SMTL ID : 5xoy.1

Crystal structure of LysK from Thermus thermophilus in complex with Lysine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-tetramer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 8 residues within 4Å: Chain A: E.136, E.137, A.138, S.141, R.174, R.248, T.312 Chain B: H.187 10 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions, 1 interactions with chain B Hydrogen bonds: A:E.136, A:S.141, A:S.141, A:T.312, A:T.312, K.1 Salt bridges: A:R.174, A:R.248, A:H.338, B:H.187 LYS.5: 8 residues within 4Å: Chain C: E.136, E.137, A.138, S.141, R.174, R.248, T.312 Chain D: H.187 10 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D, 1 Ligand-Ligand interactions Hydrogen bonds: C:E.136, C:S.141, C:S.141, C:T.312, C:T.312, K.5 Salt bridges: C:R.174, C:R.248, C:H.338, D:H.187

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: F.275, G.276, R.277 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.276, A:R.277 Salt bridges: A:R.277 SO4.3: 4 residues within 4Å: Chain B: H.233, E.236, L.237, R.238 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.236, B:L.237, B:R.238 Salt bridges: B:H.233 SO4.4: 3 residues within 4Å: Chain B: F.275, G.276, R.277 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.276, B:R.277 Water bridges: B:R.277 Salt bridges: B:R.277 SO4.6: 3 residues within 4Å: Chain C: F.275, G.276, R.277 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.276, C:R.277 Salt bridges: C:R.277 SO4.7: 4 residues within 4Å: Chain D: H.233, E.236, L.237, R.238 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.236, D:L.237, D:R.238 Salt bridges: D:H.233 SO4.8: 3 residues within 4Å: Chain D: F.275, G.276, R.277 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.276, D:R.277 Water bridges: D:R.277 Salt bridges: D:R.277

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fujita, S. et al., Crystal structure of LysK, an enzyme catalyzing the last step of lysine biosynthesis in Thermus thermophilus, in complex with lysine: Insight into the mechanism for recognition of the amino-group carrier protein, LysW. Biochem. Biophys. Res. Commun. (2017)

Release Date

2017-09-13

Peptides

[LysW]-lysine hydrolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

[LysW]-lysine hydrolase