HEADER TOXIN 05-JUL-04 1WM8 TITLE SOLUTION STRUCTURE OF BMP03 FROM THE VENOM OF SCORPION BUTHUS TITLE 2 MARTENSII KARSCH, 10 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUROTOXIN BMP03; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: POTASSIUM ION CHANNEL BLOCKER P03 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MESOBUTHUS MARTENSII; SOURCE 3 ORGANISM_COMMON: CHINESE SCORPION; SOURCE 4 ORGANISM_TAXID: 34649 KEYWDS ALPHA/BETA SCAFFOLD, TOXIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR H.WU,F.HE,Y.LI,G.WU,C.CAO,X.CHEN REVDAT 4 30-OCT-24 1WM8 1 REMARK REVDAT 3 18-APR-18 1WM8 1 REMARK REVDAT 2 24-FEB-09 1WM8 1 VERSN REVDAT 1 27-JUL-04 1WM8 0 JRNL AUTH F.HE,Y.LI,G.WU,C.CAO,H.WU JRNL TITL THREE-DIMENSIONAL STRUCTURE OF BMP03 FROM VENOM OF SCORPION JRNL TITL 2 BUTHUS MARTENSII KARSCH JRNL REF ACTA CHIM.SINICA V. 58 850 2000 JRNL REFN ISSN 0567-7351 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1B, SYBYL 6.3 REMARK 3 AUTHORS : MIKE CARLISLE, DAN STEELE, MIKE MILLER (VNMR), REMARK 3 TRIPOS, INC. (SYBYL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE ARE BASED ON A TOTAL OF REMARK 3 268 CONSTRAINTS, 241 ARE NOE-DERIVED DISTANCE CONSTRAINTS,6 REMARK 3 DIHEDRAL ANGLE CONSTRAINTS,21 DISTANCE CONSTRAINTS FROM SIX REMARK 3 HYDROGEN BONDS AND THREE DISULFIDE BONDS. REMARK 4 REMARK 4 1WM8 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000023734. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 3.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 3.7MM; 3.7MM REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1B, SYBYL(NMR TRIAD REMARK 210 MODEL) 6.3, SYBYL(DIANA PROGRAM) REMARK 210 6.3 REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 2 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 HG23 THR A 18 H CYS A 19 1.04 REMARK 500 O CYS A 24 OD1 ASN A 25 1.21 REMARK 500 O CYS A 3 HG3 GLU A 4 1.24 REMARK 500 O CYS A 19 OD1 ASP A 20 1.56 REMARK 500 REMARK 500 REMARK: NULL 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 1 HIS A 9 CE1 HIS A 9 NE2 -0.070 REMARK 500 1 ASN A 16 C PRO A 17 N 0.117 REMARK 500 2 ASN A 16 C PRO A 17 N 0.125 REMARK 500 2 VAL A 28 C VAL A 28 OXT 0.116 REMARK 500 3 HIS A 9 CE1 HIS A 9 NE2 -0.084 REMARK 500 3 VAL A 28 C VAL A 28 OXT 0.143 REMARK 500 4 ASN A 16 C PRO A 17 N 0.121 REMARK 500 4 VAL A 28 C VAL A 28 OXT 0.121 REMARK 500 6 HIS A 9 CE1 HIS A 9 NE2 -0.075 REMARK 500 6 ALA A 15 CA ALA A 15 CB -0.151 REMARK 500 6 ALA A 15 C ASN A 16 N 0.147 REMARK 500 6 ASN A 16 C PRO A 17 N 0.143 REMARK 500 6 VAL A 28 C VAL A 28 OXT 0.128 REMARK 500 7 ASN A 16 C PRO A 17 N 0.127 REMARK 500 7 VAL A 28 C VAL A 28 