PDB Short entry for 1ABT HEADER TOXIN 17-NOV-93 1ABT TITLE NMR SOLUTION STRUCTURE OF AN ALPHA-BUNGAROTOXIN(SLASH)NICOTINIC TITLE 2 RECEPTOR PEPTIDE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-BUNGAROTOXIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NICOTINIC RECEPTOR PEPTIDE; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 MOL_ID: 2 KEYWDS TOXIN EXPDTA SOLUTION NMR NUMMDL 4 AUTHOR V.J.BASUS,G.SONG,E.HAWROT REVDAT 5 16-FEB-22 1ABT 1 REMARK REVDAT 4 19-MAY-09 1ABT 1 REMARK REVDAT 3 24-FEB-09 1ABT 1 VERSN REVDAT 2 30-SEP-03 1ABT 1 JRNL DBREF REVDAT 1 31-JAN-94 1ABT 0 JRNL AUTH V.J.BASUS,G.SONG,E.HAWROT JRNL TITL NMR SOLUTION STRUCTURE OF AN ALPHA-BUNGAROTOXIN/NICOTINIC JRNL TITL 2 RECEPTOR PEPTIDE COMPLEX. JRNL REF BIOCHEMISTRY V. 32 12290 1993 JRNL REFN ISSN 0006-2960 JRNL PMID 8241115 JRNL DOI 10.1021/BI00097A004 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.F.A.PEARCE,P.PRESTON-HURLBURT,E.HAWROT REMARK 1 TITL THE ROLE OF TYROSINE AT THE LIGAND-BINDING SITE OF THE REMARK 1 TITL 2 NICOTINIC ACETYLCHOLINE RECEPTOR REMARK 1 REF PROC.R.SOC.LONDON,SER.B V. 241 207 1990 REMARK 1 REFN ISSN 0080-4649 REMARK 1 REFERENCE 2 REMARK 1 AUTH V.J.BASUS,M.BILLETER,R.A.LOVE,R.M.STROUD,I.D.KUNTZ REMARK 1 TITL STRUCTURAL STUDIES OF ALPHA-BUNGAROTOXIN. 1. REMARK 1 TITL 2 SEQUENCE-SPECIFIC 1H NMR RESONANCE ASSIGNMENTS REMARK 1 REF BIOCHEMISTRY V. 27 2763 1988 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VEMBED, GROMOS-87 REMARK 3 AUTHORS : KUNTZ (VEMBED), VAN GUNSTEREN (GROMOS-87) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NOE DATA CAME FROM SPECTRA COLLECTED AT REMARK 3 35 DEGREES AND AT 25 DEGREES CELSIUS, PH 5.8. A LIST OF ALL NMR REMARK 3 CONSTRAINTS WAS DEPOSITED IN THE PROTEIN DATA BANK TOGETHER WITH REMARK 3 THE STRUCTURE LIST. THESE CONSTRAINTS CONSISTED OF 365 REMARK 3 INTRAMOLECULAR CONSTRAINTS (146 LONG-RANGE, 155 SEQUENTIAL AND REMARK 3 64 DIHEDRAL ANGLES), AND 24 INTERMOLECULAR CONSTRAINTS BETWEEN REMARK 3 THE 74 RESIDUES OF BGTX AND THE FIRST 6 RESIDUES OF THE 12 REMARK 3 RESIDUE PEPTIDE FRAGMENT OF NACHR USED IN THIS STUDY (LISTED REMARK 3 HERE AS RESIDUES 75 B - 80 B). THE COORDINATES THAT FOLLOW ARE REMARK 3 IN FOUR SEPARATE MODELS. THE 12 RESIDUE PEPTIDE FRAGMENT OF REMARK 3 NACHR HAS BEEN MODELED FOR ONLY THE FIRST SIX RESIDUES AND HAS REMARK 3 BEEN NUMBERED AS A CONTINUATION OF THE NUMBERS FOR THE BGTX REMARK 3 PORTION OF THE COMPLEX AND GIVEN THE CHAIN IDENTIFIER 'B', AFTER REMARK 3 THE TER ENTRY SEPARATING THE COORDINATES OF THE TWO COMPONENTS REMARK 3 OF THE COMPLEX. THE AVERAGE RMS DEVIATION OF THE BACKBONE ATOMS, REMARK 3 WHEN MATCHED IN A PAIRWISE MANNER, IS 2.6 ANGSTROMS, WITH THE REMARK 3 POORLY DEFINED REGIONS OF RESIDUES 30 A - 38 A, AND 69 A - 74 A REMARK 3 OF BGTX EXCLUDED. RESTRAINT VIOLATIONS: VIOLATIONS WERE REMARK 3 CATEGORIZED ACCORDING TO SIZE. THE TOTAL NUMBER OF VIOLATIONS IN REMARK 3 EACH