SMTL ID : 4lnm.1

Structure of Escherichia coli Threonine Aldolase in Complex with Serine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

2 x PLG: N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE](Non-covalent)

PLG.1: 13 residues within 4Å: Chain B: S.6, T.57, G.58, T.59, H.83, E.136, D.166, A.168, R.169, K.197, R.308 Chain C: K.222, R.229 22 PLIP interactions: 17 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:H.83, B:E.136 Hydrogen bonds: B:S.6, B:G.58, B:T.59, B:T.59, B:H.83, B:R.169, B:R.169, B:K.197 Water bridges: B:T.59, C:K.222, C:R.229, C:R.229 Salt bridges: B:H.83, B:R.169, B:K.197, B:K.197, B:R.308, C:K.222, C:R.229 pi-Stacking: B:H.83 PLG.8: 13 residues within 4Å: Chain A: K.222, R.229 Chain D: S.6, T.57, G.58, T.59, H.83, E.136, D.166, A.168, R.169, K.197, R.308 22 PLIP interactions: 16 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:H.83, D:E.136 Hydrogen bonds: D:S.6, D:G.58, D:T.59, D:T.59, D:T.59, D:R.169, D:R.169, D:K.197 Salt bridges: D:H.83, D:R.169, D:K.197, D:K.197, D:R.308, A:K.222, A:R.229 pi-Stacking: D:H.83 Water bridges: A:K.222, A:K.222, A:R.229, A:R.229

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: T.8, T.10, S.196, T.201 Chain D: Q.230 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.8, A:T.10, A:T.10, A:S.196, A:T.201 CA.4: 6 residues within 4Å: Chain A: A.93, V.94, S.97 Chain B: A.93, V.94, S.97 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:S.97, B:S.97, H2O.10, H2O.19 CA.6: 5 residues within 4Å: Chain B: T.8, T.10, S.196, T.201 Chain C: Q.230 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:T.10, B:T.10, B:S.196, B:T.201 CA.9: 5 residues within 4Å: Chain B: Q.230 Chain C: T.8, T.10, S.196, T.201 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:T.8, C:T.10, C:T.10, C:S.196, C:T.201 CA.11: 6 residues within 4Å: Chain C: A.93, V.94, S.97 Chain D: A.93, V.94, S.97 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:S.97, C:S.97, H2O.10, H2O.19 CA.13: 5 residues within 4Å: Chain A: Q.230 Chain D: T.8, T.10, S.196, T.201 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:T.10, D:T.10, D:S.196, D:T.201

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

PLR.3: 11 residues within 4Å: Chain A: T.57, G.58, T.59, H.83, E.88, E.136, D.166, A.168, R.169, K.197 Chain D: R.229 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:H.83, A:A.168, A:K.197 Hydrogen bonds: A:G.58, A:T.59, A:T.59, A:T.59, A:R.169, A:K.197 Water bridges: A:S.196, D:K.222, D:K.222 Salt bridges: A:K.197, D:K.222, D:R.229 pi-Stacking: A:H.83 PLR.10: 11 residues within 4Å: Chain B: R.229 Chain C: T.57, G.58, T.59, H.83, E.88, E.136, D.166, A.168, R.169, K.197 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:H.83, C:A.168, C:K.197 Hydrogen bonds: C:G.58, C:T.59, C:T.59, C:R.169 Water bridges: C:S.196, B:K.222, B:K.222 Salt bridges: C:K.197, B:K.222, B:R.229 pi-Stacking: C:H.83

4 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.5: 8 residues within 4Å: Chain A: H.69, R.157, N.160, L.161, D.189, N.210, Y.213, R.216 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.157, A:R.157, A:N.210, A:Y.213 Salt bridges: A:D.189, A:D.189, A:R.216 EPE.7: 8 residues within 4Å: Chain B: H.69, N.160, A.162, D.189, N.210, D.212, Y.213, R.216 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.216 Water bridges: B:H.69, B:D.189 Salt bridges: B:D.189, B:D.189 EPE.12: 8 residues within 4Å: Chain C: H.69, R.157, N.160, L.161, D.189, N.210, Y.213, R.216 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.157, C:R.157, C:N.210, C:Y.213 Salt bridges: C:D.189, C:D.189, C:R.216 EPE.14: 8 residues within 4Å: Chain D: H.69, N.160, A.162, D.189, N.210, D.212, Y.213, R.216 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.216 Water bridges: D:H.69 Salt bridges: D:D.189, D:D.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

di Salvo, M.L. et al., On the catalytic mechanism and stereospecificity of Escherichia coli l-threonine aldolase. Febs J. (2014)

Release Date

2013-11-06

Peptides

Low-specificity L-threonine aldolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Low-specificity L-threonine aldolase

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