SMTL ID : 1xuz.1

Crystal structure analysis of sialic acid synthase (NeuB)from Neisseria meningitidis, bound to Mn2+, Phosphoenolpyruvate, and N-acetyl mannosaminitol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x MMN: 5-DEOXY-5-{[(1S)-1-HYDROXYETHYL]AMINO}-D-GLUCITOL(Non-covalent)

MMN.1: 15 residues within 4Å: Chain A: Q.55, N.74, I.79, M.83, F.112, Y.186, H.215, H.236, P.246, D.247 Chain B: T.285, A.289, R.314 Ligands: MN.2, PEP.3 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.55, A:Q.55, A:N.74, A:Y.186, A:Y.186, A:D.247, B:R.314, B:R.314 Hydrophobic interactions: B:T.285, B:A.289 MMN.4: 15 residues within 4Å: Chain A: T.285, A.289, R.314 Chain B: Q.55, N.74, I.79, M.83, F.112, Y.186, H.215, H.236, P.246, D.247 Ligands: MN.5, PEP.6 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:T.285, A:A.289 Hydrogen bonds: A:R.314, A:R.314, B:Q.55, B:Q.55, B:N.74, B:Y.186, B:Y.186, B:D.247

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: MMN.1, PEP.3 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.215, A:H.236, H2O.1, H2O.2, PEP.3 MN.5: 6 residues within 4Å: Chain B: E.25, H.215, E.234, H.236 Ligands: MMN.4, PEP.6 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:H.215, B:H.236, PEP.6, H2O.11, H2O.12

2 x PEP: PHOSPHOENOLPYRUVATE(Non-functional Binders)

PEP.3: 16 residues within 4Å: Chain A: E.25, K.53, Q.55, T.110, F.112, K.129, G.131, S.132, S.154, C.182, N.184, S.213, H.215, E.234 Ligands: MMN.1, MN.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.132, A:S.154, A:S.154, A:N.184, A:Y.186, A:S.213 Salt bridges: A:K.53, A:K.129, A:K.129, A:H.215 PEP.6: 16 residues within 4Å: Chain B: E.25, K.53, Q.55, T.110, F.112, K.129, G.131, S.132, S.154, C.182, N.184, S.213, H.215, E.234 Ligands: MMN.4, MN.5 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:S.132, B:S.154, B:S.154, B:N.184, B:Y.186, B:S.213 Salt bridges: B:K.53, B:K.129, B:K.129, B:H.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gunawan, J. et al., Structural and mechanistic analysis of sialic acid synthase NeuB from Neisseria meningitidis in complex with Mn2+, phosphoenolpyruvate, and N-acetylmannosaminitol. J.Biol.Chem. (2005)

Release Date

2004-11-02

Peptides

polysialic acid capsule biosynthesis protein SiaC: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

polysialic acid capsule biosynthesis protein SiaC

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