PDB ID or protein name

1ih9 » Zervamicin IIb

1ih9 » Zervamicin IIb
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1ih9 » Zervamicin IIb
Hydrophobic Thickness or Depth 11.5 ± 2.0 Å
Tilt Angle 74 ± 10°
ΔGtransfer -12.3 kcal/mol
Links to 1ih9 PDB Sum, PDB, SCOP, MSD, OCA, MMDB
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Resolution NMR
Other PDB entries representing this structure 1dlz
Number of subunits 1
Experimental Verification for 1ih9 » Zervamicin IIb
Orientation and membrane penetration depth of the peptide are consistent with solid-state NMR and fluorescence quenching studies (Bechinger et al. 2001, Kropacheva et al. 2005). 3D structure of the peptide was determined in DPC micelles (Shenkarev et al. 2002). The structure does not change in methanol (Shenkarev et al. 2004). Transfer energy of the peptide is strongly overestimated (experimental binding affinity is -7.8 kcal/mol, Kropacheva et al. 2005), because part of this energy must be spent to fold an alpha-helix from the coil in aqueous solution, prior to insertion of the helix into the membrane.
5 references
Bechinger B, Skladnev DA, Ogrel A, Li X, Rogozhkina EV, Ovchinnikova TV, ONeil JD, Raap J. 2001. 15N and 31P solid-state NMR investigations on the orientation of zervamicin II and alamethicin in phosphatidylcholine membranes. Biochemistry. 40:9428-37. PubMed
Kropacheva TN, Salnikov ES, Nguyen HH, Reissmann S, Yakimenko ZA, Tagaev AA, Ovchinnikova TV, Raap J. 2005. Membrane association and activity of 15/16-membered peptide antibiotics: zervamicin IIB, ampullosporin A and antiamoebin I. Biochim Biophys Acta. 1715:6-18. PubMed
Shenkarev ZO, Balashova TA, Efremov RG, Yakimenko ZA, Ovchinnikova TV, Raap J, Arseniev AS. 2002. Spatial structure of zervamicin IIB bound to DPC micelles: implications for voltage-gating. Biophys J. 82: 762-771. PubMed
Shenkarev ZO, Balashova TA, Yakimenko ZA, Ovchinnikova TV, Arseniev AS. 2004. Peptaibol zervamicin IIb structure and dynamics refinement from transhydrogen bond J couplings. Biophys J. 86: 3687-3699. PubMed
Shenkarev ZO, Paramonov AS, Balashova TA, Yakimenko ZA, Baru MB, Mustaeva LG, Raap J, Ovchinnikova TV, Arseniev AS. 2004. High stability of the hinge region in the membrane-active peptide helix of zervamicin: paramagnetic relaxation enhancement studies. Biochem Biophys Res Commun. 325: 1099-1105. PubMed
Comments on 1ih9 » Zervamicin IIb
There are small energetic differences between the surface and transmembrane arrangements of the peptide. The shown arrangement has the lowest transfer energy.