BMRB Entry 36265

Name: Three-dimensional LPS bound structure of VG16KRKP-KYE28
Published: 2019-08-29

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PDB ID: 6kbo
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36265
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Three-dimensional LPS bound structure of VG16KRKP-KYE28

Deposition date:

2019-06-26

Original release date:

2019-08-29

Authors:

Ilyas, H.; Bhunia, A.

Citation:

Citation: Ilyas, Humaira; Kim, JaeWoong; Lee, DongKuk; Malmsten, Martin; Bhunia, Anirban. "Structural insights into the combinatorial effects of antimicrobial peptides reveal a role of aromatic\u2013aromatic interactions in antibacterial synergism" J. Biol. Chem. 294, 14615-14633 (2019).
PubMed: 31383740

Assembly members:

Assembly members:
entity_1, polymer, 16 residues, 1765.157 Da.
entity_2, polymer, 28 residues, 3604.239 Da.

Natural source:

Natural source: Common Name: Dengue virus Taxonomy ID: 12637 Superkingdom: Viruses Kingdom: not available Genus/species: Flavivirus not available

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: VARGWKRKCPLFGKGG
entity_2: KYEITTIHNLFRKLTHRLFR RNFGYTLR

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
1H chemical shifts	290

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 16 residues - 1765.157 Da.

1

VAL

ALA

ARG

GLY

TRP

LYS

ARG

LYS

CYS

PRO

2

LEU

PHE

GLY

LYS

GLY

Entity 2, entity_2 28 residues - 3604.239 Da.

1

LYS

TYR

GLU

ILE

THR

ILE

HIS

ASN

LEU

2

PHE

ARG

LYS

LEU

THR

HIS

ARG

LEU

PHE

ARG

3

ARG

ASN

PHE

GLY

TYR

THR

LEU

ARG

Samples:

sample_1: VG16KRKP 0.3 ± 0.01 mM; KYE28 0.3 ± 0.01 mM; Lipopolysaccharide 10 ± 0.001 uM; H2O 90%; D2O, [U-2H], 10%

sample_conditions_1: ionic strength: 0.6 mM; pH: 4.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1

Software:

CYANA vv2.1, Guntert, Mumenthaler and Wuthrich - refinement, structure calculation

Sparky v3.113, Goddard - chemical shift assignment

TopSpin v4.0.6, Bruker Biospin - processing

NMR spectrometers:

Bruker AVANCE III 700 MHz