PDB Short entry for 2KR2 HEADER CARBOHYDRATE BINDING PROTEIN 30-NOV-09 2KR2 TITLE XENOPUS LAEVIS MALECTIN COMPLEXED WITH MALTOSE (GLCALPHA1-4GLC) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALECTIN-A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 27-213; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_COMMON: CLAWED FROG,COMMON PLATANNA,PLATANNA; SOURCE 4 ORGANISM_TAXID: 8355; SOURCE 5 GENE: MLEC, MLEC-A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET-24D KEYWDS LECTIN/CARBOHYDRATE, CARBOHYDRATE METABOLISM, ENDOPLASMIC RETICULUM, KEYWDS 2 GLYCOPROTEIN, MEMBRANE, TRANSMEMBRANE, CARBOHYDRATE BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.SCHALLUS,K.FEHER,C.MUHLE-GOLL REVDAT 3 29-JUL-20 2KR2 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 LINK SITE ATOM REVDAT 2 28-JUL-10 2KR2 1 JRNL REVDAT 1 14-JUL-10 2KR2 0 JRNL AUTH T.SCHALLUS,K.FEHER,U.STERNBERG,V.RYBIN,C.MUHLE-GOLL JRNL TITL ANALYSIS OF THE SPECIFIC INTERACTIONS BETWEEN THE LECTIN JRNL TITL 2 DOMAIN OF MALECTIN AND DIGLUCOSIDES. JRNL REF GLYCOBIOLOGY V. 20 1010 2010 JRNL REFN ISSN 0959-6658 JRNL PMID 20466650 JRNL DOI 10.1093/GLYCOB/CWQ059 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 1.2, ARIA 1.2 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), LINGE, REMARK 3 O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KR2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000101467. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0.15 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 13C; U-100% 15N] REMARK 210 MALECTIN-1, 90% H2O/10% D2O; 0.8 REMARK 210 MM [U-100% 13C; U-100% 15N] REMARK 210 MALECTIN-2, 4 MM MALTOSE REMARK 210 (GLCALPHA1-4GLC)-3, 100% D2O; REMARK 210 0.8 MM MALECTIN-4, 4 MM MALTOSE REMARK 210 (GLCALPHA1-4GLC)-5, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCA; 3D HNCACB; 3D 1H-13C REMARK 210 NOESY; 2D 1H-1H NOESY; 3D C(CO) REMARK 210 NH; 3D H(CCO)NH; 3D HCCH-TOCSY; REMARK 210 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 3 TYR A 29 CE1 TYR A 29 CZ -0.102 REMARK 500 3 TYR A 29 CZ TYR A 29 CE2 0.081 REMARK 500 4 TYR A 61 CE1 TYR A 61 CZ 0.105 REMARK 500 4 TYR A 61 CZ TYR A 61 CE2 -0.117 REMARK 500 5 TYR A 61 CE1 TYR A 61 CZ 0.124 REMARK 500 5 TYR A 61 CZ TYR A 61 CE2 -0.142 REMARK 500 5 TYR A 73 CE1 TYR A 73 CZ -0.080 REMARK 500 6 PHE A 89 CZ PHE A 89 CE2 0.118 REMARK 500 7 TYR A 29 CE1 TYR A 29 CZ -0.106 REMARK 500 7 TYR A 29 CZ TYR A 29 CE2 0.088 REMARK 500 8 TYR A 73 CE1 TYR A 73 CZ -0.098 REMARK 500 8 TYR A 73 CZ TYR A 73 CE2 0.081 REMARK 500 8 PHE A 89 CZ PHE A 89 CE2 0.120 REMARK 500 9 TYR A 29 CE1 TYR A 29 CZ -0.091 REMARK 500 9 TYR A 29 CZ TYR A 29 CE2 0.091 REMARK 500 9 TYR A 73 CE1 TYR A 73 CZ -0.088 REMARK 500 9 PHE A 89 CZ PHE A 89 CE2 0.128 REMARK 500 10 TYR A 29 CE1 TYR A 29 CZ -0.104 REMARK 500 10 TYR A 29 CZ TYR A 29 CE2 0.087 REMARK 500 11 TYR A 29 CE1 TYR A 29 CZ 0.195 REMARK 500 11 TYR A 