10 20 30 40 50 60 70 80 4R6R - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER SUGAR BINDING PROTEIN 26-AUG-14 4R6R
TITLE JACALIN-CARBOHYDRATE INTERACTIONS. DISTORTION OF THE LIGAND AS A TITLE 2 DETERMINANT OF AFFINITY.
COMPND MOL_ID: 1; COMPND 2 MOLECULE: AGGLUTININ ALPHA CHAIN; COMPND 3 CHAIN: A, C, E, G; COMPND 4 SYNONYM: JACALIN ALPHA CHAIN; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: AGGLUTININ BETA-3 CHAIN; COMPND 7 CHAIN: B, D, F, H; COMPND 8 FRAGMENT: UNP RESIDUES 2-20; COMPND 9 SYNONYM: JACALIN BETA-3 CHAIN
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARTOCARPUS INTEGER; SOURCE 3 ORGANISM_COMMON: CAMPEDAK,CHEMPEDAK; SOURCE 4 ORGANISM_TAXID: 3490; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: ARTOCARPUS INTEGER; SOURCE 7 ORGANISM_COMMON: CAMPEDAK,CHEMPEDAK; SOURCE 8 ORGANISM_TAXID: 3490
KEYWDS GALACTOSE SPECIFIC LECTIN, BETA-PRISM I FOLD, POST TRANSLATIONAL KEYWDS 2 PROTEOLYSIS, T-ANTIGEN BINDING PROTEIN, PLANT LECTINS, GALACTOSE AND KEYWDS 3 SUGAR BINDING PROTEIN, SUGAR BINDING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR K.V.ABHINAV,K.SHARMA,C.P.SWAMINATHAN,A.SUROLIA,M.VIJAYAN
REVDAT 2 25-FEB-15 4R6R 1 JRNL REVDAT 1 18-FEB-15 4R6R 0
JRNL AUTH K.V.ABHINAV,K.SHARMA,C.P.SWAMINATHAN,A.SUROLIA,M.VIJAYAN JRNL TITL JACALIN-CARBOHYDRATE INTERACTIONS: DISTORTION OF THE LIGAND JRNL TITL 2 MOLECULE AS A DETERMINANT OF AFFINITY. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 324 2015 JRNL REFN ISSN 0907-4449 JRNL PMID 25664742 JRNL DOI 10.1107/S139900471402553X
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.SANKARANARAYANAN,K.SEKAR,R.BANERJEE,V.SHARMA,A.SUROLIA, REMARK 1 AUTH 2 M.VIJAYAN REMARK 1 TITL A NOVEL MODE OF CARBOHYDRATE RECOGNITION IN JACALIN, A REMARK 1 TITL 2 MORACEAE PLANT LECTIN WITH A BETA-PRISM FOLD. REMARK 1 REF NAT.STRUCT.BIOL. V. 3 596 1996 REMARK 1 REFN ISSN 1072-8368 REMARK 1 PMID 8673603 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.A.JEYAPRAKASH,P.GEETHA RANI,G.BANUPRAKASH REDDY, REMARK 1 AUTH 2 S.BANUMATHI,C.BETZEL,K.SEKAR,A.SUROLIA,M.VIJAYAN REMARK 1 TITL CRYSTAL STRUCTURE OF THE JACALIN-T-ANTIGEN COMPLEX AND A REMARK 1 TITL 2 COMPARATIVE STUDY OF LECTIN-T-ANTIGEN COMPLEXES. REMARK 1 REF J.MOL.BIOL. V. 321 637 2002 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 12206779 REMARK 1 REFERENCE 3 REMARK 1 AUTH A.A.JEYAPRAKASH,S.KATIYAR,C.P.SWAMINATHAN,K.SEKAR,A.SUROLIA, REMARK 1 AUTH 2 M.VIJAYAN REMARK 1 TITL STRUCTURAL BASIS OF THE CARBOHYDRATE SPECIFICITIES OF REMARK 1 TITL 2 JACALIN: AN X-RAY AND MODELING STUDY. REMARK 1 REF J.MOL.BIOL. V. 332 217 2003 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 12946359 