HEADER TOXIN 20-NOV-01 1KFH TITLE SOLUTION STRUCTURE OF ALPHA-BUNGAROTOXIN BY NMR SPECTROSCOPY COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-BUNGAROTOXIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LONG NEUROTOXIN 1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BUNGARUS MULTICINCTUS; SOURCE 3 ORGANISM_COMMON: MANY-BANDED KRAIT; SOURCE 4 ORGANISM_TAXID: 8616 KEYWDS ALPHA-BUNGAROTOXIN, LONG SNAKE NEUROTOXIN, TOXIN EXPDTA SOLUTION NMR NUMMDL 13 AUTHOR L.MOISE,A.PISERCHIO,V.J.BASUS,E.HAWROT REVDAT 3 23-FEB-22 1KFH 1 REMARK REVDAT 2 24-FEB-09 1KFH 1 VERSN REVDAT 1 17-APR-02 1KFH 0 JRNL AUTH L.MOISE,A.PISERCHIO,V.J.BASUS,E.HAWROT JRNL TITL NMR STRUCTURAL ANALYSIS OF ALPHA-BUNGAROTOXIN AND ITS JRNL TITL 2 COMPLEX WITH THE PRINCIPAL ALPHA-NEUROTOXIN-BINDING SEQUENCE JRNL TITL 3 ON THE ALPHA 7 SUBUNIT OF A NEURONAL NICOTINIC ACETYLCHOLINE JRNL TITL 4 RECEPTOR. JRNL REF J.BIOL.CHEM. V. 277 12406 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 11790782 JRNL DOI 10.1074/JBC.M110320200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : MARDIGRAS 2.0, GROMOS 87 4D VERSION REMARK 3 AUTHORS : BORGIAS, B. A., AND JAMES, T. L. (MARDIGRAS), VAN REMARK 3 SCHAIK, R. C., AND VAN GUNSTEREN, W. F. (GROMOS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: TOTAL NUMBER OF RESTRAINTS USED: 657, REMARK 3 TOTAL NUMBER OF NOE RESTRAINTS: 588, REMARK 3 TOTAL NUMBER OF DIHEDRAL ANGLE RESTRAINTS: 60, REMARK 3 USED 9 HYDROGEN-BOND RESTRAINTS REMARK 4 REMARK 4 1KFH COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-01. REMARK 100 THE DEPOSITION ID IS D_1000014899. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 308 REMARK 210 PH : 5.79; 5.79 REMARK 210 IONIC STRENGTH : NO BUFFERS, PH ADJUSTED W/HCL REMARK 210 AND NAOH; NO BUFFERS, PH REMARK 210 ADJUSTED W/DCL AND NAOD REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 4MM ALPHA-BUNGAROTOXIN PH 5.79 REMARK 210 AT 288, 298, AND 308 DEGREES K; REMARK 210 4MM ALPHA-BUNGAROTOXIN PH 5.79 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; DQF-COSY; E-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : GN REMARK 210 SPECTROMETER MANUFACTURER : GE REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VEMBED 1.0 REMARK 210 METHOD USED : DISTANCE GEOMETRY, MOLECULAR REMARK 210 DYNAMICS, MATRIX RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 13 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 : 4 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 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 CYS A 33 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 2 TYR A 24 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 PHE A 32 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 3 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 6 TYR A 24 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 6 