SMTL ID : 4lnl.1

Structure of Escherichia coli Threonine Aldolase in Complex with Allo-Thr

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 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 MG.6: 5 residues within 4Å: Chain B: T.8, T.10, S.196, T.201 Chain C: Q.230 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.8, B:T.10, B:T.10, B:S.196, B:T.201 MG.7: 6 residues within 4Å: Chain A: A.93, V.94, S.97 Chain B: A.93, V.94, S.97 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:A.93, A:S.97, B:S.97, H2O.8 MG.10: 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 MG.15: 5 residues within 4Å: Chain A: Q.230 Chain D: T.8, T.10, S.196, T.201 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:T.8, D:T.10, D:T.10, D:S.196, D:T.201 MG.16: 6 residues within 4Å: Chain C: A.93, V.94, S.97 Chain D: A.93, V.94, S.97 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:A.93, C:S.97, D:S.97, H2O.26

2 x 2BO: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-threonine(Non-covalent)

2BO.2: 18 residues within 4Å: Chain A: S.6, T.8, T.57, G.58, T.59, N.62, H.83, E.88, E.136, D.166, A.168, R.169, C.194, K.197, R.308 Chain B: H.126 Chain D: R.229 Ligands: 2BK.3 29 PLIP interactions: 21 interactions with chain A, 8 interactions with chain D Hydrophobic interactions: A:E.136, A:A.168 Hydrogen bonds: A:S.6, A:G.58, A:T.59, A:T.59, A:H.83, A:R.169, A:R.169, A:K.197, D:R.229 Water bridges: A:T.57, A:N.62, A:S.196, A:K.197, A:K.197, A:R.308, A:R.308, D:Y.30, D:K.222, D:K.222, D:G.227, D:R.229 Salt bridges: A:R.169, A:K.197, A:R.308, D:K.222, D:R.229 pi-Stacking: A:H.83 2BO.11: 18 residues within 4Å: Chain B: R.229 Chain C: S.6, T.8, T.57, G.58, T.59, N.62, H.83, E.88, E.136, D.166, A.168, R.169, C.194, K.197, R.308 Chain D: H.126 Ligands: 2BK.12 28 PLIP interactions: 21 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:E.136, C:A.168 Hydrogen bonds: C:S.6, C:G.58, C:T.59, C:H.83, C:R.169, C:R.169, C:K.197, B:R.229 Water bridges: C:T.8, C:T.59, C:N.62, C:S.196, C:K.197, C:K.197, C:R.308, C:R.308, B:K.222, B:G.227, B:G.227, B:R.229 Salt bridges: C:R.169, C:K.197, C:R.308, B:K.222, B:R.229 pi-Stacking: C:H.83

2 x 2BK: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-allothreonine(Non-covalent)

2BK.3: 18 residues within 4Å: Chain A: S.6, T.8, T.57, G.58, T.59, N.62, H.83, E.88, E.136, D.166, A.168, R.169, C.194, K.197, R.308 Chain B: H.126 Chain D: R.229 Ligands: 2BO.2 29 PLIP interactions: 1 interactions with chain B, 20 interactions with chain A, 8 interactions with chain D Hydrogen bonds: B:H.126, A:S.6, A:G.58, A:T.59, A:T.59, A:R.169, A:R.169, A:K.197, D:R.229 Hydrophobic interactions: A:E.136, A:A.168 Water bridges: A:T.57, A:N.62, A:S.196, A:K.197, A:K.197, A:R.308, A:R.308, D:Y.30, D:K.222, D:K.222, D:G.227, D:R.229 Salt bridges: A:R.169, A:K.197, A:R.308, D:K.222, D:R.229 pi-Stacking: A:H.83 2BK.12: 18 residues within 4Å: Chain B: R.229 Chain C: S.6, T.8, T.57, G.58, T.59, N.62, H.83, E.88, E.136, D.166, A.168, R.169, C.194, K.197, R.308 Chain D: H.126 Ligands: 2BO.11 28 PLIP interactions: 20 interactions with chain C, 7 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: C:E.136, C:A.168 Hydrogen bonds: C:S.6, C:G.58, C:T.59, C:R.169, C:R.169, C:K.197, B:R.229, D:H.126 Water bridges: C:T.8, C:T.59, C:N.62, C:S.196, C:K.197, C:K.197, C:R.308, C:R.308, B:K.222, B:G.227, B:G.227, B:R.229 Salt bridges: C:R.169, C:K.197, C:R.308, 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.4: 9 residues within 4Å: Chain A: T.156, R.157, N.160, L.161, A.162, D.189, N.210, Y.213, R.216 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.157, A:N.210 Water bridges: A:H.69 Salt bridges: A:D.189, A:D.189, A:R.216 EPE.9: 9 residues within 4Å: Chain B: H.69, R.157, N.160, A.162, D.189, N.210, D.212, Y.213, R.216 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.160, B:N.210, B:R.216 Salt bridges: B:H.69, B:D.189, B:D.189 EPE.13: 9 residues within 4Å: Chain C: T.156, R.157, N.160, L.161, A.162, D.189, N.210, Y.213, R.216 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.157, C:N.210 Water bridges: C:R.216 Salt bridges: C:D.189, C:D.189, C:R.216 EPE.18: 9 residues within 4Å: Chain D: H.69, R.157, N.160, A.162, D.189, N.210, D.212, Y.213, R.216 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.160, D:N.210, D:R.216 Water bridges: D:H.69 Salt bridges: D:H.69, D:D.189, D:D.189

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: E.71, R.72 Chain C: E.71, R.72 Ligands: CL.14 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain A: E.71, R.72 Chain C: E.71, R.72 Ligands: CL.5 Ligand excluded by PLIP

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

PLG.8: 15 residues within 4Å: Chain B: S.6, T.8, T.57, G.58, T.59, N.62, H.83, E.88, E.136, D.166, A.168, R.169, K.197, R.308 Chain C: R.229 25 PLIP interactions: 20 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:H.83, B:E.136, B:A.168 Hydrogen bonds: B:S.6, B:G.58, B:T.59, B:R.169, B:R.169, B:K.197 Water bridges: B:P.56, B:N.62, B:H.83, B:S.196, B:K.197, B:K.197, C:K.222, C:K.222, C:K.222 Salt bridges: B:R.169, B:K.197, B:K.197, B:R.308, C:K.222, C:R.229 pi-Stacking: B:H.83 PLG.17: 15 residues within 4Å: Chain A: R.229 Chain D: S.6, T.8, T.57, G.58, T.59, N.62, H.83, E.88, E.136, D.166, A.168, R.169, K.197, R.308 26 PLIP interactions: 21 interactions with chain D, 5 interactions with chain A Hydrophobic interactions: D:H.83, D:E.136, D:A.168 Hydrogen bonds: D:S.6, D:G.58, D:T.59, D:T.59, D:R.169, D:R.169, D:K.197 Water bridges: D:P.56, D:N.62, D:H.83, D:S.196, D:K.197, D:K.197, A:K.222, A:K.222, A:K.222 Salt bridges: D:R.169, D:K.197, D:K.197, D:R.308, A:K.222, A:R.229 pi-Stacking: D:H.83

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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