REMARK 1 REFERENCE 4 REMARK 1 AUTH A.AROCKIA JEYAPRAKASH,G.JAYASHREE,S.K.MAHANTA, REMARK 1 AUTH 2 C.P.SWAMINATHAN,K.SEKAR,A.SUROLIA,M.VIJAYAN REMARK 1 TITL STRUCTURAL BASIS FOR THE ENERGETICS OF JACALIN-SUGAR REMARK 1 TITL 2 INTERACTIONS: PROMISCUITY VERSUS SPECIFICITY. REMARK 1 REF J.MOL.BIOL. V. 347 181 2005 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 15733927 REMARK 1 DOI 10.1016/J.JMB.2005.01.015 REMARK 1 REFERENCE 5 REMARK 1 AUTH Y.BOURNE,C.H.ASTOUL,V.ZAMBONI,W.J.PEUMANS,L.MENU-BOUAOUICHE, REMARK 1 AUTH 2 E.J.VAN DAMME,A.BARRE,P.ROUGE REMARK 1 TITL STRUCTURAL BASIS FOR THE UNUSUAL CARBOHYDRATE-BINDING REMARK 1 TITL 2 SPECIFICITY OF JACALIN TOWARDS GALACTOSE AND MANNOSE. REMARK 1 REF BIOCHEM.J. V. 364 173 2002 REMARK 1 REFN ISSN 0264-6021 REMARK 1 PMID 11988090
REMARK 2 REMARK 2 RESOLUTION. 1.38 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 107367 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5664 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) : 1.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.42 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7652 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.3460 REMARK 3 BIN FREE R VALUE SET COUNT : 394 REMARK 3 BIN FREE R VALUE : 0.3610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4579 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 98 REMARK 3 SOLVENT ATOMS : 437 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.03000 REMARK 3 B22 (A**2) : 1.76000 REMARK 3 B33 (A**2) : -0.73000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.061 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.064 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.050 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.296 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4794 ; 0.019 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6494 ; 1.988 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 586 ; 6.772 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 193 ;36.081 ;24.197 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 707 ;11.987 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ; 6.131 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 706 ; 0.148 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3636 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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 : NULL 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 USED IF PRESENT IN REMARK 3 THE INPUT