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 7 ARG A 36 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 8 TYR A 24 CB - CG - CD2 ANGL. DEV. = -4.9 DEGREES REMARK 500 10 LEU A 22 CB - CA - C ANGL. DEV. = -12.9 DEGREES REMARK 500 10 LEU A 22 CB - CG - CD1 ANGL. DEV. = -12.3 DEGREES REMARK 500 10 LYS A 52 N - CA - CB ANGL. DEV. = -11.1 DEGREES REMARK 500 11 TYR A 24 CB - CG - CD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 11 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 12 TYR A 24 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 13 TYR A 24 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 13 TYR A 54 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES 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 ASP A 30 -79.98 -86.28 REMARK 500 1 ALA A 31 -151.46 -92.30 REMARK 500 1 CYS A 33 -77.19 7.95 REMARK 500 1 SER A 34 82.12 -69.63 REMARK 500 1 SER A 35 -63.43 125.37 REMARK 500 1 ARG A 36 53.17 -108.59 REMARK 500 1 SER A 50 130.21 -6.21 REMARK 500 1 LYS A 51 82.04 -20.46 REMARK 500 1 TYR A 54 -29.04 128.00 REMARK 500 1 PRO A 69 -68.54 -15.92 REMARK 500 1 ARG A 72 -55.37 -136.16 REMARK 500 2 ASP A 30 -163.05 -113.85 REMARK 500 2 SER A 34 -51.43 64.09 REMARK 500 2 ARG A 36 32.25 -142.96 REMARK 500 2 LYS A 51 77.00 -67.71 REMARK 500 2 ASN A 66 71.45 -102.24 REMARK 500 2 ARG A 72 93.92 60.17 REMARK 500 3 GLU A 20 50.52 -147.12 REMARK 500 3 ALA A 31 -55.98 -28.91 REMARK 500 3 SER A 35 -49.18 150.20 REMARK 500 3 ARG A 36 85.69 102.68 REMARK 500 3 SER A 50 95.82 -69.17 REMARK 500 3 LYS A 51 115.28 -4.88 REMARK 500 3 PRO A 53 104.23 -49.28 REMARK 500 3 TYR A 54 -38.20 133.60 REMARK 500 3 PRO A 73 32.00 -63.67 REMARK 500 4 PRO A 18 159.03 -46.45 REMARK 500 4 GLU A 20 100.94 -168.94 REMARK 500 4 ASP A 30 -80.80 -84.26 REMARK 500 4 ALA A 31 -153.02 -88.40 REMARK 500 4 CYS A 33 -60.37 -5.07 REMARK 500 4 SER A 50 27.51 -75.66 REMARK 500 4 LYS A 52 -35.34 -140.56 REMARK 500 4 TYR A 54 -23.16 152.18 REMARK 500 4 ASN A 66 68.42 -101.27 REMARK 500 4 GLN A 71 -140.98 -143.95 REMARK 500 4 ARG A 72 79.00 -112.45 REMARK 500 5 GLU A 20 53.04 -140.40 REMARK 500 5 ASP A 30 -156.62 -70.73 REMARK 500 5 PHE A 32 70.72 77.84 REMARK 500 5 SER A 50 33.05 -77.96 REMARK 500 5 ASN A 66 63.67 -101.64 REMARK 500 5 LYS A 70 40.06 -79.41 REMARK 500 5 GLN A 71 159.72 176.17 REMARK 500 6 CYS A 16 87.27 -15.56 REMARK 500 6 GLU A 20 -156.32 -127.44 REMARK 500 6 ASP A 30 -81.13 -81.25 REMARK 500 6 ALA A 31 -152.25 -89.18 REMARK 500 6 CYS A 33 -43.51 -17.48 REMARK 500 6 SER A 34 73.93 -67.89 REMARK 500 REMARK 500 THIS ENTRY HAS 112 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 53 TYR A 54 2 140.01 REMARK 500 PRO A 53 TYR A 54 7 144.77 REMARK 500 PRO A 53 TYR A 54 10 141.14 REMARK 500 SER A 9 PRO A 10 11 147.20 REMARK 500 LYS A 52 PRO A 53 12 -145.58 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 TYR A 24 