29 CZ TYR A 29 CE2 -0.200 REMARK 500 12 TYR A 61 CZ TYR A 61 CE2 -0.089 REMARK 500 12 PHE A 157 CE1 PHE A 157 CZ 0.210 REMARK 500 12 PHE A 157 CZ PHE A 157 CE2 -0.183 REMARK 500 13 TYR A 29 CE1 TYR A 29 CZ 0.212 REMARK 500 13 TYR A 29 CZ TYR A 29 CE2 -0.206 REMARK 500 14 TYR A 29 CE1 TYR A 29 CZ -0.143 REMARK 500 14 TYR A 29 CZ TYR A 29 CE2 0.121 REMARK 500 15 TYR A 61 CE1 TYR A 61 CZ 0.112 REMARK 500 15 TYR A 61 CZ TYR A 61 CE2 -0.117 REMARK 500 17 TYR A 29 CE1 TYR A 29 CZ -0.119 REMARK 500 17 TYR A 29 CZ TYR A 29 CE2 0.101 REMARK 500 18 TYR A 29 CE1 TYR A 29 CZ 0.202 REMARK 500 18 TYR A 29 CZ TYR A 29 CE2 -0.183 REMARK 500 20 TYR A 61 CE1 TYR A 61 CZ 0.086 REMARK 500 20 TYR A 61 CZ TYR A 61 CE2 -0.106 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 11 TYR A 29 CE1 - CZ - OH ANGL. DEV. = -17.7 DEGREES REMARK 500 13 TYR A 29 CD1 - CE1 - CZ ANGL. DEV. = -5.9 DEGREES REMARK 500 13 TYR A 29 CE1 - CZ - OH ANGL. DEV. = -19.7 DEGREES REMARK 500 18 TYR A 29 CD1 - CE1 - CZ ANGL. DEV. = -5.5 DEGREES REMARK 500 18 TYR A 29 CE1 - CZ - OH ANGL. DEV. = -19.2 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 1 TRP A 12 117.90 -162.83 REMARK 500 1 GLU A 19 118.71 -170.53 REMARK 500 1 SER A 20 107.75 51.47 REMARK 500 1 ARG A 30 -104.78 -67.31 REMARK 500 1 LYS A 31 93.81 176.80 REMARK 500 1 PRO A 33 33.51 -98.53 REMARK 500 1 LEU A 34 -51.01 -139.08 REMARK 500 1 ARG A 37 -46.08 77.09 REMARK 500 1 TYR A 44 75.24 -105.65 REMARK 500 1 GLN A 62 -35.04 -145.67 REMARK 500 1 ARG A 65 -81.30 -100.57 REMARK 500 1 GLU A 68 -106.54 -141.43 REMARK 500 1 SER A 70 89.51 55.03 REMARK 500 1 LYS A 78 20.05 -146.83 REMARK 500 1 VAL A 92 -73.86 -124.95 REMARK 500 1 GLN A 98 49.45 73.24 REMARK 500 1 GLN A 99 -40.99 -151.36 REMARK 500 1 LYS A 100 78.88 -100.59 REMARK 500 1 LYS A 113 73.69 -109.65 REMARK 500 1 ASP A 114 62.60 158.14 REMARK 500 1 SER A 124 -128.62 73.32 REMARK 500 1 THR A 125 -171.02 58.26 REMARK 500 1 GLN A 143 -84.26 63.06 REMARK 500 1 TYR A 161 -61.00 -141.52 REMARK 500 1 ASN A 164 -85.93 -118.28 REMARK 500 1 LYS A 166 -94.02 79.86 REMARK 500 2 SER A 4 -69.77 -135.98 REMARK 500 2 GLU A 19 117.73 -165.11 REMARK 500 2 SER A 20 106.04 41.71 REMARK 500 2 LYS A 31 116.70 -33.79 REMARK 500 2 ASP A 32 73.43 40.37 REMARK 500 2 LEU A 34 -52.13 -133.91 REMARK 500 2 ARG A 37 -56.13 74.99 REMARK 500 2 ARG A 40 -126.07 -150.25 REMARK 500 2 TYR A 44 75.34 -110.42 REMARK 500 2 GLN A 62 -115.95 -139.77 REMARK 500 2 THR A 63 -84.48 56.67 REMARK 500 2 GLU A 64 133.70 82.08 REMARK 500 2 ARG A 65 -75.48 -100.23 REMARK 500 2 GLU A 68 -62.62 -157.12 REMARK 500 2 LYS A 78 17.97 -146.36 REMARK 500 2 VAL A 92 -76.03 -111.96 REMARK 500 2 GLN A 96 140.02 -171.84 REMARK 500 2 GLN A 98 49.94 72.97 REMARK 500 2 GLN A 99 -40.48 -151.33 REMARK 500 2 ASP A 114 78.84 127.65 REMARK 500 2 SER A 124 -124.09 68.09 REMARK 500 2 THR A 125 -164.09 56.07 REMARK 500 2 GLN A 143 -83.29 66.95 REMARK 500 