PDB Short entry for 1D6B HEADER TOXIN 12-OCT-99 1D6B TITLE SOLUTION STRUCTURE OF DEFENSIN-LIKE PEPTIDE-2 (DLP-2) FROM PLATYPUS TITLE 2 VENOM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEFENSIN-LIKE PEPTIDE-2; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORNITHORHYNCHUS ANATINUS; SOURCE 3 ORGANISM_COMMON: PLATYPUS; SOURCE 4 ORGANISM_TAXID: 9258; SOURCE 5 ORGAN: SPUR; SOURCE 6 TISSUE: VENOM GLAND; SOURCE 7 SECRETION: VENOM KEYWDS HELIX, ANTIPARALLEL BETA-SHEET, TOXIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.M.TORRES,G.M.DE PLATER,M.DOVERSKOG,L.C BIRINYI-STRACHAN, AUTHOR 2 G.M.NICHOLSON,C.H.GALLAGHER,P.W.KUCHEL REVDAT 4 16-FEB-22 1D6B 1 REMARK REVDAT 3 24-FEB-09 1D6B 1 VERSN REVDAT 2 01-APR-03 1D6B 1 JRNL REVDAT 1 21-JUN-00 1D6B 0 JRNL AUTH A.M.TORRES,G.M.DE PLATER,M.DOVERSKOG,L.C.BIRINYI-STRACHAN, JRNL AUTH 2 G.M.NICHOLSON,C.H.GALLAGHER,P.W.KUCHEL JRNL TITL DEFENSIN-LIKE PEPTIDE-2 FROM PLATYPUS VENOM: MEMBER OF A JRNL TITL 2 CLASS OF PEPTIDES WITH A DISTINCT STRUCTURAL FOLD. JRNL REF BIOCHEM.J. V. 348 649 2000 JRNL REFN ISSN 0264-6021 JRNL PMID 10839998 JRNL DOI 10.1042/0264-6021:3480649 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.M.TORRES,X.WANG,J.I.FLETCHER,D.ALEWOOD,P.F.ALEWOOD, REMARK 1 AUTH 2 R.SMITH,R.J.SIMPSON,G.M.NICHOLSON,S.K.SUTHERLAND, REMARK 1 AUTH 3 C.H.GALLAGHER,G.F.KING,P.W.KUCHEL REMARK 1 TITL SOLUTION STRUCTURE OF A DEFENSIN-LIKE PEPTIDE FROM PLATYPUS REMARK 1 TITL 2 VENOM REMARK 1 REF BIOCHEM.J. V. 341 785 1999 REMARK 1 REFN ISSN 0264-6021 REMARK 1 DOI 10.1042/0264-6021:3410785 REMARK 1 REFERENCE 2 REMARK 1 AUTH G.R.ZIMMERMANN,P.LEGAULT,M.E.SELSTED,A.PARDI REMARK 1 TITL SOLUTION STRUCTURE OF BOVINE NEUTROPHIL BETA-DEFENSIN-12: REMARK 1 TITL 2 THE PEPTIDE FOLD OF THE BETA-DEFENSINS IS IDENTICAL TO THAT REMARK 1 TITL 3 OF THE CLASSICAL DEFENSINS REMARK 1 REF BIOCHEMISTRY V. 34 13663 1995 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.5, X-PLOR 3.843 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 739 RESTRAINTS, 699 ARE NOE- REMARK 3 DERIVED REMARK 3 DISTANCE RESTRAINTS, 24 DIHEDRAL ANGLE RESTRAINTS, 16 DISTANCE REMARK 3 RESTRAINTS FROM REMARK 3 HYDROGEN BONDS. REMARK 4 REMARK 4 1D6B COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-OCT-99. REMARK 100 THE DEPOSITION ID IS D_1000009827. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 3.6 REMARK 210 IONIC STRENGTH : NO SALT ADDED REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM DLP-2 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY 1.3.13, DYANA 1.5 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS, REMARK 210 TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 4800 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURES WERE DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. 