PRO VAL ASN ILE GLN GLU PRO SEQRES 3 A 111 ARG GLN VAL LYS ILE ILE ALA TRP THR SER LYS THR SER SEQRES 4 A 111 VAL ALA TYR VAL THR PRO GLY ASP SER GLU THR ALA PRO SEQRES 5 A 111 VAL VAL THR VAL THR HIS ARG ASN TYR TYR GLU ARG ILE SEQRES 6 A 111 HIS ALA LEU GLY PRO ASN TYR ASN LEU VAL ILE SER ASP SEQRES 7 A 111 LEU ARG MET GLU ASP ALA GLY ASP TYR LYS ALA ASP ILE SEQRES 8 A 111 ASN THR GLN ALA ASP PRO TYR THR THR THR LYS ARG TYR SEQRES 9 A 111 ASN LEU GLN ILE TYR ARG ARG SEQRES 1 B 111 MET LYS ASP SER GLU ILE PHE THR VAL ASN GLY ILE LEU SEQRES 2 B 111 GLY GLU SER VAL THR PHE PRO VAL ASN ILE GLN GLU PRO SEQRES 3 B 111 ARG GLN VAL LYS ILE ILE ALA TRP THR SER LYS THR SER SEQRES 4 B 111 VAL ALA TYR VAL THR PRO GLY ASP SER GLU THR ALA PRO SEQRES 5 B 111 VAL VAL THR VAL THR HIS ARG ASN TYR TYR GLU ARG ILE SEQRES 6 B 111 HIS ALA LEU GLY PRO ASN TYR ASN LEU VAL ILE SER ASP SEQRES 7 B 111 LEU ARG MET GLU ASP ALA GLY ASP TYR LYS ALA ASP ILE SEQRES 8 B 111 ASN THR GLN ALA ASP PRO TYR THR THR THR LYS ARG TYR SEQRES 9 B 111 ASN LEU GLN ILE TYR ARG ARG SEQRES 1 C 111 MET LYS ASP SER GLU ILE PHE THR VAL ASN GLY ILE LEU SEQRES 2 C 111 GLY GLU SER VAL THR PHE PRO VAL ASN ILE GLN GLU PRO SEQRES 3 C 111 ARG GLN VAL LYS ILE ILE ALA TRP THR SER LYS THR SER SEQRES 4 C 111 VAL ALA TYR VAL THR PRO GLY ASP SER GLU THR ALA PRO SEQRES 5 C 111 VAL VAL THR VAL THR HIS ARG ASN TYR TYR GLU ARG ILE SEQRES 6 C 111 HIS ALA LEU GLY PRO ASN TYR ASN LEU VAL ILE SER ASP SEQRES 7 C 111 LEU ARG MET GLU ASP ALA GLY ASP TYR LYS ALA ASP ILE SEQRES 8 C 111 ASN THR GLN ALA ASP PRO TYR THR THR THR LYS ARG TYR SEQRES 9 C 111 ASN LEU GLN ILE TYR ARG ARG SEQRES 1 D 111 MET LYS ASP SER GLU ILE PHE THR VAL ASN GLY ILE LEU SEQRES 2 D 111 GLY GLU SER VAL THR PHE PRO VAL ASN ILE GLN GLU PRO SEQRES 3 D 111 ARG GLN VAL LYS ILE ILE ALA TRP THR SER LYS THR SER SEQRES 4 D 111 VAL ALA TYR VAL THR PRO GLY ASP SER GLU THR ALA PRO SEQRES 5 D 111 VAL VAL THR VAL THR HIS ARG ASN TYR TYR GLU ARG ILE SEQRES 6 D 111 HIS ALA LEU GLY PRO ASN TYR ASN LEU VAL ILE SER ASP SEQRES 7 D 111 LEU ARG MET GLU ASP ALA GLY ASP TYR LYS ALA ASP ILE SEQRES 8 D 111 ASN THR GLN ALA ASP PRO TYR THR THR THR LYS ARG TYR SEQRES 9 D 111 ASN LEU GLN ILE TYR ARG ARG SEQRES 1 E 111 MET LYS ASP SER GLU ILE PHE THR VAL ASN GLY ILE LEU SEQRES 2 E 111 GLY GLU SER VAL THR PHE PRO VAL ASN ILE GLN GLU PRO SEQRES 3 E 111 ARG GLN VAL LYS ILE ILE ALA TRP THR SER LYS THR SER SEQRES 4 E 111 VAL ALA TYR VAL THR