SMTL ID : 3gvj.1

Crystal structure of an endo-neuraminidaseNF mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

homo-trimer

Ligands

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

SLB-SIA-SIA-SIA-SIA.1: 15 residues within 4Å: Chain A: F.219, S.220, N.221, S.222, V.224, T.225, G.226, V.227, S.228, K.259, N.260, H.262 Chain B: Y.421, T.488, Y.489 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:Y.421 Hydrogen bonds: A:N.260, A:H.262 SLB-SIA-SIA-SIA-SIA.3: 15 residues within 4Å: Chain B: F.219, S.220, N.221, S.222, V.224, T.225, G.226, V.227, S.228, K.259, N.260, H.262 Chain C: Y.421, T.488, Y.489 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.260, B:H.262 Water bridges: C:Y.421 SLB-SIA-SIA-SIA-SIA.5: 15 residues within 4Å: Chain A: Y.421, T.488, Y.489 Chain C: F.219, S.220, N.221, S.222, V.224, T.225, G.226, V.227, S.228, K.259, N.260, H.262 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.260, C:H.262 Water bridges: A:Y.421

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

SLB-SIA-SIA-SIA.2: 14 residues within 4Å: Chain A: R.597, I.599, T.606, S.607, S.608, Q.613, N.630 Chain B: S.568, S.569, I.571, R.572, Q.637, S.638 Chain C: Y.581 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:S.568, B:S.568, C:Y.581, A:T.606, B:Q.637, B:S.638, A:S.608, A:N.630 Water bridges: B:R.572, B:R.572, B:R.572, A:T.606 Salt bridges: B:R.572 SLB-SIA-SIA-SIA.4: 14 residues within 4Å: Chain A: Y.581 Chain B: R.597, I.599, T.606, S.607, S.608, Q.613, N.630 Chain C: S.568, S.569, I.571, R.572, Q.637, S.638 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: A:Y.581, C:S.568, C:S.568, B:T.606, B:S.608, B:N.630, C:Q.637, C:S.638 Water bridges: C:R.572, C:R.572, C:R.572, B:T.606 Salt bridges: C:R.572 SLB-SIA-SIA-SIA.6: 14 residues within 4Å: Chain A: S.568, S.569, I.571, R.572, Q.637, S.638 Chain B: Y.581 Chain C: R.597, I.599, T.606, S.607, S.608, Q.613, N.630 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:Y.581, C:T.606, A:S.568, A:S.568, A:Q.637, A:S.638, C:S.608, C:N.630 Water bridges: C:T.606, A:R.572, A:R.572, A:R.572 Salt bridges: A:R.572

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