2 TYR A 161 -71.99 -128.99 REMARK 500 REMARK 500 THIS ENTRY HAS 519 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 6 PHE A 149 0.07 SIDE CHAIN REMARK 500 7 TYR A 73 0.05 SIDE CHAIN REMARK 500 9 TYR A 29 0.06 SIDE CHAIN REMARK 500 9 PHE A 89 0.06 SIDE CHAIN REMARK 500 11 TYR A 29 0.07 SIDE CHAIN REMARK 500 12 PHE A 102 0.07 SIDE CHAIN REMARK 500 13 TYR A 29 0.09 SIDE CHAIN REMARK 500 13 PHE A 149 0.06 SIDE CHAIN REMARK 500 16 PHE A 89 0.06 SIDE CHAIN REMARK 500 16 PHE A 102 0.06 SIDE CHAIN REMARK 500 18 TYR A 29 0.09 SIDE CHAIN REMARK 500 20 PHE A 71 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JWP RELATED DB: PDB REMARK 900 ENTRY CONTAING THE UNCOMPLEXED PROTEIN DOMAIN REMARK 900 RELATED ID: 2K46 RELATED DB: PDB REMARK 900 ENTRY CONTAINING THE PROTEIN COMPLEXED WITH NIGEROSE DBREF 2KR2 A 4 190 UNP Q6INX3 MLECA_XENLA 27 213 SEQADV 2KR2 GLY A 1 UNP Q6INX3 EXPRESSION TAG SEQADV 2KR2 ALA A 2 UNP Q6INX3 EXPRESSION TAG SEQADV 2KR2 MET A 3 UNP Q6INX3 EXPRESSION TAG SEQRES 1 A 190 GLY ALA MET SER GLY LEU ALA ASP LYS VAL ILE TRP ALA SEQRES 2 A 190 VAL ASN ALA GLY GLY GLU SER HIS VAL ASP VAL HIS GLY SEQRES 3 A 190 ILE HIS TYR ARG LYS ASP PRO LEU GLU GLY ARG VAL GLY SEQRES 4 A 190 ARG ALA SER ASP TYR GLY MET LYS LEU PRO ILE LEU ARG SEQRES 5 A 190 SER ASN PRO GLU ASP GLN VAL LEU TYR GLN THR GLU ARG SEQRES 6 A 190 TYR ASN GLU ASP SER PHE GLY TYR ASP ILE PRO ILE LYS SEQRES 7 A 190 GLU GLU GLY GLU TYR VAL LEU VAL LEU LYS PHE ALA GLU SEQRES 8 A 190 VAL TYR PHE ALA GLN SER GLN GLN LYS VAL PHE ASP VAL SEQRES 9 A 190 ARG VAL ASN GLY HIS THR VAL VAL LYS ASP LEU ASP ILE SEQRES 10 A 190 PHE ASP ARG VAL GLY HIS SER THR ALA HIS ASP GLU ILE SEQRES 11 A 190 ILE PRO ILE SER ILE LYS LYS GLY LYS LEU SER VAL GLN SEQRES 12 A 190 GLY GLU VAL SER THR PHE THR GLY LYS LEU SER VAL GLU SEQRES 13 A 190 PHE VAL LYS GLY TYR TYR ASP ASN PRO LYS VAL CYS ALA SEQRES 14 A 190 LEU PHE ILE MET LYS GLY THR ALA ASP ASP VAL PRO MET SEQRES 15 A 190 LEU GLN PRO HIS PRO GLY LEU GLU HET BGC B 1 23 HET GLC B 2 22 HETNAM BGC BETA-D-GLUCOPYRANOSE HETNAM GLC ALPHA-D-GLUCOPYRANOSE FORMUL 2 BGC C6 H12 O6 FORMUL 2 GLC C6 H12 O6 HELIX 1 1 PRO A 55 LEU A 60 1 6 HELIX 2 2 ASP A 116 GLY A 122 1 7 SHEET 1 A 6 VAL A 10 ALA A 16 0 SHEET 2 A 6 VAL A 167 LYS A 174 -1 O ILE A 172 N TRP A 12 SHEET 3 A 6 GLY A 81 ALA A 90 -1 N VAL A 86 O PHE A 171 SHEET 4 A 6 HIS A 127 LYS A 136 -1 O ILE A 133 N TYR A 83 SHEET 5 A 6 LYS A 139 VAL A 142 -1 O LYS A 139 N LYS A 136 SHEET 6 A 6 GLU A 145 THR A 148 -1 O GLU A 145 N VAL A 142 SHEET 1 B 2 HIS A 21 ASP A 23 0 SHEET 2 B 2 ILE A 27 TYR A 29 -1 O ILE A 27 N ASP A 23 SHEET 1 C 4 PHE A 71 PRO A 76 0 SHEET 2 C 4 LYS A 152 VAL A 158 -1 O LEU A 153 N ILE A 75 SHEET 3 C 4 PHE A 102 VAL A 106 -1 N ASP A 103 O VAL A 158 SHEET 4 C 4 HIS A 109 LEU A 115 -1 O HIS A 109 N VAL A 106 LINK O4 BGC B 1 C1 GLC B 2 1555 1555 1.45 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000