10 20 30 40 50 60 70 80 1WQB - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TOXIN 27-SEP-04 1WQB
TITLE THREE-DIMENSIONAL SOLUTION STRUCUTRE OF APTOTOXIN VII, FROM TITLE 2 THE VENOM OF A TRAP-DOOR SPIDER
COMPND MOL_ID: 1; COMPND 2 MOLECULE: APTOTOXIN VII; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PARALYTIC PEPTIDE VII, PP VII; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS PEPTIDE WAS CHAMICALLY SYNTHESIZED. SOURCE 4 THIS SEQUENCE OCCURS NATURALLY IN APTOSTICHUS SCHLINGERI.
KEYWDS TOXIN, SPIDER'S VENOM, CYSTEIN FRAMEWORK, CYSTINE KNOT MOTIF
EXPDTA SOLUTION NMR
NUMMDL 18
AUTHOR K.KOBAYASHI,J.-I.KIM,K.SATO,T.KOHNO
REVDAT 2 24-FEB-09 1WQB 1 VERSN REVDAT 1 13-DEC-05 1WQB 0
JRNL AUTH K.KOBAYASHI,J.-I.KIM,K.SATO,T.KOHNO JRNL TITL THREE-DIMENSIONAL SOLUTION STRUCTURE OF APTOTOXIN JRNL TITL 2 VII, FROM THE VENOM OF A TRAP-DOOR SPIDER JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 392 RESTRAINTS, 358 ARE NOE-DERIVED DISTANCE CONSTRAINTS, REMARK 3 19 DIHEDRAL ANGLE RESTRAINTS, 15 DISTANCE RESTRAINTS FROM REMARK 3 HYDROGEN BONDS AND DISULFIDE BONDS.
REMARK 4 REMARK 4 1WQB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-SEP-04. REMARK 100 THE RCSB ID CODE IS RCSB023878.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 3.5 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 10MM APTOTOXIN; 90% H2O, 10% REMARK 210 D2O; 10MM APTOTOXIN; D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY, 2D TOCSY, REMARK 210 PE-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : UXNMR 96, X-PLOR 3.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 18 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: 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 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 ARG A 6 -164.56 -124.37 REMARK 500 1 LYS A 8 12.67 -145.34 REMARK 500 1 CYS A 11 -168.50 -128.56 REMARK 500 1 CYS A 19 -170.29 -66.56 REMARK 500 1 CYS A 24 101.69 -54.14 REMARK 500 1 SER A 27 -36.59 -159.20 REMARK 500 1 PRO A 31 43.83 -81.52 REMARK 500 2 CYS A 4 -163.19 -161.21 REMARK 500 2 VAL A 7 -70.01 -57.59 REMARK 500 2 LYS A 8 -18.41 -47.40 REMARK 500 2 CYS A 11 -159.32 -116.71 REMARK 500 2 PRO A 17 -166.30 -69.86 REMARK 500 2 CYS A 19 172.67 -48.50 REMARK 500 2 SER A 27 -78.91 -154.05 REMARK 500 3 LEU A 2 -93.05 50.06 REMARK 500 3 ARG A 6 -163.17 -114.40 REMARK 500 3 LYS A 8 32.91 172.20 REMARK 500 3 ALA A 10 104.66 -54.67 REMARK 500 3 CYS A 11 -159.58 -103.18 REMARK 500 3 GLU A 15 -158.27 -108.14 REMARK 500 3 CYS A 19 152.92 -44.47 REMARK 500 3 CYS A 24 90.51 -59.58 REMARK 500 3 SER A 27 -48.25 -160.39 REMARK 500 4 CYS A 4 -152.24 -104.30 REMARK 500 4 VAL A 7 -83.17 -41.86 REMARK 500 4 LYS A 8 -27.52 -36.95 