SMTL ID : 6ppy.1

Crystal structure of NeuNAc oxime complexed with NeuB, an N-acetylneuraminate synthase from Neisseria meningitidis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x OVY: (2E,4S,5R,6R,7S,8R)-5-(acetylamino)-4,6,7,8,9-pentahydroxy-2-(hydroxyimino)nonanoic acid (non-preferred name)(Non-covalent)

OVY.1: 26 residues within 4Å: Chain A: E.25, I.28, K.53, Q.55, N.74, I.79, I.82, M.83, T.110, F.112, K.129, G.131, S.132, G.133, S.154, M.157, N.184, Y.186, H.215, H.236, P.246, D.247 Chain B: T.285, F.288, A.289, R.314 20 PLIP interactions: 15 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Q.55, A:N.74, A:N.74, A:T.110, A:K.129, A:S.132, A:S.132, A:S.154, A:N.184, A:Y.186, A:H.236, B:R.314, B:R.314 Water bridges: A:S.213, A:H.215 Salt bridges: A:K.53, A:K.129 Hydrophobic interactions: B:T.285, B:F.288, B:A.289 OVY.2: 26 residues within 4Å: Chain A: T.285, F.288, A.289, R.314 Chain B: E.25, I.28, K.53, Q.55, N.74, I.79, I.82, M.83, T.110, F.112, K.129, G.131, S.132, G.133, S.154, M.157, N.184, Y.186, H.215, H.236, P.246, D.247 20 PLIP interactions: 15 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Q.55, B:N.74, B:N.74, B:T.110, B:K.129, B:S.132, B:S.132, B:S.154, B:N.184, B:Y.186, B:H.236, A:R.314, A:R.314 Water bridges: B:S.213, B:H.215 Salt bridges: B:K.53, B:K.129 Hydrophobic interactions: A:T.285, A:F.288, A:A.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Popovic, V. et al., NeuNAc Oxime: A Slow-Binding and Effectively Irreversible Inhibitor of the Sialic Acid Synthase NeuB. Biochemistry (2019)

Release Date

2019-10-02

Peptides

N-acetylneuraminate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

N-acetylneuraminate synthase

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