SMTL ID : 3ael.1

Reaction intermediate structure of Entamoeba histolytica methionine gamma-lyase 1 containing methionine imine-pyridoxamine-5'-phosphate and alpha-amino-alpha, beta-butenoic acid-pyridoxal-5'-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

1 x 4LM: (2E)-2-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}but-2-enoic acid(Non-covalent)

4LM.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: Y.53, R.55 Ligands: MEE.2 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:Y.108, A:T.182, A:V.331, 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 Salt bridges: A:K.205, A:K.205, A:R.367, D:R.55 pi-Stacking: A:Y.108

1 x MEE: METHANETHIOL(Non-covalent)

MEE.2: 3 residues within 4Å: Chain A: Y.108 Chain D: L.56 Ligands: 4LM.1 No protein-ligand interaction detected (PLIP)

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

SO4.3: 1 residues within 4Å: Chain A: R.176 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.176, A:R.176, A:R.176 Salt bridges: A:R.176 SO4.6: 1 residues within 4Å: Chain B: R.176 5 PLIP interactions: 5 interactions with chain B Water bridges: B:Q.96, B:R.176, B:R.176, B:R.176 Salt bridges: B:R.176 SO4.8: 2 residues within 4Å: Chain C: F.94, R.176 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.176 Salt bridges: C:R.176 SO4.11: 1 residues within 4Å: Chain D: R.176 2 PLIP interactions: 2 interactions with chain D Water bridges: D:Q.96 Salt bridges: D:R.176

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 1 residues within 4Å: Chain A: K.312 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.312 GOL.9: 1 residues within 4Å: Chain C: K.312 No protein-ligand interaction detected (PLIP)

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

2LM.5: 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 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.108, B:Y.108 Hydrogen bonds: B:S.82, B:G.83, B:M.84, B:N.155, B:N.155, B:S.204, B:K.205, B:S.332 Water bridges: B:D.180 Salt bridges: B:K.205, B:K.205, B:R.367, C:R.55 2LM.7: 22 residues within 4Å: Chain B: F.44, Y.53, R.55 Chain C: 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 19 PLIP interactions: 16 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:Y.108, C:T.182, B:Y.53 Hydrogen bonds: C:S.82, C:G.83, C:M.84, C:N.155, C:N.155, C:T.182, C:S.202, C:S.204, C:K.205, C:S.332, B:Y.53 Salt bridges: C:K.205, C:K.205, C:R.367, B:R.55 pi-Stacking: C:Y.108 2LM.10: 22 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, F.183, S.202, S.204, K.205, I.214, G.215, V.331, S.332, L.333, T.347, R.367 16 PLIP interactions: 15 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:Y.108, D:Y.108, D:T.182 Hydrogen bonds: D:S.82, D:G.83, D:M.84, D:N.155, D:S.202, 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

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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