10 20 30 40 50 60 70 80 1X6A - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER PROTEIN BINDING 17-MAY-05 1X6A
TITLE SOLUTION STRUCTURES OF THE SECOND LIM DOMAIN OF HUMAN LIM- TITLE 2 KINASE 2 (LIMK2)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIM DOMAIN KINASE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIM DOMAIN; COMPND 5 SYNONYM: LIMK-2; COMPND 6 EC: 2.7.1.-; COMPND 7 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: LIMK2; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P040921-12; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS
KEYWDS LIM-KINASE 2, ZINC FINGER DOMAIN, STRUCTURAL GENOMICS, KEYWDS 2 NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND KEYWDS 3 FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI, PROTEIN BINDING
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR N.NAMEKI,A.SASAGAWA,T.TOMIZAWA,S.KOSHIBA,M.INOUE,T.KIGAWA, AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE AUTHOR 3 (RSGI)
REVDAT 2 24-FEB-09 1X6A 1 VERSN REVDAT 1 17-NOV-05 1X6A 0
JRNL AUTH N.NAMEKI,A.SASAGAWA,T.TOMIZAWA,S.KOSHIBA,M.INOUE, JRNL AUTH 2 T.KIGAWA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURES OF THE SECOND LIM DOMAIN OF JRNL TITL 2 HUMAN LIM-KINASE 2 (LIMK2) JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OPALP 1.2 REMARK 3 AUTHORS : KORADI, R.,BILLETER, M.,GUNTERT, P. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1X6A COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-MAY-05. REMARK 100 THE RCSB ID CODE IS RCSB024432.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.3MM LIM DOMAIN U-15N, 13C; REMARK 210 20MM D-TRIS-HCL(PH 7.0); 100MM REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3; REMARK 210 0.05MM ZNCL2, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, 3D_ REMARK 210 13C-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, NMRPIPE REMARK 210 20030801, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9295, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION, STRUCTURES REMARK 210 WITH THE LOWEST ENERGY, REMARK 210 STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 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 7 CYS A 70 CB - CA - C ANGL. DEV. = 9.8 DEGREES REMARK 500 17 CYS A 70 CB - CA - C ANGL. DEV. = 7.5 DEGREES REMARK 500 19 CYS A 21 CA - CB - SG ANGL. DEV. = 9.0 DEGREES REMARK 500 19 CYS A 70 CB - CA - C ANGL. DEV. = 8.6 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 PHE A 14 -50.11 -138.32 REMARK 500 1 THR A 26 -37.36 -143.87 REMARK 500 1 ASP A 53 77.26 -67.27 REMARK 500 1 ALA A 56 103.42 -55.69 REMARK 500 1 SER A 76 13.67 55.16 REMARK 500 1 SER A 80 -78.62 -83.98 REMARK 500 2 SER A 2 78.38 40.21 REMARK 500 2 TYR A 10 50.57 -152.82 REMARK 500 2 GLU A 34 -0.96 82.21 REMARK 500 2 LYS A 48 -1.62 66.38 REMARK 500 2 SER A 79 -165.67 -121.38 REMARK 500 3 THR A 26 -56.54 -131.53 REMARK 500 3 GLU A 34 6.67 84.04 REMARK 500 3 ALA A 63 76.10 -67.66 REMARK 500 3 SER A 80 -56.56 -163.61 REMARK 500 4 HIS A 19 21.95 -64.50 REMARK 500 4 THR A 26 -70.68 -127.36 REMARK 500 4 GLU A 34 -1.83 76.52 REMARK 