SMTL ID : 5vye.1

Crystal Structure of L-Threonine Aldolase from Pseudomonas putida

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-tetramer

Ligands

4 x PLR: (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE(Non-covalent)

PLR.1: 15 residues within 4Å: Chain A: N.12, N.63, G.64, T.65, N.68, H.89, E.94, T.143, E.147, D.174, A.176, R.177, K.207 Chain B: Y.35, S.239 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:H.89, A:T.143, A:A.176 Hydrogen bonds: A:N.63, A:G.64, A:T.65, A:T.65, A:R.177, A:K.207, B:Y.35 Water bridges: A:N.68, A:E.214, A:E.214, B:K.232, B:K.232 pi-Stacking: A:H.89 PLR.3: 16 residues within 4Å: Chain A: Y.35, S.239 Chain B: N.12, N.63, G.64, T.65, N.68, H.89, E.94, T.143, E.147, D.174, A.176, R.177, K.207, E.214 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:H.89, B:T.143, B:E.147, B:A.176 Hydrogen bonds: B:G.64, B:T.65, B:T.65, B:T.65, B:R.177, B:R.177, A:Y.35 Water bridges: B:N.68, B:K.207, B:E.214, A:K.232 Salt bridges: B:K.207 pi-Stacking: B:H.89 PLR.5: 16 residues within 4Å: Chain C: N.12, N.63, G.64, T.65, N.68, H.89, E.94, T.143, E.147, D.174, A.176, R.177, T.206, K.207 Chain D: Y.35, S.239 17 PLIP interactions: 15 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:H.89, C:T.143, C:E.147, C:A.176 Hydrogen bonds: C:G.64, C:T.65, C:T.65, C:R.177, C:K.207, D:Y.35, D:S.239 Water bridges: C:N.63, C:N.63, C:N.68, C:G.213 Salt bridges: C:K.207 pi-Stacking: C:H.89 PLR.7: 15 residues within 4Å: Chain C: Y.35, S.239 Chain D: N.12, N.63, G.64, T.65, N.68, H.89, T.143, E.147, D.174, A.176, R.177, K.207, E.214 18 PLIP interactions: 15 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:H.89, D:T.143 Hydrogen bonds: D:G.64, D:T.65, D:T.65, D:T.65, D:H.89, D:R.177, D:R.177, D:K.207, C:Y.35, C:S.239 Water bridges: D:N.63, D:N.68, D:E.214, C:K.232 Salt bridges: D:K.207 pi-Stacking: D:H.89

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: A.73, S.74, L.75, C.76, Q.77, E.225, R.230 Chain C: Q.77, Y.79 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:Q.77, C:Y.79, A:A.73, A:Q.77, A:R.230, A:R.230 Water bridges: C:Y.79 GOL.4: 8 residues within 4Å: Chain B: A.73, S.74, L.75, C.76, Q.77, R.230 Chain D: Q.77, Y.79 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:A.73, B:R.230, B:R.230, D:Q.77 Water bridges: B:Q.77, B:L.223, B:E.225, B:E.225, D:Y.79 GOL.6: 9 residues within 4Å: Chain A: Q.77, Y.79 Chain C: A.73, S.74, L.75, C.76, Q.77, L.223, R.230 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:S.74, C:R.230, A:Q.77 Water bridges: C:A.73, C:L.75, C:C.76, C:Q.77, C:Q.77, C:Q.77, C:Q.77, C:R.230 GOL.8: 9 residues within 4Å: Chain B: Q.77, Y.79 Chain D: A.73, S.74, L.75, C.76, Q.77, E.225, R.230 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:Q.77, D:R.230, B:Q.77, B:Q.77, B:Y.79 Water bridges: D:Q.77, D:Q.77, D:R.230, B:Y.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beaudoin, S.F. et al., Crystal Structure of L-Threonine Aldolase from Pseudomonas putida. To Be Published

Release Date

2018-06-27

Peptides

L-threonine aldolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-threonine aldolase