SMTL ID : 3ju4.1

Crystal Structure Analysis of EndosialidaseNF at 0.98 A Resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 0.98 Å

Oligo State

homo-trimer

Ligands

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

SLB.1: 8 residues within 4Å: Chain A: R.597, I.599, T.606, S.607, S.608, Q.613, N.630 Chain C: Y.581 15 PLIP interactions: 12 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, B:Q.637, B:Q.637, B:Q.637 SLB.8: 8 residues within 4Å: Chain A: Y.581 Chain B: R.597, I.599, T.606, S.607, S.608, Q.613, N.630 15 PLIP interactions: 12 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, C:Q.637, C:Q.637, C:Q.637 SLB.15: 8 residues within 4Å: Chain B: Y.581 Chain C: R.597, I.599, T.606, S.607, S.608, Q.613, N.630 15 PLIP interactions: 3 interactions with chain A, 12 interactions with chain C Water bridges: A:Q.637, A:Q.637, A:Q.637, C:T.606, C:S.607 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

15 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: R.356, G.357, T.358, H.388 Ligand excluded by PLIP CL.3: 7 residues within 4Å: Chain A: A.87, W.88, P.89, G.461, G.463, V.464, G.479 Ligand excluded by PLIP CL.4: 7 residues within 4Å: Chain A: R.356, G.357, S.365, V.386, H.387, H.388, T.389 Ligand excluded by PLIP CL.5: 7 residues within 4Å: Chain A: G.559, H.560 Chain B: I.563, R.564, S.566, S.573, E.574 Ligand excluded by PLIP CL.6: 6 residues within 4Å: Chain A: E.285, H.287, Y.301, H.302, E.341, P.342 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: R.356, G.357, T.358, H.388 Ligand excluded by PLIP CL.10: 7 residues within 4Å: Chain B: A.87, W.88, P.89, G.461, G.463, V.464, G.479 Ligand excluded by PLIP CL.11: 7 residues within 4Å: Chain B: R.356, G.357, S.365, V.386, H.387, H.388, T.389 Ligand excluded by PLIP CL.12: 7 residues within 4Å: Chain B: G.559, H.560 Chain C: I.563, R.564, S.566, S.573, E.574 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain B: E.285, H.287, Y.301, H.302, E.341, P.342 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain C: R.356, G.357, T.358, H.388 Ligand excluded by PLIP CL.17: 7 residues within 4Å: Chain C: A.87, W.88, P.89, G.461, G.463, V.464, G.479 Ligand excluded by PLIP CL.18: 7 residues within 4Å: Chain C: R.356, G.357, S.365, V.386, H.387, H.388, T.389 Ligand excluded by PLIP CL.19: 7 residues within 4Å: Chain A: I.563, R.564, S.566, S.573, E.574 Chain C: G.559, H.560 Ligand excluded by PLIP CL.20: 6 residues within 4Å: Chain C: E.285, H.287, Y.301, H.302, E.341, P.342 Ligand excluded by PLIP

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

NA.7: 7 residues within 4Å: Chain A: T.82, Y.84, N.86, H.503, S.505, D.506 Chain C: R.532 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.84, A:N.86 NA.14: 7 residues within 4Å: Chain A: R.532 Chain B: T.82, Y.84, N.86, H.503, S.505, D.506 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.86, B:D.506 NA.21: 7 residues within 4Å: Chain B: R.532 Chain C: T.82, Y.84, N.86, H.503, S.505, D.506 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.82, C:N.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schulz, E.C. et al., Structure analysis of endosialidase NF at 0.98 A resolution. Acta Crystallogr.,Sect.D (2010)

Release Date

2010-02-02

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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