REMARK 4 REMARK 4 4R6R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-SEP-14. REMARK 100 THE RCSB ID CODE IS RCSB086969.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : SI(111) MONOCHROMATOR. REMARK 200 OPTICS : BENT COLLIMATING MIRROR AND REMARK 200 TOROID REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 113064 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.82400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1KU8 REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 8000, 0.1M HEPES, PH 7.4; 10% REMARK 280 (V/V) ISOPROPANOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 40.12500 REMARK 290 SMTRY3 2 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, G, H 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 VAL B 19 REMARK 465 SER B 20 REMARK 465 GLU D 2 REMARK 465 GLN D 3 REMARK 465 LYS D 18 REMARK 465 VAL D 19 REMARK 465 SER D 20 REMARK 465 GLU F 2 REMARK 465 VAL F 19 REMARK 465 SER F 20 REMARK 465 GLU H 2 REMARK 465 GLN H 3 REMARK 465 VAL H 19 REMARK 465 SER H 20
REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 74 CG OD1 ND2 REMARK 470 LYS C 21 CG CD CE NZ REMARK 470 LYS C 90 CG CD CE NZ REMARK 470 LYS C 91 CG CD CE NZ REMARK 470 GLN H 8 CG CD OE1 NE2
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 TRP B 15 CE2 TRP B 15 CD2 0.086 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 ARG G 13 NE - CZ - NH2 ANGL. DEV. = -3.7 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 THR A 23 -85.10 -126.97 REMARK 500 PHE C 9 -167.40 -129.74 REMARK 500 THR C 23 -97.96 -129.99 REMARK 500 THR E 23 -92.11 -113.46 REMARK 500 THR G 23 -98.96 -130.01 REMARK 500 THR G 49 -169.81 -110.59 REMARK 500 REMARK 500 REMARK: NULL
REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 147 A 201
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 147 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPA A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 147 E 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 147 G 201
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JAC RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH ALPHA-METHYL-D-GALACTOSIDE. REMARK 900 RELATED ID: 1UGW RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH D-GALACTOSIDE. REMARK 900 RELATED ID: 1KU8 RELATED DB: PDB REMARK 900 NATIVE JACALIN STRUCTURE. REMARK 900 RELATED ID: 1M26 RELATED DB: PDB REMARK 900 JACALIN COMPLEXED WITH T-ANTIGEN. REMARK 900 RELATED ID: 1UH0 RELATED DB: PDB REMARK 900 JACALIN COMPLEXED WITH ME-ALPHA-GALNAC. REMARK 900 RELATED ID: 1UGY RELATED DB: PDB REMARK 900 JACALIN COMPLEXED WITH MELLIBIOSE. REMARK 900 RELATED ID: 4R6N RELATED DB: PDB REMARK 900 RELATED ID: 4R6O RELATED DB: PDB REMARK 900 RELATED ID: 4R6P RELATED DB: PDB REMARK 900 RELATED ID: 4R6Q RELATED DB: PDB
