10 20 30 40 50 60 70 80 2DCX - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ANTIMICROBIAL PROTEIN 17-JAN-06 2DCX
TITLE NMR SOLUTION STRUCTURE OF THE DERMASEPTIN ANTIMICROBIAL TITLE 2 PEPTIDE ANALOG NC12-K4S4(1-13)A
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DERMASEPTIN-4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-13; COMPND 5 SYNONYM: DS IV; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS IS A TRUNCATED, MUTATED SEQUENCE OF A SOURCE 4 PEPTIDE THAT OCCURS NATURALLY IN THE SOUTH AMERICAN TREE SOURCE 5 FROG, PHYLLOMEDUSA SAUVAGEI.
KEYWDS ALPHA-HELIX, PEPTIDE, ANTIMICROBIAL PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 15
AUTHOR D.E.SHALEV,S.ROTEM,A.FISH,A.MOR
REVDAT 3 24-FEB-09 2DCX 1 VERSN REVDAT 2 25-APR-06 2DCX 1 JRNL REVDAT 1 28-FEB-06 2DCX 0
JRNL AUTH D.E.SHALEV,S.ROTEM,A.FISH,A.MOR JRNL TITL CONSEQUENCES OF N-ACYLATION ON STRUCTURE AND JRNL TITL 2 MEMBRANE BINDING PROPERTIES OF DERMASEPTIN JRNL TITL 3 DERIVATIVE K4-S4-(1-13) JRNL REF J.BIOL.CHEM. V. 281 9432 2006 JRNL REFN ISSN 0021-9258 JRNL PMID 16407175 JRNL DOI 10.1074/JBC.M513051200
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.856 REMARK 3 AUTHORS : NILGES, KUSZEWSKI AND BRNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE DERIVED FROM 241 REMARK 3 NOE CONSTRAINTS; 109 INTRARESIDUAL; 44 I+1; 19 I+2; 39 I+3; 30 REMARK 3 LONG-RANGE.
REMARK 4 REMARK 4 2DCX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JAN-06. REMARK 100 THE RCSB ID CODE IS RCSB025266.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 78 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.2MM PEPTIDE; 20:1 MOLAR REMARK 210 RATIO OF DPC-D38 (CAMBRIDGE REMARK 210 ISOTOPE LABORATORIES, INC., REMARK 210 USA); 0.02% NAN3 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY, 2D TOCSY, 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.1, SPARKY 3, X-PLOR REMARK 210 3.856, PROCHECK REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY, STRUCTURES WITH THE REMARK 210 LEAST 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 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 1 ALA A 13 C ALA A 13 O -0.143 REMARK 500 8 ALA A 13 C ALA A 13 O 0.184 REMARK 500 15 ALA A 13 C ALA A 13 O 0.121 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 6 ALA A 13 N - CA - CB ANGL. DEV. = -9.4 DEGREES REMARK 500 8 ALA A 13 CB - CA - C ANGL. DEV. = 23.6 DEGREES REMARK 500 8 ALA A 13 N - CA - CB ANGL. DEV. = -8.9 DEGREES REMARK 500 8 ALA A 13 N - CA - C ANGL. DEV. = -17.4 DEGREES REMARK 500 15 ALA A 13 CB - CA - C ANGL. DEV. = 13.0 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 LEU A 2 52.72 89.65 REMARK 