PRO GLY ASP SER GLU THR ALA PRO SEQRES 5 E 111 VAL VAL THR VAL THR HIS ARG ASN TYR TYR GLU ARG ILE SEQRES 6 E 111 HIS ALA LEU GLY PRO ASN TYR ASN LEU VAL ILE SER ASP SEQRES 7 E 111 LEU ARG MET GLU ASP ALA GLY ASP TYR LYS ALA ASP ILE SEQRES 8 E 111 ASN THR GLN ALA ASP PRO TYR THR THR THR LYS ARG TYR SEQRES 9 E 111 ASN LEU GLN ILE TYR ARG ARG SEQRES 1 F 111 MET LYS ASP SER GLU ILE PHE THR VAL ASN GLY ILE LEU SEQRES 2 F 111 GLY GLU SER VAL THR PHE PRO VAL ASN ILE GLN GLU PRO SEQRES 3 F 111 ARG GLN VAL LYS ILE ILE ALA TRP THR SER LYS THR SER SEQRES 4 F 111 VAL ALA TYR VAL THR PRO GLY ASP SER GLU THR ALA PRO SEQRES 5 F 111 VAL VAL THR VAL THR HIS ARG ASN TYR TYR GLU ARG ILE SEQRES 6 F 111 HIS ALA LEU GLY PRO ASN TYR ASN LEU VAL ILE SER ASP SEQRES 7 F 111 LEU ARG MET GLU ASP ALA GLY ASP TYR LYS ALA ASP ILE SEQRES 8 F 111 ASN THR GLN ALA ASP PRO TYR THR THR THR LYS ARG TYR SEQRES 9 F 111 ASN LEU GLN ILE TYR ARG ARG HET CL C 500 1 HET CL E 600 1 HETNAM CL CHLORIDE ION FORMUL 7 CL 2(CL 1-) FORMUL 9 HOH *393(H2 O) HELIX 1 1 HIS A 58 TYR A 62 5 5 HELIX 2 2 ARG A 80 ALA A 84 5 5 HELIX 3 3 GLU B 25 ARG B 27 5 3 HELIX 4 4 HIS B 58 TYR B 62 5 5 HELIX 5 5 GLU C 25 ARG C 27 5 3 HELIX 6 6 HIS C 58 TYR C 62 5 5 HELIX 7 7 ARG C 80 ALA C 84 5 5 HELIX 8 8 GLU D 25 ARG D 27 5 3 HELIX 9 9 HIS D 58 TYR D 62 5 5 HELIX 10 10 ARG D 80 ALA D 84 5 5 HELIX 11 11 GLU E 25 ARG E 27 5 3 HELIX 12 12 HIS E 58 TYR E 62 5 5 HELIX 13 13 ARG E 80 ALA E 84 5 5 HELIX 14 14 HIS F 58 TYR F 62 5 5 HELIX 15 15 ARG F 80 ALA F 84 5 5 SHEET 1 A 6 PHE A 7 ILE A 12 0 SHEET 2 A 6 THR A 99 TYR A 109 1 O ASN A 105 N VAL A 9 SHEET 3 A 6 GLY A 85 THR A 93 -1 N ILE A 91 O THR A 100 SHEET 4 A 6 VAL A 29 THR A 35 -1 N LYS A 30 O ASN A 92 SHEET 5 A 6 SER A 39 THR A 44 -1 O VAL A 43 N ILE A 32 SHEET 6 A 6 VAL A 53 VAL A 56 -1 O THR A 55 N TYR A 42 SHEET 1 B 3 VAL A 17 PHE A 19 0 SHEET 2 B 3 LEU A 74 ILE A 76 -1 O LEU A 74 N PHE A 19 SHEET 3 B 3 ILE A 65 ALA A 67 -1 N HIS A 66 O VAL A 75 SHEET 1 C 6 ILE B 6 ILE B 12 0 SHEET 2 C 6 THR B 99 TYR B 109 1 O ASN B 105 N VAL B 9 SHEET 3 C 6 GLY B 85 THR B 93 -1 N ILE B 91 O THR B 100 SHEET 4 C 6 VAL B 29 THR B 35 -1 N ILE B 31 O ASN B 92 SHEET 5 C 6 SER B 39 THR B 44 -1 O ALA B 41 N TRP B 34 SHEET 6 C 6 VAL B 53 VAL B 56 -1 O VAL B 53 N THR B 44 SHEET 1 D 3 VAL B 17 PHE B 19 0 SHEET 2 D 3 LEU B 74 ILE B 76 -1 O LEU B 74 N PHE B 19 SHEET 3 D 3 ILE B 65 ALA B 67 -1 N HIS B 66 O VAL B 75 SHEET 1 E 6 PHE C 7 ILE C 12 0 