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PDBsum entry 2b8h

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Hydrolase PDB id
2b8h
Jmol
Contents
Protein chains
388 a.a.
Ligands
NAG ×4
NAG-NAG ×4
NAG-NAG-BMA-MAN-
MAN-MAN-MAN-MAN-
MAN
×3
SO4 ×29
GOL ×3
NAG-NAG-BMA-MAN-
MAN-MAN-MAN-MAN-
MAN-MAN
Metals
_CL ×4
Waters ×1373

References listed in PDB file
Key reference
Title Structure of a calcium-Deficient form of influenza virus neuraminidase: implications for substrate binding.
Authors B.J.Smith, T.Huyton, R.P.Joosten, J.L.Mckimm-Breschkin, J.G.Zhang, C.S.Luo, M.Z.Lou, N.E.Labrou, T.P.Garrett.
Ref. Acta Crystallogr D Biol Crystallogr, 2006, 62, 947-952. [DOI no: 10.1107/S0907444906020063]
PubMed id 16929094
Abstract
The X-ray structure of influenza virus neuraminidase (NA) isolated from whale, subtype N9, has been determined at 2.2 A resolution and contains a tetrameric protein in the asymmetric unit. In structures of NA determined previously, a calcium ion is observed to coordinate amino acids near the substrate-binding site. In three of the NA monomers determined here this calcium is absent, resulting in structural alterations near the substrate-binding site. These changes affect the conformation of residues that participate in several key interactions between the enzyme and substrate and provide at a molecular level the basis of the structural and functional role of calcium in substrate and inhibitor binding. Several sulfate ions were identified in complex with the protein. These are located in the active site, occupying the space reserved for the substrate (sialic acid) carboxylate, and in positions leading away from the substrate-binding site. These sites offer a new opportunity for the design of inhibitors of influenza virus NA.
Figure 1.
Figure 1 Ribbon diagram of the calcium-binding site and structural changes between calcium-bound (green, chain A) and calcium-free (cyan, chain B; pink, chain C; tan, chain D) forms of NA. The loops L1 (245-251), L2 (295-298) and L3 (343-344) adopt different conformations in the four monomers. In the calcium-bound form, the protein backbone carbonyl O atoms of Asp293, Gly297 and Asn347 and the side-chain carboxylate of Asp324 all bind the calcium cation (yellow sphere). In the calcium-free form of chain B, the carbonyl groups of Gly297 and Asn347 are shown to be flipped from the conformation observed in the calcium-bound form.
The above figure is reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 947-952) copyright 2006.
PROCHECK
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