500 1 TRP A 3 -42.25 -134.13 REMARK 500 1 LYS A 9 -18.53 169.06 REMARK 500 1 LYS A 12 96.44 57.80 REMARK 500 2 LEU A 2 59.52 81.82 REMARK 500 2 TRP A 3 -43.40 -132.91 REMARK 500 2 LYS A 9 -18.60 167.58 REMARK 500 2 LYS A 12 14.19 58.56 REMARK 500 3 TRP A 3 -45.89 -136.36 REMARK 500 3 LYS A 4 -28.16 -38.05 REMARK 500 3 LEU A 6 -37.29 -39.43 REMARK 500 3 LEU A 7 42.98 -107.67 REMARK 500 3 LYS A 9 -19.55 165.48 REMARK 500 4 LEU A 2 57.93 75.68 REMARK 500 4 LYS A 9 -23.45 171.87 REMARK 500 4 LYS A 12 -68.00 68.28 REMARK 500 5 LEU A 2 59.55 82.06 REMARK 500 5 TRP A 3 -43.92 -132.74 REMARK 500 5 LYS A 9 -18.80 168.68 REMARK 500 5 LYS A 12 -69.54 62.79 REMARK 500 6 TRP A 3 -43.26 -137.00 REMARK 500 6 LYS A 4 -27.40 -38.58 REMARK 500 6 LEU A 6 -36.35 -37.63 REMARK 500 6 LYS A 9 -29.99 164.23 REMARK 500 6 VAL A 10 -89.16 -39.70 REMARK 500 6 LEU A 11 50.05 172.74 REMARK 500 7 LEU A 2 52.77 -111.48 REMARK 500 7 LYS A 9 -21.94 174.09 REMARK 500 7 LYS A 12 91.30 62.58 REMARK 500 8 LEU A 2 74.85 68.78 REMARK 500 8 TRP A 3 -38.35 -147.58 REMARK 500 8 LYS A 9 -20.56 164.13 REMARK 500 8 LYS A 12 96.94 48.37 REMARK 500 9 LEU A 2 54.03 76.23 REMARK 500 9 LYS A 9 -22.12 170.84 REMARK 500 9 LYS A 12 82.87 51.12 REMARK 500 10 LEU A 2 60.22 81.08 REMARK 500 10 TRP A 3 -41.77 -133.76 REMARK 500 10 LYS A 9 -19.13 177.81 REMARK 500 10 LYS A 12 94.21 62.25 REMARK 500 11 LYS A 9 -24.26 -179.79 REMARK 500 11 LYS A 12 89.06 62.03 REMARK 500 12 LYS A 8 -35.98 -39.90 REMARK 500 12 LYS A 9 23.23 -175.55 REMARK 500 12 LYS A 12 -67.74 67.73 REMARK 500 13 LEU A 7 39.18 -84.04 REMARK 500 13 LYS A 9 -19.55 174.83 REMARK 500 13 VAL A 10 12.46 -69.33 REMARK 500 13 LYS A 12 95.17 62.42 REMARK 500 14 LEU A 2 89.16 65.52 REMARK 500 14 TRP A 3 -34.18 -158.13 REMARK 500 14 LEU A 7 46.92 -109.15 REMARK 500 14 LYS A 9 -22.32 174.57 REMARK 500 14 LYS A 12 -64.02 67.87 REMARK 500 15 LEU A 2 57.74 78.64 REMARK 500 15 LYS A 8 -19.77 -47.47 REMARK 500 15 LYS A 9 -16.33 172.49 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 DOA A 0
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DD6 RELATED DB: PDB REMARK 900 NON-ACYLATED PEPTIDE ANALOG, K4-S4(1-13)A
DBREF 2DCX A 1 13 UNP P80280 DMS4_PHYSA 1 13
SEQADV 2DCX LYS A 4 UNP P80280 MET 4 ENGINEERED
SEQRES 1 A 14 ALA LEU TRP LYS THR LEU LEU LYS LYS VAL LEU LYS ALA SEQRES 2 A 14 NH2
HET NH2 A 14 3 HET DOA A 0 38
HETNAM NH2 AMINO GROUP HETNAM DOA 12-AMINO-DODECANOIC ACID
FORMUL 1 NH2 H2 N FORMUL 2 DOA C12 H25 N O2
LINK N ALA A 1 C DOA A 0 1555 1555 1.34 LINK C ALA A 13 N NH2 A 14 1555 1555 1.15
SITE 1 AC1 3 ALA A 1 LEU A 2 TRP A 3
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