1QFB - Header Asymmetric Unit

HEADER TOXIN 08-APR-99 1QFB

TITLE THE CYCLIC PEPTIDE CONTRYPHAN-R FROM CONUS RADIATUS

COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (CONTRYPHAN-R); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CONTRYPHAN; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: HYDROXYPROLINE AT POSITION 3 (HYP), D- COMPND 7 CONFIGURED TRP AT POSITION 4 (TPD), C- TERMINALLY AMIDATED

SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. SOURCE 4 THE SEQUENCE OF THIS PEPTIDE IS NATURALLY FOUND IN THE SOURCE 5 VENOM DUCT OF CONUS RADIATUS (CONE SHELL).

KEYWDS CYCLIC PEPTIDE, DISULFIDE BRIDGE, D-CONFIGURATION, CONUS KEYWDS 2 PEPTIDE, STIFF-TAIL SYNDROME, VENOM DUCT PEPTIDE, TOXIN

EXPDTA SOLUTION NMR

NUMMDL 20

AUTHOR P.K.PALLAGHY,A.P.MELNIKOVA,E.C.JIMENEZ,B.M.OLIVERA, AUTHOR 2 R.S.NORTON

REVDAT 3 24-FEB-09 1QFB 1 VERSN REVDAT 2 03-NOV-99 1QFB 1 SOURCE JRNL REMARK REVDAT 1 29-SEP-99 1QFB 0

JRNL AUTH P.K.PALLAGHY,A.P.MELNIKOVA,E.C.JIMENEZ,B.M.OLIVERA, JRNL AUTH 2 R.S.NORTON JRNL TITL SOLUTION STRUCTURE OF CONTRYPHAN-R, A NATURALLY JRNL TITL 2 OCCURRING DISULFIDE-BRIDGED OCTAPEPTIDE CONTAINING JRNL TITL 3 D-TRYPTOPHAN: COMPARISON WITH PROTEIN LOOPS. JRNL REF BIOCHEMISTRY V. 38 11553 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10471307 JRNL DOI 10.1021/BI990685J

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.C.JIMENEZ,B.M.OLIVERA,W.R.GRAY,L.J.CRUZ REMARK 1 TITL CONTRYPHAN IS A D-TRYPTOPHAN-CONTAINING CONUS REMARK 1 TITL 2 PEPTIDE REMARK 1 REF J.BIOL.CHEM. V. 271 28002 1996 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.271.45.28002

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT WAS PERFORMED IN THE REMARK 3 CHARMM19 FORCE FIELD WITH A BOX OF EXPLICIT WATER MOLECULES REMARK 3 TREATED WITH PBC.

REMARK 4 REMARK 4 1QFB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-APR-99. REMARK 100 THE RCSB ID CODE IS RCSB000814.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278.0 REMARK 210 PH : 3.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 90% WATER/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, TCOSY, DQFCOSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING, ENERGY REMARK 210 MINIMISATION IN CHARMM19 REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST NOE & TOTAL ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR 1H NMR REMARK 210 SPECTROSCOPY ON A SYNTHETIC SAMPLE.