500 4 CYS A 47 -8.37 -142.43 REMARK 500 4 ASP A 53 3.81 -63.24 REMARK 500 4 HIS A 62 39.91 38.99 REMARK 500 4 ALA A 63 -16.55 -148.61 REMARK 500 4 SER A 76 49.06 -89.49 REMARK 500 5 SER A 5 34.56 -71.50 REMARK 500 5 SER A 6 14.36 59.75 REMARK 500 5 THR A 26 -50.25 -125.66 REMARK 500 5 PRO A 78 -166.29 -74.98 REMARK 500 6 ASP A 53 43.97 -75.44 REMARK 500 6 GLN A 61 48.66 38.27 REMARK 500 6 ALA A 63 -38.66 -147.43 REMARK 500 7 SER A 5 41.96 -148.81 REMARK 500 7 TYR A 10 -49.58 -163.61 REMARK 500 7 LYS A 13 151.01 174.72 REMARK 500 7 PHE A 14 -67.47 -120.81 REMARK 500 7 GLU A 34 13.13 53.57 REMARK 500 7 CYS A 41 40.99 -143.47 REMARK 500 7 GLN A 61 44.65 34.35 REMARK 500 7 HIS A 62 36.23 39.03 REMARK 500 7 ALA A 63 -11.92 -143.64 REMARK 500 7 SER A 76 0.69 -65.13 REMARK 500 8 SER A 3 -168.96 -165.00 REMARK 500 8 LYS A 8 59.73 -145.25 REMARK 500 8 TYR A 10 -23.38 -150.11 REMARK 500 8 SER A 22 -16.12 81.11 REMARK 500 8 GLU A 34 -9.48 87.43 REMARK 500 8 LYS A 48 -7.85 71.78 REMARK 500 8 GLN A 61 -6.83 -55.91 REMARK 500 8 ALA A 63 7.86 80.09 REMARK 500 9 HIS A 19 19.80 -64.83 REMARK 500 9 SER A 22 -3.35 67.33 REMARK 500 9 THR A 26 -8.01 -143.05 REMARK 500 9 GLU A 34 -5.13 60.28 REMARK 500 9 ASP A 53 10.59 -69.10 REMARK 500 9 GLN A 61 46.08 38.85 REMARK 500 9 HIS A 62 23.84 44.03 REMARK 500 10 HIS A 19 31.12 -73.53 REMARK 500 10 SER A 22 -8.52 70.69 REMARK 500 10 GLU A 34 -3.41 76.41 REMARK 500 10 GLU A 40 1.34 -64.14 REMARK 500 10 LYS A 48 -0.27 62.35 REMARK 500 10 GLN A 61 1.45 -60.79 REMARK 500 10 SER A 79 1.16 -61.73 REMARK 500 11 GLU A 40 4.42 -61.39 REMARK 500 11 ALA A 63 49.18 -80.24 REMARK 500 12 LYS A 48 -0.09 64.42 REMARK 500 12 ASP A 53 49.96 -81.48 REMARK 500 12 ASP A 55 -150.54 -92.66 REMARK 500 12 ALA A 63 62.11 -68.78 REMARK 500 13 LYS A 8 -77.02 -158.72 REMARK 500 13 TYR A 10 -22.08 -163.02 REMARK 500 13 PHE A 14 32.31 -77.30 REMARK 500 13 SER A 22 -13.00 70.82 REMARK 500 13 THR A 26 29.58 43.87 REMARK 500 13 GLN A 61 28.42 48.33 REMARK 500 13 HIS A 62 -36.03 71.50 REMARK 500 14 SER A 5 161.81 170.81 REMARK 500 14 TYR A 10 -30.39 -139.30 REMARK 500 14 PHE A 14 65.08 -118.48 REMARK 500 14 GLU A 34 -0.62 77.29 REMARK 500 14 GLU A 40 6.71 -62.77 REMARK 500 14 LYS A 48 5.39 58.40 REMARK 500 14 HIS A 62 19.15 57.11 REMARK 500 15 SER A 5 157.29 174.64 REMARK 500 15 SER A 22 60.28 63.51 REMARK 500 15 GLU A 34 2.92 88.54 REMARK 500 15 HIS A 62 -165.09 -70.85 REMARK 500 15 ALA A 63 47.93 -101.19 REMARK 500 16 GLU A 34 10.18 53.97 REMARK 500 16 ASP A 53 20.47 -74.01 REMARK 500 16 ASP A 55 -165.27 -118.40 REMARK 500 16 GLN A 61 24.90 48.35 REMARK 500 17 SER A 3 79.85 -150.15 REMARK 500 17 SER A 6 -40.68 -160.19 REMARK 500 17 LYS A 8 78.33 -151.02 REMARK 500 17 ASP A 9 100.67 -54.72 REMARK 500 17 SER A 22 -0.05 65.77 REMARK 500 17 GLU A 34 -20.88 93.90 REMARK 500 17 GLU A 40 3.44 -64.13 REMARK 500 17 ASP A 53 12.17 -60.68 REMARK 500 17 ALA A 63 69.37 -67.28 REMARK 500 18 THR A 26 -65.54 55.72 REMARK 500 18 GLU A 34 -15.92 105.44 REMARK 500 18 GLU A 40 0.36 -62.58 REMARK 500 18 ALA A 63 95.15 -50.43 REMARK 500 19 SER A 6 -97.21 -140.38 REMARK 500 19 SER A 22 -2.58 72.28 REMARK 500 19 CYS A 47 -11.48 -140.44 REMARK 500 19 GLN A 61 171.51 -51.85 REMARK 500 19 ALA A 63 19.07 46.64 REMARK 500 19 SER A 79 152.22 -43.59 REMARK 500 20 SER A 3 109.11 -165.07 REMARK 500 20 GLU A 34 12.60 53.54 REMARK 500 20 PHE A 35 -148.45 -128.87 REMARK 500 20 ALA A 63 68.53 -68.10 REMARK 500 20 SER A 80 33.60 -144.86 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 1 TYR A 37 0.10 SIDE_CHAIN REMARK 500 3 TYR A 37 0.07 SIDE_CHAIN REMARK 500 3 TYR A 66 0.06 SIDE_CHAIN REMARK 500 6 TYR A 10 0.07 SIDE_CHAIN REMARK 500 16 TYR A 66 0.07 SIDE_CHAIN REMARK 500 17 TYR A 57 0.07 SIDE_CHAIN REMARK 500 18 TYR A 10 0.09 SIDE_CHAIN REMARK 500 20 TYR A 10 0.08 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 18 SG REMARK 620 2 CYS A 21 SG 82.0 REMARK 620 3 HIS A 38 ND1 79.9 72.0 REMARK 620 4 CYS A 41 SG 92.6 152.2 134.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 44 SG REMARK 620 2 CYS A 47 SG 83.9 REMARK 620 3 CYS A 67 SG 95.3 138.7 REMARK 620 4 CYS A 70 SG 122.8 145.2 66.7 REMARK 620 N 1 2 3
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 201 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 401
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSI002010509.1 RELATED DB: TARGETDB
DBREF 1X6A A 8 75 UNP P53671 LIMK2_HUMAN 62 129
SEQADV 1X6A GLY A 1 UNP P53671 CLONING ARTIFACT SEQADV 1X6A SER A 2 UNP P53671 CLONING ARTIFACT SEQADV 1X6A SER A 3 UNP P53671 CLONING ARTIFACT SEQADV 1X6A GLY A 4 UNP P53671 CLONING ARTIFACT SEQADV 1X6A SER A 5 UNP P53671 CLONING ARTIFACT SEQADV 1X6A SER A 6 UNP P53671 CLONING ARTIFACT SEQADV 1X6A GLY A 7 UNP P53671 CLONING ARTIFACT SEQADV 1X6A SER A 76 UNP P53671 CLONING ARTIFACT SEQADV 1X6A GLY A 77 UNP P53671 CLONING ARTIFACT SEQADV 1X6A PRO A 78 UNP P53671 CLONING ARTIFACT SEQADV 1X6A SER A 79 UNP P53671 CLONING ARTIFACT SEQADV 1X6A SER A 80 UNP P53671 CLONING ARTIFACT SEQADV 1X6A GLY A 81 UNP P53671 CLONING ARTIFACT
SEQRES 1 A 81 GLY SER SER GLY SER SER GLY LYS ASP TYR TRP GLY LYS SEQRES 2 A 81 PHE GLY GLU PHE CYS HIS GLY CYS SER LEU LEU MET THR SEQRES 3 A 81 GLY PRO PHE MET VAL ALA GLY GLU PHE LYS TYR HIS PRO SEQRES 4 A 81 GLU CYS PHE ALA CYS MET SER CYS LYS VAL ILE ILE GLU SEQRES 5 A 81 ASP GLY ASP ALA TYR ALA LEU VAL GLN HIS ALA THR LEU SEQRES 6 A 81 TYR CYS GLY LYS CYS HIS ASN GLU VAL VAL SER GLY PRO SEQRES 7 A 81 SER SER GLY
HET ZN A 201 1 HET ZN A 401 1
HETNAM ZN ZINC ION
FORMUL 2 ZN 2(ZN 2+)
HELIX 1 1 GLY A 68 SER A 76 1 9
SHEET 1 A 2 TYR A 57 LEU A 59 0 SHEET 2 A 2 LEU A 65 CYS A 67 -1 O TYR A 66 N ALA A 58
LINK ZN ZN A 201 SG CYS A 18 1555 1555 3.29 LINK ZN ZN A 201 SG CYS A 21 1555 1555 3.18 LINK ZN ZN A 201 ND1 HIS A 38 1555 1555 2.52 LINK ZN ZN A 201 SG CYS A 41 1555 1555 3.13 LINK ZN ZN A 401 SG CYS A 44 1555 1555 3.17 LINK ZN ZN A 401 SG CYS A 47 1555 1555 3.03 LINK ZN ZN A 401 SG CYS A 67 1555 1555 3.05 LINK ZN ZN A 401 SG CYS A 70 1555 1555 3.16
SITE 1 AC1 4 CYS A 18 CYS A 21 HIS A 38 CYS A 41 SITE 1 AC2 4 CYS A 44 CYS A 47 CYS A 67 CYS A 70
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