SMTL ID : 2ya5.1

Crystal structure of Streptococcus pneumoniae NanA (TIGR4) in complex with sialic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x SIA: N-acetyl-alpha-neuraminic acid(Non-covalent)

SIA.1: 17 residues within 4Å: Chain A: R.48, I.49, R.67, D.73, I.117, D.118, D.135, I.143, F.144, Y.291, L.299, Q.303, E.348, R.364, Y.396, R.422, Y.453 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.117 Hydrogen bonds: A:R.67, A:D.73, A:D.73, A:D.73, A:D.118, A:Q.303, A:R.364, A:Y.396 Water bridges: A:D.73, A:Y.291, A:Y.291 Salt bridges: A:R.48, A:R.364, A:R.422 SIA.6: 17 residues within 4Å: Chain B: R.48, I.49, R.67, D.73, I.117, D.118, D.135, I.143, F.144, Y.291, L.299, Q.303, E.348, R.364, Y.396, R.422, Y.453 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.117 Hydrogen bonds: B:R.48, B:R.67, B:D.73, B:D.73, B:D.118, B:Q.303, B:E.348 Water bridges: B:D.73, B:D.73, B:D.73, B:E.348, B:E.348 Salt bridges: B:R.48, B:R.364, B:R.422

5 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 6 residues within 4Å: Chain A: Y.241, S.242, D.243, D.244, T.248, W.249 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.243, A:D.244, A:D.244 FMT.3: 5 residues within 4Å: Chain A: P.257, M.258, V.259, K.260, A.261 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.257 Water bridges: A:A.261 FMT.4: 2 residues within 4Å: Chain A: K.54, Q.457 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.457 Water bridges: A:E.458 FMT.7: 5 residues within 4Å: Chain B: Y.241, S.242, D.243, D.244, T.248 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.243, B:D.244, B:S.250 FMT.8: 4 residues within 4Å: Chain B: P.281, H.282, R.285, D.311 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.282, B:R.285

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

CL.5: 6 residues within 4Å: Chain A: G.217, N.218, F.221, K.225, T.226, S.227 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain B: G.217, N.218, F.221, K.225, T.226, S.227 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gut, H. et al., Structural Basis for Streptococcus Pneumoniae Nana Inhibition by Influenza Antivirals Zanamivir and Oseltamivir Carboxylate. J.Mol.Biol. (2011)

Release Date

2011-04-27

Peptides

NEURAMINIDASE A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NEURAMINIDASE A

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