SMTL ID : 8j6n.1 (2 other biounits)

Crystal structure of Cystathionine gamma-lyase in complex with compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x TVJ: [6-methyl-4-[(~{E})-(oxamoylhydrazinylidene)methyl]-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate(Non-covalent)

TVJ.1: 20 residues within 4Å: Chain A: S.82, G.83, L.84, Y.107, E.150, N.154, D.180, T.182, F.183, S.202, T.204, K.205, M.215, E.332, S.333, L.334, T.348, R.368 Chain D: Y.53, R.55 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:Y.107 Hydrogen bonds: A:G.83, A:L.84, A:Y.107, A:N.154, A:T.182, A:S.202, A:S.202, A:S.202, A:T.204, A:K.205, A:K.205, A:E.332, A:S.333, A:R.368, A:R.368, D:Y.53 Salt bridges: A:K.205, D:R.55 TVJ.3: 19 residues within 4Å: Chain B: S.82, G.83, L.84, Y.107, E.150, N.154, D.180, T.182, F.183, S.202, T.204, K.205, E.332, S.333, L.334, T.348, R.368 Chain C: Y.53, R.55 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:Y.107 Hydrogen bonds: B:G.83, B:L.84, B:Y.107, B:Y.107, B:N.154, B:S.202, B:K.205, B:K.205, B:S.333, B:R.368, B:R.368 Water bridges: B:E.150, B:D.180 Salt bridges: B:K.205, C:R.55 TVJ.5: 19 residues within 4Å: Chain B: Y.53, R.55 Chain C: S.82, G.83, L.84, Y.107, E.150, N.154, D.180, T.182, F.183, S.202, T.204, K.205, E.332, S.333, L.334, T.348, R.368 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:Y.107 Hydrogen bonds: C:G.83, C:L.84, C:N.154, C:T.182, C:S.202, C:T.204, C:K.205, C:K.205, C:E.332, C:S.333, C:R.368, C:R.368 Water bridges: C:D.180, C:D.180 Salt bridges: C:K.205, B:R.55 TVJ.7: 19 residues within 4Å: Chain A: Y.53, R.55 Chain D: S.82, G.83, L.84, Y.107, E.150, N.154, D.180, T.182, F.183, S.202, T.204, K.205, E.332, S.333, L.334, T.348, R.368 19 PLIP interactions: 17 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:Y.107 Hydrogen bonds: D:G.83, D:L.84, D:Y.107, D:Y.107, D:Y.107, D:N.154, D:S.202, D:S.202, D:S.202, D:K.205, D:E.332, D:S.333, D:R.368, D:R.368, A:Y.53 Water bridges: D:E.150 Salt bridges: D:K.205, A:R.55

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: H.92, L.93, L.94, L.232 Chain D: V.117, E.120, F.121 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.92 Water bridges: A:R.228, A:R.228 GOL.4: 7 residues within 4Å: Chain B: H.92, L.93, L.94, L.232 Chain C: V.117, E.120, F.121 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.93 Water bridges: B:K.95, B:K.95, B:R.228, B:R.228 GOL.6: 6 residues within 4Å: Chain B: R.116, E.120 Chain C: H.92, L.93, L.94, L.232 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.93 Water bridges: C:R.228, C:R.228 GOL.8: 7 residues within 4Å: Chain A: V.117, E.120, F.121 Chain D: H.92, L.93, L.94, L.232 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:H.92 Water bridges: D:R.228, D:R.228, A:E.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Echizen, H. et al., Discovery of a cystathionine gamma-lyase (CSE) selective inhibitor targeting active-site pyridoxal 5'-phosphate (PLP) via Schiff base formation. Sci Rep (2023)

Release Date

2024-02-14

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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