SMTL ID : 5afd.1

Native structure of N-acetylneuramininate lyase (sialic acid aldolase) from Aliivibrio salmonicida

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: S.19 Chain B: I.84, L.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.19, A:S.19 Water bridges: A:S.19 GOL.5: 3 residues within 4Å: Chain A: I.84, L.88 Chain B: S.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.19, B:S.19 Water bridges: B:S.19 GOL.9: 3 residues within 4Å: Chain C: S.19 Chain D: I.84, L.88 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.19, C:S.19 Water bridges: C:S.19 GOL.13: 3 residues within 4Å: Chain C: I.84, L.88 Chain D: S.19 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.19, D:S.19 Water bridges: D:S.19

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: I.51, A.81, L.82, G.106, P.107, C.108 Chain B: F.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.81, A:C.108 Water bridges: A:I.105 EDO.3: 3 residues within 4Å: Chain A: M.1, K.2, L.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.2, A:K.2 EDO.4: 4 residues within 4Å: Chain A: V.192, D.193, E.194, S.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.193, A:D.193 EDO.6: 7 residues within 4Å: Chain A: F.109 Chain B: I.51, A.81, L.82, G.106, P.107, C.108 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.81, B:C.108 Water bridges: B:I.105 EDO.7: 3 residues within 4Å: Chain B: M.1, K.2, L.100 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.2, B:K.2 EDO.8: 4 residues within 4Å: Chain B: V.192, D.193, E.194, S.210 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.193, B:D.193 EDO.10: 7 residues within 4Å: Chain C: I.51, A.81, L.82, G.106, P.107, C.108 Chain D: F.109 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:A.81, C:C.108 Water bridges: C:I.105 EDO.11: 3 residues within 4Å: Chain C: M.1, K.2, L.100 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.2, C:K.2 EDO.12: 4 residues within 4Å: Chain C: V.192, D.193, E.194, S.210 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.193, C:D.193 EDO.14: 7 residues within 4Å: Chain C: F.109 Chain D: I.51, A.81, L.82, G.106, P.107, C.108 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:A.81, D:C.108 Water bridges: D:I.105 EDO.15: 3 residues within 4Å: Chain D: M.1, K.2, L.100 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.2, D:K.2 EDO.16: 4 residues within 4Å: Chain D: V.192, D.193, E.194, S.210 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.193, D:D.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gurung, M.K. et al., Features and structure of a cold active N-acetylneuraminate lyase. Plos One (2019)

Release Date

2016-03-02

Peptides

N-ACETYLNEURAMINATE LYASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

N-ACETYLNEURAMINATE LYASE