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 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 CD1 - NE1 - CE2 ANGL. DEV. = 7.5 DEGREES REMARK 500 1 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 7.9 DEGREES REMARK 500 1 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -6.7 DEGREES REMARK 500 2 TRP A 7 CB - CG - CD1 ANGL. DEV. = -8.3 DEGREES REMARK 500 2 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 6.5 DEGREES REMARK 500 2 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 7.9 DEGREES REMARK 500 2 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 3 TRP A 7 CB - CG - CD1 ANGL. DEV. = -8.1 DEGREES REMARK 500 3 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 7.7 DEGREES REMARK 500 3 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 7.7 DEGREES REMARK 500 3 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 4 TRP A 7 CB - CG - CD1 ANGL. DEV. = -8.9 DEGREES REMARK 500 4 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 7.5 DEGREES REMARK 500 4 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 8.5 DEGREES REMARK 500 4 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 5 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 7.7 DEGREES REMARK 500 5 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 7.0 DEGREES REMARK 500 5 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 6 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 6.9 DEGREES REMARK 500 7 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 8.1 DEGREES REMARK 500 7 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 7.7 DEGREES REMARK 500 7 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 8 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 7.4 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. = -6.8 DEGREES REMARK 500 9 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 7.7 DEGREES REMARK 500 9 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 8.1 DEGREES REMARK 500 9 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 10 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 7.4 DEGREES REMARK 500 10 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 7.6 DEGREES REMARK 500 10 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 11 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 7.5 DEGREES REMARK 500 11 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 7.0 DEGREES REMARK 500 12 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 7.4 DEGREES REMARK 500 12 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 13 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 7.8 DEGREES REMARK 500 13 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 8.5 DEGREES REMARK 500 13 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -7.4 DEGREES REMARK 500 14 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 7.4 DEGREES REMARK 500 14 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 7.4 DEGREES REMARK 500 14 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 15 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 7.6 DEGREES REMARK 500 15 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 6.7 DEGREES REMARK 500 15 TRP A 7 NE1 - CE2 - CD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 16 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 7.6 DEGREES REMARK 500 16 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 6.8 DEGREES REMARK 500 17 TRP A 7 CB - CG - CD1 ANGL. DEV. = -8.6 DEGREES REMARK 500 17 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 7.5 DEGREES REMARK 500 18 TRP A 7 CD1 - NE1 - CE2 ANGL. DEV. = 7.8 DEGREES REMARK 500 18 TRP A 7 NE1 - CE2 - CZ2 ANGL. DEV. = 6.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 56 ANGLE DEVIATIONS. 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 NH2 A 9

DBREF 1QFB A 1 8 PIR A43097 2144177 1 8

SEQRES 1 A 9 GLY CYS HYP DTR GLU PRO TRP CYS NH2

MODRES 1QFB HYP A 3 PRO 4-HYDROXYPROLINE

HET HYP A 3 15 HET DTR A 4 24 HET NH2 A 9 3

HETNAM HYP 4-HYDROXYPROLINE HETNAM DTR D-TRYPTOPHAN HETNAM NH2 AMINO GROUP

HETSYN HYP HYDROXYPROLINE

FORMUL 1 HYP C5 H9 N O3 FORMUL 1 DTR C11 H12 N2 O2 FORMUL 1 NH2 H2 N

SSBOND 1 CYS A 2 CYS A 8 1555 1555 2.02

LINK C CYS A 2 N HYP A 3 1555 1555 1.31 LINK C HYP A 3 N DTR A 4 1555 1555 1.30 LINK C DTR A 4 N GLU A 5 1555 1555 1.30 LINK C CYS A 8 N NH2 A 9 1555 1555 1.30

CISPEP 1 CYS A 2 HYP A 3 1 -10.36 CISPEP 2 CYS A 2 HYP A 3 2 -1.26 CISPEP 3 CYS A 2 HYP A 3 3 -9.20 CISPEP 4 CYS A 2 HYP A 3 4 -7.12 CISPEP 5 CYS A 2 HYP A 3 5 -8.97 CISPEP 6 CYS A 2 HYP A 3 6 -9.51 CISPEP 7 CYS A 2 HYP A 3 7 -1.09 CISPEP 8 CYS A 2 HYP A 3 8 10.09 CISPEP 9 CYS A 2 HYP A 3 9 -4.90 CISPEP 10 CYS A 2 HYP A 3 10 -1.27 CISPEP 11 CYS A 2 HYP A 3 11 -11.93 CISPEP 12 CYS A 2 HYP A 3 12 -4.99 CISPEP 13 CYS A 2 HYP A 3 13 -6.63 CISPEP 14 CYS A 2 HYP A 3 14 -10.04 CISPEP 15 CYS A 2 HYP A 3 15 -10.11 CISPEP 16 CYS A 2 HYP A 3 16 10.70 CISPEP 17 CYS A 2 HYP A 3 17 1.36 CISPEP 18 CYS A 2 HYP A 3 18 -10.77 CISPEP 19 CYS A 2 HYP A 3 19 3.31 CISPEP 20 CYS A 2 HYP A 3 20 -1.54

SITE 1 AC1 2 TRP A 7 CYS A 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