OXT 0.124 REMARK 500 9 HIS A 9 CE1 HIS A 9 NE2 -0.078 REMARK 500 9 ASN A 16 C PRO A 17 N 0.115 REMARK 500 9 VAL A 28 C VAL A 28 OXT 0.117 REMARK 500 10 HIS A 9 CE1 HIS A 9 NE2 -0.070 REMARK 500 10 VAL A 28 C VAL A 28 OXT 0.125 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 6 CA - CB - SG ANGL. DEV. = -12.6 DEGREES REMARK 500 1 ALA A 15 N - CA - CB ANGL. DEV. = 9.0 DEGREES REMARK 500 2 CYS A 3 CA - CB - SG ANGL. DEV. = 9.2 DEGREES REMARK 500 2 PRO A 7 CA - N - CD ANGL. DEV. = 9.6 DEGREES REMARK 500 2 VAL A 23 CA - CB - CG1 ANGL. DEV. = 9.3 DEGREES REMARK 500 3 ALA A 15 N - CA - CB ANGL. DEV. = 8.4 DEGREES REMARK 500 4 ASP A 21 CB - CA - C ANGL. DEV. = 12.2 DEGREES REMARK 500 5 CYS A 6 CA - CB - SG ANGL. DEV. = -12.2 DEGREES REMARK 500 5 HIS A 9 CB - CG - CD2 ANGL. DEV. = -11.0 DEGREES REMARK 500 5 ASP A 20 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 5 ASN A 25 N - CA - CB ANGL. DEV. = -10.9 DEGREES REMARK 500 6 ASP A 20 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 7 CYS A 3 CB - CA - C ANGL. DEV. = 14.0 DEGREES REMARK 500 7 PRO A 7 CA - N - CD ANGL. DEV. = 9.2 DEGREES REMARK 500 7 PRO A 7 N - CA - CB ANGL. DEV. = -8.9 DEGREES REMARK 500 8 GLU A 4 N - CA - CB ANGL. DEV. = 11.1 DEGREES REMARK 500 8 ASP A 20 CB - CG - OD1 ANGL. DEV. = -6.2 DEGREES REMARK 500 8 CYS A 24 CA - C - O ANGL. DEV. = -13.7 DEGREES REMARK 500 8 CYS A 24 O - C - N ANGL. DEV. = 9.6 DEGREES REMARK 500 9 GLU A 5 N - CA - CB ANGL. DEV. = 11.7 DEGREES REMARK 500 9 ASP A 21 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 10 CYS A 24 CA - CB - SG ANGL. DEV. = -11.9 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 GLU A 4 -55.28 145.80 REMARK 500 1 LYS A 11 72.86 -34.30 REMARK 500 1 LYS A 13 -52.41 130.56 REMARK 500 1 ALA A 15 -169.97 127.68 REMARK 500 1 ASN A 16 -90.91 155.17 REMARK 500 1 PRO A 17 -129.15 -48.35 REMARK 500 1 THR A 18 -167.76 -69.46 REMARK 500 1 ASP A 20 55.75 74.78 REMARK 500 1 ASP A 21 -151.07 71.17 REMARK 500 1 VAL A 23 170.89 -57.24 REMARK 500 1 ASN A 25 -162.12 158.65 REMARK 500 1 ASN A 27 -46.93 148.55 REMARK 500 2 GLU A 4 -55.09 159.66 REMARK 500 2 LYS A 11 70.02 -33.95 REMARK 500 2 LYS A 13 -59.08 136.17 REMARK 500 2 ALA A 15 -163.75 137.92 REMARK 500 2 ASN A 16 -102.11 141.70 REMARK 500 2 PRO A 17 -131.98 -41.13 REMARK 500 2 THR A 18 -170.08 -69.69 REMARK 500 2 ASP A 20 54.37 85.26 REMARK 500 2 ASP A 21 -159.68 66.19 REMARK 500 2 VAL A 23 172.93 -52.54 REMARK 500 2 ASN A 25 -153.76 155.02 REMARK 500 2 ASN A 27 -42.86 154.81 REMARK 500 3 GLU A 4 -63.15 166.82 REMARK 500 3 CYS A 6 -72.68 -41.72 REMARK 500 3 LYS A 11 84.72 -53.24 REMARK 500 3 LYS A 13 -62.20 