SMTL ID : 3gvl.1

Crystal Structure of endo-neuraminidaseNF

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

homo-trimer

Ligands

3 x SLB- SIA: N-acetyl-alpha-neuraminic acid-(2-8)-N-acetyl-beta-neuraminic acid(Non-covalent)

SLB-SIA.1: 11 residues within 4Å: Chain A: F.219, S.220, N.221, S.222, A.223, T.225, G.226, V.227, S.228 Chain B: T.488, Y.489 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:T.488, B:Y.489 Water bridges: B:R.109, B:S.493, A:N.218, A:S.222, A:N.248 Hydrogen bonds: A:S.220, A:N.221, A:N.221, A:S.228, A:S.222, A:A.223, A:G.226, A:V.227, A:S.228, A:S.228 SLB-SIA.3: 11 residues within 4Å: Chain B: F.219, S.220, N.221, S.222, A.223, T.225, G.226, V.227, S.228 Chain C: T.488, Y.489 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:S.220, B:N.221, B:N.221, B:S.228, B:S.222, B:A.223, B:G.226, B:V.227, B:S.228, B:S.228 Water bridges: B:N.218, B:S.222, C:R.109, C:S.493, B:N.248 Hydrophobic interactions: C:T.488, C:Y.489 SLB-SIA.5: 11 residues within 4Å: Chain A: T.488, Y.489 Chain C: F.219, S.220, N.221, S.222, A.223, T.225, G.226, V.227, S.228 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:T.488, A:Y.489 Water bridges: A:R.109, A:S.493, C:N.218, C:S.222, C:N.248 Hydrogen bonds: C:S.220, C:N.221, C:N.221, C:S.228, C:S.222, C:A.223, C:G.226, C:V.227, C:S.228, C:S.228

3 x SLB: N-acetyl-beta-neuraminic acid(Non-covalent)

SLB.2: 7 residues within 4Å: Chain A: R.597, I.599, T.606, S.608, Q.613, N.630 Chain C: Y.581 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.599 Hydrogen bonds: A:R.597, A:T.606, A:S.608, A:S.608, A:S.608, A:S.608, A:Q.613, A:Q.613, A:N.630 Water bridges: A:T.606, A:S.607, A:S.607, B:Q.637, B:Q.637, B:Q.637 SLB.4: 7 residues within 4Å: Chain A: Y.581 Chain B: R.597, I.599, T.606, S.608, Q.613, N.630 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:I.599 Hydrogen bonds: B:R.597, B:T.606, B:S.608, B:S.608, B:S.608, B:S.608, B:Q.613, B:Q.613, B:N.630 Water bridges: B:T.606, B:S.607, B:S.607, C:Q.637, C:Q.637, C:Q.637 SLB.6: 7 residues within 4Å: Chain B: Y.581 Chain C: R.597, I.599, T.606, S.608, Q.613, N.630 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:I.599 Hydrogen bonds: C:R.597, C:T.606, C:S.608, C:S.608, C:S.608, C:S.608, C:Q.613, C:Q.613, C:N.630 Water bridges: C:T.606, C:S.607, C:S.607, A:Q.637, A:Q.637, A:Q.637

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schulz, E.C. et al., Structural basis for the recognition and cleavage of polysialic acid by the bacteriophage K1F tailspike protein EndoNF. J.Mol.Biol. (2010)

Release Date

2010-03-02

Peptides

Endo-N-acetylneuraminidase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Endo-N-acetylneuraminidase

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