PDB Short entry for 5NQ4 HEADER TOXIN 19-APR-17 5NQ4 TITLE CYTOTOXIN-1 IN DPC-MICELLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOTOXIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOTOXIN I,CTI; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NAJA OXIANA; SOURCE 3 ORGANISM_COMMON: CENTRAL ASIAN COBRA; SOURCE 4 ORGANISM_TAXID: 8657; SOURCE 5 EXPRESSION_SYSTEM: NAJA OXIANA; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 8657 KEYWDS CYTOLYTIC PEPTIDE, COBRA VENOM, CYTOTOXYC ACTIVITY, THREE-FINGER KEYWDS 2 PROTEIN, TOXIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.V.DUBOVSKII,M.A.DUBINNYI,P.E.VOLYNSKY,Y.E.PUSTOVALOVA,A.G.KONSHINA, AUTHOR 2 Y.N.UTKIN,R.G.EFREMOV,A.S.ARSENIEV REVDAT 4 08-MAY-19 5NQ4 1 REMARK REVDAT 3 16-JAN-19 5NQ4 1 JRNL REVDAT 2 21-FEB-18 5NQ4 1 ATOM REVDAT 1 13-DEC-17 5NQ4 0 JRNL AUTH P.V.DUBOVSKII,M.A.DUBINNYI,P.E.VOLYNSKY,Y.E.PUSTOVALOVA, JRNL AUTH 2 A.G.KONSHINA,Y.N.UTKIN,A.S.ARSENIEV,R.G.EFREMOV JRNL TITL IMPACT OF MEMBRANE PARTITIONING ON THE SPATIAL STRUCTURE OF JRNL TITL 2 AN S-TYPE COBRA CYTOTOXIN. JRNL REF J. BIOMOL. STRUCT. DYN. V. 36 3463 2018 JRNL REFN ESSN 1538-0254 JRNL PMID 28990854 JRNL DOI 10.1080/07391102.2017.1389662 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.V.DUBOVSKII,D.M.LESOVOY,M.A.DUBINNYI,A.G.KONSHINA, REMARK 1 AUTH 2 Y.N.UTKIN,R.G.EFREMOV,A.S.ARSENIEV REMARK 1 TITL INTERACTION OF THREE-FINGER TOXINS WITH PHOSPHOLIPID REMARK 1 TITL 2 MEMBRANES: COMPARISON OF S- AND P-TYPE CYTOTOXINS. REMARK 1 REF BIOCHEM. J. V. 387 807 2005 REMARK 1 REFN ESSN 1470-8728 REMARK 1 PMID 15584897 REMARK 1 DOI 10.1042/BJ20041814 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 1.0.6 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 517 NOE REMARK 3 CONSTRAINTS, 160 HUDROGEN BOND AND 24 DISULFIDE BOND CONSTRAINTS, REMARK 3 AND 236 CONSTRAINTS FOR 193 ANGLES REMARK 4 REMARK 4 5NQ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-APR-17. REMARK 100 THE DEPOSITION ID IS D_1200004515. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 323; 323 REMARK 210 PH : 6.0; 6.0 REMARK 210 IONIC STRENGTH : 50; 50 REMARK 210 PRESSURE : 1 BAR; 1 BAR REMARK 210 SAMPLE CONTENTS : 3.0 MM NO CYTOTOXIN-1, 180.0 MM REMARK 210 FULLY DEUTERATED REMARK 210 DODECYLPHOSPHOCHOLINE, 50 MM NO REMARK 210 POTASSIUM CHLORIDE, 50 M NO H2O, REMARK 210 5.5 M 99.9%-DEUTERATED D2O, 0.01 REMARK 210 UM NO HCL, 90% H2O/10% D2O; 3.0 REMARK 210 MM NO CYTOTOXIN-1, 180.0 MM REMARK 210 FULLY DEUTERATED REMARK 210 DODECYLPHOSPHOCHOLINE, 50 MM NO REMARK 210 POTASSIUM CHLORIDE, 55 M 100%- REMARK 210 DEUTERATED D2O, 0.01 UM NO HCL, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D DQF-COSY; DIFFUSION REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX; UNITY REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, NMRPIPE REMARK 210 2001.085.20.47, XEASY 1.2.11 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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 