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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
