SMTL ID : 6ppz.1

Crystal structure of NeuB, an N-acetylneuraminate synthase from Neisseria meningitidis, in complex with manganese, inorganic phosphate, and N-acetylmannosamine (NeuB.Mn2+.Pi.ManNAc)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x MN9: 2-(ACETYLAMINO)-2-DEOXY-D-MANNOSE(Non-covalent)

MN9.1: 15 residues within 4Å: Chain A: Q.55, P.72, N.74, M.83, F.112, Y.186, H.236, P.246, D.247 Chain B: T.285, F.288, A.289, R.314 Ligands: MN.2, PO4.3 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Q.55, A:Q.55, A:N.74, A:Y.186, A:H.236, A:D.247, B:R.314 Water bridges: A:I.28, A:K.53, B:R.314 Hydrophobic interactions: B:T.285, B:F.288, B:A.289 MN9.4: 15 residues within 4Å: Chain A: T.285, F.288, A.289, R.314 Chain B: Q.55, P.72, N.74, M.83, F.112, Y.186, H.236, P.246, D.247 Ligands: MN.5, PO4.6 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Q.55, B:Q.55, B:N.74, B:Y.186, B:H.236, B:D.247, A:R.314 Water bridges: B:I.28, B:K.53, A:R.314 Hydrophobic interactions: A:T.285, A:F.288, A:A.289

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 6 residues within 4Å: Chain A: E.25, H.215, E.234, H.236 Ligands: MN9.1, PO4.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.215 MN.5: 6 residues within 4Å: Chain B: E.25, H.215, E.234, H.236 Ligands: MN9.4, PO4.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.215

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 12 residues within 4Å: Chain A: K.129, G.131, S.132, S.154, C.182, N.184, Y.186, S.213, H.215, E.234 Ligands: MN9.1, MN.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.132, A:S.154, A:S.154, A:S.154, A:N.184, A:S.213 Water bridges: A:K.129 Salt bridges: A:K.129, A:H.215 PO4.6: 12 residues within 4Å: Chain B: K.129, G.131, S.132, S.154, C.182, N.184, Y.186, S.213, H.215, E.234 Ligands: MN9.4, MN.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.132, B:S.154, B:S.154, B:S.154, B:N.184, B:S.213 Water bridges: B:K.129 Salt bridges: B:K.129, B:H.215

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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