HEADER ANTIMICROBIAL PROTEIN 26-JUN-19 6KBO TITLE THREE-DIMENSIONAL LPS BOUND STRUCTURE OF VG16KRKP-KYE28. COMPND MOL_ID: 1; COMPND 2 MOLECULE: VG16KRKP; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEPARIN COFACTOR 2; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: HELIX-D; COMPND 9 SYNONYM: KYE28; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: DENGUE VIRUS; SOURCE 4 ORGANISM_TAXID: 12637; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606 KEYWDS ANTIMICROBIAL PEPTIDE, NUCLEAR MAGNETIC SPECTROSCOPY, PEPTIDE KEYWDS 2 SYNERGISM, LIPOPOLYSACCHARIDE (LPS), BACTERIAL MEMBRANE, KEYWDS 3 ANTIMICROBIAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR H.ILYAS,A.BHUNIA REVDAT 3 14-JUN-23 6KBO 1 REMARK REVDAT 2 26-FEB-20 6KBO 1 JRNL REVDAT 1 14-AUG-19 6KBO 0 JRNL AUTH H.ILYAS,J.KIM,D.LEE,M.MALMSTEN,A.BHUNIA JRNL TITL STRUCTURAL INSIGHTS INTO THE COMBINATORIAL EFFECTS OF JRNL TITL 2 ANTIMICROBIAL PEPTIDES REVEAL A ROLE OF AROMATIC-AROMATIC JRNL TITL 3 INTERACTIONS IN ANTIBACTERIAL SYNERGISM. JRNL REF J.BIOL.CHEM. V. 294 14615 2019 JRNL REFN ESSN 1083-351X JRNL PMID 31383740 JRNL DOI 10.1074/JBC.RA119.009955 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA V2.1 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6KBO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1300012686. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : 0.6 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.3 MM 1H, NATURAL ABUNDANCE REMARK 210 VG16KRKP, 0.3 MM 1H, NATURAL REMARK 210 ABUNDANCE KYE28, 55.55 M 1H, REMARK 210 NATURAL ABUNDANCE WATER, 10 UM REMARK 210 1H, NATURAL ABUNDANCE REMARK 210 LIPOPOLYSACCHARIDE, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 4.0.6, SPARKY 3.113, REMARK 210 CYANA V2.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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: 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 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 ALA A 2 65.32 -115.51 REMARK 500 1 LYS A 8 -77.78 -58.73 REMARK 500 1 PRO A 10 36.83 -69.78 REMARK 500 1 TYR B 2 -55.20 -120.24 REMARK 500 1 THR B 15 122.65 -34.05 REMARK 500 1 HIS B 16 97.84 -48.13 REMARK 500 1 ARG B 17 -50.42 -123.90 REMARK 500 2 LYS A 8 -79.99 -65.86 REMARK 500 2 PRO A 10 38.36 -69.66 REMARK 500 2 ARG B 17 32.63 -96.63 REMARK 500 3 LYS A 8 -76.24 -59.08 REMARK 500 3 PRO A 10 37.10 -69.68 REMARK 500 3 ASN B 22 -57.04 -123.94 REMARK 500 4 ALA A 2 69.57 -115.43 REMARK 500 4 LYS A 6 -54.35 -121.12 REMARK 500 4 LYS A 8 -77.73 -59.48 REMARK 500 4 PRO A 10 37.01 -69.74 REMARK 500 4 ASN B 9 -60.17 -92.02 REMARK 500 4 LYS B 13 -72.17 -120.29 REMARK 500 4 HIS B 16 -120.22 -117.36 REMARK 500 4 ASN B 22 -53.47 -121.89 REMARK 500 5 LYS A 8 -75.25 -49.60 REMARK 500 5 PRO A 10 36.59 -69.66 REMARK 500 5 ARG B 12 -74.78 -76.02 REMARK 500 5 LEU B 14 102.18 -44.59 REMARK 500 5 THR B 15 -92.05 -100.20 REMARK 500 5 HIS B 16 -83.37 -123.67 REMARK 500 5 PHE B 19 -51.81 -121.93 REMARK 500 5 ASN B 22 -55.20 -122.98 REMARK 500 6 LYS A 8 -75.89 -49.03 REMARK 500 6 PRO A 10 36.41 -69.78 REMARK 500 6 LYS B 13 -74.43 -120.09 REMARK 500 6 HIS B 16 -100.81 -122.29 REMARK 500 6 ASN B 22 -57.76 -123.59 REMARK 500 7 ALA A 2 65.12 -100.42 REMARK 500 7 LYS A 6 -58.03 -120.89 REMARK 500 7 LYS A 8 -75.95 -54.86 REMARK 500 7 PRO A 10 37.30 -69.75 REMARK 500 7 LYS B 13 -74.98 -105.33 REMARK 500 7 LEU B 14 -122.12 -116.79 REMARK 500 7 THR B 15 -90.90 -121.17 REMARK 500 7 ARG B 17 -52.75 -120.87 REMARK 500 7 ASN B 22 -53.40 -123.22 REMARK 500 8 LYS A 8 -70.75 -50.29 REMARK 500 8 PRO A 10 37.52 -69.76 REMARK 500 8 ARG B 12 -83.43 -44.77 REMARK 500 8 THR B 15 -94.45 -56.04 REMARK 500 8 ARG B 17 -64.94 -121.68 REMARK 500 8 LEU B 18 3.23 -68.86 REMARK 500 8 ASN B 22 -61.77 -122.77 REMARK 500 REMARK 500 THIS ENTRY HAS 89 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36265 RELATED DB: BMRB REMARK 900 THREE-DIMENSIONAL LPS BOUND STRUCTURE OF VG16KRKP-KYE28. DBREF 6KBO A 1 16 PDB 6KBO 6KBO 1 16 DBREF 6KBO B 1 28 UNP P05546 HEP2_HUMAN 192 219 SEQRES 1 A 16 VAL ALA ARG GLY TRP LYS ARG LYS CYS PRO LEU PHE GLY SEQRES 2 A 16 LYS GLY GLY SEQRES 1 B 28 LYS TYR GLU ILE THR THR ILE HIS ASN LEU PHE ARG LYS SEQRES 2 B 28 LEU THR HIS ARG LEU PHE ARG ARG ASN PHE GLY TYR THR SEQRES 3 B 28 LEU ARG HELIX 1 AA1 TYR B 2 ILE B 7 1 6 HELIX 2 AA2 ARG B 17 ASN B 22 1 6 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