SMTL ID : 3gvk.1

Crystal structure of endo-neuraminidase NF mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-trimer

Ligands

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

SLB-SIA-SIA.1: 14 residues within 4Å: Chain A: T.284, E.285, H.302, G.304, D.305, V.306, R.309, P.337, D.338, E.341, T.358, R.359, R.362, N.459 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.337 Hydrogen bonds: A:R.309, A:R.309, A:D.338, A:R.362, A:E.341 Water bridges: A:V.306, A:R.309, A:R.309, A:R.359, A:R.356, A:R.356, A:R.407, A:R.407, A:S.460 Salt bridges: A:R.359, A:R.407 SLB-SIA-SIA.2: 13 residues within 4Å: Chain A: F.219, S.220, N.221, S.222, V.224, T.225, G.226, V.227, S.228, G.229 Chain C: K.170, T.488, Y.489 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:K.170, A:N.221, A:G.226, A:S.228 SLB-SIA-SIA.4: 14 residues within 4Å: Chain B: T.284, H.302, G.304, D.305, V.306, A.307, R.309, P.337, D.338, E.341, T.358, R.359, R.362, N.459 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:R.309, B:R.309, B:D.338, B:D.338, B:R.362, B:E.341 Water bridges: B:R.309, B:R.309, B:W.88, B:A.110, B:S.340, B:R.356, B:R.356, B:R.356, B:R.356, B:R.407, B:R.407, B:R.420, B:N.459, B:N.459 Salt bridges: B:R.359, B:R.407 SLB-SIA-SIA.5: 14 residues within 4Å: Chain A: K.170, T.488, Y.489, S.493 Chain B: F.219, S.220, N.221, S.222, V.224, T.225, G.226, V.227, S.228, G.229 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.221, A:K.170, B:G.226, B:S.228 Water bridges: B:S.220, A:K.170 SLB-SIA-SIA.7: 13 residues within 4Å: Chain C: T.284, H.302, G.304, D.305, V.306, R.309, P.337, D.338, E.341, T.358, R.359, R.362, N.459 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.305, C:R.309, C:R.309, C:D.338, C:D.338, C:T.358, C:R.362, C:E.341 Water bridges: C:R.309, C:R.407, C:R.407 Salt bridges: C:R.359, C:R.407 SLB-SIA-SIA.8: 14 residues within 4Å: Chain B: K.170, T.488, Y.489, S.493 Chain C: F.219, S.220, N.221, S.222, V.224, T.225, G.226, V.227, S.228, G.229 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.221, C:G.226, C:S.228

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

SLB-SIA.3: 11 residues within 4Å: Chain A: R.597, I.599, T.606, S.607, S.608, Q.613, N.630 Chain B: Y.581, R.625 Chain C: Q.637, S.638 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: A:I.599, B:Y.581 Hydrogen bonds: A:R.597, A:T.606, A:S.608, A:Q.613, A:Q.613, A:S.608, A:N.630, C:Q.637, C:S.638 SLB-SIA.6: 11 residues within 4Å: Chain A: Q.637, S.638 Chain B: R.597, I.599, T.606, S.607, S.608, Q.613, N.630 Chain C: Y.581, Y.644 6 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: B:I.599, C:Y.581 Hydrogen bonds: B:R.597, B:T.606, B:S.608, B:S.608, B:Q.613, B:Q.613, B:S.608, B:N.630, A:Q.637, A:S.638 Water bridges: C:N.645, C:N.645 SLB-SIA.9: 10 residues within 4Å: Chain A: Y.581 Chain B: Q.637, S.638 Chain C: R.597, I.599, T.606, S.607, S.608, Q.613, N.630 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.599 Hydrogen bonds: C:R.597, C:T.606, C:S.608, C:S.608, C:Q.613, C:Q.613, B:Q.637, B:S.638, C:S.608, C:N.630 Water bridges: C:S.607, C:T.609

3 x NA: SODIUM ION(Non-functional Binders)

NA.10: 8 residues within 4Å: Chain A: T.82, P.83, Y.84, N.86, H.503, S.505, D.506 Chain B: R.532 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.84 NA.11: 8 residues within 4Å: Chain B: T.82, P.83, Y.84, N.86, H.503, S.505, D.506 Chain C: R.532 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.86 NA.12: 8 residues within 4Å: Chain A: R.532 Chain C: T.82, P.83, Y.84, N.86, H.503, S.505, D.506 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.506

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
B

C
C

Endo-N-acetylneuraminidase