HG SER A 46 O VAL A 49 1.52 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 LYS A 5 -145.09 -95.03 REMARK 500 1 PRO A 8 47.26 -75.05 REMARK 500 1 GLU A 16 93.51 -40.18 REMARK 500 1 ASN A 19 15.90 -144.82 REMARK 500 1 MET A 27 -73.89 62.69 REMARK 500 2 LYS A 5 -153.47 -84.98 REMARK 500 2 PRO A 8 46.79 -74.96 REMARK 500 2 GLU A 16 93.53 -38.99 REMARK 500 2 ASN A 19 16.18 -145.53 REMARK 500 2 MET A 27 -76.03 60.77 REMARK 500 2 ASN A 55 21.40 -143.76 REMARK 500 2 ARG A 58 30.59 75.47 REMARK 500 3 LYS A 5 -141.66 -87.81 REMARK 500 3 PRO A 8 47.41 -74.92 REMARK 500 3 ILE A 9 -56.92 -123.74 REMARK 500 3 CYS A 14 78.20 -117.74 REMARK 500 3 GLU A 16 93.13 -40.25 REMARK 500 3 ASN A 19 -39.59 -147.32 REMARK 500 3 MET A 27 -74.79 62.20 REMARK 500 3 ASN A 55 18.22 -144.51 REMARK 500 4 LYS A 5 -151.01 -87.66 REMARK 500 4 PRO A 8 47.38 -75.05 REMARK 500 4 GLU A 16 90.21 -38.04 REMARK 500 4 MET A 27 83.61 43.54 REMARK 500 4 SER A 28 150.29 91.37 REMARK 500 4 ASN A 55 17.71 -141.61 REMARK 500 5 PRO A 8 47.10 -75.01 REMARK 500 5 CYS A 14 75.74 -119.90 REMARK 500 5 GLU A 16 94.64 -35.48 REMARK 500 5 ASN A 19 18.76 -145.90 REMARK 500 5 MET A 27 -74.22 63.07 REMARK 500 6 LYS A 5 -152.02 -90.81 REMARK 500 6 PRO A 8 47.05 -74.90 REMARK 500 6 CYS A 14 77.13 -119.38 REMARK 500 6 GLU A 16 91.80 -38.15 REMARK 500 6 MET A 27 -73.57 62.32 REMARK 500 7 LYS A 5 -150.10 -96.33 REMARK 500 7 PRO A 8 47.66 -75.00 REMARK 500 7 GLU A 16 92.35 -40.85 REMARK 500 7 ASN A 19 -39.88 -147.41 REMARK 500 7 MET A 27 95.95 38.17 REMARK 500 7 SER A 28 127.18 66.19 REMARK 500 7 ASN A 55 20.14 -146.17 REMARK 500 8 LYS A 5 -143.75 -86.43 REMARK 500 8 PRO A 8 46.95 -75.05 REMARK 500 8 CYS A 14 77.06 -118.48 REMARK 500 8 GLU A 16 89.65 -36.45 REMARK 500 8 MET A 27 -77.53 61.87 REMARK 500 8 ASN A 55 37.45 -147.44 REMARK 500 8 ARG A 58 32.45 73.48 REMARK 500 REMARK 500 THIS ENTRY HAS 129 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5NPN RELATED DB: PDB REMARK 900 THE CURRENT ENTRY IS THE SAME TOXIN, BUT IN DIFFERENT ENVIRONMENT REMARK 900 RELATED ID: 34125 RELATED DB: BMRB REMARK 900 CYTOTOXIN-1 IN DPC-MICELLE DBREF 5NQ4 A 1 60 UNP P01451 3SA1_NAJOX 1 60 SEQRES 1 A 60 LEU LYS CYS ASN LYS LEU VAL PRO ILE ALA TYR LYS THR SEQRES 2 A 60 CYS PRO GLU GLY LYS ASN LEU CYS TYR LYS MET PHE MET SEQRES 3 A 60 MET SER ASP LEU THR ILE PRO VAL LYS ARG GLY CYS ILE SEQRES 4 A 60 ASP VAL CYS PRO LYS ASN SER LEU LEU VAL LYS TYR VAL SEQRES 5 A 60 CYS CYS ASN THR ASP ARG CYS ASN FORMUL 2 HOH *(H2 O) SHEET 1 AA1 2 LYS A 2 ASN A 4 0 SHEET 2 AA1 2 TYR A 11 THR A 13 -1 O LYS A 12 N CYS A 3 SHEET 1 AA2 3 LYS A 35 ILE A 39 0 SHEET 2 AA2 3 LEU A 20 MET A 26 -1 N TYR A 22 O GLY A 37 SHEET 3 AA2 3 VAL A 49 CYS A 54 -1 O LYS A 50 N PHE A 25 SSBOND 1 CYS A 3 CYS A 21 1555 1555 2.00 SSBOND 2 CYS A 14 CYS A 38 1555 1555 2.02 SSBOND 3 CYS A 42 CYS A 53 1555 1555 2.07 SSBOND 4 CYS A 54 CYS A 59 1555 1555 1.99 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