REMARK 500 4 CYS A 11 -162.40 -114.01 REMARK 500 4 PRO A 13 -92.34 -72.16 REMARK 500 4 TRP A 16 95.98 -34.97 REMARK 500 4 PRO A 17 -169.54 -74.61 REMARK 500 4 CYS A 19 155.88 -41.68 REMARK 500 4 CYS A 24 97.37 -57.00 REMARK 500 4 ASP A 25 -96.10 -78.80 REMARK 500 4 SER A 27 -53.75 -160.38 REMARK 500 4 PRO A 31 43.60 -80.66 REMARK 500 5 ALA A 5 -154.19 -101.27 REMARK 500 5 LYS A 8 37.78 -84.90 REMARK 500 5 PRO A 13 -154.14 -69.65 REMARK 500 5 TRP A 14 41.46 -82.22 REMARK 500 5 GLU A 15 -138.51 -91.00 REMARK 500 5 TRP A 16 106.28 -50.05 REMARK 500 5 CYS A 19 169.71 -48.01 REMARK 500 5 CYS A 24 103.56 -57.04 REMARK 500 5 ASP A 25 48.55 -85.33 REMARK 500 5 SER A 27 -58.66 -160.13 REMARK 500 5 PRO A 31 45.01 -81.53 REMARK 500 6 ALA A 5 -158.97 -82.16 REMARK 500 6 ARG A 6 -158.13 -153.20 REMARK 500 6 LYS A 8 -21.33 173.55 REMARK 500 6 GLU A 15 -94.17 -112.33 REMARK 500 6 CYS A 18 175.41 70.74 REMARK 500 6 SER A 27 -33.53 -161.39 REMARK 500 7 ARG A 6 -156.10 -80.13 REMARK 500 7 PRO A 17 -158.81 -72.55 REMARK 500 7 CYS A 19 -166.27 -59.63 REMARK 500 7 SER A 27 -53.95 -126.35 REMARK 500 8 VAL A 7 -70.49 -49.88 REMARK 500 8 LYS A 8 -26.02 -39.49 REMARK 500 8 GLU A 15 -159.45 -135.42 REMARK 500 8 PRO A 17 -159.51 -74.46 REMARK 500 8 CYS A 18 139.60 -171.42 REMARK 500 8 CYS A 19 174.17 -47.31 REMARK 500 8 LYS A 23 105.71 -160.47 REMARK 500 8 SER A 27 -63.80 -160.06 REMARK 500 9 LEU A 2 -133.40 -60.03 REMARK 500 9 CYS A 4 75.63 -160.36 REMARK 500 9 ALA A 5 -145.99 -69.89 REMARK 500 9 LYS A 8 37.54 164.49 REMARK 500 9 GLU A 15 -84.20 -143.56 REMARK 500 9 PRO A 17 -155.89 -72.78 REMARK 500 9 CYS A 18 113.21 -169.03 REMARK 500 9 CYS A 19 155.86 -39.84 REMARK 500 9 SER A 27 -52.08 -149.96 REMARK 500 10 LYS A 8 37.99 164.27 REMARK 500 10 PRO A 13 -93.09 -71.51 REMARK 500 10 CYS A 19 -159.07 -75.63 REMARK 500 10 CYS A 24 105.62 -52.79 REMARK 500 10 SER A 27 13.93 -156.60 REMARK 500 11 LEU A 2 -32.57 -177.95 REMARK 500 11 ARG A 6 -157.58 -84.57 REMARK 500 11 LYS A 8 43.40 168.67 REMARK 500 11 ALA A 10 83.10 -67.50 REMARK 500 11 GLU A 15 -151.51 -137.64 REMARK 500 11 CYS A 19 -170.36 -69.49 REMARK 500 11 CYS A 24 90.94 -61.02 REMARK 500 11 SER A 27 -34.30 -160.23 REMARK 500 11 CYS A 29 101.96 -56.07 REMARK 500 12 LEU A 2 -52.49 169.92 REMARK 500 12 LYS A 8 -21.73 174.44 REMARK 500 12 TRP A 14 14.25 -147.69 REMARK 500 12 GLU A 15 -70.46 -103.81 REMARK 500 12 PRO A 17 -160.43 -73.20 REMARK 500 12 CYS A 19 -173.71 -51.84 REMARK 500 12 SER A 27 -55.05 -149.03 REMARK 500 13 ARG A 6 -157.60 -89.79 REMARK 500 13 LYS A 8 54.16 168.52 REMARK 500 13 GLU A 15 -63.40 -120.99 REMARK 500 13 CYS A 19 -171.41 -54.90 REMARK 500 13 CYS A 24 101.92 -51.77 REMARK 500 13 CYS