DBREF 4R6R A 1 133 UNP P18670 LECA_ARTIN 1 133 DBREF 4R6R B 2 20 UNP P18673 LECB3_ARTIN 2 20 DBREF 4R6R C 1 133 UNP P18670 LECA_ARTIN 1 133 DBREF 4R6R D 2 20 UNP P18673 LECB3_ARTIN 2 20 DBREF 4R6R E 1 133 UNP P18670 LECA_ARTIN 1 133 DBREF 4R6R F 2 20 UNP P18673 LECB3_ARTIN 2 20 DBREF 4R6R G 1 133 UNP P18670 LECA_ARTIN 1 133 DBREF 4R6R H 2 20 UNP P18673 LECB3_ARTIN 2 20
SEQRES 1 A 133 GLY LYS ALA PHE ASP ASP GLY ALA PHE THR GLY ILE ARG SEQRES 2 A 133 GLU ILE ASN LEU SER TYR ASN LYS GLU THR ALA ILE GLY SEQRES 3 A 133 ASP PHE GLN VAL VAL TYR ASP LEU ASN GLY SER PRO TYR SEQRES 4 A 133 VAL GLY GLN ASN HIS LYS SER PHE ILE THR GLY PHE THR SEQRES 5 A 133 PRO VAL LYS ILE SER LEU ASP PHE PRO SER GLU TYR ILE SEQRES 6 A 133 MET GLU VAL SER GLY TYR THR GLY ASN VAL SER GLY TYR SEQRES 7 A 133 VAL VAL VAL ARG SER LEU THR PHE LYS THR ASN LYS LYS SEQRES 8 A 133 THR TYR GLY PRO TYR GLY VAL THR SER GLY THR PRO PHE SEQRES 9 A 133 ASN LEU PRO ILE GLU ASN GLY LEU ILE VAL GLY PHE LYS SEQRES 10 A 133 GLY SER ILE GLY TYR TRP LEU ASP TYR PHE SER MET TYR SEQRES 11 A 133 LEU SER LEU SEQRES 1 B 19 GLU GLN SER GLY ILE SER GLN THR VAL ILE VAL GLY PRO SEQRES 2 B 19 TRP GLY ALA LYS VAL SER SEQRES 1 C 133 GLY LYS ALA PHE ASP ASP GLY ALA PHE THR GLY ILE ARG SEQRES 2 C 133 GLU ILE ASN LEU SER TYR ASN LYS GLU THR ALA ILE GLY SEQRES 3 C 133 ASP PHE GLN VAL VAL TYR ASP LEU ASN GLY SER PRO TYR SEQRES 4 C 133 VAL GLY GLN ASN HIS LYS SER PHE ILE THR GLY PHE THR SEQRES 5 C 133 PRO VAL LYS ILE SER LEU ASP PHE PRO SER GLU TYR ILE SEQRES 6 C 133 MET GLU VAL SER GLY TYR THR GLY ASN VAL SER GLY TYR SEQRES 7 C 133 VAL VAL VAL ARG SER LEU THR PHE LYS THR ASN LYS LYS SEQRES 8 C 133 THR TYR GLY PRO TYR GLY VAL THR SER GLY THR PRO PHE SEQRES 9 C 133 ASN LEU PRO ILE GLU ASN GLY LEU ILE VAL GLY PHE LYS SEQRES 10 C 133 GLY SER ILE GLY TYR TRP LEU ASP TYR PHE SER MET TYR SEQRES 11 C 133 LEU SER LEU SEQRES 1 D 19 GLU GLN SER GLY ILE SER GLN THR VAL ILE VAL GLY PRO SEQRES 2 D 19 TRP GLY ALA LYS VAL SER SEQRES 1 E 133 GLY LYS ALA PHE ASP ASP GLY ALA PHE THR GLY ILE ARG SEQRES 2 E 133 GLU ILE ASN LEU SER TYR ASN LYS GLU THR ALA ILE GLY SEQRES 3 E 133 ASP PHE GLN VAL VAL TYR ASP LEU ASN GLY SER PRO TYR SEQRES 4 E 133 VAL GLY GLN ASN HIS LYS SER PHE ILE THR GLY PHE THR SEQRES 5 E 133 PRO VAL LYS ILE SER LEU ASP PHE PRO SER GLU TYR ILE SEQRES 6 E 133 MET GLU VAL SER GLY TYR THR GLY ASN VAL SER GLY TYR SEQRES 7 E 133 VAL VAL VAL ARG SER LEU THR PHE LYS THR ASN LYS LYS SEQRES 8 E 133 THR TYR GLY PRO TYR GLY VAL THR SER GLY THR PRO PHE SEQRES 9 E 133 ASN LEU PRO ILE GLU ASN GLY LEU ILE VAL GLY PHE LYS SEQRES 10 E 133 GLY SER ILE GLY TYR TRP LEU ASP TYR PHE SER MET TYR SEQRES 11 E 133 LEU SER LEU SEQRES 1 F 19 GLU GLN