SMTL ID : 5tsu.1 (1 other biounit)

Active conformation for Engineered human cystathionine gamma lyase (E59N, R119L, E339V) to depleting methionine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

1 x MET: METHIONINE(Non-covalent)

MET.1: 8 residues within 4Å: Chain A: Y.131, N.178, K.229, V.356, S.357, R.392 Chain B: N.76, Y.77 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.178, A:S.357 Salt bridges: A:R.392

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

SO4.2: 3 residues within 4Å: Chain A: K.182, P.315, Q.316 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.316 Salt bridges: A:K.182 SO4.3: 7 residues within 4Å: Chain B: Y.131, N.178, K.229, S.357, L.358, T.372, R.392 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.131, B:N.178, B:S.357 Salt bridges: B:R.392 SO4.5: 9 residues within 4Å: Chain D: Y.131, N.178, K.229, V.356, S.357, L.358, E.366, T.372, R.392 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.178, D:S.357 Salt bridges: D:R.392

1 x LPI: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-methionine(Covalent)

LPI.4: 19 residues within 4Å: Chain C: S.106, G.107, L.108, Y.131, E.174, N.178, D.204, T.206, S.226, T.228, K.229, M.239, V.356, S.357, L.358, T.372, R.392 Chain D: Y.77, R.79 15 PLIP interactions: 2 interactions with chain D, 13 interactions with chain C Hydrophobic interactions: D:Y.77, C:Y.131 Salt bridges: D:R.79, C:K.229, C:K.229, C:R.392 Hydrogen bonds: C:S.106, C:G.107, C:L.108, C:N.178, C:S.226, C:S.357, C:S.357 Water bridges: C:D.204 pi-Stacking: C:Y.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yan, W. et al., Structural Snapshots of an Engineered Cystathionine-gamma-lyase Reveal the Critical Role of Electrostatic Interactions in the Active Site. Biochemistry (2017)

Release Date

2017-10-11

Peptides

Cystathionine gamma-lyase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Cystathionine gamma-lyase

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