10 20 30 40 50 60 70 80 1DG0 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TOXIN 22-NOV-99 1DG0
TITLE NMR STRUCTURE OF DES[GLY1]-CONTRYPHAN-R CYCLIC PEPTIDE TITLE 2 (MAJOR FORM)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DES[GLY1]-CONTRYPHAN-R; COMPND 3 CHAIN: A
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CONUS RADIATUS; SOURCE 3 ORGANISM_TAXID: 61198
KEYWDS CYCLIC PEPTIDE, DISULFIDE BRIDGE, D-TRYPTOPHAN, CIS-TRANS KEYWDS 2 ISOMERISM, CONTRYPHAN, TOXIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR P.K.PALLAGHY,W.HE,E.C.JIMENEZ,B.M.OLIVERA,R.S.NORTON
REVDAT 2 24-FEB-09 1DG0 1 VERSN REVDAT 1 09-SEP-03 1DG0 0
JRNL AUTH P.K.PALLAGHY,W.HE,E.C.JIMENEZ,B.M.OLIVERA, JRNL AUTH 2 R.S.NORTON JRNL TITL STRUCTURES OF THE CONTRYPHAN FAMILY OF CYCLIC JRNL TITL 2 PEPTIDES. ROLE OF ELECTROSTATIC INTERACTIONS IN JRNL TITL 3 CIS-TRANS ISOMERISM JRNL REF BIOCHEMISTRY V. 39 12845 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 11041849 JRNL DOI 10.1021/BI0010930
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: EM IN CHARMM-19 FORCE-FIELD WITH REMARK 3 EXPLICIT BOX OF H2O TREATED WITH PBC
REMARK 4 REMARK 4 1DG0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-NOV-99. REMARK 100 THE RCSB ID CODE IS RCSB010052.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 2.9 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 5.0 MM REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY, E-COSY, REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 1.3, XEASY 1.3.13 REMARK 210 METHOD USED : SIMULATED ANNEALING & ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 5 TRP A 7 CG TRP A 7 CD2 -0.104 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 1 TRP A 7 CG - CD1 - NE1 ANGL. DEV. = -6.4 DEGREES REMARK 500 1 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 8.1 DEGREES REMARK 500 1 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 10.8 DEGREES REMARK 500 1 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -7.2 DEGREES REMARK 500 1 TRP A 7 CG - CD2 - CE3 ANGL. DEV. = -6.5 DEGREES REMARK 500 2 TRP A 7 CG - CD1 - NE1 ANGL. DEV. = -6.5 DEGREES REMARK 500 2 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 8.4 DEGREES REMARK 500 2 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 10.3 DEGREES REMARK 500 2 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -7.2 DEGREES REMARK 500 2 TRP A 7 CG - CD2 - CE3 ANGL. DEV. = -5.6 DEGREES REMARK 500 3 TRP A 7 CG - CD1 - NE1 ANGL. DEV. = -6.8 DEGREES REMARK 500 3 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 8.2 DEGREES REMARK 500 3 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 9.5 DEGREES REMARK 500 3 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 4 TRP A 7 CG - CD1 - NE1 ANGL. DEV. = -6.3 DEGREES REMARK 500 4 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 8.0 DEGREES REMARK 500 4 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 9.6 DEGREES REMARK 500 4 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -7.2 DEGREES REMARK 500 4 TRP A 7 CG - CD2 - CE3 ANGL. DEV. = -5.9 DEGREES REMARK 500 5 TRP A 7 CG - CD1 - NE1 ANGL. DEV. = -7.1 DEGREES REMARK 500 5 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 8.3 DEGREES REMARK 500 5 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 9.5 DEGREES REMARK 500 5 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -6.7 DEGREES REMARK 500 5 TRP A 7 CG - CD2 - CE3 ANGL. DEV. = -5.5 DEGREES REMARK 500 6 TRP A 7 CG - CD1 - NE1 ANGL. DEV. = -6.5 DEGREES REMARK 500 6 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 8.5 DEGREES