SMTL ID : 1lw5.1

X-ray structure of L-Threonine Aldolase (low-specificity) in complex with glycine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: T.12, T.14, S.202, A.207 Chain D: Q.236 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.12, A:T.14, A:T.14, A:S.202, A:A.207 CA.2: 5 residues within 4Å: Chain A: Q.236 Chain D: T.12, T.14, S.202, A.207 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.12, D:T.14, D:S.202 CA.4: 5 residues within 4Å: Chain B: Q.236 Chain C: T.12, T.14, S.202, A.207 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:T.12, C:T.14, C:T.14, C:S.202, C:A.207 CA.5: 2 residues within 4Å: Chain B: N.330, E.333 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.333, H2O.9, H2O.13, H2O.13, H2O.16 CA.10: 5 residues within 4Å: Chain B: T.12, T.14, S.202, A.207 Chain C: Q.236 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.12, B:T.14, B:T.14, B:S.202, B:A.207 CA.12: 2 residues within 4Å: Chain D: N.330, E.333 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.333, H2O.33, H2O.33

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

CL.3: 4 residues within 4Å: Chain A: Q.75, R.76 Chain B: Q.75, R.76 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain B: K.15, R.21 Chain C: E.28, V.29 Ligand excluded by PLIP CL.7: 5 residues within 4Å: Chain B: A.27, E.28, V.29 Chain C: K.15, R.21 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain C: Q.75, R.76 Chain D: Q.75, R.76 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: K.15, R.21 Chain D: E.28, V.29 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: E.28, V.29 Chain D: K.15, R.21 Ligand excluded by PLIP

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

PLG.8: 16 residues within 4Å: Chain B: S.10, S.61, G.62, T.63, N.66, H.87, E.92, E.139, D.172, A.174, R.175, M.198, K.203, R.320 Chain C: R.235 Ligands: PLP.9 22 PLIP interactions: 5 interactions with chain C, 17 interactions with chain B Water bridges: C:K.228, C:K.228, C:R.235, B:P.60, B:S.61, B:T.63, B:N.143, B:N.143, B:S.202 Salt bridges: C:K.228, C:R.235, B:R.175, B:R.320 Hydrophobic interactions: B:H.87, B:E.139, B:A.174 Hydrogen bonds: B:S.10, B:G.62, B:T.63, B:R.175, B:R.175 pi-Stacking: B:H.87 PLG.11: 17 residues within 4Å: Chain B: R.235 Chain C: S.10, T.12, S.61, G.62, T.63, N.66, H.87, E.92, E.139, N.143, D.172, A.174, R.175, M.198, K.203, R.320 24 PLIP interactions: 6 interactions with chain B, 18 interactions with chain C Water bridges: B:K.228, B:R.235, B:R.235, B:R.235, C:T.63, C:T.63, C:H.87, C:S.202, C:R.320, C:R.320 Salt bridges: B:K.228, B:R.235, C:R.175, C:R.320 Hydrophobic interactions: C:H.87, C:E.139, C:A.174 Hydrogen bonds: C:S.10, C:G.62, C:T.63, C:N.143, C:R.175, C:R.175 pi-Stacking: C:H.87 PLG.16: 16 residues within 4Å: Chain A: R.235 Chain D: S.10, S.61, G.62, T.63, N.66, H.87, E.92, E.139, N.143, D.172, A.174, R.175, M.198, K.203, R.320 26 PLIP interactions: 20 interactions with chain D, 6 interactions with chain A Hydrophobic interactions: D:H.87, D:E.139, D:A.174 Hydrogen bonds: D:S.10, D:G.62, D:T.63, D:T.63, D:N.66, D:N.143, D:R.175, D:R.175 Water bridges: D:T.63, D:H.87, D:S.202, D:S.211, D:R.320, D:R.320, A:K.228, A:K.228, A:R.235, A:R.235 Salt bridges: D:R.175, D:R.320, A:K.228, A:R.235 pi-Stacking: D:H.87

1 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.9: 14 residues within 4Å: Chain B: S.61, G.62, T.63, N.66, H.87, E.92, E.139, D.172, A.174, R.175, M.198, K.203 Chain C: R.235 Ligands: PLG.8 15 PLIP interactions: 4 interactions with chain C, 11 interactions with chain B Water bridges: C:K.228, C:K.228, B:P.60, B:S.61, B:T.63, B:S.202 Salt bridges: C:K.228, C:R.235 Hydrophobic interactions: B:H.87, B:E.139 Hydrogen bonds: B:G.62, B:T.63, B:R.175, B:R.175 pi-Stacking: B:H.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kielkopf, C.L. et al., X-ray Structures of Threonine Aldolase Complexes: Structural Basis of Substrate Recognition. Biochemistry (2002)

Release Date

2002-12-11

Peptides

L-allo-threonine aldolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

L-allo-threonine aldolase

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