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 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 HG2 GLU A 21 HB2 CYS A 24 1.18 REMARK 500 HG3 GLU A 21 H ASN A 23 1.25 REMARK 500 HG12 VAL A 15 H CYS A 16 1.28 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 MET A 2 -165.70 70.75 REMARK 500 1 PHE A 4 -119.04 154.55 REMARK 500 1 GLU A 5 84.26 13.82 REMARK 500 1 MET A 6 -108.66 -43.99 REMARK 500 1 ALA A 8 115.83 -23.11 REMARK 500 1 SER A 13 72.82 81.05 REMARK 500 1 ASP A 18 133.30 -35.54 REMARK 500 1 ALA A 28 176.26 -47.04 REMARK 500 1 TRP A 29 73.81 40.17 REMARK 500 1 THR A 30 137.01 159.14 REMARK 500 1 ARG A 35 12.88 -67.06 REMARK 500 1 GLU A 41 -73.01 -50.69 REMARK 500 2 MET A 2 77.58 -51.73 REMARK 500 2 PHE A 3 -126.66 -137.50 REMARK 500 2 PHE A 4 76.50 86.22 REMARK 500 2 GLU A 5 69.28 -1.85 REMARK 500 2 MET A 6 -93.83 -36.74 REMARK 500 2 ALA A 8 129.69 -21.78 REMARK 500 2 PRO A 26 96.29 -44.22 REMARK 500 2 ALA A 28 -171.58 -62.71 REMARK 500 2 TRP A 29 75.44 40.10 REMARK 500 2 THR A 30 157.49 162.88 REMARK 500 2 ARG A 35 17.52 -60.12 REMARK 500 2 GLU A 41 -74.01 -42.63 REMARK 500 3 PHE A 3 65.29 -102.22 REMARK 500 3 MET A 6 -134.66 -52.91 REMARK 500 3 ALA A 8 103.35 -30.80 REMARK 500 3 CYS A 9 -25.95 -31.20 REMARK 500 3 SER A 13 77.43 61.78 REMARK 500 3 PRO A 26 99.92 -47.66 REMARK 500 3 ALA A 28 177.58 -52.44 REMARK 500 3 TRP A 29 72.89 39.76 REMARK 500 3 THR A 30 150.06 165.11 REMARK 500 3 ARG A 35 12.48 -64.99 REMARK 500 3 GLU A 41 -76.10 -56.24 REMARK 500 4 PHE A 4 109.89 67.32 REMARK 500 4 GLU A 5 83.45 170.70 REMARK 500 4 MET A 6 -138.70 -54.60 REMARK 500 4 GLN A 7 -149.59 -127.18 REMARK 500 4 CYS A 9 -24.60 -33.60 REMARK 500 4 SER A 11 10.05 -56.30 REMARK 500 4 SER A 13 65.51 89.51 REMARK 500 4 PRO A 26 108.49 -52.86 REMARK 500 4 MET A 27 76.15 -103.39 REMARK 500 4 ALA A 28 -166.74 -46.54 REMARK 500 4 TRP A 29 66.11 36.34 REMARK 500 4 THR A 30 147.87 153.09 REMARK 500 4 ARG A 35 15.65 -66.52 REMARK 500 5 PHE A 3 39.46 -98.49 REMARK 500 5 PHE A 4 56.51 -93.90 REMARK 500 REMARK 500 THIS ENTRY HAS 262 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1B8W RELATED DB: PDB DBREF 1D6B A 1 42 UNP P82140 DLP2_ORNAN 1 42 SEQRES 1 A 42 ILE MET PHE PHE GLU MET GLN ALA CYS TRP SER HIS SER SEQRES 2 A 42 GLY VAL CYS ARG ASP LYS SER GLU ARG ASN CYS LYS PRO SEQRES 3 A 42 MET ALA TRP THR TYR CYS GLU ASN ARG ASN GLN LYS CYS SEQRES 4 A 42 CYS GLU TYR HELIX 1 1 ALA A 8 SER A 13 1 6 SHEET 1 A 2 VAL A 15 ASP A 18 0 SHEET 2 A 2 GLN A 37 CYS A 40 -1 N LYS A 38 O ARG A 17 SSBOND 1 CYS A 9 CYS A 39 1555 1555 2.03 SSBOND 2 CYS A 16 CYS A 32 1555 1555 2.03 SSBOND 3 CYS A 24 CYS A 40 1555 1555 2.03 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