REMARK 500 6 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 10.4 DEGREES REMARK 500 6 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -7.3 DEGREES REMARK 500 6 TRP A 7 CG - CD2 - CE3 ANGL. DEV. = -5.7 DEGREES REMARK 500 7 TRP A 7 CG - CD1 - NE1 ANGL. DEV. = -6.5 DEGREES REMARK 500 7 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 8.4 DEGREES REMARK 500 7 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 9.7 DEGREES REMARK 500 7 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -7.3 DEGREES REMARK 500 7 TRP A 7 CG - CD2 - CE3 ANGL. DEV. = -5.7 DEGREES REMARK 500 8 TRP A 7 CG - CD1 - NE1 ANGL. DEV. = -7.0 DEGREES REMARK 500 8 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 8.5 DEGREES REMARK 500 8 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 9.8 DEGREES REMARK 500 8 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -7.1 DEGREES REMARK 500 8 TRP A 7 CG - CD2 - CE3 ANGL. DEV. = -5.4 DEGREES REMARK 500 9 TRP A 7 CG - CD1 - NE1 ANGL. DEV. = -6.4 DEGREES REMARK 500 9 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 7.9 DEGREES REMARK 500 9 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 9.4 DEGREES REMARK 500 9 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 9 TRP A 7 CG - CD2 - CE3 ANGL. DEV. = -5.6 DEGREES REMARK 500 10 TRP A 7 CG - CD1 - NE1 ANGL. DEV. = -6.7 DEGREES REMARK 500 10 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 8.2 DEGREES REMARK 500 10 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 10.0 DEGREES REMARK 500 10 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -7.1 DEGREES REMARK 500 10 TRP A 7 CG - CD2 - CE3 ANGL. DEV. = -5.7 DEGREES REMARK 500 11 TRP A 7 CG - CD1 - NE1 ANGL. DEV. = -6.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 99 ANGLE DEVIATIONS. 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 4 PRO A 6 20.77 -75.83 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QFB RELATED DB: PDB REMARK 900 STRUCTURE OF CONTRYPHAN-R REMARK 900 RELATED ID: 1DFY RELATED DB: PDB REMARK 900 STRUCTURE OF ALTERNATE FORM OF CONTRYPHAN-SM (MAJOR FORM - REMARK 900 CIS) REMARK 900 RELATED ID: 1DFZ RELATED DB: PDB REMARK 900 STRUCTURE OF ALTERNATE FORM OF CONTRYPHAN-SM (MINOR FORM - REMARK 900 TRANS)
SEQRES 1 A 7 CYS HYP DTR GLN PRO TRP CY3
MODRES 1DG0 HYP A 3 PRO 4-HYDROXYPROLINE MODRES 1DG0 CY3 A 8 CYS 2-AMINO-3-MERCAPTO-PROPIONAMIDE
HET HYP A 3 15 HET DTR A 4 24 HET CY3 A 8 13
HETNAM HYP 4-HYDROXYPROLINE HETNAM DTR D-TRYPTOPHAN HETNAM CY3 2-AMINO-3-MERCAPTO-PROPIONAMIDE
HETSYN HYP HYDROXYPROLINE
FORMUL 1 HYP C5 H9 N O3 FORMUL 1 DTR C11 H12 N2 O2 FORMUL 1 CY3 C3 H8 N2 O S
LINK C CYS A 2 N HYP A 3 1555 1555 1.32 LINK SG CYS A 2 SG CY3 A 8 1555 1555 2.02 LINK C HYP A 3 N DTR A 4 1555 1555 1.31 LINK C DTR A 4 N GLN A 5 1555 1555 1.30 LINK C TRP A 7 N CY3 A 8 1555 1555 1.31
CISPEP 1 CYS A 2 HYP A 3 1 -10.45 CISPEP 2 CYS A 2 HYP A 3 2 -10.52 CISPEP 3 CYS A 2 HYP A 3 3 -11.63 CISPEP 4 CYS A 2 HYP A 3 4 -9.06 CISPEP 5 CYS A 2 HYP A 3 5 -8.99 CISPEP 6 CYS A 2 HYP A 3 6 -9.62 CISPEP 7 CYS A 2 HYP A 3 7 -3.96 CISPEP 8 CYS A 2 HYP A 3 8 -10.49 CISPEP 9 CYS A 2 HYP A 3 9 -5.69 CISPEP 10 CYS A 2 HYP A 3 10 -3.79 CISPEP 11 CYS A 2 HYP A 3 11 -10.56 CISPEP 12 CYS A 2 HYP A 3 12 -2.56 CISPEP 13 CYS A 2 HYP A 3 13 -2.63 CISPEP 14 CYS A 2 HYP A 3 14 -10.56 CISPEP 15 CYS A 2 HYP A 3 15 -11.49 CISPEP 16 CYS A 2 HYP A 3 16 -10.98 CISPEP 17 CYS A 2 HYP A 3 17 -10.48 CISPEP 18 CYS A 2 HYP A 3 18 8.66 CISPEP 19 CYS A 2 HYP A 3 19 -2.59 CISPEP 20 CYS A 2 HYP A 3 20 -7.03
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