BMRB: 36265

Three-dimensional LPS bound structure of VG16KRKP-KYE28

Authors

Ilyas, H., Bhunia, A.

Assembly

VG16KRKP, Heparin cofactor 2

Entity

1. VG16KRKP, Heparin cofactor 2, entity 1 (polymer, Thiol state: all free), 16 monomers, 1760.116 Da Detail

VARGWKRKCP LFGKGG

2. VG16KRKP, Heparin cofactor 2, entity 2 (polymer, Thiol state: not present), 28 monomers, 3595.166 Da Detail

KYEITTIHNL FRKLTHRLFR RNFGYTLR

Total weight

5355.282 Da

Max. entity weight

3595.166 Da

Source organism

Dengue virus , Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 83.6 %, Completeness (bb): 95.7 % Detail

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Polymer type: polypeptide(L)

	Total	1H
All	83.6 % (254 of 304)	83.6 % (254 of 304)
Backbone	95.7 % (88 of 92)	95.7 % (88 of 92)
Sidechain	78.3 % (166 of 212)	78.3 % (166 of 212)
Aromatic	73.7 % (28 of 38)	73.7 % (28 of 38)
Methyl	90.5 % (19 of 21)	90.5 % (19 of 21)

1. entity 1

VARGWKRKCP LFGKGG

2. entity 2

KYEITTIHNL FRKLTHRLFR RNFGYTLR

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.01) atm, Temperature 298 (±0.01) K, pH 4.5 (±0.02), Details 0.3 mM 1H, Natural Abundance VG16KRKP, 0.3 mM 1H, Natural Abundance KYE28, 55.55 M 1H, Natural Abundance Water, 10 uM 1H, Natural Abundance Lipopolysaccharide, 90% H2O/10% D2O

#	Name	Isotope labeling	Type	Concentration
1	VG16KRKP	natural abundance	protein	0.3 (±0.01) mM
2	KYE28	natural abundance	protein	0.3 (±0.01) mM
3	Lipopolysaccharide	natural abundance		10 (±0.001) uM
4	H2O	natural abundance	solvent	90 %
5	D2O	[U-2H]	solvent	10 %

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Calculated from 15 models in PDB: 6KBO, Strand ID: A, B Detail

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Release date

2019-08-05

Citation

Structural insights into the combinatorial effects of antimicrobial peptides reveal a role of aromatic-aromatic interactions in antibacterial synergism
Ilyas, H., Kim, J., Lee, D., Malmsten, M., Bhunia, A.
J. Biol. Chem. (2019), 294, 14615-14633, PubMed 31383740 , DOI 10.1074/jbc.RA119.009955 , Abstract

Related entities 1. VG16KRKP, Heparin cofactor 2, entity 1, : 63 entities Detail

Related entities 2. VG16KRKP, Heparin cofactor 2, entity 2, : 1 : 7 : 4 : 2 : 11 entities Detail

Interaction partners 2. VG16KRKP, Heparin cofactor 2, entity 2, : 5 : 1 interactors Detail

Experiments performed 2 experiments Detail