SMTL ID : 3aej.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-tetramer

Ligands

3 x AA5: N-[(3-HYDROXY-2-METHYL-5-{[(TRIHYDROXYPHOSPHORANYL)OXY]METHYL}PYRIDIN-4-YL)METHYLENE]METHIONINE(Non-covalent)

AA5.1: 23 residues within 4Å: Chain A: 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 D: F.44, Y.53, R.55 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:Y.108 Hydrogen bonds: A:S.82, A:G.83, A:M.84, A:N.155, A:T.182, A:S.202, A:S.204, A:S.332, D:Y.53 Salt bridges: A:K.205, A:R.367, D:R.55 pi-Stacking: A:Y.108 AA5.4: 21 residues within 4Å: Chain B: 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, T.347, R.367 Chain C: F.44, Y.53, R.55 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.108, B:Y.108, B:Y.108 Hydrogen bonds: B:S.82, B:G.83, B:M.84, B:N.155, B:S.202, B:S.204, B:S.332 Salt bridges: B:K.205, B:K.205, B:R.367, C:R.55 AA5.9: 23 residues within 4Å: Chain A: F.44, Y.53, R.55 Chain D: 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 14 PLIP interactions: 13 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:Y.108 Hydrogen bonds: D:S.82, D:G.83, D:M.84, D:N.155, D:S.202, D:S.204, D:S.332, D:S.332 Salt bridges: D:K.205, D:K.205, D:R.367, A:R.55 pi-Stacking: D:Y.108

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

SO4.2: 1 residues within 4Å: Chain A: R.176 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.176, 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:Q.96 Salt bridges: B:R.176 SO4.7: 2 residues within 4Å: Chain C: F.94, R.176 2 PLIP interactions: 2 interactions with chain C Water bridges: C:F.94 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:S.313

1 x MET: METHIONINE(Non-covalent)

MET.6: 10 residues within 4Å: Chain B: F.44, Y.53 Chain C: Y.108, N.155, K.205, V.331, S.332, L.333, T.347, R.367 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.108, C:T.347 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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