SHEET 2 E 6 THR C 99 TYR C 109 1 O GLN C 107 N VAL C 9 SHEET 3 E 6 GLY C 85 THR C 93 -1 N ILE C 91 O THR C 100 SHEET 4 E 6 VAL C 29 THR C 35 -1 N LYS C 30 O ASN C 92 SHEET 5 E 6 SER C 39 THR C 44 -1 O ALA C 41 N TRP C 34 SHEET 6 E 6 VAL C 53 VAL C 56 -1 O VAL C 53 N THR C 44 SHEET 1 F 3 VAL C 17 PHE C 19 0 SHEET 2 F 3 LEU C 74 ILE C 76 -1 O LEU C 74 N PHE C 19 SHEET 3 F 3 ILE C 65 ALA C 67 -1 N HIS C 66 O VAL C 75 SHEET 1 G 6 PHE D 7 ILE D 12 0 SHEET 2 G 6 THR D 99 TYR D 109 1 O TYR D 109 N GLY D 11 SHEET 3 G 6 GLY D 85 THR D 93 -1 N ILE D 91 O THR D 100 SHEET 4 G 6 VAL D 29 THR D 35 -1 N ILE D 31 O ASN D 92 SHEET 5 G 6 SER D 39 THR D 44 -1 O ALA D 41 N TRP D 34 SHEET 6 G 6 VAL D 53 VAL D 56 -1 O VAL D 53 N THR D 44 SHEET 1 H 3 VAL D 17 PHE D 19 0 SHEET 2 H 3 LEU D 74 ILE D 76 -1 O LEU D 74 N PHE D 19 SHEET 3 H 3 ILE D 65 ALA D 67 -1 N HIS D 66 O VAL D 75 SHEET 1 I 6 PHE E 7 ILE E 12 0 SHEET 2 I 6 THR E 99 TYR E 109 1 O ASN E 105 N VAL E 9 SHEET 3 I 6 GLY E 85 THR E 93 -1 N ILE E 91 O THR E 100 SHEET 4 I 6 VAL E 29 THR E 35 -1 N ILE E 31 O ASN E 92 SHEET 5 I 6 SER E 39 THR E 44 -1 O ALA E 41 N TRP E 34 SHEET 6 I 6 VAL E 53 VAL E 56 -1 O VAL E 53 N THR E 44 SHEET 1 J 3 VAL E 17 PHE E 19 0 SHEET 2 J 3 LEU E 74 ILE E 76 -1 O LEU E 74 N PHE E 19 SHEET 3 J 3 ILE E 65 ALA E 67 -1 N HIS E 66 O VAL E 75 SHEET 1 K 6 PHE F 7 ILE F 12 0 SHEET 2 K 6 THR F 99 TYR F 109 1 O GLN F 107 N VAL F 9 SHEET 3 K 6 GLY F 85 THR F 93 -1 N ILE F 91 O THR F 100 SHEET 4 K 6 VAL F 29 THR F 35 -1 N ILE F 31 O ASN F 92 SHEET 5 K 6 SER F 39 THR F 44 -1 O VAL F 43 N ILE F 32 SHEET 6 K 6 VAL F 53 VAL F 56 -1 O THR F 55 N TYR F 42 SHEET 1 L 3 VAL F 17 PHE F 19 0 SHEET 2 L 3 LEU F 74 ILE F 76 -1 O LEU F 74 N PHE F 19 SHEET 3 L 3 ILE F 65 ALA F 67 -1 N HIS F 66 O VAL F 75 CISPEP 1 GLY A 69 PRO A 70 0 -1.86 CISPEP 2 ASP A 96 PRO A 97 0 -1.03 CISPEP 3 GLY B 69 PRO B 70 0 -0.20 CISPEP 4 ASP B 96 PRO B 97 0 2.23 CISPEP 5 GLY C 69 PRO C 70 0 -5.74 CISPEP 6 GLY D 69 PRO D 70 0 -14.77 CISPEP 7 ASP D 96 PRO D 97 0 5.42 CISPEP 8 GLY E 69 PRO E 70 0 -6.44 CISPEP 9 ASP E 96 PRO E 97 0 10.17 CISPEP 10 GLY F 69 PRO F 70 0 3.59 CISPEP 11 ASP F 96 PRO F 97 0 6.82 SITE 1 AC1 1 ARG C 110 SITE 1 AC2 1 ARG E 110 CRYST1 61.013 170.982 148.527 90.00 90.00 90.00 C 2 2 21 48 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 0.016390 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005849 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006733 0.00000