CATEGORY WAS ADDED, AND THAT NUMBER DIVIDED BY 4 TO REMARK 3 DETERMINE THE AVERAGE NUMBER OF VIOLATIONS PER STRUCTURE FOR REMARK 3 EACH CATEGORY. VIOLATION RANGE AVERAGE NUMBER OF VIOLATIONS REMARK 3 (ANGSTROMS) VIOLATION >0.7 5.0 0.7>=VIOLATION >0.6 6.0 0.6>= REMARK 3 VIOLATION >0.5 5.75 0.5>=VIOLATION >0.4 9.5 0.4>=VIOLATION >0.3 REMARK 3 17.0 0.3>=VIOLATION >0.2 16.5 0.2>=VIOLATION >0.1 18.0. TO REMARK 3 SIMPLIFY THE CALCULATIONS, ONLY THE FIRST SIX AMINO ACIDS (185 - REMARK 3 190) OF THE DODECAPEPTIDE WERE INCORPORATED INTO THE STRUCTURE REMARK 3 OF THE COMPLEX. THIS WAS APPROPRIATE AS NO INTERMOLECULAR NOE'S REMARK 3 AND NO LONG-RANGE INTRAMOLECULAR NOE'S WERE ASSIGNED INVOLVING REMARK 3 PEPTIDE RESIDUES 191 - 196. THE COORDINATES ARE PRESENTED IN REMARK 3 FOUR SEPARATE MODELS, WITH TER STATEMENTS TO SEPARATE THE BGTX REMARK 3 PART OF THE COMPLEX FROM THE NACHR PORTION OF THE COMPLEX. ALL REMARK 3 STRUCTURES WERE MATCHED IN CARTESIAN SPACE SUCH THAT THE RMSD REMARK 3 BETWEEN THEM WAS MINIMIZED, WITH THE EXCLUSION OF RESIDUES 30 A - REMARK 3 38 A, AND 69 A - 74 A OF BGTX. REMARK 4 REMARK 4 1ABT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170632. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-4 REMARK 465 RES C SSSEQI REMARK 465 THR B 81 REMARK 465 CYS B 82 REMARK 465 CYS B 83 REMARK 465 PRO B 84 REMARK 465 ASP B 85 REMARK 465 THR B 86 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 TYR A 24 N - CA - C ANGL. DEV. = 16.6 DEGREES REMARK 500 2 TYR A 24 CB - CG - CD2 ANGL. DEV. = -4.8 DEGREES REMARK 500 2 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 TYR B 79 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 3 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 3 TYR A 54 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 3 TYR B 79 CB - CG - CD2 ANGL. DEV. = -5.2 DEGREES REMARK 500 4 TYR A 24 CA - CB - CG ANGL. DEV. = 12.5 DEGREES REMARK 500 4 TYR A 24 CB - CG - CD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 4 TYR A 24 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 TYR B 79 CB - CG - CD2 ANGL. DEV. = -5.2 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 CYS A 3 -138.70 -131.50 REMARK 500 1 ALA A 13 81.59 -68.85 REMARK 500 1 THR A 15 94.43 -69.73 REMARK 500 1 GLU A 20 -163.54 -119.26 REMARK 500 1 ASN A 21 13.90 -65.75 REMARK 500 1 TYR A 24 -84.80 -18.63 REMARK 500 1 ARG A 25 82.64 -2.20 REMARK 500 1 TRP A 28 -156.55 -146.34 REMARK 500 1 CYS A 29 116.38 -25.34 REMARK 500 1 ASP A 30 87.68 72.36 REMARK 500 1 PHE A 32 43.71 23.10 REMARK 500 1 CYS A 33 51.78 26.40 REMARK 500 1 SER A 34 -90.85 -166.74 REMARK 500 1 ARG A 36 100.85 70.41 REMARK 500 1 VAL A 39 95.62 -67.13 REMARK 500 1 PRO A 53 108.82 -59.40 REMARK 500 1 TYR A 54 88.74 -64.76 REMARK 500 1 SER A 61 -73.50 -79.23 REMARK 500 1 ASP A 63 76.38 71.97 REMARK 500 1 LYS A 64 -76.00 59.55 REMARK 500 1 CYS A 65 -64.20 56.64 REMARK 500 1 HIS A 68 -66.78 -18.45 REMARK 500 1 PRO A 69 -178.35 -66.47 REMARK 500 1 GLN A 71 75.33 -66.03 REMARK 500 2 CYS A 3 -124.05 -169.87 REMARK 500 2 THR A 6 -77.24 55.67 REMARK 500 2 ALA A 7 -80.63 -0.58 REMARK 500 2 THR A 8 37.19 -78.39 REMARK 500 2 PRO A 10 79.21 -69.23 REMARK 500 2 ILE A 11 114.83 65.30 REMARK 500 2 THR A 15 109.40 -57.42 REMARK 500 2 GLU A 20 53.12 20.15 REMARK 500 2 LYS A 26 -161.81 179.76 REMARK 500 2 ALA A 31 -53.70 72.56 REMARK 500 2 PHE A 32 -98.46 -49.63 REMARK 500 2 CYS A 33 -78.55 62.97 REMARK 500 2 ARG A 36 105.77 63.23 REMARK 500 2 LYS A 38 82.73 51.10 REMARK 500 2 GLU A 41 -167.68 -165.76 REMARK 500 2 LEU A 42 164.29 179.36 REMARK 500 2 ALA A 46 5.62 -62.44 REMARK 500 2 PRO A 49 88.51 -66.59 REMARK 500 2 LYS A 51 -5.24 84.40 REMARK 500 2 PRO A 53 106.95 -54.18 REMARK 500 2 TYR A 54 88.71 -65.88 REMARK 500 2 ASP A 63 -160.45 46.44 REMARK 500 2 LYS A 64 58.24 -67.74 REMARK 500 2 LYS A 70 -77.37 -28.56 REMARK 500 2 GLN A 71 -37.59 56.50 REMARK 500 2 TYR B 79 61.72 -100.30 REMARK 500 REMARK 500 THIS ENTRY HAS 96 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 TYR A 24 ARG A 25 1 -131.03 REMARK 500 GLU A 41 LEU A 42 2 134.97 REMARK 500 LYS A 38 VAL A 39 3 145.32 REMARK 500 VAL A 39 VAL A 40 4 -149.67 REMARK 500 VAL A 40 GLU A 41 4 128.73 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 HIS A 4 0.16 SIDE CHAIN REMARK 500 1 TYR A 24 0.15 SIDE CHAIN REMARK 500 1 PHE A 32 0.08 SIDE CHAIN REMARK 500 1 TYR A 54 0.10 SIDE CHAIN REMARK 500 1 HIS A 68 0.14 SIDE CHAIN REMARK 500 1 TYR B 80 0.07 SIDE CHAIN REMARK 500 2 TYR A 24 0.15 SIDE CHAIN REMARK 500 2 TYR B 79 0.09 SIDE CHAIN REMARK 500 3 TYR A 24 0.07 SIDE CHAIN REMARK 500 3 TYR B 79 0.19 SIDE CHAIN REMARK 500 3 TYR B 80 0.07 SIDE CHAIN REMARK 500 4 ARG A 36 0.07 SIDE CHAIN REMARK 500 4 HIS A 68 0.10 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 1 GLU A 56 11.41 REMARK 500 3 HIS A 4 10.34 REMARK 500 3 THR A 5 11.03 REMARK 500 3 ALA A 7 -10.34 REMARK 500 3 SER A 12 10.34 REMARK 500 3 TYR A 24 10.32 REMARK 500 3 ARG A 36 11.42 REMARK 500 3 LYS A 38 15.60 REMARK 500 3 PRO A 49 10.99 REMARK 500 3 LYS A 51 -10.60 REMARK 500 3 CYS A 65 -12.44 REMARK 500 4 VAL A 40 11.33 REMARK 500 REMARK 500 REMARK: NULL DBREF 1ABT A 1 74 UNP P60615 NXL1A_BUNMU 1 74 DBREF 1ABT B 75 86 UNP P02710 ACHA_TORCA 209 220 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 SEQRES 1 B 12 LYS HIS TRP VAL TYR TYR THR CYS CYS PRO ASP THR HELIX 1 1 ASP A 30 SER A 34 5 5 SHEET 1 S1 2 ILE A 1 THR A 5 0 SHEET 2 S1 2 SER A 12 CYS A 16 -1 O SER A 12 N THR A 5 SHEET 1 S2 3 VAL A 39 ALA A 45 0 SHEET 2 S2 3 LEU A 22 TRP A 28 -1 N LEU A 22 O ALA A 45 SHEET 3 S2 3 GLU A 56 CYS A 60 -1 O GLU A 56 N MET A 27 SSBOND 1 CYS A 3 CYS A 23 1555 1555 2.03 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 2.04 CISPEP 1 CYS A 29 ASP A 30 1 17.57 CISPEP 2 TYR A 24 ARG A 25 4 9.57 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