HEADER TOXIN 22-NOV-99 1DFY TITLE NMR STRUCTURE OF CONTRYPHAN-SM CYCLIC PEPTIDE (MAJOR FORM-CIS) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CONTRYPHAN-SM; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CONUS STERCUSMUSCARUM; SOURCE 3 ORGANISM_TAXID: 89452 KEYWDS CYCLIC PEPTIDE, DISULFIDE BRIDGE, D-TRYPTOPHAN, CIS-TRANS ISOMERISM, KEYWDS 2 CONTRYPHAN, TOXIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.K.PALLAGHY,W.HE,E.C.JIMENEZ,B.M.OLIVERA,R.S.NORTON REVDAT 3 24-JUN-20 1DFY 1 SOURCE REMARK DBREF LINK REVDAT 2 24-FEB-09 1DFY 1 VERSN REVDAT 1 01-MAY-02 1DFY 0 JRNL AUTH P.K.PALLAGHY,W.HE,E.C.JIMENEZ,B.M.OLIVERA,R.S.NORTON JRNL TITL STRUCTURES OF THE CONTRYPHAN FAMILY OF CYCLIC PEPTIDES. ROLE JRNL TITL 2 OF ELECTROSTATIC INTERACTIONS IN CIS-TRANS ISOMERISM. JRNL REF BIOCHEMISTRY V. 39 12845 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 11041849 JRNL DOI 10.1021/BI0010930 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 1.3, X-PLOR 3 REMARK 3 AUTHORS : BRUKER (XWINNMR), BRUNGER (X-PLOR) 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 1DFY 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 DEPOSITION ID IS D_1000010050. 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 : XEASY 1.3.13 REMARK 210 METHOD USED : SIMULATED ANNEALING & ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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 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: 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 7 DTR A 4 CG DTR A 4 CD2 -0.103 REMARK 500 17 DTR A 4 CG DTR A 4 CD2 -0.107 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 DTR A 4 CG - CD1 - NE1 ANGL. DEV. = -7.7 DEGREES REMARK 500 1 DTR A 4 CD1 - NE1 - CE2 ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DTR A 4 NE1 - CE2 - CZ2 ANGL. DEV. = 9.1 DEGREES REMARK 500 1 DTR A 4 NE1 - CE2 - CD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 TRP A 7 CG - CD1 - NE1 ANGL. DEV. = -7.3 DEGREES REMARK 500 1 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 9.6 DEGREES REMARK 500 1 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 9.7 DEGREES REMARK 500 1 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -7.1 DEGREES REMARK 500 2 DTR A 4 CG - CD1 - NE1 ANGL. DEV. = -7.2 DEGREES REMARK 500 2 DTR A 4 CD1 - NE1 - CE2 ANGL. DEV. = 7.9 DEGREES REMARK 500 2 DTR A 4 NE1 - CE2 - CZ2 ANGL. DEV. = 8.5 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. = 7.6 DEGREES REMARK 500 2 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 8.0 DEGREES REMARK 500 3 DTR A 4 CG - CD1 - NE1 ANGL. DEV. = -7.8 DEGREES REMARK 500 3 DTR A 4 CD1 - NE1 - CE2 ANGL. DEV. = 8.5 DEGREES REMARK 500 3 DTR A 4 NE1 - CE2 - CZ2 ANGL. DEV. = 8.4 DEGREES REMARK 500 3 TRP A 7 CG - CD1 - NE1 ANGL. DEV. = -6.9 DEGREES REMARK 500 3 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 7.4 DEGREES REMARK 500 3 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 8.1 DEGREES REMARK 500 4 DTR A 4 CG - CD1 - NE1 ANGL. DEV. = -7.0 DEGREES REMARK 500 4 DTR A 4 CD1 - NE1 - CE2 ANGL. DEV. = 8.2 DEGREES REMARK 500 4 DTR A 4 NE1 - CE2 - CZ2 ANGL. DEV. = 8.8 DEGREES REMARK 500 4 DTR A 4 NE1 - CE2 - CD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 4 TRP A 7 CG - CD1 - NE1 ANGL. DEV. = -6.5 DEGREES REMARK 500 4 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 7.9 DEGREES