SMTL ID : 6rd1.1

Ruminococcus gnavus sialic acid aldolase catalytic lysine mutant in complex with sialic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

homo-tetramer

Ligands

4 x SI3: 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid(Non-covalent)

SI3.1: 16 residues within 4Å: Chain A: A.44, Y.76, G.79, S.80, S.81, Y.170, S.200, G.223, P.224, D.225, E.226, G.241, G.242, T.243, M.287, Y.288 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.80, A:S.81, A:S.81, A:Y.170, A:Y.170, A:G.223, A:G.223, A:D.225, A:G.242, A:Y.288 Water bridges: A:Y.76, A:Y.76, A:G.79, A:Y.288 SI3.2: 18 residues within 4Å: Chain B: A.44, Y.76, G.79, S.80, S.81, Y.170, I.172, S.200, G.223, P.224, D.225, E.226, I.240, G.241, G.242, T.243, M.287, Y.288 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.172 Hydrogen bonds: B:S.80, B:S.81, B:S.81, B:S.81, B:Y.170, B:Y.170, B:G.223, B:D.225, B:E.226, B:I.240, B:G.242 Water bridges: B:G.79, B:Y.288 SI3.3: 16 residues within 4Å: Chain C: A.44, Y.76, G.79, S.80, S.81, Y.170, S.200, G.223, P.224, D.225, E.226, G.241, G.242, T.243, M.287, Y.288 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:S.80, C:S.81, C:S.81, C:Y.170, C:G.223, C:G.223, C:D.225, C:G.242, C:Y.288, C:Y.288 Water bridges: C:G.79 SI3.4: 18 residues within 4Å: Chain D: A.44, Y.76, G.79, S.80, S.81, Y.170, I.172, S.200, G.223, P.224, D.225, E.226, I.240, G.241, G.242, T.243, M.287, Y.288 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:I.172 Hydrogen bonds: D:S.80, D:S.81, D:S.81, D:S.81, D:Y.170, D:G.223, D:D.225, D:E.226, D:I.240, D:G.242, D:Y.288 Water bridges: D:Y.76, D:G.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bell, A. et al., Elucidation of a sialic acid metabolism pathway in mucus-foraging Ruminococcus gnavus unravels mechanisms of bacterial adaptation to the gut. Nat Microbiol (2019)

Release Date

2019-09-25

Peptides

Putative N-acetylneuraminate lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Putative N-acetylneuraminate lyase

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