SER GLY ILE SER GLN THR VAL ILE VAL GLY PRO SEQRES 2 F 19 TRP GLY ALA LYS VAL SER SEQRES 1 G 133 GLY LYS ALA PHE ASP ASP GLY ALA PHE THR GLY ILE ARG SEQRES 2 G 133 GLU ILE ASN LEU SER TYR ASN LYS GLU THR ALA ILE GLY SEQRES 3 G 133 ASP PHE GLN VAL VAL TYR ASP LEU ASN GLY SER PRO TYR SEQRES 4 G 133 VAL GLY GLN ASN HIS LYS SER PHE ILE THR GLY PHE THR SEQRES 5 G 133 PRO VAL LYS ILE SER LEU ASP PHE PRO SER GLU TYR ILE SEQRES 6 G 133 MET GLU VAL SER GLY TYR THR GLY ASN VAL SER GLY TYR SEQRES 7 G 133 VAL VAL VAL ARG SER LEU THR PHE LYS THR ASN LYS LYS SEQRES 8 G 133 THR TYR GLY PRO TYR GLY VAL THR SER GLY THR PRO PHE SEQRES 9 G 133 ASN LEU PRO ILE GLU ASN GLY LEU ILE VAL GLY PHE LYS SEQRES 10 G 133 GLY SER ILE GLY TYR TRP LEU ASP TYR PHE SER MET TYR SEQRES 11 G 133 LEU SER LEU SEQRES 1 H 19 GLU GLN SER GLY ILE SER GLN THR VAL ILE VAL GLY PRO SEQRES 2 H 19 TRP GLY ALA LYS VAL SER
HET 147 A 201 12 HET EDO A 202 4 HET EDO A 203 4 HET EDO A 204 4 HET EDO A 205 4 HET EDO A 206 4 HET IPA A 207 4 HET EDO C 201 4 HET EDO C 202 4 HET EDO C 203 4 HET EDO C 204 4 HET EDO D 101 4 HET 147 E 201 21 HET 147 G 201 21
HETNAM 147 1-O-[P-NITROPHENYL]-BETA-D-GALACTOPYRANOSE HETNAM EDO 1,2-ETHANEDIOL HETNAM IPA ISOPROPYL ALCOHOL
HETSYN EDO ETHYLENE GLYCOL HETSYN IPA 2-PROPANOL
FORMUL 9 147 3(C12 H15 N O8) FORMUL 10 EDO 10(C2 H6 O2) FORMUL 15 IPA C3 H8 O FORMUL 23 HOH *437(H2 O)
SHEET 1 A 8 LYS A 2 ASP A 5 0 SHEET 2 A 8 LEU A 112 ILE A 120 -1 O ILE A 120 N LYS A 2 SHEET 3 A 8 LEU A 124 SER A 132 -1 O SER A 128 N LYS A 117 SHEET 4 A 8 VAL B 10 GLY B 16 -1 O VAL B 12 N MET A 129 SHEET 5 A 8 THR C 102 ASN C 110 -1 O PRO C 107 N GLY B 13 SHEET 6 A 8 ILE C 65 VAL C 75 -1 N THR C 72 O THR C 102 SHEET 7 A 8 TYR C 78 THR C 88 -1 O LYS C 87 N MET C 66 SHEET 8 A 8 THR C 92 GLY C 97 -1 O TYR C 93 N PHE C 86 SHEET 1 B 4 SER A 37 VAL A 40 0 SHEET 2 B 4 ILE A 25 LEU A 34 -1 N TYR A 32 O TYR A 39 SHEET 3 B 4 GLY A 11 TYR A 19 -1 N ASN A 16 O GLN A 29 SHEET 4 B 4 THR A 52 SER A 57 -1 O THR A 52 N TYR A 19 SHEET 1 C 8 THR A 92 GLY A 97 0 SHEET 2 C 8 TYR A 78 THR A 88 -1 N PHE A 86 O TYR A 93 SHEET 3 C 8 ILE A 65 VAL A 75 -1 N MET A 66 O LYS A 87 SHEET 4 C 8 THR A 102 ASN A 110 -1 O LEU A 106 N VAL A 68 SHEET 5 C 8 VAL D 10 TRP D 15 -1 O GLY D 13 N PRO A 107 SHEET 6 C 8 LEU C 124 SER C 132 -1 N MET C 129 O VAL D 12 SHEET 7 C 8 LEU C 112 ILE C 120 -1 N VAL C 114 O TYR C 130 SHEET 8 C 8 LYS C 2 ASP C 5 -1 N LYS C 2 O ILE C 120 SHEET 1 D 4 SER C 37 HIS C 44 0 SHEET 2 D 4 ILE C 25 LEU C 34 -1 N LEU C 34 O SER C 37 SHEET 3 D 4 GLY C 11 TYR C 19 -1 N ASN C 16 O GLN C 29 SHEET 4 D 4 THR C 52 SER C 57 -1 O ILE C 56 N ILE C 15 SHEET 1 E 8 LYS E 2 ASP E 5 0 