SMTL ID : 4bwl.1

Structure of the Y137A mutant of E. coli N-acetylneuraminic acid lyase in complex with pyruvate, N-acetyl-D-mannosamine and N- acetylneuraminic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

3 x SI3: 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid(Post Translational Modification)

SI3.1: 16 residues within 4Å: Chain A: Y.50, G.53, S.54, T.55, I.146, L.149, K.172, T.174, G.196, Y.197, D.198, E.199, I.213, G.214, S.215, F.259 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.149, A:K.172 Hydrogen bonds: A:S.54, A:T.55, A:T.55, A:K.172, A:T.174, A:G.196, A:D.198, A:S.215, A:S.215 Salt bridges: A:K.172 SI3.2: 16 residues within 4Å: Chain B: A.18, Y.50, G.53, S.54, T.55, K.172, T.174, G.196, Y.197, D.198, E.199, I.213, G.214, S.215, V.258, F.259 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:K.172, B:I.213 Hydrogen bonds: B:S.54, B:T.55, B:T.55, B:T.55, B:T.55, B:K.172, B:G.196, B:D.198, B:I.213, B:S.215, B:S.215 Salt bridges: B:K.172 SI3.6: 15 residues within 4Å: Chain D: Y.50, G.53, S.54, T.55, L.149, K.172, T.174, G.196, Y.197, D.198, E.199, I.213, G.214, S.215, F.259 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:K.172, D:F.259 Hydrogen bonds: D:S.54, D:T.55, D:T.55, D:T.55, D:K.172, D:G.196, D:G.196, D:D.198, D:S.215 Salt bridges: D:K.172

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 3 residues within 4Å: Chain B: D.177 Chain D: Y.197, I.200 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.178 1PE.5: 2 residues within 4Å: Chain A: D.177 Chain C: Y.197 No protein-ligand interaction detected (PLIP)

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

MN9.4: 12 residues within 4Å: Chain C: I.146, L.149, K.172, T.174, G.196, Y.197, D.198, E.199, I.213, G.214, S.215, F.259 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.259 Hydrogen bonds: C:T.174, C:D.198, C:D.198, C:I.213, C:S.215, C:S.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Daniels, A.D. et al., The Reaction Mechanism of N-Acetylneuraminic Acid Lyase Revealed by a Combination of Crystallography, Qm/Mm Simulation and Mutagenesis. Acs Chem.Biol. (2014)

Release Date

2014-02-19

Peptides

N-ACETYLNEURAMINATE LYASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

N-ACETYLNEURAMINATE LYASE