HEADER DNA BINDING PROTEIN 06-FEB-02 1KZ0 TITLE SOLUTION STRUCTURE OF THE THIRD HELIX OF ANTENNAPEDIA HOMEODOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTENNAPEDIA PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL FRAGMENT OF ANTENNAPEDIA HOMEODOMAIN; COMPND 5 SYNONYM: PENETRATIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE WAS SYNTHETIZED IN SOLID-PHASE USING SOURCE 4 THE BOC-CHEMISTRY. THE SOURCE OF THIS PEPTIDE IS NATURALLY FOUND IN SOURCE 5 DROSOPHILA MELANOGASTER (FRUIT FLY). KEYWDS IRREGULAR HELIX, TURN-LIKE PARTS AT THE BEGINNING AND AT THE END, DNA KEYWDS 2 BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 26 AUTHOR A.CZAJLIK,E.MESKO,B.PENKE,A.PERCZEL REVDAT 4 23-FEB-22 1KZ0 1 REMARK REVDAT 3 24-FEB-09 1KZ0 1 VERSN REVDAT 2 19-JUN-02 1KZ0 1 JRNL REVDAT 1 20-FEB-02 1KZ0 0 JRNL AUTH A.CZAJLIK,E.MESKO,B.PENKE,A.PERCZEL JRNL TITL INVESTIGATION OF PENETRATIN PEPTIDES. PART 1. THE JRNL TITL 2 ENVIRONMENT DEPENDENT CONFORMATIONAL PROPERTIES OF JRNL TITL 3 PENETRATIN AND TWO OF ITS DERIVATIVES. JRNL REF J.PEPT.SCI. V. 8 151 2002 JRNL REFN ISSN 1075-2617 JRNL PMID 11991205 JRNL DOI 10.1002/PSC.380 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 97.2, X-PLOR 3.851 REMARK 3 AUTHORS : SAN DIEGO, MSI (FELIX), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 553 NOE-DERIVED RESTRAINTS REMARK 4 REMARK 4 1KZ0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-02. REMARK 100 THE DEPOSITION ID IS D_1000015487. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 3 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5MM PEPTIDE; 90% TFED2, 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 97.2, X-PLOR 3.851 REMARK 210 METHOD USED : SIMULATED ANNEALING AND REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 26 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS 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 O ILE A 5 HD21 ASN A 9 1.57 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 GLN A 2 -152.60 -126.86 REMARK 500 1 TRP A 6 -98.30 -41.17 REMARK 500 1 PHE A 7 -9.37 -56.86 REMARK 500 1 LYS A 13 45.39 -78.59 REMARK 500 1 TRP A 14 -165.33 -113.40 REMARK 500 2 GLN A 2 -156.51 -130.00 REMARK 500 2 TRP A 6 -99.00 -41.01 REMARK 500 2 PHE A 7 -9.87 -56.14 REMARK 500 2 LYS A 13 43.55 -78.89 REMARK 500 2 TRP A 14 -161.51 -111.99 REMARK 500 3 GLN A 2 -146.56 -114.69 REMARK 500 3 ILE A 3 36.63 70.06 REMARK 500 3 TRP A 6 -99.00 -41.16 REMARK 500 3 PHE A 7 -9.87 -56.16 REMARK 500 3 LYS A 13 45.16 -79.21 REMARK 500 3 TRP A 14 -161.27 -111.68 REMARK 500 4 TRP A 6 -98.88 -41.34 REMARK 500 4 PHE A 7 -9.79 -56.47 REMARK 500 4 LYS A 13 44.76 -78.26 REMARK 500 4 TRP A 14 -164.99 -113.22 REMARK 500 5 GLN A 2 -158.47 -127.55 REMARK 500 5 TRP A 6 -98.83 -40.85 REMARK 500 5 PHE A 7 -9.90 -56.24 REMARK 500 5 LYS A 13 45.16 -79.69 REMARK 500 5 TRP A 14 -162.38 -111.40 REMARK 500 6 GLN A 2 -157.08 -127.18 REMARK 500 6 TRP A 6 -99.08 -40.79 REMARK 500 6 PHE A 7 -9.98 -56.08 REMARK 500 6 LYS A 13 39.36 -68.75 REMARK 500 6 TRP A 14 -162.90 -111.58 REMARK 500 7 GLN A 2 -160.26 -127.09 REMARK 500 7 TRP A 6 -99.18 -40.82 REMARK 500 7 LYS A 13 45.36 -80.61 REMARK 500 7 TRP A 14 -162.26 -111.87 REMARK 500 