A 29 108.13 -54.81 REMARK 500 14 LEU A 2 -27.23 173.15 REMARK 500 14 CYS A 4 -167.00 -160.01 REMARK 500 14 ARG A 6 -153.50 -79.81 REMARK 500 14 LYS A 8 33.64 175.41 REMARK 500 14 ALA A 10 97.07 -64.88 REMARK 500 14 TRP A 14 35.29 -159.87 REMARK 500 14 GLU A 15 -73.38 -79.77 REMARK 500 14 CYS A 19 -169.56 -53.17 REMARK 500 14 SER A 27 11.67 -157.53 REMARK 500 14 CYS A 29 95.43 -63.64 REMARK 500 15 ARG A 6 -150.53 -79.93 REMARK 500 15 VAL A 7 49.46 -83.91 REMARK 500 15 LYS A 8 34.36 173.46 REMARK 500 15 TRP A 14 22.81 -147.49 REMARK 500 15 GLU A 15 -159.95 -93.59 REMARK 500 15 CYS A 19 174.67 -48.30 REMARK 500 15 ASP A 25 45.54 -87.96 REMARK 500 15 SER A 27 -44.28 -157.59 REMARK 500 16 LEU A 2 -88.76 -65.62 REMARK 500 16 ALA A 5 153.21 -48.30 REMARK 500 16 ARG A 6 -166.99 -107.25 REMARK 500 16 LYS A 8 -29.56 -178.33 REMARK 500 16 TRP A 14 44.10 -105.63 REMARK 500 16 GLU A 15 -88.60 -104.41 REMARK 500 16 CYS A 24 90.26 -53.35 REMARK 500 16 SER A 27 -36.26 -160.62 REMARK 500 17 LYS A 8 33.23 -179.71 REMARK 500 17 PRO A 13 -90.06 -72.11 REMARK 500 17 TRP A 16 89.58 49.20 REMARK 500 17 CYS A 19 -176.47 -54.19 REMARK 500 17 ASP A 25 -72.54 -79.80 REMARK 500 17 SER A 27 -63.99 -160.75 REMARK 500 18 LEU A 2 -72.97 -33.75 REMARK 500 18 CYS A 4 -159.91 -104.39 REMARK 500 18 ARG A 6 -156.55 -83.15 REMARK 500 18 LYS A 8 35.22 173.05 REMARK 500 18 PRO A 13 -92.22 -72.13 REMARK 500 18 CYS A 18 171.68 -56.48 REMARK 500 18 CYS A 24 97.84 -54.00 REMARK 500 18 ASP A 25 -135.00 -79.61 REMARK 500 18 SER A 27 -39.07 -160.06 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 ARG A 6 0.22 SIDE_CHAIN REMARK 500 2 ARG A 6 0.31 SIDE_CHAIN REMARK 500 3 ARG A 6 0.31 SIDE_CHAIN REMARK 500 4 ARG A 6 0.31 SIDE_CHAIN REMARK 500 6 ARG A 6 0.28 SIDE_CHAIN REMARK 500 7 ARG A 6 0.30 SIDE_CHAIN REMARK 500 8 ARG A 6 0.19 SIDE_CHAIN REMARK 500 9 ARG A 6 0.22 SIDE_CHAIN REMARK 500 11 ARG A 6 0.15 SIDE_CHAIN REMARK 500 12 ARG A 6 0.32 SIDE_CHAIN REMARK 500 13 ARG A 6 0.32 SIDE_CHAIN REMARK 500 14 ARG A 6 0.25 SIDE_CHAIN REMARK 500 15 ARG A 6 0.16 SIDE_CHAIN REMARK 500 16 ARG A 6 0.09 SIDE_CHAIN REMARK 500 17 ARG A 6 0.32 SIDE_CHAIN REMARK 500 18 ARG A 6 0.29 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 1WQB A 1 32 UNP P49271 TXP7_APTSC 1 32
SEQRES 1 A 32 TRP LEU GLY CYS ALA ARG VAL LYS GLU ALA CYS GLY PRO SEQRES 2 A 32 TRP GLU TRP PRO CYS CYS SER GLY LEU LYS CYS ASP GLY SEQRES 3 A 32 SER GLU CYS HIS PRO GLN
SHEET 1 A 2 LYS A 23 CYS A 24 0 SHEET 2 A 2 CYS A 29 HIS A 30 -1 O HIS A 30 N LYS A 23
SSBOND 1 CYS A 4 CYS A 19 1555 1555 2.02 SSBOND 2 CYS A 11 CYS A 24 1555 1555 2.02 SSBOND 3 CYS A 18 CYS A 29 1555 1555 2.02
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