SHEET 2 E 8 LEU E 112 ILE E 120 -1 O ILE E 120 N LYS E 2 SHEET 3 E 8 LEU E 124 SER E 132 -1 O ASP E 125 N SER E 119 SHEET 4 E 8 VAL F 10 GLY F 16 -1 O VAL F 12 N MET E 129 SHEET 5 E 8 THR G 102 ASN G 110 -1 O PRO G 107 N GLY F 13 SHEET 6 E 8 ILE G 65 VAL G 75 -1 N VAL G 68 O LEU G 106 SHEET 7 E 8 TYR G 78 THR G 88 -1 O LYS G 87 N MET G 66 SHEET 8 E 8 THR G 92 TYR G 96 -1 O TYR G 93 N PHE G 86 SHEET 1 F 4 SER E 37 VAL E 40 0 SHEET 2 F 4 ILE E 25 LEU E 34 -1 N LEU E 34 O SER E 37 SHEET 3 F 4 GLY E 11 TYR E 19 -1 N ASN E 16 O GLN E 29 SHEET 4 F 4 THR E 52 SER E 57 -1 O ILE E 56 N ILE E 15 SHEET 1 G 8 THR E 92 GLY E 97 0 SHEET 2 G 8 TYR E 78 THR E 88 -1 N PHE E 86 O TYR E 93 SHEET 3 G 8 ILE E 65 VAL E 75 -1 N GLU E 67 O LYS E 87 SHEET 4 G 8 THR E 102 ASN E 110 -1 O LEU E 106 N VAL E 68 SHEET 5 G 8 VAL H 10 GLY H 16 -1 O GLY H 13 N PRO E 107 SHEET 6 G 8 LEU G 124 SER G 132 -1 N MET G 129 O VAL H 12 SHEET 7 G 8 LEU G 112 ILE G 120 -1 N VAL G 114 O TYR G 130 SHEET 8 G 8 LYS G 2 ASP G 5 -1 N LYS G 2 O ILE G 120 SHEET 1 H 4 SER G 37 VAL G 40 0 SHEET 2 H 4 ILE G 25 LEU G 34 -1 N LEU G 34 O SER G 37 SHEET 3 H 4 GLY G 11 TYR G 19 -1 N ASN G 16 O GLN G 29 SHEET 4 H 4 THR G 52 SER G 57 -1 O ILE G 56 N ILE G 15
CISPEP 1 PHE A 60 PRO A 61 0 4.32 CISPEP 2 GLY A 94 PRO A 95 0 7.89 CISPEP 3 GLY B 13 PRO B 14 0 2.09 CISPEP 4 PHE C 60 PRO C 61 0 1.53 CISPEP 5 GLY C 94 PRO C 95 0 3.15 CISPEP 6 GLY D 13 PRO D 14 0 9.26 CISPEP 7 PHE E 60 PRO E 61 0 7.03 CISPEP 8 GLY E 94 PRO E 95 0 4.71 CISPEP 9 GLY F 13 PRO F 14 0 0.24 CISPEP 10 PHE G 60 PRO G 61 0 2.40 CISPEP 11 GLY G 94 PRO G 95 0 -2.84 CISPEP 12 GLY H 13 PRO H 14 0 7.79
SITE 1 AC1 6 GLY A 1 TYR A 78 GLY A 121 TYR A 122 SITE 2 AC1 6 TRP A 123 ASP A 125 SITE 1 AC2 2 LYS A 55 HOH A 306 SITE 1 AC3 6 LEU A 34 ASN A 35 SER A 37 ASP E 6 SITE 2 AC3 6 PHE E 9 TYR E 39 SITE 1 AC4 3 THR A 23 SER A 76 HOH A 317 SITE 1 AC5 3 PRO A 38 VAL A 40 EDO C 201 SITE 1 AC6 4 PHE A 4 ASP A 5 GLN A 42 HIS A 44 SITE 1 AC7 4 ASN A 74 GLY A 101 THR A 102 HOH A 410 SITE 1 AC8 2 EDO A 205 TRP C 123 SITE 1 AC9 4 TYR C 19 PRO C 95 TYR C 96 GLY C 97 SITE 1 BC1 4 PHE C 51 THR C 52 PRO C 53 HOH C 375 SITE 1 BC2 4 SER D 4 TYR G 64 ASN G 110 GLY G 111 SITE 1 BC3 8 GLY E 1 SER E 76 TYR E 78 VAL E 80 SITE 2 BC3 8 GLY E 121 TYR E 122 TRP E 123 ASP E 125 SITE 1 BC4 10 GLY C 1 TYR C 78 VAL C 79 HOH C 322 SITE 2 BC4 10 GLY G 1 TYR G 78 GLY G 121 TYR G 122 SITE 3 BC4 10 TRP G 123 ASP G 125
CRYST1 58.440 80.250 62.970 90.00 107.68 90.00 P 1 21 1 8
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 0.017112 0.000000 0.005454 0.00000
SCALE2 0.000000 0.012461 0.000000 0.00000
SCALE3 0.000000 0.000000 0.016668 0.00000