0.07 SIDE CHAIN REMARK 500 1 TYR A 54 0.07 SIDE CHAIN REMARK 500 2 TYR A 24 0.12 SIDE CHAIN REMARK 500 3 TYR A 24 0.07 SIDE CHAIN REMARK 500 3 PHE A 32 0.10 SIDE CHAIN REMARK 500 4 TYR A 24 0.10 SIDE CHAIN REMARK 500 6 TYR A 24 0.08 SIDE CHAIN REMARK 500 6 TYR A 54 0.06 SIDE CHAIN REMARK 500 7 PHE A 32 0.08 SIDE CHAIN REMARK 500 8 TYR A 24 0.14 SIDE CHAIN REMARK 500 8 TYR A 54 0.10 SIDE CHAIN REMARK 500 9 TYR A 24 0.12 SIDE CHAIN REMARK 500 9 TYR A 54 0.11 SIDE CHAIN REMARK 500 10 TYR A 24 0.07 SIDE CHAIN REMARK 500 10 PHE A 32 0.11 SIDE CHAIN REMARK 500 11 TYR A 24 0.12 SIDE CHAIN REMARK 500 11 TYR A 54 0.08 SIDE CHAIN REMARK 500 12 TYR A 24 0.10 SIDE CHAIN REMARK 500 12 TYR A 54 0.07 SIDE CHAIN REMARK 500 13 TYR A 24 0.09 SIDE CHAIN REMARK 500 13 TYR A 54 0.19 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 4 SER A 50 -11.26 REMARK 500 5 SER A 50 -10.17 REMARK 500 10 LEU A 22 -12.43 REMARK 500 11 HIS A 4 10.55 REMARK 500 11 PRO A 10 10.93 REMARK 500 11 LEU A 42 10.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KC4 RELATED DB: PDB REMARK 900 1KC4 CONTAINS ALPHA-BUNGAROTOXIN BOUND TO A 19-RESIDUE FRAGMENT OF REMARK 900 THE ALPHA7 SUBUNIT OF THE CHICK NEURONAL NICOTINIC ACETYLCHOLINE REMARK 900 RECEPTOR. DBREF 1KFH A 1 74 UNP P60615 NXL1A_BUNMU 1 74 SEQRES 1 A 74 ILE VAL CYS HIS THR THR ALA THR SER PRO ILE SER ALA SEQRES 2 A 74 VAL THR CYS PRO PRO GLY GLU ASN LEU CYS TYR ARG LYS SEQRES 3 A 74 MET TRP CYS ASP ALA PHE CYS SER SER ARG GLY LYS VAL SEQRES 4 A 74 VAL GLU LEU GLY CYS ALA ALA THR CYS PRO SER LYS LYS SEQRES 5 A 74 PRO TYR GLU GLU VAL THR CYS CYS SER THR ASP LYS CYS SEQRES 6 A 74 ASN PRO HIS PRO LYS GLN ARG PRO GLY SHEET 1 A 2 VAL A 2 THR A 5 0 SHEET 2 A 2 SER A 12 THR A 15 -1 O VAL A 14 N CYS A 3 SHEET 1 B 3 GLY A 37 ALA A 45 0 SHEET 2 B 3 LEU A 22 PHE A 32 -1 N LYS A 26 O GLU A 41 SHEET 3 B 3 GLU A 56 CYS A 60 -1 O CYS A 60 N CYS A 23 SSBOND 1 CYS A 3 CYS A 23 1555 1555 2.04 SSBOND 2 CYS A 16 CYS A 44 1555 1555 2.04 SSBOND 3 CYS A 29 CYS A 33 1555 1555 2.04 SSBOND 4 CYS A 48 CYS A 59 1555 1555 2.04 SSBOND 5 CYS A 60 CYS A 65 1555 1555 2.03 CISPEP 1 SER A 9 PRO A 10 1 -0.13 CISPEP 2 SER A 9 PRO A 10 2 1.58 CISPEP 3 LYS A 52 PRO A 53 2 -11.78 CISPEP 4 SER A 9 PRO A 10 3 2.41 CISPEP 5 SER A 9 PRO A 10 4 -2.13 CISPEP 6 SER A 9 PRO A 10 5 -1.38 CISPEP 7 LYS A 52 PRO A 53 5 -10.92 CISPEP 8 SER A 9 PRO A 10 6 2.61 CISPEP 9 SER A 9 PRO A 10 7 4.14 CISPEP 10 LYS A 52 PRO A 53 7 -0.08 CISPEP 11 SER A 9 PRO A 10 8 0.57 CISPEP 12 SER A 9 PRO A 10 9 9.13 CISPEP 13 LYS A 52 PRO A 53 9 -21.69 CISPEP 14 ARG A 72 PRO A 73 9 -6.55 CISPEP 15 SER A 9 PRO A 10 10 -1.46 CISPEP 16 LYS A 52 PRO A 53 10 -4.21 CISPEP 17 ARG A 72 PRO A 73 10 -12.57 CISPEP 18 SER A 9 PRO A 10 12 2.87 CISPEP 19 SER A 9 PRO A 10 13 1.53 CISPEP 20 LYS A 52 PRO A 53 13 -11.51 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