SMTL ID : 3aem.1

Reaction intermediate structure of Entamoeba histolytica methionine gamma-lyase 1 containing Michaelis complex and methionine imine-pyridoxamine-5'-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

3 x 2LM: (2E)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]-4-(methylsulfanyl)butanoic acid(Non-covalent)

2LM.1: 22 residues within 4Å: Chain A: S.82, G.83, M.84, I.87, Y.108, E.151, N.155, D.180, T.182, S.202, S.204, K.205, I.214, G.215, V.331, S.332, L.333, T.347, R.367 Chain D: F.44, Y.53, R.55 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:Y.108, A:T.182, D:Y.53 Hydrogen bonds: A:S.82, A:G.83, A:M.84, A:N.155, A:N.155, A:T.182, A:S.202, A:S.204, A:K.205, A:S.332, D:Y.53, D:Y.53 Salt bridges: A:K.205, A:K.205, A:R.367, D:R.55 pi-Stacking: A:Y.108 2LM.4: 23 residues within 4Å: Chain B: S.82, G.83, M.84, I.87, Y.108, E.151, N.155, D.180, T.182, F.183, S.202, S.204, K.205, I.214, G.215, V.331, S.332, L.333, T.347, R.367 Chain C: F.44, Y.53, R.55 16 PLIP interactions: 2 interactions with chain C, 14 interactions with chain B Hydrogen bonds: C:Y.53, B:S.82, B:G.83, B:M.84, B:N.155, B:S.202, B:S.204, B:K.205, B:S.332 Salt bridges: C:R.55, B:K.205, B:K.205, B:R.367 Hydrophobic interactions: B:Y.108, B:Y.108 Water bridges: B:T.111 2LM.9: 21 residues within 4Å: Chain A: Y.53, R.55 Chain D: S.82, G.83, M.84, I.87, Y.108, E.151, N.155, D.180, T.182, S.202, S.204, K.205, I.214, G.215, V.331, S.332, L.333, T.347, R.367 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:Y.108, D:Y.108, D:T.182, A:Y.53 Hydrogen bonds: D:S.82, D:G.83, D:M.84, D:N.155, D:S.204, D:K.205, D:S.332 Water bridges: D:T.111 Salt bridges: D:K.205, D:K.205, D:R.367, A:R.55

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

SO4.2: 1 residues within 4Å: Chain A: R.176 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.176 Salt bridges: A:R.176 SO4.5: 1 residues within 4Å: Chain B: R.176 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.176 Salt bridges: B:R.176 SO4.7: 1 residues within 4Å: Chain C: R.176 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.176 Salt bridges: C:R.176 SO4.10: 1 residues within 4Å: Chain D: R.176 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.176

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain A: K.312 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.312 GOL.8: 1 residues within 4Å: Chain C: K.312 1 PLIP interactions: 1 interactions with chain C Water bridges: C:K.312

1 x MET: METHIONINE(Non-covalent)

MET.6: 11 residues within 4Å: Chain B: F.44, Y.53, L.56 Chain C: Y.108, N.155, K.205, V.331, S.332, L.333, T.347, R.367 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:Y.53 Hydrogen bonds: C:N.155, C:S.332, C:S.332 Salt bridges: C:R.367

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karaki, T. et al., Crystal structure of Entamoeba histolytica methionine gamma-lyase 1. To be published

Release Date

2011-02-09

Peptides

Methionine gamma-lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Methionine gamma-lyase

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