146.05 REMARK 500 3 ALA A 15 -165.74 140.63 REMARK 500 3 ASN A 16 -104.55 147.70 REMARK 500 3 PRO A 17 -127.15 -50.55 REMARK 500 3 THR A 18 -165.87 -69.40 REMARK 500 3 ASP A 20 57.07 99.89 REMARK 500 3 ASP A 21 -158.19 53.18 REMARK 500 3 VAL A 23 170.75 -48.45 REMARK 500 3 ASN A 25 -164.71 140.64 REMARK 500 3 ASN A 27 -47.97 159.03 REMARK 500 4 GLU A 4 -62.76 170.24 REMARK 500 4 MET A 8 -73.23 -33.35 REMARK 500 4 HIS A 9 -39.85 -36.71 REMARK 500 4 CYS A 10 -36.35 -39.63 REMARK 500 4 LYS A 11 79.55 -52.34 REMARK 500 4 LYS A 13 -48.86 144.36 REMARK 500 4 ALA A 15 -168.41 152.25 REMARK 500 4 ASN A 16 -115.91 143.01 REMARK 500 4 PRO A 17 -135.77 -53.73 REMARK 500 4 THR A 18 -167.97 -64.58 REMARK 500 4 ASP A 20 50.27 102.53 REMARK 500 4 ASP A 21 -168.30 61.50 REMARK 500 4 VAL A 23 154.46 -40.50 REMARK 500 REMARK 500 THIS ENTRY HAS 117 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 ASN A 16 PRO A 17 1 -146.47 REMARK 500 ASN A 16 PRO A 17 2 -140.98 REMARK 500 ASN A 16 PRO A 17 3 -131.45 REMARK 500 ASN A 16 PRO A 17 4 -140.93 REMARK 500 PRO A 17 THR A 18 4 -139.11 REMARK 500 ASN A 16 PRO A 17 5 -143.62 REMARK 500 ASN A 16 PRO A 17 6 -142.16 REMARK 500 PRO A 17 THR A 18 6 -142.59 REMARK 500 ASN A 16 PRO A 17 7 -144.89 REMARK 500 ALA A 15 ASN A 16 8 142.84 REMARK 500 ASN A 16 PRO A 17 8 -139.82 REMARK 500 ASN A 16 PRO A 17 9 -143.42 REMARK 500 ASN A 16 PRO A 17 10 -133.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DU9 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURES OF BMP02, A NATURAL SCORPION TOXIN WHICH BLOCKS REMARK 900 APAMIN-SENSITIVE CALCIUM-ACTIVATED POTASSIUM CHANNEL REMARK 900 RELATED ID: 1ACW RELATED DB: PDB REMARK 900 SOLUTION STRUCTURES OF P01, A NATURAL SCORPION PEPTIDE STRUCTURALLY REMARK 900 ANALOGUS TO SCORPION TOXINS SPECIFIC FOR APAMIN-SENSITIVE POTASSIUM REMARK 900 CHANNEL REMARK 900 RELATED ID: 1PNH RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF P05-NH2,A SCORPION TOXIN ANALOG WITH HIGH REMARK 900 AFFINITY FOR THE APAMIN-SENSITIVE POTASSIUM CHANNEL REMARK 900 RELATED ID: 1SCY RELATED DB: PDB REMARK 900 SOLUTION STRUCTURES OF SCYLLATOXIN,A SCORPION TOXIN WITH HIGH REMARK 900 AFFINITY FOR APAMIN-SENSITIVE CALCIUM-ACTIVATED POTASSIUM CHANNEL DBREF 1WM8 A 1 28 UNP Q9U8D1 SCP3_MESMA 29 56 SEQRES 1 A 28 VAL GLY CYS GLU GLU CYS PRO MET HIS CYS LYS GLY LYS SEQRES 2 A 28 ASN ALA ASN PRO THR CYS ASP ASP GLY VAL CYS ASN CYS SEQRES 3 A 28 ASN VAL HELIX 1 1 PRO A 7 LYS A 11 5 5 SSBOND 1 CYS A 3 CYS A 19 1555 1555 2.07 SSBOND 2 CYS A 6 CYS A 24 1555 1555 2.03 SSBOND 3 CYS A 10 CYS A 26 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 MODEL 1