REMARK 500 4 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 9.1 DEGREES REMARK 500 4 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 5 DTR A 4 CG - CD1 - NE1 ANGL. DEV. = -7.0 DEGREES REMARK 500 5 DTR A 4 CD1 - NE1 - CE2 ANGL. DEV. = 8.3 DEGREES REMARK 500 5 DTR A 4 NE1 - CE2 - CZ2 ANGL. DEV. = 8.5 DEGREES REMARK 500 5 DTR A 4 NE1 - CE2 - CD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 5 TRP A 7 CG - CD1 - NE1 ANGL. DEV. = -6.4 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. = 8.7 DEGREES REMARK 500 6 DTR A 4 CG - CD1 - NE1 ANGL. DEV. = -6.9 DEGREES REMARK 500 6 DTR A 4 CD1 - NE1 - CE2 ANGL. DEV. = 8.3 DEGREES REMARK 500 6 DTR A 4 NE1 - CE2 - CZ2 ANGL. DEV. = 10.3 DEGREES REMARK 500 6 DTR A 4 NE1 - CE2 - CD2 ANGL. DEV. = -7.0 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. = 7.6 DEGREES REMARK 500 6 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 8.0 DEGREES REMARK 500 7 DTR A 4 CG - CD1 - NE1 ANGL. DEV. = -7.7 DEGREES REMARK 500 7 DTR A 4 CD1 - NE1 - CE2 ANGL. DEV. = 8.3 DEGREES REMARK 500 7 DTR A 4 NE1 - CE2 - CZ2 ANGL. DEV. = 9.8 DEGREES REMARK 500 7 DTR A 4 NE1 - CE2 - CD2 ANGL. DEV. = -6.6 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. = 7.8 DEGREES REMARK 500 7 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 8.3 DEGREES REMARK 500 7 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 150 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 1 HYP A 3 -168.40 -65.10 REMARK 500 2 HYP A 3 -167.01 -64.98 REMARK 500 3 HYP A 3 -174.98 -62.04 REMARK 500 4 HYP A 3 -169.56 -70.24 REMARK 500 6 HYP A 3 -169.11 -62.65 REMARK 500 8 HYP A 3 -178.13 -60.65 REMARK 500 10 HYP A 3 -168.16 -67.55 REMARK 500 10 PRO A 6 -9.95 -55.90 REMARK 500 12 HYP A 3 -171.10 -64.98 REMARK 500 14 HYP A 3 176.45 -59.79 REMARK 500 14 PRO A 6 -6.04 -58.93 REMARK 500 15 HYP A 3 -178.35 -57.42 REMARK 500 20 HYP A 3 -172.75 -60.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DFZ RELATED DB: PDB REMARK 900 STRUCTURE OF ALTERNATIVE FORM OF CONTRYPHAN-SM (MINOR FORM - TRANS) REMARK 900 RELATED ID: 1DG0 RELATED DB: PDB REMARK 900 STRUCTURE OF DES[GLY1]-CONTRYPHAN-R REMARK 900 RELATED ID: 1QFB RELATED DB: PDB REMARK 900 STRUCTURE OF CONTRYPHAN-R DBREF 1DFY A 1 8 PDB 1DFY 1DFY 1 8 SEQRES 1 A 8 GLY CYS HYP DTR GLN PRO TRP CY3 MODRES 1DFY HYP A 3 PRO 4-HYDROXYPROLINE MODRES 1DFY DTR A 4 TRP D-TRYPTOPHAN MODRES 1DFY 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 1.31 LINK SG CYS A 2 SG CY3 A 8 1555 1555 2.02 LINK C HYP A 3 N DTR A 4 1555 1555 1.30 LINK C DTR A 4 N GLN A 5 1555 1555 1.31 LINK C TRP A 7 N CY3 A 8 1555 1555 1.31 CISPEP 1 CYS A 2 HYP A 3 1 -9.76 CISPEP 2 CYS A 2 HYP A 3 2 -10.76 CISPEP 3 CYS A 2 HYP A 3 3 -10.16 CISPEP 4 CYS A 2 HYP A 3 4 -3.62 CISPEP 5 CYS A 2 HYP A 3 5 1.50 CISPEP 6 CYS A 2 HYP A 3 6 -8.27 CISPEP 7 CYS A 2 HYP A 3 7 -0.91 CISPEP 8 CYS A 2 HYP A 3 8 -6.35 CISPEP 9 CYS A 2 HYP A 3 9 2.21 CISPEP 10 CYS A 2 HYP A 3 10 -2.44 CISPEP 11 CYS A 2 HYP A 3 11 -3.31 CISPEP 12 CYS A 2 HYP A 3 12 -9.19 CISPEP 13 CYS A 2 HYP A 3 13 1.44 CISPEP 14 CYS A 2 HYP A 3 14 -1.45 CISPEP 15 CYS A 2 HYP A 3 15 -10.21 CISPEP 16 CYS A 2 HYP A 3 16 7.36 CISPEP 17 CYS A 2 HYP A 3 17 4.49 CISPEP 18 CYS A 2 HYP A 3 18 0.66 CISPEP 19 CYS A 2 HYP A 3 19 -11.05 CISPEP 20 CYS A 2 HYP A 3 20 -11.82 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