8 GLN A 2 -156.43 -125.57 REMARK 500 8 TRP A 6 -98.72 -40.66 REMARK 500 8 PHE A 7 -9.76 -56.32 REMARK 500 8 LYS A 13 45.06 -80.28 REMARK 500 8 TRP A 14 -161.92 -111.79 REMARK 500 9 GLN A 2 -156.16 -124.68 REMARK 500 9 TRP A 6 -99.15 -40.74 REMARK 500 9 LYS A 13 45.10 -80.98 REMARK 500 9 TRP A 14 -161.95 -110.97 REMARK 500 10 GLN A 2 -156.42 -127.97 REMARK 500 10 TRP A 6 -98.57 -41.28 REMARK 500 10 PHE A 7 -9.28 -56.97 REMARK 500 10 LYS A 13 44.11 -79.38 REMARK 500 10 TRP A 14 -162.03 -111.27 REMARK 500 11 GLN A 2 -138.25 -116.16 REMARK 500 11 ILE A 3 34.16 70.45 REMARK 500 REMARK 500 THIS ENTRY HAS 118 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 1 ARG A 1 0.24 SIDE CHAIN REMARK 500 1 ARG A 10 0.16 SIDE CHAIN REMARK 500 1 ARG A 11 0.31 SIDE CHAIN REMARK 500 2 ARG A 1 0.28 SIDE CHAIN REMARK 500 2 ARG A 10 0.29 SIDE CHAIN REMARK 500 2 ARG A 11 0.32 SIDE CHAIN REMARK 500 3 ARG A 1 0.23 SIDE CHAIN REMARK 500 3 ARG A 10 0.23 SIDE CHAIN REMARK 500 3 ARG A 11 0.31 SIDE CHAIN REMARK 500 4 ARG A 1 0.21 SIDE CHAIN REMARK 500 4 ARG A 10 0.30 SIDE CHAIN REMARK 500 4 ARG A 11 0.31 SIDE CHAIN REMARK 500 5 ARG A 1 0.27 SIDE CHAIN REMARK 500 5 ARG A 10 0.22 SIDE CHAIN REMARK 500 5 ARG A 11 0.32 SIDE CHAIN REMARK 500 6 ARG A 1 0.26 SIDE CHAIN REMARK 500 6 ARG A 10 0.22 SIDE CHAIN REMARK 500 6 ARG A 11 0.31 SIDE CHAIN REMARK 500 7 ARG A 1 0.24 SIDE CHAIN REMARK 500 7 ARG A 10 0.28 SIDE CHAIN REMARK 500 7 ARG A 11 0.31 SIDE CHAIN REMARK 500 8 ARG A 1 0.24 SIDE CHAIN REMARK 500 8 ARG A 10 0.28 SIDE CHAIN REMARK 500 8 ARG A 11 0.32 SIDE CHAIN REMARK 500 9 ARG A 1 0.26 SIDE CHAIN REMARK 500 9 ARG A 10 0.26 SIDE CHAIN REMARK 500 9 ARG A 11 0.31 SIDE CHAIN REMARK 500 10 ARG A 1 0.19 SIDE CHAIN REMARK 500 10 ARG A 10 0.31 SIDE CHAIN REMARK 500 10 ARG A 11 0.32 SIDE CHAIN REMARK 500 11 ARG A 1 0.24 SIDE CHAIN REMARK 500 11 ARG A 10 0.27 SIDE CHAIN REMARK 500 11 ARG A 11 0.31 SIDE CHAIN REMARK 500 12 ARG A 1 0.23 SIDE CHAIN REMARK 500 12 ARG A 10 0.30 SIDE CHAIN REMARK 500 12 ARG A 11 0.31 SIDE CHAIN REMARK 500 13 ARG A 1 0.24 SIDE CHAIN REMARK 500 13 ARG A 10 0.23 SIDE CHAIN REMARK 500 13 ARG A 11 0.31 SIDE CHAIN REMARK 500 14 ARG A 1 0.29 SIDE CHAIN REMARK 500 14 ARG A 10 0.29 SIDE CHAIN REMARK 500 14 ARG A 11 0.32 SIDE CHAIN REMARK 500 15 ARG A 1 0.21 SIDE CHAIN REMARK 500 15 ARG A 10 0.25 SIDE CHAIN REMARK 500 15 ARG A 11 0.31 SIDE CHAIN REMARK 500 16 ARG A 1 0.30 SIDE CHAIN REMARK 500 16 ARG A 10 0.32 SIDE CHAIN REMARK 500 16 ARG A 11 0.31 SIDE CHAIN REMARK 500 17 ARG A 1 0.23 SIDE CHAIN REMARK 500 17 ARG A 10 0.27 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 78 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HOM RELATED DB: PDB REMARK 900 1HOM CONTAINS THE ENTIRE HOMEODOMAIN REMARK 900 RELATED ID: 1KZ2 RELATED DB: PDB REMARK 900 THIRD HELIX[W6F,W14F] OF ANTENNAPEDIA HOMEODOMAIN REMARK 900 RELATED ID: 1KZ5 RELATED DB: PDB REMARK 900 THIRD HELIX OF ANTENNAPEDIA HOMEODOMAIN DERIVATIVE, 4 DELETIONS DBREF 1KZ0 A 1 16 UNP P02833 ANTP_DROME 50 65 SEQRES 1 A 16 ARG GLN ILE LYS ILE TRP PHE GLN ASN ARG ARG MET LYS SEQRES 2 A 16 TRP LYS LYS HELIX 1 1 ILE A 5 MET A 12 1 8 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 MODEL 1